Meeting of the Minds 2016 by Carnegie Mellon University in Qatar

eeting of the Minds is an annual symposium at Carnegie Mellon University that gives students an opportunity to

present their research and project work to a wide audience of faculty, fellow students, family members, industry representatives and the larger community. Students use posters, videos and other visual aids to present their work in a manner that can be easily understood by both experts and non experts. Through this experience, students learn how to bridge the gap between conducting research and presenting it to a wider audience. A review committee consisting of industry experts and faculty members from other universities will review the presentations and choose the best projects and posters. Awards and certificates are presented to the winners.

Table of Contents

Page

A Message from Dean Ilker Baybars

Carnegie Mellon University in Qatar Leadership

Judges

Biological Sciences Posters

• Possible Alternative to Chimeric Placental and Intestinal Alkaline Phosphatase in the Treatment of Acute Kidney Disease

• Inhibition of Bacterial Alkaline Phosphatase by L-Phenylalanine

• Development of Educational Protein Assay for Secondary Schools in Qatar

• Characterizing a Novel Bacillus-like Phage from Qatar’s Sand

• Role of DNAJB3/ HSP-40 in Maintaining Metabolic Homeostasis

• The Effect of pH on the Activity and Affinity of Alkaline Phosphatase

• Analysis of Microbiome in Water Systems in Doha

• Comparison of Kinetic Behavior Between E. coli and Calf-Intestinal Alkaline Phosphatase Using Nitrophenyl Phosphate (NPP)

• Effect of Aspartame on Malate Aspartate Shuttle in MDCK Cells

• Isolation, Purification, and Complete Genome Sequence of Bayan Bacteriophage, a Potential Therapeutic Tool for Tuberculosis

20 22 24

• Acute Toxicity of Saccharine on Proximal Tubular Kidney Cells

• Inhibition of Human Placental Alkaline Phosphatase (PLAP) by L-Phenylalanine

• Temporal Patterns in Qatar’s Particulate Air Pollution

• Annotation of Qatar’s Novel Bacillus-like Phage Genome

• Microbiology-based Educational Kit for High School Students in Qatar

Computer Science Posters

• Computer Assisted Learning Using Foreign Language Material

• Device-to-Device Communication in the Internet of Things: Providing Development Guidelines for IoT Enthusiasts.

36 38

• Wireless Eruptions - Reprogramming Wireless Sensor Networks: Challenges and Approaches

• CheckMyStack Vulnerability Detection Tool for the Qatari Web

• Software Defined Networking in Wireless Networks Using a Raspberry Pi

• Applying Recurrent Neural Network for Arabic Named Entity Recognition

• An In-Car Speech-based Interactive Recitation Correction System

• Tweets about Qatar: Who’s Setting the Agenda?

• Social Media Image Analysis for Public Health

General Education Posters

• Graceful Trees and Parking Functions

Information Systems Posters

• Helping Qatar’s Disabled: Identifying our Web Accessibility Problems

• Designing Services in Healthcare: A Research Collaboration with Hamad General Hospital

56 58

Postgraduate Posters

• A Leg in the Future of Hive Mind Programming

• A Web-based Framework For Arabic Text Diacritization Annotation

• Alice in the Middle East: Computing Curriculum for K-12

• Cumulus: A Distributed Flexible Computing Testbed for Edge Cloud Computational Offloading

• Detecting and Tracking Attacks in Mobile Edge Computing Platforms

• Drone-Be-Gone: Agile Low-Cost Vision-Based UAV Cyber Physical Testbed

• Extending the Range via Ad-hoc Communication for Cooperative Robotic Watercraft

• GraphSim: A Distributed and Adaptive Graph Simulation System

• NEXCEL: A Deductive Spreadsheet

• The OptDiac Project: Guidelines and Framework for a Large Scale Arabic Diacritized Corpus

• Effect of Wave Interference on Richtmyer-Meshkov Instability

• Teacher Development for Student Reading

• A Study of Visual Metaphors on Arab e-Commerce Websites

• Websites as Cultural Expressions: A Multimodal Analysis of Arabic e-Commerce Websites

A Message from Dean Ilker Baybars The Meeting of the Minds student research symposium is a highlight of the academic year, a celebration of the ingenuity, hard work, scientific exploration and intellectual curiosity that characterizes students in all disciplines at Carnegie Mellon University in Qatar. Research is an essential element of the undergraduate experience. For some students, the process of hypothesis, experimentation and analysis will inspire them to pursue further study, perhaps even a career in scientific research. For others, the intellectual rigor of research is invaluable experience in problem solving, and they can apply these skills in their professional careers, regardless of the industry. The fundamental process of scientific research is to bring together creativity and reason. The work that CMU-Q students are presenting is a showcase of this process: each project shows originality of thought and careful analysis. I encourage you to explore the projects, ask questions and learn about the unique perspectives that our students bring to scientific questions. The entire CMU-Q community can be exceptionally proud of this body of work.

Kind regards,

Ilker Baybars Dean and CEO Carnegie Mellon University in Qatar

Carnegie Mellon University in Qatar

Leadership

Ilker Baybars Dean and CEO

John Oâ&#x20AC;&#x2122;Brien Associate Dean

Selma Limam Mansar Associate Dean, Education

Kemal Oflazer Associate Dean, Research

Contact:

Deanâ&#x20AC;&#x2122;s Office: deans-office@qatar.cmu.edu

Research Office:

cmuq-research@qatar.cmu.edu

Admission Office:

ug-admission@qatar.cmu.edu

Media Inquiries:

mpr@qatar.cmu.edu

Judges External Judges •

Dr. Hadi Abderrahim, Managing Director, Qatar BioBank

•

Hayfa Ahmed, Research Manager, Qatar Science and Technology Park

•

Haya Al-Ghanim, Innovation Director, Qatar Science and Technology Park

•

Dr. Kai-Henrik Barth, Senior Assistant Dean, Georgetown University in Qatar

•

Dr. Omar Boukhris, Postaward Administrator, Qatar National Research Fund

•

Dr. Hassan Bazzi, Assistant Dean for Research, Texas A&M University at Qatar

•

Dr. Sebti Foufou, Professor and Head, Computer Science and Engineering Department, Qatar University

•

Dr. Thomas Groegler, Head of Innovation Center, Siemens

•

Dr. Mohamed Hefeeda, Principal Scientist, Qatar Computing Research Institute

•

Dr. Henning Horn, Assistant Professor, Hamad Bin Khalifa University

•

Dr. Qutaibah Malluhi, Director, KINDI Center for Computing Research, Qatar University

•

Batool Mohammed, Engineer, Vodafone

•

Dr. Alessandro Moschitti, Principal Scientist, Qatar Computing Research Institute

•

Dr. Walid Qoronflech, Director of Biotechnology Development, Qatar Biomedical Research Institute

•

Dr. Kareem Sakallah, Chief Scientist, Qatar Computing Research Institute

•

Dr. Klaus Schoenbach, Associate Dean for Research, Northwestern University in Qatar

•

Dr. Munir Tag, Program Manager, ICT, Qatar National Research Fund

•

Dr. Sarah Vieweg, Scientist, Qatar Computing Research Institute

•

Dr. Ingmar Weber, Senior Scientist, Qatar Computing Research Institute

•

Dr. Barak Yehya, Expert, Ministry of Development Planning and Statistics

Carnegie Mellon University in Qatar Judges •

Dr. Houda Bouamor

•

Dr. Anis Charfi

•

Dr. Hasan Demirkoparan

•

Dr. Fuad Farooqi

•

Dr. Susan Hagan

•

Dr. Kemal Oflazer

•

Dr. Ihab Younis

Special Awards Carnegie Mellon University in Qatar acknowledges and thanks the Ministry of Development Planning and Statistics and Qatar National Research Fund for recognizing students and researchers with special awards.

Note: All student and advisor affiliations in the posters are with Carnegie Mellon University in Qatar unless otherwise noted.

Possible Alternative to Chimeric Placental and Intestinal Alkaline Phosphatase in the Treatment of Acute Kidney Disease Authors Abdulrahman Al-Subaiey Dana Al-Eshaq

Advisor Annette Vincent

Category Biological Sciences

Abstract Human placental alkaline phosphatase (PLAP) and bacterial alkaline phosphatase (E. coli AP) are dimeric zinc-metallo enzymes that are both known to be thermostable. Alkaline phosphatase hydrolyzes the colorless p-nitrophenolphosphate (pNPP) into the yellow p-nitrophenol. Thus, the activity of alkaline phosphatase can be detected at 410 nm at which p-nitrophenol maximally absorbs using a spectrophotometer. The goal of this study is to determine which enzyme is more thermostable by measuring the activity of PLAP and E. coli C6318 alkaline phosphatase at an optimal temperature and two extreme temperatures. The activity of the two enzyme isoforms were measured in the presence of 0.1–0.5 mM pNPP at temperatures of 37°, 80°, and 90° C. Our hypothesis was supported by the data we obtained that shows a significant difference in the activity after incubation at 80°C, indicating that E. coli C6318 alkaline phosphatase is more thermostable than PLAP. This discovery expands the toolbox of scientists interested in thermostable enzymes for therapeutic or research purposes such as the construction of an E. coli AP/Intestinal AP chimera to treat diseases such as Acute Kidney Disease.

Figure 1: Human Kidneys

Figure 2: LPS Structure

In a study by Kiffer-Moreira, et al., 2014, a chimeric alkaline phosphatase (ChimAP) was developed, composed of the thermostable human placental alkaline phosphatase and the intestinal alkaline phosphatase that targets bacterial LPS, or lipopolysaccharide. ChimAP demonstrated high thermostability with a narrower substrate specificity than the parents and demonstrated high selectivity for the bacterial substrate LPS. LPS is an endotoxin found on the surface of gram-negative bacteria. Acute Kidney Disease, which is the abrupt loss of kidney function, has been highly associated with presence of LPS. ChimAP is capable of dephosphorylating LPS, causing it to become inactive. ChimAP is being investigated for its therapeutic properties for inflammatory bowel disease, gut dybioses, and acute kidney disease (Kiffer-Moreira et al., 2014). AM-Pharma, the company that manufactures ChimAP has completed a Phase I clinical trial and confirmed a good safety and tolerability profile in healthy individuals. The company began a Phase II proof-of-concept clinical trial on patients with sepsis-associated AKD in the U.S. and in Europe to identity the best dosage (Kiffer-Moreira et al., 2014).

Significance

The goal of this project was to compare the thermostability of E. coli C6318 alkaline phosphatase with that of the human placental (PLAP). We hypothesized that the E. coli AP is more thermostable than PLAP since during the purification process of E. coli AP, it was exposed to 80°C to facilitate protein denaturation yet remained active. If the hypothesis is supported, that could pave the way to developing a more thermostable chimeric alkaline phosphatase, composed of the E. coli AP and Human Intestinal AP that could be purified using heat denaturation, which is a feasible and affordable purification strategy. This may result in affordable production of Chimeric Alkaline Phosphatase, were it to become a commercialized and standardized medicine for people suffering from Acute Kidney Disease and other gut diseases.

Our study on E. coli AP

Human placental alkaline phosphatase (PLAP) and bacterial alkaline phosphatase (E. coli AP) are dimeric zinc-metallo enzymes that are both known to be thermostable. Alkaline phosphatase hydrolyzes the colorless p-nitrophenolphosphate (pNPP) into the yellow p-nitrophenol. Thus, the activity of alkaline phosphatase can be detected at 410 nm at which pnitrophenol maximally absorbs using a spectrophotometer. The goal of this study is to determine which enzyme is more thermostable by measuring the activity of PLAP and E. coli C6318 alkaline phosphatase at an optimal temperature and two extreme temperatures. The activity of the two enzyme isoforms were measured in the presence of 0.1–0.5 mM pNPP at temperatures of 37°, 80°, and 90° C. Our hypothesis was supported by the data we obtained that shows a significant difference in the activity after incubation at 80°C, indicating that E. coli C6318 alkaline phosphatase is more thermostable than PLAP (Vincent, 2015). This discovery expands the toolbox of scientists interested in thermostable enzymes for therapeutic or research purposes.

Abstract

2.00E-04

4.00E-04

6.00E-04

Enzyme Units, mg

8.00E-04

1.00E-03

1.20E-03

2.00E-03

4.00E-03

6.00E-03

1.00E-02

Enzyme Units, mg

8.00E-03

1.20E-02

1.40E-02

1.60E-02

1.80E-02

0.09

0.14

0.19

0.24

0.29

0.5

2.5

Concentration of pNPP, mM

1.5

3.5

4.5

Figure 5: Michaelis-Menten Plot of Human Placental Alkaline Phosphatase. Graph of Activity, µmol NP/min, against Concentration of pNPP, mM. Enzyme amount used was 0.5 µg. Substrate Saturation occurred at 0.5 mM.

0 0.00E+00

Figure 4: Enzyme Saturation Curve of E. coli alkaline phosphatase. Excess pNPP, 11.2 mM, was used with varying units of E. coli AP, in mg. Enzyme saturation occurred at 7.81 x 10-3 mg of enzyme.

0 0.00E+00

Figure 3: Enzyme Saturation Curve of Human Placental Alkaline Phosphatase. Excess pNPP, 11.2 mM, was used with varying units of PLAP, in mg. Enzyme saturation occurred at 5 x 10-4 mg of enzyme.

Data

•  To test for thermostability, each enzyme was incubated for 10 min in DEA buffer (100 mM Diethanolamine, 5 mM MgCl2, pH 9.5) at three different temperatures: 37º, 80º and 90º, and the initial activity was measured at each temperature per enzyme in triplicates.

•  The Agilent 8453 UV-Vis Spectrophotometer, was used to measure enzyme activities by rate of dephosphorylation of pNPP to nitrophenol at 410nm.

•  PLAP (Sigma, St Louis) was used in this study, whereas bacterial AP was extracted from E. coli C6318 and purified using ammonium sulfate precipitation followed by ion-exchange column chromatography.

Methods

0.2

0.6

Concentration of pNPP, mM

0.4

0.8

1.2

0.2

-0.2

0.5

2.5

Concentration of pNPP, mM

1.5

y = 0.3713x + 0.029 R² = 0.9986

3.5

-0.2

-0.1

0.2

0.6

Concentration of pNPP, mM

0.4

y = 0.6763x + 0.0057 R² = 0.99841

0.8

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

80°C

T-test value: 0.038

90°C

T-test value: 0.124

PLAP

E. coli AP

Figure 9: Human Placental Alkaline Phosphatase & E. coli Alkaline Phosphatase Average Activity Across All Substrate Concentrations . Graph of Activity in µmol NP/min vs. temperature °C. The amount of enzyme used for PLAP: 0.5 µg. The amount of enzyme used for E. coli: 7.81 µg.

-0.2

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

Figure 8: Hanes Plot of E. coli C6318 Alkaline Phosphatase. Concentration of pNPP in mM/Enzyme Activity in µmol NP/min vs. Concentration of pNPP, mM. Km = 8.428 mM pNPP; Vmax = 0.0125 µmol pNPP/min

-0.5

0.4

0.6

0.8

1.2

1.4

1.6

1.8

1.2

4.5

Figure 7: Hanes Plot of Human Placental Alkaline Phosphatase. Concentration of pNPP in mM/Enzyme Activity in µmol NP/min vs. Concentration of pNPP, mM. Km = 0.0782 mM pNPP; Vmax = 0.2016 µmol pNPP/min

0.1

0.12

0.14

0.16

0.18

0.2

0.22

0.24

0.26

Figure 6: Michaelis-Menten Plot of E. coli C6318 Alkaline Phosphatase. Graph of Activity, µmol NP/min, vs. Concentration of pNPP, mM. Enzyme amount used was 7.81 µg. Substrate Saturation occurred at 0.2 mM pNPP.

Abdulrahman Al-Subaiey, Dana Al-Eshaq, Dr. Annette Vincent Carnegie Mellon University Qatar

1. Kiffer-Moreira, T., Sheen, C. R., Gasque, K. C. da S., Bolean, M., Ciancaglini, P., van Elsas, A., Millán, J. L. 2014. Catalytic Signature of a Heat-Stable, Chimeric Human Alkaline Phosphatase with Therapeutic Potential. PLoS ONE, 9(2), e89374. 2. Vincent, A. 2016. Techniques in Biochemistry Lecture. Carnegie Mellon University Qatar.

References

Chloe Glynn, Maya Kemaldean, Rayan Mahmoud, Aya Abd Elaal

Acknowledgments

Figure 10: Structure of ChimAP

The thermostability-conferring crown domain of E. coli AP will be fused to the IAP. This chimera utilizes a relatively small portion of the enzyme therefore should be easily fused onto IAP.

Create the E.coli AP/IAP chimera to study functionality

The structure of the E. coli AP was unavailable, therefore amino acid sequence homology was performed. BLAST of PLAP and IAP amino acid sequences revealed that the two proteins share 87% identity with a 93% query cover. BLAST of E. coli AP with IAP amino acid sequences revealed a 27% identity and 87% query cover.

Assess the success of an E. coli AP/IAP chimera through structural comparisons.

Future Work – Computational Studies

The hypothesis is supported by the data as the t-test clearly shows a significant difference between the enzyme activities of the Human Placental Alkaline Phosphatase and the E. coli C6318 Alkaline Phosphatase after 80° C incubation for 10 minutes, proving that E. coli Alkaline Phosphatase is more thermostable than Human Placental Alkaline Phosphatase.

Conclusion

Statistical Significance of Thermostability Difference •  Difference between PLAP and E. coli AP Activity across pNPP concentrations of 0.1, 0.25, and 0.5 mM at 37 and 90°C were found to be insignificant. T-test values: 0.109, 0.124, respectively. •  Difference between PLAP and E. coli AP across pNPP concentrations of 0.1, 0.25, and 0.5 mM at 80 °C were found to be significant as the t-test value was determined to be 0.038.

Enzyme Affinity •  E. Coli C6318 Alkaline Phosphatase has higher affinity towards the substrate pNPP in comparison to Human Placental Alkaline Phosphatase.

Analysis

Possible Alternative to Chimeric Placental and Intestinal Alkaline Phosphatase in the Treatment of Acute Kidney Disease

Activity, umoles pNPP/min Activity, umoles NP/min Activity, umol NP/min

Activity, umol NP/min Concentration of NP/Activity, mM/ umol/min Concentration of NP mM/Activity, mM/ umol/min Activity, umol NP/min

Inhibition of Bacterial Alkaline Phosphatase by L-Phenylalanine

Authors Alya Al-Kurbi Reem Hasnah

Advisor Annette Vincent

Category Biological Sciences

Abstract The goal of this experiment is to analyze and determine whether L-phenylalanine will inhibit the enzyme activity of the bacterial strain C6318 alkaline phosphatase similarly as intestinal and placental alkaline phosphatase 1. We predict to see inhibition of bacterial alkaline phosphatase at pH 8.0 and 37째C which will cause the enzyme activity to decrease by observing a decrease in Vmax in the reciprocal plot at 450 nm measured using Agilent Model 8453 UV-Vis spectrophotometer. Enzyme velocity was measured using different L-phenylalanine concentration 0.5, 5, 10, and 30 mM. The rate of reaction decreased from 0.12 to 0.099 abs/min as more concentrated amount of L-phenylalanine was added into the reaction.

●  Same thing was done for substrate saturation curve using different concentrations of substrate (0.1 -‐ 3mM) keeping enzyme amount constant (4.1 x 10-‐5 mg) in Diethanolamine buffer pH 8.0 at 37°C. ●  The maximum amount of enzyme (4.1 x 10-‐5 mg) and substrate concentrations (3mM) were used to create different stock solutions with varying concentrations of l-‐phenylalanine inhibitor (0.5-‐ 30mM). ●  Lineweaver-‐Burke plot was created from the Michaelis-‐ Menton plot of the inhibitor curve to determine effect on Km and Vmax values

●  The maximum amount of enzyme concentration required for non-‐limiting enzyme activity of the isolated, puriUied bacterial strain C6318 alkaline phosphatase that was isolated in lab 2 is 4.1 x 10-‐5. Different amounts of enzyme were added (4.1 x 10-‐6 – 4.5 x 10 -‐5 mg) keeping substrate concentration (11.2mM) constant in Diethanolamine buffer, measuring the absorbance at 450nm every 30 second for at least 2 min using Agilent Model 8453 UV-‐Vis spectrophotometer.

Methods

The goal of this experiment is to analyze and determine whether L-‐phenylalanine will inhibit the enzyme activity of the bacterial strain C6318 alkaline phosphatase similarly as intestinal and placental alkaline phosphatase 1. We predict to see inhibition of bacterial alkaline phosphatase at pH 8.0 and 37°C which will cause the enzyme activity to decrease by observing a decrease in Vmax in the reciprocal plot at 450 nm measured using Agilent Model 8453 UV-‐Vis spectrophotometer . Enzyme velocity was measured using different L-‐phenylalanine concentration 0.5, 5, 10, and 30 mM. The rate of reaction decreased from 0.12 to 0.099 abs/min as more concentrated amount of L-‐phenylalanine was added into the reaction.

Abstract

Figure 3: Double reciprocal plot of Substrate Saturation curve of day-‐ 1.

Figure 2: Michaelis Menton plot of Bacterial Alkaline Phosphatase substrate (pNPP). Reaction was carried at 37C, pH 8.0 using diethylalanine buffer with a constant enzyme amounts 0.000045 mg (50ul) with Uinal reaction volume being 300ul varying substrate concentration. Absorbance was measured at 450nm every 10 seconds for 3 minutes using Agilent Model 8453 UV-‐Vis spectrophotometer.

Figure 1: Saturation curve of Bacterial Alkaline Phosphatase. Reaction was carried at 37C, pH 8.0 using Diethanolamine buffer with a maximum substrate concentration 11.2mM with Uinal reaction volume being 300ul . Absorbance was measured at 450nm every 10 seconds for 3 minutes using Agilent Model 8453 UV-‐Vis spectrophotometer.

Results

Discussion

1/[S] (mM)

y = 0.0053x + 0.0088 R² = 0.87997

y = 0.0391x - 0.0262 R² = 0.98169

For the purpose of this mini project, enzyme concentration have to be Uixed, in order for the concentration of the inhibitor to be the only variable factor affecting the rate of the reaction. From the enzyme saturation curve we choose maximum enzyme concentration after which it reached zero order kinetics, where no change in Vmax occurred with changing enzyme concentrations. Enzyme concentration used was From the Michaelis-‐Menton plot it is observed that as the substrate concentrations increases that rate of reaction increases till it reaches saturation were increasing substrate concentration no longer affects rate of reaction. From this plot Lineweaver-‐Burke plot was plotted since it provide more accurate results regarding the Km and Vmax of the reaction. 1/Km value is the X-‐intercept, thus, the Km value is 1.49mM. However, 1/Vmax is the Y-‐intercept, so, the Vmax value is 38.17 umol/min. Km value obtained from the Lineweaver-‐Burke plot is 1.49mM for the isolated and puriUied bacterial alkaline phosphatase in lab 2, however, the published Km value for the pure bacterial alkaline phosphatase is 0.031mM which is much smaller than what we obtained. Thus, there appears to be no relationship between the Km value and the r-‐squared value of the regression line since the r-‐square value is 0.98 which is almost 1, but the obtained Km value was very different than the published value Km value obtained from Hanes plot in Uigure 3 is 0.27mM ( Vincent, A. 2016) which is close to the published value than to the value obtained from the Lineweaver-‐Burke plot in day 1 (1.49mM). However, Vmax obtained from Uigure 3 is 0.30 which is close to the published value (1 umol/min) than to the value obtained from Lineweaver-‐Burke plot (38.17 umol/min). The Hanes plot is better to use for the determination of kinetic parameters than the Lineweaver-‐Burke plot because it is more accurate 2.This is because the advantages to use Hanes plot is that it allow for both Km and Vmax to be estimated accurately since data are more spread across the plot. However, one of the disadvantage of using Hanes plot is that any inaccurate measurement of substrate concentration will be exaggerated since its used on both axis 1.

-0.05

0.05

0.1

0.15

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Figure 4: Reciprocal plot of the Effect of L-‐phenylalanine on reaction rate of bacterial Alkaline Phosphatase. Overlaid with Hanes plot of substrate saturation curve.

Carnegie Mellon University – Qatar, Biological Sciences program Advisor: Dr. Annette Vincent

Alya Al-‐Kurbi and Reem Hasnah

1-‐ Medicinal Chemistry — Understanding Enzyme Kinetics. (2014). PharmaFactz. Retrieved 8 March 2016, from http://pharmafactz.com/medicinal-‐chemistry-‐understanding-‐enzyme-‐ kinetics/ 2-‐ Bioinformatics, Biology and Computing: Michaelis-‐Menten Enzyme Kinetics. (2016). Dan-‐thornton.blogspot.qa. Retrieved 8 March 2016, from http://dan-‐thornton.blogspot.qa/2013/06/introduction-‐this-‐study-‐is-‐ look-‐at.html 3-‐ Vincent, A. 2016. Enzyme kinetics lecture slides. 4-‐ ENZYME KINETICS: CHARACTERIZATION OF THE ENZYME ALKALINE PHOSPHATASE. (2016). Retrieved 16 February 2016, from http://www.acad.carleton.edu/curricular/BIOL/classes/bio126/ Documents/Lab_3.pdf 5-‐ Fernley, H N, and P G Walker. "Inhibition Of Alkaline Phosphatase By L-‐ Phenylalanine". Biochem. J. 116.3 (1970): 543-‐544. Web.

References

Previous studies were made on the inhibition effect of L-‐ phenylalanine inhibition of intestinal and placental alkaline phosphatase. This project was made to Uind out the effect of L-‐ phenylalanine on bacterial alkaline phosphatase. After measuring the reactions of alkaline phosphatase with increasing L-‐phenylalanine concentration (0.5-‐30 mM)we observed a decreased in the rate of reaction of bacterial alkaline phosphatase (0.099 abs/ min). In conclusion L-‐phenylalanine had an inhibition effect on bacterial alkaline phosphatase. The physiological function of bacterial alkaline phosphatase, is to dephosphorylate phosphate groups. So, if a mutation occurred in bacterial alkaline phosphatase that would negatively impact the bacterial cell, it can be inhibited by L-‐ phenylalanine.

Conclusion

The R-‐squared value of the reciprocal plot of l-‐phenylalanine inhibition is 0.879. This regression value means that results are not very accurate. However they contain some errors, these errors can be overcome by carrying out triplicates to each concentration. Also by taking more values in-‐between the range that was taken, so that the data can be tightened up. Our data is very variable, however it had allowed us to obtain the type of inhibition The R-‐squared value of the reciprocal plot of l-‐phenylalanine inhibition is 0.879. This regression value means that results are not very accurate. However they contain some errors, these errors can be overcome by carrying out triplicates to each concentration. Also by taking more values in-‐between the range that was taken, so that the data can be tightened up. Our data is very variable, as the range of inhibitor concentration is very large. However, it had allowed us to obtain the type of inhibition, as seen in the overlaying Uig. both the Vmax and the Km have changed in the presence of the inhibitor.

Inhibition of Bacterial Alkaline phosphatase by L-‐Phenylalanine

1/Velocity (umol/min)

Development of Educational Protein Assay for Secondary Schools in Qatar Author Aya Gaballa

Advisor Annette Vincent

Category Biological Sciences

Abstract This goal of this project was to create a marketable educational protein assay kit to complement the Qatar high school biology curriculum and promote the concept of active learning. The kit is comprised of three sections. The first section takes the students through plotting the standard curve through conducting serial dilutions. The second section of the kit involves an unknown solution that contains a concentration of BSA that is within the standard curve. The third section of the kit is used to provide a visual representation of the amount of protein present in a variety of food samples using a color chart. The Bradford reagent was created in the lab. Students use the reagent and the kit components to create standards of concentrations 0.5mg/ml, 0.25mg/ml, 0.125mg/ml, and 0.0625mg/ml. The standards were found to be reproducible. In addition to the color chart, a manual included in the kit will feature both the English version as well as the Arabic translation. The kit has been implemented in a scientific teaching laboratory for ninth grade students at Qatar Academy.

Development of EducaGonal Protein Assay for Secondary Schools in Qatar

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Aya Gaballa, Dr. AnneMe Vincent

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Biological Sciences Program, Carnegie Mellon University in Qatar

INTRODUCTION The goal of this project was to create a marketable educational protein assay kit to complement the Qatar secondary school Biology curriculum and promote the concept of active learning. A survey conducted among students in the local schools indicated that 91% of them felt that inquiry and practical based Biology lessons promoted critical thinking. Therefore, the aim of this project was to create an easy-to-use educational kit to complement Biology lessons on proteins. The kit makes use of the interaction that occurs between Coomassie Brilliant Blue dye and proteins, which results in a change in color of the dye. Consequently, the concentration of the protein was analyzed by measuring the color change quantitatively and visually to ensure that the difference between each sample was visible without the need of any advanced tools. A manual will be provided with the kit containing a color chart of the colors and the absorbances since most schools do not possess spectrophotometers. The kit is comprised of three sections. The first section takes the students through plotting the standard curve through conducting serial dilutions. The second section of the kit involves an unknown solution that contains a concentration of BSA that within the standard curve. The third section of the kit is the protein extraction section. This section used phosphate saline buffer with SDS (PBS-SDS) to extract protein from food samples. The kit is then used to provide a visual representation of the amount of protein present in a variety of food samples.

RESULTS Quality Testing of Bradford

will Figure 1: Standards (left to right): Blank, 0.0625mg/ml, 0.125mg/ml, 0.25mg/ml, and 0.5mg/ml

Section 1: Standard Curve A stock solution of 10mg/ml Bovine Serum Albumin (BSA) is provided. The students must first conduct a 10fold dilution to achieve a stock concentration of 1mg/ml BSA. A series of two-fold dilutions is then carried out to achieve concentrations of 0.5mg/ml, 0.25mg/ml, 0.125mg/ ml, and 0.0625mg/ml.

0 0.118

0.09750

0.221

0.18750

0.389

0.37500

0.508

0.125

0.1250

0.240

0.2500

0.414

0.5000

0.702

You refo cre

Section 3: Food Samples Food samples utilized in the experiment yielded results comparable with the provided color chart. In some cases, the resulting colors were outside or below the color range of the chart. In such cases, it is possible to perform further dilutions to the solution.

Absorbance Value

Blank

0.0625

Figure 3:

unknown solutions measured at 595nm

0.03125

Absorbance Value 0

You A pa TEX

Section 2: Unknown Solution . Table 2: Absorbance values for Concentration (mg/ml)

Concentration (mg/ml) Blank

Adj The req

Section 1: Standard Curve Once the solutions were created, they were analyzed using spectrophotometric analysis in order to ensure that they were valid quantitatively as well as visually. The standards were found to be reproducible. .

MATERIALS AND METHODS The Bradford reagent was created in the lab by mixing Coomassie Blue (Sigma) with ethanol, phosphoric acid, and distilled water. An appropriate formulation was concooted that is reproducible as well as increased storage life.

Table 1: Absorbance values for standard solutions measured at 595nm

Figure 2:

In addition to the color charts, a manual will provide simple scientific explanations of the staining mechanisms and the extraction methods as well as some general information regarding proteins contained in food. The manual will feature both the English version as well as the Arabic translation. 25

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Section 2: Unknown Solution The unknown solutions will be randomly distributed within the kit. The possible unknown solutions are of concentrations 0.375mg/ml, 0.1875mg/ml, 0.0975mg/ml, and 0.03125mg/ml BSA solutions.

RESEARCH POSTER PRESENTATION DESIGN ÂŠ 2015

www.PosterPresentations.com

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Section 3: Food Samples In order to test the food samples, extraction solution (PBS-SDS) is added to cover the sample by around 2cm. The tube must be shaken well and left for half an hour for the debris to settle. Using a Pasteur pipette, 0.25ml of the top of the solution will be taken and placed in a separate tube with 5ml Coomassie Blue. The students are then required to utilize the provided manual in order to determine the concentration of protein in the food sample.

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Figure 4: Student feedback. The kit was implemented in a scientific teaching laboratory for ninth grade students at Qatar Academy where 55 students participated in the class. Student feedback was collected from 21 students after they had used the kit.

ACKNOWLEDGEMENTS We would like to thank Maya Kemaldean, Bernadette, and Maria Navarro for their assistance, and Qatar Academy, for their participation.

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Characterizing a Novel Bacillus-like Phage from Qatar’s Sand Author Aya Abdelaal

Advisor Annette Vincent

Category Biological Sciences

Abstract The goal of the research is to use bacteriophages extracted from Qatar’s sand in water treatment to disinfect the water from microbial bacterial and other bacteria that were used to detoxify the water. This will replace the use of chlorine, which is more difficult to remove and high concentrations of which are harmful to the body. The model host chosen is Arthobacter bacteria, which is a denitrification bacteria, as it is similar to the bacteria used in water treatment. Three factors have been varied in order to obtain the highest phage titer. First, growth Media and incubation temperature of Arthrobacter used for plaque formation, secondly, type of plates and Top Agar used for plaque formation, lastly incubation temperature for plaque formation. Higher phage titer was obtained when the culture was grown in LB media at 37°C using PYCA plates and incubating the plates at 37°C. PYCA plates containing CaCl2 formed clearer plaques, indicating dominance of the lytic state. Therefore, addition of calcium in the top agar and the plates aided in the phages’ shift from the lysogenic cycle to the lytic cycle. The genome was then sequenced using Next generation sequencer Ion S5 (Life Technologies) and 1,059,168 reads were obtained. Future work will focus on annotating the genome and characterizing it.

Characterizing a novel Bacillus-like Phage from Qatar’s Sand Aya Abdelaal, Annette Vincent

Results II:

Introduction:

B: Type of plates and Top Agar used for plaque formation:

A bacteriophage is a virus that infects a bacteria, it uses the bacteria as a host to further replicate by controlling the replication and protein synthesis machinery of the cell. Bacteriophages are used in the treatment of bacterial infections. This results from phages invading the bacteria, as they undergo a lytic cycle, where the replication and protein synthesis machinery is used to produce virions, that later cause the cell to lyse, thus killing the bacteria. This research explores the potential of the use of bacteriophages in the treatment of water, to disinfect the water from microbial bacterial and other bacteria that were used to detoxify the water . This will replace the use of chlorine, which is more difficult to remove and high concentrations of which are harmful for the body. Phages can then be easily removed using a filter, this will provide an Eco friendly technique for water purification.

•  LB top agar in 1mM CaCl2 and PYCA top agar. It was concluded that the top agar that resulted in the highest titer was LB top agar in 1mM CaCl2. •  LB and PYCA plates were used for pour plating and it was concluded that PYCA plates result in highest phage titer. A

C: Incubation temperature for plaque formation: •  The plates were incubated at 32°C and 37°C, bigger burst size was obtained when the plates were incubated at 37°C . A

Objectives:

DNA extraction and genome sequencing: •  The phage DNA was extracted from phage lysate using QIAamp MinElute Virus Spin kit. •  The genome was sequenced using Next generation sequencer Ion S5 (Life Technologies)and 1,059,168 reads were obtained.

Genome assembly and genomic annotation:

Materials and Methods

•  The Genome was assembled using different assemblers like Mira-4.0.2, SOAPdenovo2 and SPAdes-3.7.0. However, SPAdes-3.7.0 produced the biggest contig length 43K base pair. •  DNA master was used for annotation and it predicted 67 genes. •  The predicted genes were blasted against protein data base and these genes were predicted: DNA-binding protein [Bacillus cereus], peptidase S74,Haemolysin XhlA [Bacillus subtilis],cell division protein FtsK [Bacillus thuringiensis], integrase,transcriptional regulator [Bacillus thuringiensis], AraC family transcriptional regulator and holin.

Luria Broth Media (LB): tryptone, yeast extract and NaCl Smeg media: Middlebrook 7H9 broth base with supplements of albumin, dextrose and salts PYCA plates: Peptone, Agar, Yeast Extract

Isolate Sand Bacteriophage 1.  Plaques were picked from previous samples through suction technique using sterile pasture pipets or pipet tips. Then resuspended in 100ul of phage buffer 2.  The plaques suspension was serially diluted to obtain 10-1, 10-2, 10-3, 10-4 dilutions. 3.  0.5ml of saturated Arthrobacter culture was added to each dilution. 4.  4.5ml of Top agar was add and then pour plated on PYCA plates. 2

67_2

DNA Extraction from phage Lysate 1

Figure 4: 100 Phage plated on PYCA plates using 0.5ml saturated Arthrobacter grown in SMEG media at 37°C and 4.5ml LB Top Agar in 1mM CaCl 2 . The plates were incubated overnight at 32°C (A) and 37°C (B).

Genomic Annotation

•  To identify optimum plaque formation conditions, this includes growth media for the host culture, incubation temperature of the host culture, type of plates and Top agar used for plaque formation. Lastly, incubation temperature after pour plating. •  Purify and extract the phage’s DNA from several high titer plates and Sequence the genome of the phage and analyze the genome of the phage.

67_2

Figure 3: 100 Phage plated on PYCA plates(A) and LB plates (B) using 0.5ml saturated Arthrobacter grown in SMEG media at 37°C and 4.5ml LB Top Agar in 1mM CaCl2. The plates were incubated overnight at 37°C.

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Microscopic Phage Images:

Figure 1: Electron microscopy image of Bacillus-like phage from Qatar’s Sand

•  Plaques formed using LB plates produced unclear plaques, this unclearness is an indication of persistence of the lysogenic state and not the lytic state. In the lysogenic state the phage genome gets incorportated into the host genome and replicates along with the cell cycle, thus remaining in a dormant state. On the other hand, in the lystic cycle, the phage uses the replication and protein synthesis machinery to produce more phages, that will later lead to lysis. In contrast, PYCA plates containing CaCl2 formed clearer plaques, indicating dominance of the lytic state. Therefore, addition of calcium in the top agar and the plates aided in the phages’ shift from the lysogenic cycle to the lytic cycle. This correlates with previous work4, where calcium was shown to be essential for the penetration of the phage’s genome into the host. •  Incubation temperature of 32°C for the plates was adapted from infection of lambda phage to Arthrobacter. However, the sand’s phage required a higher temperature at 37°C to cause lysis and the formation of plaques. This might be due to a mutation in a protein involved in lysis, causing a shift in temperature.

Optimizing plaque formation conditions A: Growth Media and incubation temperature of Arthrobacter used for plaque formation: •  The culture was grown in LB media and SMEG media, each at 30°C and 37°C. •  Higher phage titer was obtained when the culture was grown in LB media at 37°C. A

References:

1.  Mc Grath S and van Sinderen D (editors). (2007 2.  Ben Burrowes, David R Harper, Joseph Anderson, Malcolm McConville& Mark C Enright (2011) Bacteriophage therapy: potential uses in the control of antibiotic-resistant pathogens, Expert Review of Anti-infective Therapy, 9:9, 775-785 3.  Chhibber S, Kaur T, Kaur S. Essential role of calcium in the infection process of broad-spectrum methicillin-resistant Staphylococcus aureus bacteriophage. J Basic Microbiol. 2014 Aug;54(8):775-80. doi: 10.1002/jobm.201300051. Epub 2013 May 20. PubMed PMID: 23686366. Steensma HY, Blok J. Effect of calcium ions on the infection of Bacillus 4.  Steensma HY, Blok J. Effect of calcium ions on the infection of Bacillus subtilis by bacteriophage SF 6. J Gen Virol. 1979 Feb;42(2):305-14. PubMed PMID: 106092.

Acknowledgments: Figure2: 100(A), 10-1(B) and 10-2(C) Phage plated on PYCA plates using 0.5ml host grown in LB media (right) at 30°C (Top) and 37°C (bottom) and SMEG media (left) at 30°C (Top) and 37°C (bottom), 4.5ml LB Top Agar without CaCl2. The plates were incubated overnight at 32°C (Top) and 37°C (bottom).

67_1

Discussion and Conclusion: Results I:

18 19 20 21 22 23 24 25 Kilobases�of�Extracted�from�FastA�Library�aya�final�contigs.fasta_Ann

1.  5ml of phage buffer in 1mM CaCl2 was added to high phage titer plates and incubated at 37°C overnight. 2 3 4 5a metal 6 7spreader. 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 2.  Top agar was1 scrapped using Kilobases�of�Extracted�from�FastA�Library�aya�final�contigs.fasta_Annotated 3.  The lysate was centrifuged at 8000rpm for 10min to remove the cells. Figure 5: Genomic predictions of the phage 43K contig using DNA master. 4.  The lysate was filtered through 0.22mm low protein binding filter 5.  The phages were concentrated through centrifugation at 32500 rpm for 30 min. 6.  The DNA was extracted using QIAamp MinElute Virus Spin kit. 12

The following people and corporations, without which this would not have been possible, deserve special thanks and recognition for their efforts: Dr. Valentine Ilyin, Maya Kemaldean, BernadetteCaruana, Umm kulthum Umlai, Chloe Glynn, Mohammad El allam

Role of DNAJB3/ HSP-40 in Maintaining Metabolic Homeostasis Author Bushra Memon

Advisors Mohammed Dehbi (Qatar Biomedical Research Institute) Gordon Rule

Category Biological Sciences

Abstract DNAJB3, a member of the Heat Shock Protein-40 co-chaperone, was recently shown to be down-regulated in obese and diabetic individuals. The c-Jun NH2-terminal kinase (JNK) stress kinase and the IKK inflammatory kinase are two key enzymes that phosphorylate and inactivate the insulin receptor substrate and thereby, convert it into a poor substrate of the insulin receptor in response to insulin and ultimately leading to Type 2 Diabetes. Interestingly, the reduced expression of DNAJB3/ HSP-40 in patients was reversed on physical exercise. Previous studies have also shown that DNAJB3 binds to JNK and abrogated its activation following stress induction with palmitic acid. Because JNK activates transcription factor AP-1 that causes expression of pro-apoptotic proteins, we hypothesize that by binding to JNK and inactivating it, DNAJB3 leads to the inactivation of AP-1 and consequently protects against stress-induced apoptosis. Previous studies have confirmed DNAJB3â&#x20AC;&#x2122;s interaction with IKKB by co-immunoprecipitating them together, however the functional consequence of such interaction remains to be elucidated. Given the destructive role of JNK and IKKB stress kinases in aggravating insulin resistance by direct phosphorylation of the Insulin Receptor Substrate thus impeding insulin signaling, abrogating the activity of JNK and IKKB kinases to down-regulate the activation of pro-apoptotic genes and expression of inflammatory cytokine production is an important approach to control insulin resistance. Our data gives us promising insight into the key role played by the heat shock protein DNAJB3 in maintaining metabolic homeostasis shows a significant effect on inactivation of the apoptotic and inflammatory pathways by reducing the degree of activation of AP-1 and NF-kB transcription factors. DNAJB3â&#x20AC;&#x2122;s previously shown binding with JNK and IKKB could therefore inactivate JNK and IKKB decreasing their ability to phosphorylate AP-1 and IKBa respectively. Given the current world scenario where the number of people affected by obesity and diabetes is constantly increasing, the research project serves to be an important step towards determining potential therapeutic intervention at initial developmental stages of Obesity, Type 2 Diabetes and Insulin Resistance.

Chronic ER stress

Increased Inflammation

T2D

Impaired Insulin Signaling

Beta Cell Dysfunction

Defects in Heat Shock Response

Phosphorylation of AP-1

Transcription of pro-apoptotic factors Apoptosis

www.PosterPresentations.com

DNAJB3

Activation of IKKB (IKKB-p)

Phosphorylation of IKBa

HDAC4

Release and translocation of NF-kB to nucleus Transcription of inflammatory cytokines

Previous studies have confirmed DNAJB3’s interaction with IKKB by co-immunoprecipitating them together [4], however the functional consequence of such interaction remains to be elucidated. NFkB forms an inert complex with IKBa (substrate of IKK) in the cytoplasm and is translocated inside the nucleus when IKBa is phosphorylated by IKKB in the presence of stress where it activates the expression of various inflammatory genes. The recent finding that DNAJB3 interacts with histone deacetylase 4 (HDAC-4) protein, an epigenetic factor that deacetylates histone and certain nonhistone proteins (unpublished results) and that HDAC-4 inhibit IKK inflammatory pathway points to the assessment of the functional significance of formation of DNAJB3-HDAC4 complex under stressed conditions in attenuating inflammation.

Effect of DNAJB3/ HSP-40 on IKKB mediated Inflammatory Pathway

DNAJB3

Activation of JNK (JNK-p)

Previous studies have also shown that DNAJB3 binds to JNK and abrogated its activation following stress induction with palmitic acid.[4] Because JNK activates transcription factor AP-1 that causes expression of pro-apoptotic proteins, we hypothesize we that by binding to JNK and inactivating it, DNAJB3 leads to the inactivation of AP-1 and consequently protects against stress-induced apoptosis. Functional assays based on Luciferase reporter system driven by AP-1 transcription factor. We expect that DNAJB3 will abrogate the expression of AP-1 dependent luciferase activity in response to JNK inducers.

Effect of DNAJB3/ HSP-40 on JNK mediated Apoptotic Pathway

HSP-40/ DNAJB3 and its Clinical Significance DNAJB3; a member of the HSP-40 co-chaperone was recently shown to be downregulated in obese and diabetic individuals. Interestingly, the reduced expression of this protein in patients was reversed on physical exercise. [3]

HSP-40/ DNAJB3 interaction with JNK and IKK pathway

The c-Jun NH2-terminal kinase (JNK) stress kinase and the IKK inflammatory kinase are two key enzymes that phosphorylate and inactivate the insulin receptor substrate and thereby, converting it to a poor substrate of the insulin receptor in response to insulin and ultimately leading to T2D. [2]

Stress Kinases and Insulin Resistance

HSR is orchestrated by the induction of a set of proteins called heat shock proteins (HSPs) that play a fundamental role in restoring normal protein homeostasis and preventing multiorgan dysfunction. Recent evidence indicates that HSPs exert anti-inflammatory, anti-stress and anti-apoptotic activities in response to metabolic stress. In diabetic conditions, the expression of certain forms of HSPs is significantly reduced in a manner that correlates with the degree of insulin resistance. Consistent with these observations, interventions that restore the normal expression of HSPs improved the clinical outcomes and attenuated various forms of metabolic stress. [1]

Role of Heat Shock Response

Vicious Cycle of Type 2 Diabetes Progression

Given the current world scenario where the number of people affected by obesity and diabetes is constantly increasing, the research project serves to be an important step towards determining potential therapeutic intervention at initial developmental stages of Obesity, Type 2 Diabetes and Insulin Resistance.

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C2C12 cells were transfected with either pCMV-CRYAB, p-CMV-DNAJB3 or pCDNA-eGFP using calcium phosphate method and treated with 050ug/ml Tunicamycin overnight. Change in cell viability was measured using Promega G5420 Non Radioactive MTT Proliferation Assay kit, formazan product was solubilized with 10%SDS and absorbance was measured after 3 hours at 550nm.

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Co-transfection of DNAJB3(A) or HDAC4(B) with p-NF-kB-luc reporter vector in HEK293 cells inhibited activation and translocation of NF-kB and prevented its binding to the NF-kB recognition site on the reporter vector on induction of ER stress using 5uM PMA overnight for increasing amounts of DNA for transfection(A and B), as measured by Bright Glo Luciferase Assay System E2620 kit from Promega.

Fig. 3: NF-kB driven Luciferase functional assay shows DNAJB3 overexpression inhibits NF-kB activation in HEK293 cells

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Co-transfection of DNAJB3 (B) or HDAC4 (C)with p-AP-1-luc reporter vector in HEK293 cells inhibited phosphorylation of AP-1 and prevented its binding to the AP-1 recognition site on the reporter vector on induction of ER stress in a dose dependent manner using different concentrations of PMA(A) as well as DNA for transfection(B) (C), as measured by Bright Glo Luciferase Assay Screen Shot 2016-04-10 at 10.51.26 AM System E2620 kit from Promega.

Fig. 3: AP-1 driven Luciferase functional assay shows DNAJB3 and HDAC4 overexpression both inhibit AP-1 activation in HEK293 cells

(A) AP-1 transcription factor recognition site (7copies) driven luciferase gene expression (B) NF-kB transcription factor recognition site (3copies) driven luciferase gene expression as reporter vectors.

LUCIFERASE

TATA

AP-1 RECOGNITION SITE (enhancer)

Fig. 2: Reporter Vectors for Luciferase Functional Assay

RESULTS

Fig. 1: MTT proliferation assay shows DNAJB3 overexpression protects against stress-induced apoptosis in C2C12 myoblasts % change in viability compared to control Average RLU Average RLU

INTRODUCTION

METHODS

(3) ESTIMATION OF TRANSFECTION EFFICIENCY

(2) INCUBATION WITH TRANSFECTION MEDIA

(1) TRANSFECTION

(4) SPLITTING IN 96 WELLS, STRESS INDUCTION, LUCIFERASE or MTT ASSAY

REFERENCES

[1] Hooper, Philip L., and Paul L. Hooper. “Inflammation, Heat Shock Proteins, and Type 2 Diabetes.” Cell Stress & Chaperones 14.2 (2009) [2] Chaudhari, Namrata et al. “A Molecular Web: Endoplasmic Reticulum Stress, Inflammation, and Oxidative Stress.” Frontiers in Cellular Neuroscience 8 (2014) [3] Abubaker, Jehad et al. “DNAJB3/HSP-40 Cochaperone Is Downregulated in Obese Humans and Is Restored by Physical Exercise.” Ed. Ferenc Gallyas.PLoS ONE 8.7 (2013) [4] Abu-Farha, Mohamed et al. “DNAJB3/HSP-40 Cochaperone Improves Insulin Signaling and Enhances Glucose Uptake in Vitro through JNK Repression.”Scientific Reports 5 (2015): [5] Westerheide, Sandy D. et al. “Stress-Inducible Regulation of Heat Shock Factor 1 by the Deacetylase SIRT1.” Science (New York, N.Y.) 323.5917 (2009)

With certain studies establishing the regulation of Heat Shock Response by Deacetylases like Sirtuins that activate Heat Shock Factor-1[5], we are also exploring the effect of HDAC4 on activation HSF-1 to give an insight into how HDAC4 may be regulating Heat Shock Response.

With respect to recent unpublished data showing DNAJB3 and HDAC4 interaction, cotransfection studies for DNAJB3 and HDAC4 together with NF-kB or AP-1 needs to be done to evaluate the functional significance of DNAJB3 and HDAC4 complex in attenuating the activity of AP-1 and NF-kB. Following the inhibition of AP-1 and NF-kB activity, the role of DNAJB3 and HDAC4 overexpression on other pathways dependent on AP-1 and NFkB activation like FasL (Fas Ligand) that has binding sites for AP-1 and NFkB in its promoter and is a key player Fas-FasL dependent apoptotic pathway using reporter vectors with FasL promoter for NFkB and AP-1 binding sites. This approach will allow us to evaluate the physiological impact of DNAJB3 and HDAC4’s inhibition of AP-1 and NFkB.

While we were able to elucidate the functional significance of DNAJB3’s interaction with JNK and IKKB, our data also points towards the similar role played by HDAC4 in downregulating inflammatory and apoptotic pathways (Fig. 3B and 4B). Similar to DNAJB3, HDAC4 also attenuates AP-1 phosphorylation (Fig. 3B) thereby inhibiting AP-1 dependent expression of pro-apoptotic genes. We were able to confirm previously shown inhibition of NF-kB by HDAC4 overexpression and thereby control inflammation on stress induction (Fig. 4B).

Given the destructive role of JNK and IKKB stress kinases in aggravating insulin resistance by direct phosphorylation of the Insulin Receptor Substrate thus impeding insulin signaling, abrogating the activity of JNK and IKKB kinases to downregulate the activation of proapoptotic genes and expression of inflammatory cytokine production is an important approach to control insulin resistance. The heat shock protein DNAJB3 shows a significant effect on inactivation of the apoptotic and inflammatory pathways by reducing the degree of activation of AP-1 and NF-kB transcription factors. DNAJB3’s previously shown binding with JNK and IKKB could therefore inactivate JNK and IKKB decreasing their ability to phosphorylate AP-1 and IKBa respectively.

The promising results from MTT viability assay (Fig.1) suggested a protective role played by DNAJB3/ HSP-40 co-chaperone in combating stress induced inflammation and thereby preventing apoptosis in C2C12 myoblasts. The stable viability trend for hDNAJB3 transfected C2C12 on increasing Tunicamycin concentration and thereby stress and apoptosis compared to eGFP and CRYAB controls suggest DNAJB3 may be able to combat the irregular glycosylation and protein misfolding caused by Tunicamycin in C2C12. This prevention of apoptosis by DNAJB3 emphasized the need for carrying out pathway specific functional assays based on key research findings to identify molecular targets of DNAJB3.

CONCLUSION & FUTURE DIRECTION

Luciferase Functional Assay: HEK293 cells co-transfected with pAP-1-luc or pNF-kB (Fig. 2A and 2B) and pCMV-hDNAJB3 or pCMV-hHDAC4 in varying DNA amounts and split into 96 well opaque white plates at 20,000cells/well. Cells were then treated with 5uM PMA for stress induction overnight and luciferase expression was then quantified using Brigh Glo Dual Luciferase Assay system from Promega E2620 and luminescence was measured at 550-575nm.

MTT Assay for Cell Viability: pCMV-DNAJB3 or pCMV-CRYAB transfected C2C12 cells were split in 96 wells and treated with Tunicamycin or PMA to induce stress and apoptosis. Change in viability was then measured using Promega’s Aqueous Non Radioactive MTT Proliferation Assay kit G5420. MTT incubation was done for 3-4 hours and cells were solubilized with 10% SDS for absorbance reading at 550nm.

Transfection: C2C12 or HEK293 were transfected with vectors like pCMV, pCMVhDNAJB3, pCMV-hHDAC4, pCMV-hCRYAB, pCDNA-eGFP, pAP1-Luc or pNF-kBLuc using calcium phosphate-DNA precipitation in 2xHBS pH 7. Transfection efficiency was determined by spiking the DNA content with pCDNA-eGFP followed by estimation using confocal microscopy.

Cell Culture : C2C12 Myoblastss or Human Embryonic Kidney cells (HEK293) were cultured in DMEM + Glutamax culture media from Gibco Life Technologies, supplemented with 10% Fetal Bovine Serum and 1% 100X Penicillin Streptomycin from Gibco, Life Technologies. Cells were passaged at 70-80% confluency using 1X Trypsin-EDTA solution from Gibco.

By: Bushra Memon Supervisor: Dr. Mohammed Dehbi2 , Co- advisor: Dr. Gordon Rule3 1Biological Sciences Program, Carnegie Mellon University Qatar , Class of 2016 2Principal Investigator, Diabetes Research Group, Qatar Biomedical Research Institute 3Biological Sciences Program, Carnegie Mellon University Qatar

Role of DNAJB3/HSP-40 in Maintaining Metabolic Homeostasis 1

Average RLU Average RLU

The Effect of pH on the Activity and Affinity of Alkaline Phosphatase Authors Ettaib El Marabti Zamra Zahir Ali Abouelghar

Advisor Annette Vincent

Category Biological Sciences

Abstract The goal of our project was to determine the effect of pH on the activity of E. coli 6318 alkaline phosphatase (AP) and to finally obtain its optimal pH. Different prokaryotes have evolved APs that function optimally at different pHs. Since the E.coli 6318 was grown in LB with a pH of 7.4, we were interested in determining if this LB environment caused any changes in the reported optimal pH of E. coli AP, which is pH 8.0. We hypothesized that the optimal activity of AP will be at the reported value of pH 8. However, we were also interested in determining if pH 7 will change our hypothesis because of the E. coliâ&#x20AC;&#x2122;s pH 7.4 LB environment. Thus, 3 different pHs (7, 8 and 10) were tested using Tris-HCl buffers. The goal was achieved by constructing an enzyme saturation curve and a substrate saturation curve to obtain the amount of enzyme and substrate to be used for our assays, respectively. A Lineweaver-Burke plot was constructed based on the MichaelisMenton plot at pH 8, to determine the Km and Vmax values. A Michaelis-Menton and Lineweaver-Burke plot were also constructed at pH 7. However, there was not enough enzyme to do this for pH 10. We found that the optimal pH of AP was consistent with the literature value of pH 8, although the activity did not significantly decrease at pHs 7 and 10. The Km of AP was 7.41mM and 33.02mM at pH 8 and pH 7 respectively. Both values were significantly higher than the reported value of 0.013mM. The Vmax at pH 8 was 0.56 umol/min/ mg while at pH 7 it was 0.875 umol/min/mg. These results are contradictory with the findings that the optimal activity is at pH 8. Thus, it can be concluded that these results are not reliable because more data points need to be measured in order to be able to see a statistically significant difference.

Methods

Figure 2: Lineweaver-Burke plot using a constant concentration of pure E.coli Alkaline Phosphatase. Using the reciprocal of the reaction rates determined and the reciprocal of pNPP concentration the following curve was plotted and its equation was used to determine the Vmax and Km for pure E. coli AP.

Figure 1: Enzyme saturation curve using different units of enzyme at a constant substrate concentration of 11.2 mM Using different concentrations of AP from AP peak fraction the following plot was performed. The pNPP concentration was kept constant at a final concentration 11.2 mM. Each concentration of AP gave a different initial reaction rate that was measured at 405 nm wavelength using a microplate reader.

pH 7 29.61

8.39

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pH 7 9.31 x 10-3

7.01x10-3

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Figure 4: Lineweaver-Burke plot of AP activity at pH 8 and pH 7

Figure 3: Comparison of the reaction rate of Alkaline phosphatase from E. coli C6318 at different pH values The buffer used was Tris-HCl at the different pHs mentioned, and the abs/min was measured for 3 minutes using a microplate reader.

Table 1: The effect of pH on Km and Vmax on alkaline phosphatase isolated from E. coli C6318

Data

0.0436 ug/ml was the enzyme concentration used for the Michaelis-Menton substrate saturation curve. For this curve, the substrate concentrations were varied from 5mM to 60mM and the abs/min was obtained in triplicates at a pH of 8. This was done to obtain the substrate concentration that could be used for the pH assay, where the substrate should not be limiting. Using this plot, an inverse Lineweaver-Burke plot was created, and the Vmax and Km were calculated using the intercepts. The Michaelis-Menton and Lineweaver-Burke plot process was repeated for a pH of 7, in order to obtain the Km and Vmax at this pH. The optimal enzyme and substrate concentrations obtained from the above plots were used

Evaluating kinetic parameters Km and Vmax

The enzyme saturation curve was obtained by keeping the substrate concentration constant at 11.2mM, and varying the concentrations of enzyme. This was done in order to determine the concentration of enzyme at the point of saturation to be used for the Michaelis-Menton plot. The substrate, with a final concentration of 11.2mM, the diethanolamine buffer and the respective volumes of the enzyme were added to microplate wells and triplicates of the change in absorbance over time were obtained immediately using the microplate reader, for each enzyme concentration. The abs/min was obtained at a wavelength of 405nm over a period of 3 minutes for each sample.

Enzyme saturation curve

The goal of our project was to determine the effect of pH on the activity of E. coli 6318 alkaline phosphatase (AP). Different prokaryotes have evolved APs that function optimally at different pHs. Since the E.coli 6318 was grown in LB with a pH of 7.4, we were interested in determining if this pH environment caused any changes as the reported optimal pH of E. coli AP, is pH 8.0. Thus, activity of AP at two different pHs (7 and 8) was measured by quantitating the dephosphorylation of pnitrophenol phosphate into nitrophenol. A Lineweaver-Burke plot was constructed based on the Michaelis-Menton plot at pH 8, to determine the Km and Vmax values. A Michaelis-Menton and Lineweaver-Burke plot was also constructed at pH 7. We found that the optimal pH of AP was consistent with the literature value of pH 8, although the activity did not significantly decrease at lower pH . The Km of AP was 7.41mM and 33.02mM at pH 8 and pH 7 respectively. However, the Vmax at pH 8 was 0.56 umol/min/mg while at pH 7 it was 0.875 umol/min/mg illustrating that the enzyme was more active at lower pH.

Abstract

We would like to thank Jayden Park and Hamad Al-Hail for providing the purified bacterial Alkaline phosphatase. We would also like to thank Maya Kemaldean and Maria Bernales for their support

Acknowledgements

2. Dowd EJ, Riggs SD. A comparison of estimates of Michaelis-Menten kinetic constants from various linear transformations. J Biological Chemistry [Internet]. 1965 Feb; 240:863-869.

1. The effect of substrate concentration on enzyme activity [Internet]. University College London; [cited 2016 March 07]. Available from http://www.ucl.ac.uk/ ~ucbcdab/enzass/substrate.htm

References

AP in E. coli is important in the recycling of nutrients such as phosphates which are obtained from the environment, and is needed for growth and survival. Thus, the AP activity must be able to function optimally at the environmental conditions in the habitat of the bacteria. Since LB has a pH of 7.4, coupled with the fact that the reported value for E.coli is a pH 8, we hypothesized that the activity will be optimal between these two pHs. However, we cannot make an accurate conclusion based on our results due to the contradictory data.

Conclusion

Figure 3 indicates that the highest reaction rate occurs at pH 8 which is reported in the literature as the optimal pH for AP activity. By observing the trend of the curve in Figure 3, the activity decreases at pH 7 and 10. However, by performing the t-test and comparing activities at pH 10 and 7 to that at the optimal pH 8 we concluded that the observed decrease is not statistically significant. Then in order to test the effect of pH on Km and Vmax, a Michaelis-Menton plot and a Lineweaver-Burke plot was constructed at pH 7. The latter was used to calculate the Km and Vmax. The Km was calcu-ated to be 29.61 mM while the Vmax was 9.31 x 10-3 umol/min. The Km was higher at pH 7 compared to that calculated at pH 8 (8.39 mM) and also to the reported Km value of 0.013 mM, which might indicate that pH decreases the affinity of AP to pNPP. Nevertheless, due to the fact that pH 7 had only 3 data points, we cannot have high confidence in the previous conclusion as it may not have high statistical significance. In

Enzyme saturation was performed by keeping pNPP concentration constant while changing the amount of AP to generate the enzyme saturation curve to determine to amount of enzyme needed. The reaction rate obeyed first order kinetics where it increased steadily as the concentration of enzyme increased. After determining the concentration from the enzyme saturation assay, a substrate concentration assay (Michaelis-Menton plot) was performed. In this assay, the determined enzyme concentration was kept constant while the concentration of substrate (pNPP) was increased. Ideally, this was to be done until the reaction rate stabilized at Vmax. This was done to determine Km and Vmax of AP in addition to the pNPP concentration required to reach Vmax in order to avoid pNPP from being limiting, in our following experiment. The Michaelis-Menton plot obeyed first order kinetics and the reaction rate increased with increasing pNPP concentration. However, it kept increasing till 60 mM and so Vmax was not reached. Nevertheless, by plotting the reciprocal Lineweaver-Burke plot we obtained the Vmax and Km. The Lineweaver Burke plot had an R2 value of 0.953 and using the equation of this curve y = 1196.1x + 142.53 we calculated Vmax to be 7.01 x 10-3 umol/min, and Km 8.39 mM at a pH of 8. The calculated Km for AP 8.39 mM, which is higher than the reported value of 0.013 mM. This is because, although the R squared values were good, only 3 data points were used for the plot which might be the reason for the high R2. The data could be tightened up by increasing the number of data points and decreasing the standard deviation in each data point. There is high variability in our data which can be observed through the large error bars especially in the Lineweaver-Burke plots (Figure 4). Consequently, the obtained Km values are too high due to the inaccuracy of the Lineweaver-Burke plot and the variability in the data.

Analysis

Analysis of Microbiome in Water Systems in Doha

Authors Farah AbdelAziz F. Zamra Zahir

Advisors Basem Shomar (Qatar Environment and Energy Research Institute) Azhar Siddique (Qatar Environment and Energy Research Institute) Annette Vincent

Category Biological Sciences

Abstract The diversity of the microbiome and the different roles it plays in the ecosystem is vast. They can range from benefiting humans such as aiding the digestive system or they can have harmful effects. Of interest is the microbiome that inhabit water systems. Helicobacter pylori and other microorganisms are leading causes of water borne diseases in developing nations. Therefore, water filters play an important role in eliminating these bacteria to a varying extent. The purpose of this project is to carry out taxonomic classification of bacteria present in water systems in Doha. This is achieved through different biological techniques such as microbiology, DNA isolation, PCR and next-generation sequencing. DNA was extracted directly from Granular activated carbon (GAC) filters and water samples collected at various stages of the water system were further cultured. Morphological data obtained from cultured samples demonstrate the important use of water filters as they reduce the bacteria in water and in this way they reduce water contamination. DNA quality was evaluated using PCR targeting the 16S rDNA region of the bacterial genome. 92% (11 out of 12 samples) of the DNA isolated using the PicopureTM and modified Qiagen kits were amplifiable therefore affirming the DNA quality. Future work involves sequencing hypervariable regions on the 16S region to identify the taxonomy of the microbiome. Consequently, bacteriophages can be applied in order to eliminate these bacteria and provide clean water in a chemical free manner.

Introduction

www.PosterPresentations.com

Figure1. Stages of sampling through the water system

GAC filters

Water supply to household

Water supply to city

Stage 4: Samples were directly collected from GAC filters

Stage 3: Samples were collected after passing through filters

Stage 2: Samples were collected before passing through filters

Stage 1: Water samples were collected before passing through households

Microbiome play an important role in the environment as they have diverse effects on both the community and humans. Several waterborne diseases are a result of microbes such as Helicobacter pylori which can result in detrimental effects to individuals. Therefore, water filters are essential to eliminate bacteria for safe consumption. Different types of filters remove bacteria to varying extents. However, these filter units have finite lifespans. The purpose of this project is to identify the microbial population in household water systems in Doha, Qatar using a set of molecular biology techniques. Consequently, upon taxonomic classification of the microbes, host range analysis with bacteriophages will be tested in an attempt to eliminate possible pathogenic bacteria. Samples were collected from four different stages in the local water system which use granular activated carbon (GAC) filters. The first and second stages involved collecting the water samples before they pass through the filter. The third stage was carried out by directly collecting samples from the GAC filters for DNA extraction. The fourth stage involved collecting the water samples after passing through the filter. The water samples from the first, second, and fourth stages were then cultured to isolate bacterial colonies from which DNA was isolated. To further assess the quality of the isolated DNA, PCR was performed on the 16S rDNA regions of the bacterial genome before sequencing.

1201 1201

UB341F UB1541R

CCTACGGGAGGCAGCAG

Primer Sequence

AAGGAGGTGATCCAACCACA

0.2mM 0.2uM 0.2uM 5 ng 1 unit To make up total reaction volume of 50µl

Forward Primer Reverse Primer DNA (5ng/rxn) Taq (1unit/rxn) Sterile nuclease free water

94 94 53 72 72 4

Initial Denaturing Denaturing Annealing Extension Final Extension Hold

Hold

10 minutes

90 seconds

2 minutes

45 seconds

3 minutes

Temperature Time (°C)

Step

x35

Cycles

1X buffer

Table 3. PCR thermocycling conditions

Final concentration/amount

Reagent

Melti ng Point (⁰C) 58.2

10 x Master Mix (100mM Tris-HCl, 15mM MgCl2, 500mM KCl; pH8.3) dNTPs

Table 2. PCR reaction mixture

Expected Product Size (bp)

Primer Pair

Table 1. Primers used for PCR

Qualitating isolated DNA using 16S rDNA primers: A set of primers was used for PCR in order to amplify the 16S rDNA of the rrnH operon between nucleotide number 341 and 1541 region on the bacterial genome. 16 tubes were prepared in total that included each of the DNA samples along with their controls.

Isolation of DNA from GAC: Isolation of bacterial DNA from three GAC samples was done using the procedure developed for QIAaMP DNA stool mini kit and QIAaMP DNA blood midikit. The extracted DNA was reprecipitated using CH3COONa/Ethanol precipitation protocol.

DNA extraction from cultured bacteria: The PicoPure™ DNA extraction kit (Life Technologies) was used to isolate genomic DNA from the bacterial samples. The extracted DNA was further purified through treatment with RNase A (10 mg/mL) at 37⁰C for 30 minutes and precipitated overnight at 20⁰C using CH3COONa/Ethanol. The precipitated DNA was resuspended in nuclease free water and quantitated using Qubit.

Culturing bacteria from water samples from stages 1-3: The water samples that were obtained before and after filtration were further cultured on R2A agar. 100mL of each sample was passed through a 0.45uM membrane and cultured for 3 days at 36.5 ⁰C . In addition, 100uL and 1mL of the samples were spread over R2A agar plates and incubated for 3 days at 36.5 ⁰C .

Materials and Methods

Single colony

0.0544 0.0400 Less than 0.5 0.224 0.636 2.90 1.44 0.532 5.02 4.70 15.6

Concentration (ng/uL)

Two different midi gels were performed for PCR products. The first gel contained bands for the control lane along with the DNA samples. This could have been due to contamination, mishandling of the pipette tips, or formation of primer dimers. As a result, new reagents were prepared and diluted and the control tubes were separated from the tubes containing the DNA samples. Consequently, a second gel was run. Positive results were obtained as no bands were shown for the control lane and bands were observed for the DNA samples.

PCR gel analysis

g: Isolated bacterial DNA from a cultured sample; stage2.

f: Isolated bacterial DNA from a cultured sample; stage 1.

d, e, h, and i: Isolated bacterial DNA from cultured samples; stage 3.

a, b, and c: Isolated bacterial DNA; stage 4

x GAC #1a GAC #2b GAC #3c 2-Af 2-Bg 2-Cd 3-Ce 4-Af 4-Bg 4-Ch 7-Ci

Type of DNA sample

Figure 2: Images of the different colonies that were used for isolating the different DNA samples. Different volumes of the samples were plated on LB medium and stored at 4 ⁰C, resulting in different colors and sizes of colonies on each plate. a) 4-C sample was obtained from Al-Muntazah. The water was used for drinking. 100uL of the water sample was injected into the plate and small bright orange colonies were obtained. b) 3-C sample was obtained from Fareej AbdelAziz. 100uL of the sample was injected and as a result multiple densely populated colonies were formed that resulted in a white dense color. c) 4-A sample was obtained from the same place as 4-C. 1mL of the sample was injected and the same result appeared for 4-A as in 3-C. d) 7-C sample was obtained from Almuntazah. 100uL of the sample was injected and as a result different colonies were obtained with different sizes, numbers, and colors. There were 85 small colonies that contained orange color, 19 small colonies with a yellow color, and 3 colonies of a white color. e) 4-B sample was obtained from the same location as 4-C sample. 1mL of the sample was injected and as a result 4 large orange colonies were observed and many small orange colonies were observed around the edge of the plate. Table4. Concentrations of the DNA samples using Qubit

Biofilm (multiple colonies that stick to each other)

Results

1: Carnegie Mellon University, Qatar 2: Qatar Environment and Energy Research Institute (QEERI)

Our special thanks go to Maya Kemaldean, Bernadette Bernales, and Maria Navarro for their valuable help and support during our laboratory work.

Acknowledgments

Qiagen (2012). QIAamp DNA Stool Handbook. Retrieved from: www.qiagen.com Qiagen (2010). Isolation of bacterial DNA from soil using the QIAamp® DNA Stool Mini Kit and QIAamp DNA Blood Midi Kit. Life Technologies (2010). Arcturus ® PicoPure ® DNA Extraction Kit Manual. ThermoFisher Scientific. Qubit ® 3.0 Fluorometer. GATC Biotech Manual (2016).

References

Figure4. Hyper-variable regions of Bacteria

Each of the samples from each stage contained different sized colonies with different colors. Bacterial colonies were still obtained after passing through the filters but were smaller in size compared to the ones that were collected before filtration. As a result, it is crucial to install water filters as they reduce the number of bacterial colonies. Furthermore, it is necessary to change the filters throughout time as DNA isolated from the filters indicated the accumulation of bacteria. Filters will eliminate as much of the bacteria as possible and ensure a safe and clean water supply. By studying the genes and therefore the function of the microbiome through computational tools, water-related diseases can be eliminated. As a part of future work, sequencing of the isolated DNA will be performed in order to identify the type of bacteria. This can be achieved by sequencing specific hypervariable regions on the 16S rDNA to allow taxonomic analysis. These regions are unique to each type of bacteria and act as their fingerprints. Bacteriophages can then be applied to kill the bacteria which is an alternative to the use of antibiotics or chlorine.

Conclusion

Figure 3. 16s rDNA PCR products using agarose gel electrophoresis. Lanes 1, 3, 5 are products from GAC samples; Lanes 7, 9,11 are from Stage C colonies and Lanes 13, 15 from Stages A and B respectively. L is the 1kb ladder (NEB). The even number lanes are the controls that do not contain template DNA. The presence of a band at 1201bp indicates amplifiable DNA.

A 1.2% agarose gel was stained with ethidium bromide and the gel was run for 1 hour at 100V in Tris/borate EDTA buffer. PCR products were run alongside a DNA ladder and products of size 1201 bp were observed in most of the isolated DNA samples. This as a result affirms the quality of the isolated DNA.

Farah AbdelAziz1, F. Zamra Zahir1, Basem Shomar2, Azhar Siddique2, Annette Vincent1

Analysis of Microbiome in Water Systems in Doha

Comparison of Kinetic Behavior Between E. coli and Calf-Intestinal Alkaline Phosphatase Using Nitrophenyl Phosphate (NPP) Authors Dana Abou Samhadaneh Khawla Al-Darwish

Advisor Annette Vincent

Category Biological Sciences

Abstract Intestinal alkaline phosphatase (IAP) is crucial in maintaining intestinal homeostasis and health through interactions with the resident microbiota, diet and the gut. IAPâ&#x20AC;&#x2122;s role in the intestine is to dephosphorylate toxic microbial ligands such as lipopolysaccharides, hence, allowing for a healthy gut microflora. The goal of the project was to investigate and compare the kinetic behavior of mammalian alkaline phosphatase isolated from calf-intestines (CIAP) and Bacterial E. coli alkaline phosphatase (BAP). This was carried out using a UV-spectrophotometer to measure the enzyme activity of AP, using NPP as a substrate. The optimal enzyme and substrate concentrations were then used to measure the enzyme activity over a span of 1-2 minutes. It was found that the Km and Vmax for CIAP are 1.33 mM and 0.27 umol/min, respectively; whereas the Km and Vmax for BAP are 0.22 mM and 0.0097 umol/min, respectively. Therefore, it was concluded that mammalian AP is more efficient than bacterial AP; however, it has lower affinity towards NPP.

Effect of Aspartame on Malate Aspartate Shuttle in MDCK Cellsfortlessly Author Maryam Aghadi

Advisor Annette Vincent

Category Biological Sciences

Abstract Aspartame is a low calorie sweetener widely used in diet beverages. Studies in the past have shown that the long-term exposure of aspartame to mouse PC12 neuronal cells have resulted in mitochondrial mediated apoptosis. As kidney cells serve as a natural filter of the blood and are involved in waste removal; therefore the purpose of this study was to determine the effect of aspartame on kidney cells. In order to see the activity of intracellular dehydrogenases upon exposure to aspartame, MTT (4,5-dimethylthiazol-2-yl-2, 5-diphenyltetrazolium bromide) assay was carried out, and it showed elevated activity of dehydrogenases upon exposure to 250ug/ml aspartame for 0.5 and 1 hour. Moreover, functional analysis of intracellular dehydrogenases showed no effect in the presence and absence of aspartame, which indicated absence of any direct effect of aspartame on the functionality of dehydrogenases. As aspartate, a metabolic product of aspartame, is a precursor of malate in the malate aspartate, therefore participation of aspartame in the malate aspartate shuttle was hypothesized. It was validated by the quantification of the level of pyruvate in the cells, which showed a 2000 fold elevation upon exposure to 250ug/ml aspartame for 1 hour. Moreover, pyruvate levels were dropped to baseline levels on inhibiting aspartameâ&#x20AC;&#x2122;s conversion to the precursor of malate, which confirmed participation of aspartame in the malate aspartate shuttle. In order to determine the underlying effects caused by shuttleâ&#x20AC;&#x2122;s hyperactivity, intracellular stress level was evaluated by quantification of intracellular reactive oxygen species, which showed elevated levels over the time upon exposure to 250ug/ml aspartame.

Isolation, Purification, and Complete Genome Sequence of Bayan Bacteriophage, a Potential Therapeutic Tool for Tuberculosis Authors Najlaa Al-Thani Dana Al-Eshaq

Advisors Annette Vincent Valentin Ilyin

Category Biological Sciences

Abstract Mycobacteriophages are viruses that infect mycobacterial hosts, such as Mycobacterium tuberculosis and Mycobacterium smegmatis. Phages are widely used in research as tools to transport genetic material by constructing vectors as well as other experimental genetic purposes. Many studies have been conducted to study the therapeutic potential of phages that target and lyse tuberculosis-causing bacteria, Mycobacterium tuberculosis. To date, in vitro studies were successful, yet animal models are to be tested in order to validate the implementation of this phage therapy. The goal of this project was to isolate and purify a novel mycobacteriophage from the soil samples, and ultimately extract the phage nucleic acid to be able to sequence and annotate its genome. Mycobacteriophage Bayan was isolated from soil samples taken from Devonshire Road in Pittsburgh, Pennsylvania. Phage DNA was extracted from the purified high-titer phage lysate, by phenol chloroform extraction. Full Annotation of phage genome was done on DNAMaster, from which the synthase protein was found to be present in this phage could be able to alter the DNA composition of M. tuberculosis, a cousin of M. smegmatis.

Figure 1: Alignment scores of Bayan mycobacterium phage

Fastq file was imported and the reads were aligned using SoapDENOVA 2 program with optimum k-mer size equal to 53. Coverage was then reduced to 60, two contigs were produced and sequence was run again with SoapDENOVA. Blast with NCBI against nr database revealed match with Mycobacterium Phage Meezee Complete Genome.

Genome Assembly

A soil enriched phage containing sample was collected to which M. smegmatis was added to infect. A single plaque was picked, after pour plating, for further rounds of isolation and purification 5. Then, high titer phage solution was harvested by performing 10-web plates infection. A final phage titer of 1.48 – 2 x109pfu/mL was achieved. Phages were imaged using an electron microscope. Using the high-titer phage lysate, phenol chloroform extraction technique 1 was conducted to extract phage DNA. Final concentration of DNA purified was 312ng/µl. The genome was sequenced via MiSeq platform (Illumina), using the 2 × 150-bp protocol yielding paired-end reads. Following sequencing, raw BCL (binary base call) files were retrieved from the MiSeq platform and called into fastqs by Casava v1.8.3 (Illumina).

Methods

Mycobacteriophages are viruses that infect mycobacterial hosts, such as Mycobacterium tuberculosis and Mycobacterium smegmatis 1. Phages are widely used in research as tools to transport genetic material by constructing vectors as well as other experimental genetic purposes 5. Many studies have been conducted to study the therapeutic potential of phages that target and lyse tuberculosis-causing bacteria, Mycobacterium tuberculosis. To date, in vitro studies were successful, yet animal models are to be tested in order to validate the implementation of this phage therapy. The goal if this project was to isolate and purify a novel mycobacteriophage from the soil samples, and ultimately extract the phage nucleic acid to be able to sequence and annontate its genome. Mycobacteriophage Bayan was isolated from soil samples taken from Devonshire Road in Pittsburgh, Pennsylvania.

Introduction

Figure 4: Sequence Alignment of Contig 2 Showing Similarities with Mycobacterium Tuberculosis Thymidylate Synthase.

Query 173 LPNMTNSPMVVTGNHRAWRYVIKARWHEAADAEIRSLAGELLKQLREIAPHTYQDI 228 LPN T + +VVTGN+RAWR+ I R E AD EIR LA E L+QL +AP + D Sbjct 175 LPNATETRIVVTGNYRAWRHFIAMRASEHADVEIRRLAIECLRQLAAVAPAVFADF 230

Query 120 KDLIDAPGRGYFRAKELLEEIQHASAEAYDELVTI----YAE---AGLGRKKAREAARAV 172 +D D + +L E A+ Y EL+ +A+ A L RK+AR+AARAV Sbjct 123 EDDADL--------RHILTEAADAARATYSELLAKLEAKFADQPNAILRRKQARQAARAV 174

Query 61 HILDVGHESVLEHASATFYIEA-SRSVLTELERHRHLSFSVVSQRYVDPTELGVHEPPAV 119 HI+DVGH SVLEHAS +FYI SRS EL RHRH S+S +SQRYV + V PP + Sbjct 63 HIIDVGHFSVLEHASVSFYITGISRSCTHELIRHRHFSYSQLSQRYVPEKDSRVVVPPGM 122

Alignment statistics for match #1 Score Expect Method Identities Positives Gaps 180 bits(456) 7e-55 Compositional matrix adjust. 110/236(47%) 141/236(59%) 20/236(8%) Query 1 MKVKLIASTVLEDPYWAGTGYEDSGTPSSADELAEFAGRNCYRSFSRPNPATRENVDYLK 60 ++V+LIA T P + G P+ L EFAGR CY+S+S+PNP T N YL+ Sbjct 7 LRVQLIAKTDFLAPPDVPWTTDADGGPA----LVEFAGRACYQSWSKPNPKTATNAGYLR 62

Chain A, Crystal Structure Of Mycobacterium Tuberculosis Thymidylate Synthase X Bound To Fdump And Fad Sequence ID: pdb|3GWC|ALength: 258Number of Matches: 1

Figure 3: Complete annotation of contig 1 (right) and contig 2 (left)

Figure 2: Electron Micrographs of Bayan Bacteriophage.

Data

Najlaa Al-Thani, Dana Al-Eshaq, Annette Vincent, Valentin Ilyin Biological Sciences Program, Carnegie Mellon University Qatar

1. 2.

PCI DNA Extraction: Phagehunting Protocols (2013) phagesdb.org Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., & Yuan, J. et al. (2015). Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 4(1). http://dx.doi.org/10.1186/s13742-015-0069-2 Lawrence, J. (2007). Lawrence Lab HomePage. Lawrence Lab/Computer Programs. Retrieved 29 March 2016, from http://cobamide2.bio.pitt.edu/ Loren Baugh, Isabelle Phan, Darren W. Begley, Matthew C. Clifton, et. al. (2015) Increasing the structural coverage of tuberculosis drug targets, Tuberculosis, Volume 95, Issue 2, Pages 142-148, ISSN 1472-9792, http://dx.doi.org/10.1016/j.tube.2014.12.003. SEA-PHAGE Lab Manual.(2013) Howard Hughes Medical Institute

References

We would like to thank Maya Kemaldean and Chloe Glynn for the technical support. We will also like to thank the Genomics Core Facility at Weill-Cornell Medical College in Qatar for the sequencing work..

Acknowledgments

The increased prevalence of antibiotic resistance amongst disease causing bacteria has led to new frontiers in phage therapy. Phage therapy is a potential alternative therapy to antibiotics as these bacteriophages lyse, and thus, kills their infectious bacteria hosts. In this study, using a nonpathogenic mycobacterium strain, a potential bacteriophage that could infect and lyse Mycobacterium tuberculosis was identified. Through annotation of the phage genome, the presence of a gene closely linked to this pathogenic bacteria was identified.

Conclusion

• Turbid phages were observed which could indicate that Bayan phage is a temperate phage 5. • Annotation of phage genome was done on DNAMaster (3). Each protein of the set of genes from both contigs obtained from assembly were blasted against both pdb and nr databases. Results were recorded and full annotation of genome was complete. • Blast on pdb database of gene 36 in contig 2 showed similarities to Mycobacterium tuberculosis Thymidylate Synthase 4.

Discussion

Figure 5: Plaque morphology of Bayan phage was turbid.

Data

Isolation, Purification, and Complete Genome Sequence of Bayan Bacteriophage, a Potential Therapeutic Tool for Tuberculosis

Acute Toxicity of Saccharine on Proximal Tubular Kidney Cells Author Rayan Hashim

Advisor Annette Vincent

Category Biological Sciences

Abstract In the early 1970s, saccharine was linked to bladder cancer in laboratory rats. Therefore, the aim of this project was to further investigate the effects of saccharine on the renal system, more specifically on proximal tubular kidney cells. Saccharine is present in many commercially available artificial sweeteners, for example, the HPLC analysis showed that saccharine makes up 3% of Sweet and Low content. At 7.5, 3, 1.5, 0.3 and 0.15 Îźg/ml of saccharine, it was found that the viability of MDCK II decrease over short time period incubation. Assessing the apoptotic markers suggests that the cells were not undergoing programmed cell death, neither DNA fragmentation nor cleavage of Poly ADP ribose polymerase (PARP).

Saccharin is a relatively new FDA approved nonnutritive sweetener found in many commercial sweeteners like Sweet and Low. [1] It was placed on the list of potential carcinogens until 2000 due to previous studies that showed the development of bladder cancer in rats after a saccharine based diet. The study was conducted on Madin-Darby Canine Kidney epithelial cells II (MDCK) because they are precursors of bladder in the renal system and the organ responsible for blood filtration and removal of drugs, such as saccharine from the system. The assays used to assess the cell viability were: (3-(4,5-dimethylthiazol-2-yl)-2,3diphenyltetrazolium bromide (MTT) assay, Nucleosomal fragmentation assay and Poly ADP ribose polymerase (PARP) assay.

Introduction

In the early 1970s, saccharin was linked to bladder cancer in laboratory rats. [1] Therefore, the aim of this project was to further investigate the effects of Saccharine on renal system, more specifically on proximal tubular kidney cells. Saccharine is present in many commercially available artificial sweetener, for example, the HPLC analysis showed that saccharine makes up 3% of Sweet and Low content. At 7.5, 3, 1.5, 0.3 and 0.15 μg/ml of saccharine, it was found that the viability of MDCK II decrease over short time period incubation. Assessing the apoptotic markers suggest that the cells were not undergoing programmed cell death, neither DNA fragmentation nor cleavage of Poly ADP ribose polymerase (PARP).

Abstract

Rayan Hashim rmahmoud@qatar.cmu.edu

* *

Figure 3: Nucleosomal fragmentation for MDCK cells after exposure to Saccharine on 0.7% agarose gel in 1X TBE buffer. The gel ran for 1.5 hours at 100 V. Figure Key: 1.1kb ladder, 2. Positive control (cycloheximide), 4. Negative Control (Culture media), 6. 7.5ug/ml of saccharine, 8. 0.15ug/ml of saccharine

Figure 4: PARP assay for MDCK cells after exposure to saccharine for 30 minutes. Figure Key: 1. SeeBlue +2 protein ladder 2. Positive Control (DMEM) 3. Negative Control (PBS) 4. Negative Control (Culture Media) 5. 250ug/ml Sweet and Low for 24hr 6. 5ug/ml Sweet and Low for 24hr 7. 250ug/ml Sweet and Low for 0.5hr 8. 5ug/ml Sweet and Low for 0.5hr

Figure 2: Cell viability of MDCK cells measured by MTT assay. A) The MTT results after exposure to various concentrations of saccharine for 30 minutes. B) The MTT results after exposure to to various concentrations of Sweet and Low for 24 hours. The absorbance was measured at 550nm using a micro-plate reader. Each data bar represents the mean of data from three wells (n=3) with error bars representing the SEM. Negative control wells didn’t contain additive while the positive control contained DMEM. Stars indicates P-value less than 0.05.

Figure 1: HPLC analysis of the saccharine content in Sweet and Low sweetener. A) The HPLC result obtained in a phosphate buffer (pH 4.3) : acetonitrile mobile phase of 80:20 ratio. B) The standard curve of analytical saccharine standards ranging between 5 and 250 μg/ml.

Results

Carnegie Mellon University in Qatar Biological Sciences Program

1. Reuber, M D. “Carcinogenicity of Saccharin.” Environmental Health Perspectives 25 (1978): 173–200. Print.

References

Conclusion

In conclusion, the effect of Saccharine on MDCK cells was investigated using MTT assay, PARP and nucleosomal fragmentation assay. A decrease in cell viability was observed upon exposure to saccharine and Sweet & Low sweetener for short time intervals. This cell response is possibly due to the inactivation of the metal protein-cofactors such as Zinc and Magnesium. Current research is focusing on the mechanism of enzyme deactivation by saccharine.

and incubated with AP coupled antibodies.

incubation with saccharine, transferred on PVDF membrane

PARP: Proteins were extracted from cells after 30 minutes of

genomic DNA extraction from mammalian cells protocol.

MDCK cells after 30 minute exposure to saccharine using

Nucleosomal fragmentation: DNA was extracted from the

measured at 570 nm.

wells were exposed to saccharine. The absorbance was then

Cell viability assay: 10,000 cells per well in 96-well plate, the

were incubated in 5% CO2 at 37oC incubator.

Bovine Serum, 1% Penicillin and DMEM. The culture flasks

Cell culture: The MDCK cells were cultured in 10% Fetal

phosphate buffer (pH 4.3) : acetonitrile mobile phase of 80:20

HPLC: Samples of sweet and low were analysed in a

Methods

Annette Vincent, Ph.D annettev@qatar.cmu.edu

Acute toxicity of Saccharine on Proximal Tubular Kidney Cells

Inhibition of Human Placental Alkaline Phosphatase (PLAP) by L-Phenylalanine Authors Asma Al-Naama Safa Salim

Advisor Annette Vincent

Category Biological Sciences

Abstract Alkaline phosphatase (AP) is an enzyme present in the periplasmic space that catalyzes the hydrolysis of phosphomonoesters resulting in the release of inorganic phosphate and alcohol at alkaline pH. Placental Alkaline Phosphatase (PLAP) isoenzyme is a product of the same gene, with small differences due to postgenetic modifications. Rise in the activity of AP in the body has been associated with bone diseases, liver diseases, hyperthyroidism, and malignant processes. L-phenylalanine is an uncompetitive inhibitor of AP, that is, it binds to the enzyme-substrate complex, rather than to the free enzyme. However, not a lot is known about the enzymatic, physical, and immunological characteristics of PLAP. Thus, our goal was to determine the kinetic parameters (Km and Vmax) of PLAP, and to study the effect of L-phenylalanine on the activity of PLAP, in the presence of p-Nitrophenyl Phosphate (pNPP) as the substrate, using the standard enzyme assay. The dephosphorylation of pNPP by PLAP produces nitrophenol, which can be colorimetrically measured at 450nm. Our hypothesis was that L-phenylalanine would uncompetitively inhibit PLAP with pNPP as the substrate using 1M diethanolamine, 0.5mM MgCl2, pH 9.8 buffer. Based on the enzyme saturation curve, 0.0150mg was chosen to be the amount of PLAP that would be used for all enzymatic reactions. Based on the Lineweaver Burke plot in the absence of inhibitor, the Km was calculated to be 4.53mM, and the Vmax was calculated to be 0.0894umol/min. Based on the Lineweaver Burke plot in the presence of inhibitor, the Km was calculated to be 0.0384mM, and the Vmax was calculated to be 5.16E-03umol/min. Thus, we successfully determined the kinetic parameters of PLAP, and concluded that PLAP is uncompetitively inhibited by L-phenylalanine.

ABSTRACT

Michaelis-Menton plot and Lineweaver Burke plot in the presence of inhibitor: In order to determine the effect of L-phenylalanine on the activity of PLAP, the enzyme assay was carried out by using 0.0500mg of PLAP enzyme and 5mM of L-phenylalanine inhibitor, and varying the substrate concentration from 0.1-5mM. The reaction was carried out in 1M diethanolamine, 0.5M MgCl2, pH 9.8 buffer at 37oC. The Michaelis-Menton plot was then constructed, and its reciprocal produced the Lineweaver Burke plot, which allows determining the Km and Vmax in presence of L-phenylalanine.

Lineweaver Burke plot in the absence of inhibitor: The reciprocal of the Michaelis-Menton plot produced the Lineweaver Burke plot (1/(reaction velocity) vs. 1/(substrate concentration)), which allows determining the Km and Vmax.

Michaelis-Menton plot in the absence of inhibitor: After determining the enzyme concentration from the enzyme saturation curve, the Michaelis-Menton plot, which is the reaction velocity (umol/min) vs. substrate concentration (mM), was constructed by varying the substrate concentration from 0.1-5mM, and using 0.0500mg of PLAP. The reaction was carried out in 1M diethanolamine, 0.5M MgCl2, pH 9.8 buffer at 37oC.

Enzyme saturation curve: The enzyme saturation curve, which is the reaction velocity (umon/min) vs. amount of enzyme (mg), was prepared by using excess pNPP substrate at a concentration of 11.2mM, and varying the amount of PLAP enzyme from 0.0010.05mg. The reaction was carried out in 1M diethanolamine, 0.5M MgCl2, pH 9.8 buffer at 37oC. This step ensures that the enzyme is not the limiting reagent in the reaction.

METHODS

Alkaline phosphatase (AP) is an enzyme present in the periplasmic space that catalyzes the hydrolysis of phosphomonoesters resulting in the release of inorganic phosphate and alcohol at alkaline pH. Placental Alkaline Phosphatase (PLAP) isoenzyme is a product of the same gene, with small differences due to post-genetic modifications. Rise in the activity of AP in the body has been associated with bone diseases, liver diseases, hyperthyroidism, and malignant processes. L-phenylalanine is an uncompetitive inhibitor of AP, that is, it binds to the enzyme-substrate complex, rather than to the free enzyme. However, not a lot is known about the enzymatic, physical, and immunological characteristics of PLAP. Thus, our goal was to determine the kinetic parameters (Km and Vmax) of PLAP, and to study the effect of L-phenylalanine on the activity of PLAP, in the presence of p-Nitrophenyl Phosphate (pNPP) as the substrate, using the standard enzyme assay. he dephosphorylation of pNPP by PLAP produces nitrophenol, which can be colorimetrically measured at 450nm. Our hypothesis was that, L-phenylalanine would uncompetitively inhibit PLAP with pNPP as the substrate using 1M diethanolamine, 0.5mM MgCl2, pH 9.8 buffer. Based on the enzyme saturation curve, 0.0150mg was chosen to be the amount of PLAP that would be used for all enzymatic reactions. Based on the Lineweaver Burke plot in the absence of inhibitor, the Km was calculated to be 4.53mM, and the Vmax was calculated to be 0.0894umol/min. Based on the Lineweaver Burke plot in the presence of inhibitor, the Km was calculated to be 0.0384mM, and the Vmax was calculated to be 5.16E-03umol/min. Thus, we successfully determined the kinetic parameters of PLAP, and concluded that PLAP is uncompetitively inhibited by L-phenylalanine.

Figure 4: Bar graphs showing decrease in the Km and Vmax values in the presence of 5mM L-phenylalanine

Figure 3: Overlay Of Lineweaver Burke plots in the presence and absence of inhibitor (L-phenylalanine). In the presence of L-phenylalanine, reaction was carried out by holding PLAP concentration constant at 0.05mg/mL, Lphenylalanine concentration at 5mM, and varying the substrate concentration (0.1-5mM), in 1M diethanolamine, 0.5M MgCl2 buffer at 37°C, pH 9.8. Final reaction volume was 300uL. Stock solutions for inhibitor were prepared in 0.5M TrisHCl ,pH 8.0 buffer, and stock solutions for substrate were prepared in 0.5M Tris-HCl ,pH 9.0 buffer. Absorbances were measured in triplicates at 450nm at 1 second-intervals for 3 minutes, using Agilent 8453 UV-Vis spectrophotometer.

Figure 2: Lineweaver Burke plot in the absence of inhibitor. Reaction was carried out by holding PLAP concentration constant at 0.05mg/mL, and varying the substrate concentration (0.1-5mM), in 1M diethanolamine, 0.5M MgCl2 buffer at 37°C, pH 9.8. Final reaction volume was 300uL. Stock solutions for substrate were prepared in 0.5M Tris-HCl, pH 9.0 buffer. Absorbances were measured in triplicates at 450nm at 1 second-intervals for 3 minutes, using Agilent 8453 UVVis spectrophotometer.

Figure 1: Enzyme saturation curve for PLAP. Reaction was carried out by holding pNPP concentration constant at 11.2mM, and varying the amount of enzyme (0.001-0.05mg), in 1M diethanolamine, 0.5M MgCl2 buffer at 37°C, pH 9.8. Final reaction volume was 300uL. Absorbance was measured in duplicates at 450nm at 1 second-intervals for 3 minutes, using Agilent 8453 UV-Vis spectrophotometer.

RESULTS

Annette Vincent, Asma Al-Naama, & Safa Salim Biological Sciences Program, Carnegie Mellon University, Qatar

● Dean, R.L. (2006). Kinetic studies with alkaline phosphatase in the presence and absence of inhibitors and divalent cations. [Cited March 7, 2016]. Retrieved from: http://onlinelibrary.wiley. com/doi/10.1002/bmb.2002.494030060138/full#fig6 ● Komoda, T., Hokari S., Sonoda, M., Sakagishi, Y., & Tamura, T. (1982). L-phenylalanine Inhibition of Human Alkaline Phosphatases with p-nitrophenyl Phosphate as Substrate. [Cited March 1, 2016]. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/7139925 ● UCL. The Effect of Substrate Concentration on Enzyme Activity. [Cited March 7, 2016]. Retrieved from: http://www.ucl.ac.uk/~ucbcdab/enzass/substrate.htm

REFERENCES

We would like to thank Maya and Rayan Mahmoud for their support and guidance.

ACKNOWLEDGMENTS

● To test the effective therapy of pheylalanine on diseases associated with increased AP acitivity

● Determine the kinetic parameters of PLAP at different pH’s and temperatures, and using different substrates

● Determine the effect of varying concentrations of L-phenylalanine on PLAP, and determine the threshold of inhibition of PLAP by Lphenylalanine

FUTURE DIRECTIONS

● Thus, our hypothesis that L-phenylalanine would uncompetitively inhibit PLAP with pNPP as the substrate using 1M diethanolamine, 0.5mM MgCl2, pH 9.8 buffer was proven correct, as a decrease in the values of Km and Vmax of PLAP was observed on the addition of L-phenylalanine.

● By performing t-test for the Km and Vmax for values obtained in the presence and absence of inhibitor, the p-value was determined to be 0.174 for both Km and Vmax. Since, the p-value is greater than 0.05, there is weak evidence to reject the null hypothesis.

● As displayed in figure 4, in the presence of 5mM L-phenylalanine, both the Vmax and Km decreased in comparison to when the inhibitor was not added. This agrees with the inhibition kinetics of an uncompetitve inhibitor.

● By constructing the Lineweaver Burke plot for the addition of the inhibitor L-phenylalanine, the Km was calculated to be 0.0384mM, and the Vmax was calculated to be 5.16E-03umol/min.

● From the Lineweaver Burke plot (figure 2), the Vmax and the Km were calculated to be 0.0894umol/min and 4.53mM respectively.

● As observed in figure 1, the maximum rate of the reaction was 0.0490 umol/min for 0.0500mg of PLAP, which has been determined to be the point at which plateau was reached. Thus, the point just before the plateau, which is where the amount of enzyme was 0.0150mg, was chosen to be the amount of enzyme that would be used for further reactions.

ANALYSIS

Inhibition of Human Placental Alkaline Phosphatase (PLAP) by L-phenylalanine

Temporal Patterns in Qatarâ&#x20AC;&#x2122;s Particulate Air Pollution Authors Syed Abbas Mehdi Nourhan ElKhatib Advisor Terrance Murphy

Category Biological Sciences

Abstract Throughout Qatar the particulate air quality concentrations are high due to dust, road traffic, construction and industries. This study presents data and seeks to interpret the patterns observed for particulate matter (PM2.5 and PM10) concentrations collected for 350 days from April 2015 â&#x20AC;&#x201C; March 2016. These concentrations were measured by two Met One BAM-1020 instruments. The Air Quality Index (AQI) was calculated from these data according to the Environmental Protection Agency USA (EPA) AQI standards. The results show a correlation in the variation of PM10 concentrations and day-of-week/time-of-day. PM2.5 displayed consistent results with low variations independent of day-of-week/time-of-day patterns shown by PM.

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Fig. 2: AQI Scale for PM10 and PM2.5 developed by EPA

Fig. 1: Location of Met One BAM-1020 instruments GPS: 25.325858, 51.420848

Particulate matter (PM) refers to tiny particles present in the air. These particles are classified according to size as coarse, fine, and ultrafine. Coarse particles are less than 10 microns in diameter (PM10). Fine particles are less than or equal to 2.5 microns in diameter (PM2.5). Ultrafine particles are smaller than 0.1 micron (100 nm) in diameter. The concentrations of PM2.5 and PM10 were measured near Education City from April 2015 - March 2016(Fig. 1). The Air Quality Index (AQI) for this period was calculated using the PM data by an algorithm developed by the EPA (Fig. 2).

INTRODUCTION

Throughout Qatar the particulate air quality concentrations are high due to dust, road traffic, construction and industries. This study presents data and seeks to interpret the patterns observed for particulate matter (PM2.5 and PM10) concentrations collected for 350 days from April 2015 – March 2016. These concentrations were measured by two Met One BAM-1020 instruments. The Air Quality Index (AQI) was calculated from these data according to the Environmental Protection Agency USA (EPA) AQI standards. The results show a correlation in the variation of PM10 concentrations and day-of-week/time-of-day. PM2.5 displayed consistent results with low variations independent of day-ofweek/time-of-day patterns shown by PM10.

ABSTRACT

31-Jul

1-Sep

Date

1-Oct

31-Oct

30-Nov 30-Dec

29-Jan

2-Mar

AQI Range: 0..50

AQI Range: 50..100

AQI Range: 100..150

AQI Range: 150..200

AQI Range: 200..300

30-Jul

Date

31-Aug 30-Sep

30-Oct

Fig. 4: PM2.5 monthly average concentrations

0 28-Mar 27-Apr 27-May 26-Jun

100

120

140

160

180

5-Jan

4-Feb

7-Mar

AQI Range: 100..150 AQI Range: 50..100 AQI Range: 0..50

AQI Range: 150..200

Time (hours)

PM10 Concentrations hourly from April 2015- March 2016

Fig. 5: PM10 hourly average concentrations

100

150

200

250

300

350

400

EPA AQI

100

150

Fall: September, October, November

Spring: March, April, May

Summer: June, July, August

Fig. 6: PM2.5 average concentrations during meteorological seasons

Spring

Summer

Fall

Winter

Winter: December, January, February

Meteorological Seasons from April 2015- March 2016

The AQI for the study from April 2015 till March 2016 shows great variability, ranging from 34 to 341. There were only 3 days that can be characterized as good quality according to EPA standards. The yearly average for April 2015-March 2016 of PM2.5 (Fig. 4) (47 ± 22 μg/m³, n = 313) and PM10 (Fig. 3) (183 ± 91 μg/m³, n = 349) rose by 5.2% and 19.7% respectively [April 2014-March 2015 (PM2.5 45 ± 30 μg/m³, n = 379, 153 ± 89 μg/m³, n = 372)]. The increase can be attributed to the recent construction activity in the vicinity of the station. The Winter of 2015-2016 experienced moderate AQI throughout, this can be linked to the intermittent rain experienced during the season that contributed to settling the dust particles. The Summer displayed consistently high AQI which can be linked to the strong winds carrying the dust giving rise in the PM10 concentrations. The PM10 (Fig. 5) concentrations for each hour from April 2015-March 2016 shows considerable variation but consistently high PM10 concentrations during the duration of the work hours(7 a.m. to 6 p.m.). However, the PM2.5 (Fig. 6) concentrations for each hour throughout the year were consistent, with relatively lower variation.

RESULTS AND DISCUSSION

Fig. 3: PM10 monthly average concentrations

0 29-Mar 28-Apr 28-May 27-Jun

100

150

200

250

300

350

400

450

500

Two Met One BAM-1020 instruments were used to measure hourly PM2.5 and PM10 concentrations in micrograms per cubic meter (μg/m³). The data collected was analyzed using Microsoft Excel and the EPA Air Quality Index (AQI) (Fig. 2) for each day was calculated using a Java algorithm. Statistical analysis of the data was performed to assess particulate air pollution patterns near the station. PM10 Concentrations PM2.5 Concentrations

METHOD AND INSTRUMENTATION

PM10 concentrations (μg/m³)

Advisor: Terrance Murphy, Ph.D.

Syed Abbas Mehdi, Nourhan ElKhatib, Biological Sciences Program, CMU-Q

TEMPORAL PATTERNS IN QATAR’S PARTICULATE AIR POLLUTION

PM2.5 concentrations (μg/m³) Time ( Meteorological Seasons)

Concentrations (μg/m³ )

Time (Days)

Image Courtesy of Google Maps U.S. EPA. REVISED AIR QUALITY STANDARDS FOR PARTICLE POLLUTION AND UPDATES TO THE AIR QUALITY INDEX (AQI). Available at http://www.epa.gov/ttn/naaqs/standards/pm/s_pm_index.html Pope III, C. A., & Dockery, D. W. (2006). Health effects of fine particulate air pollution: lines that connect. Journal of the Air & Waste Management Association, 56(6), 709-742. Chow, J. C., Watson, J. G., Fujita, E. M., Lu, Z., Lawson, D. R., & Ashbaugh, L. L. (1994). Temporal and spatial variations of PM 2.5 and PM 10 aerosol in the southern California air quality study. Atmospheric Environment, 28(12), 2061-2080.

Sharjeel Khan CMU-Q, Computer Science Baljit Singh CMU-Q, Computer Science Graduate Syed Hasan Mehdi CMU-Q, Information Systems John-Charles Baucom, TA, Biological Sciences Program Yazan Abu Hijleh

ACKNOWLEDGEMENTS

1. 2.

REFERENCES

•Winter of 2015-2016 experienced moderate AQI due to the rain that settled dust particles •Summer experienced consistent high AQI caused by strong winds carrying dust •Results have shown that most of the AQI values are between 101-150 in the unhealthy for sensitive people range •PM10 shows high concentrations during work hours and distinct drop in concentration on Fridays •It is recommended to enforce stricter guidelines for construction activities to improve the Air Quality Index.

CONCLUSION

Fig. 8: PM10 daily concentrations

Time (Day)

PM10 Daily Average Concentrations from April 2015- March 2016 195 190 185 180 175 170 165 160 155 150 145

The particulate matter concentrations for different days of the week for the period of April 2015-March 2016 show a low value for PM10 (Fig. 8) on Friday due to less traffic. Surprisingly, high concentrations were detected for Saturday which could be linked to the construction activity in the vicinity of the station. For the rest of the week PM10 concentrations are consistently high. PM2.5 (Fig. 7) concentrations are inconsistent with the patterns shown by PM10 due to different sources and environmental factors affecting the rise in concentrations.

Fig. 7: PM2.5 daily concentrations

50 49 48 47 46 45 44 43 42 41

PM2.5 Daily Average Concentrations from April 2015March 2016 Concentrations (μg/m³ )

Annotation of Qatar’s Novel Bacillus-like Phage Genome Author Umm-Kulthum Umlai

Advisors Annette Vincent Valentin Ilyin

Category Biological Sciences

Abstract In this era of increasing antibiotic resistance, we are running out of time as common bacterial infections are progressively rejecting drugs that would be standard for treatment. It is due to these reasons that research regarding bacteriophages, viruses that infect bacteria, has seen a sudden revival. The study of these viruses is virtually new, and thus requires a significant effort; there is a novel, virtually untapped resource of genes and proteins that could greatly benefit our understanding of genomes and be used as treatments to bacterial infections that are resistant to antibiotics. Thus, studying the bacteriophages is of great importance. The Science Education Alliance- Phage Hunters Advancing Genomics and Evolutionary Science (SEA- PHAGES) headed by Dr. Graham Hatful from the Howard Hughes Medical Institute (HHMI), University of Pittsburgh and Carnegie Mellon University has begun a nationwide educational initiative to discover, categorize and study the billions of bacteriophages that surround us. This initiative aims to create a thorough database containing genomic data for as many bacteriophages as possible. The same protocols and procedures from the SEA-PHAGES program were applied to search for bacteriophages in Qatar within the sand and soil at Carnegie Mellon University in Qatar. This is the first research of its kind to be carried out in Qatar and possibly in the Gulf region. Bacteriophages, which infect host bacteria Arthrobacter sp., were discovered in the sand from Al Rayyan, Doha Qatar. Genome analysis has shown a number of interesting things about this phage, including its chimeric incorporation of genes from both B.cereus and B. thuringiensis (Bt), soil dwelling bacteria. These bacteria have toxic properties to humans (B.cereus) and insects (Bt), so by studying the phage proteins in more detail we can identify individual proteins that protect against the pathogenicity of these bacteria or determine whether the phage transfers proteins of pathogenicity to these organisms. Transmission electron microscopy imaging has allowed us to visualize the phage and the morphology displayed in the images strongly suggest its characterization as being from the siphoviridae family of phages which are dsDNA containing bacteriophage with an icosahedral head.

Umm-Kulthum Umlai, Annette Vincent Ph.D & Valentin Ilyin Ph.D

Biological Science Program, Carnegie Mellon University in Qatar. Doha, Qatar _ ______________________________________________________________________________________________

_______________________________________________________________________________________________

Results and Data

Objectives

_______________________________________________________________________________________

________________________________________________________________________________________________

The phage contains double stranded DNA and appears to be from the siphoviridae dsDNA family of viruses.The Arthrobacter infecting phage appears to have Bacillus-like phage properties, with genes sharing high similarity with phages that infect pathogenic bacteria such as Bacillus cereus, B.anthracis, B.subtilis, B.licheniformis as well as non-pathogenic forms such as common agricultural bacteria B.thuringenisis (Bt). Thus it is easy to imagine the significance and use of a phage that could fight such Bacillus infections. The genes found in the bacteriophage contig include genes transcribing structural components, metabolic proteins, DNA packaging proteins as well as viral enzymes that allow infection into host bacteria .Some of the enzymes and proteins found include:

Bacteriophages are viruses that are parasitic to bacteria (Figure 1). Identification of these phages and their potential as a therapeutic tool against specific antibiotic-resistant pathogenic bacteria has substantial impact. Therefore we aim to sequence, assemble, annotate and model the genes and proteins comprising the genome of the bacteriophage discovered in Qatar.

Table 1: Some BLASTn results from NCBI non-redundant database of the FASTA file of Phage DNA sequence results

____________________________________________________________

Background

Enzyme

Identity

Query Function[5] Cover

Holin

100%

100% The protein encoded for by this gene forms pores in the 2.1 host bacterial cell membrane, using lysins to break down E-44 the peptidoglycan in bacterial cell walls

Integrase/Lysin

100%

100% allows the insertion of phage DNA into the host genome 0.00

Phosphoglycolate phosphotase

82.1%

91.1% Encodes an enzyme which catalyzes conversion of 2phosphoglycolate into glycolate and phosphate

0.00

Phage tail protein

99.5%

100% gene encoding major tail protein

0.00

Phage tail tape measure protein

99.1%

100% The length of this gene is the length of the phage’s tail

0.00

_______________________________________________________

In this era of increasing antibiotic resistance (WHO)[1], we are running out of time as common bacterial infections are progressively rejecting drugs that would be standard for treatment. There is a novel, virtually untapped resource of genes and proteins in the bacteriophage genomes’ that could greatly benefit our understanding of of new proteins and be used for treatments. It is due to these reasons that research regarding bacteriophages has seen a sudden revival. ____________________________________________________________

Introduction

_______________________________________________________

The Science Education Alliance (SEA) Phage Hunters Advancing Genomics and Evolutionary Science, or PHAGES[2], is a national educational initiative in the United States, funded by the Howard Hughes Medical Institute (HHMI) and led by Professor Graham Hatfull from the University of Pittsburgh. This project is built around the discovery and analysis of mycobacteriophages in the biodiversity of the United States as a course for university undergraduates. The project allows students the discovery of a new species through research laboratory work, encouraging further interest in the sciences. Similar research is now being carried out in Qatar at CMUQ to discover bacteriophages within the ecology of the country. This is the first research of its kind to be carried out in Qatar and possibly in the Gulf region. The initial objectives of this research were to simply determine the presence of bacteriophages within soil samples from Qatar. Simultaneously however we were also interested in seeing the results with a sand sample obtained locally. The investigation was initially carried out using the host bacteria Mycobacterium smegmatis, a nonpathogenic bacteria closely related to Mycobacterium tuberculosis which is responsible for causing Tuberculosis. This was done using the pour plating techniques (Figure 2). We were looking for mycobacteriophages at first. However, upon several unsuccessful attempts with this bacteria, we switched to a common soildwelling bacteria Arthrobacter sp. and this yielded positive results for the sand samples.

Figure 3: Transmission electron microscopy image of the novel phage. Morphology suggests the phage belongs to a siphoviridae family, with a ~120nm length tail and ~50nm diameter icosahedral head _______________________________________________________________________________________

Methods

_______________________________________________________________________________________

After discovering the phage in the sand from Al Rayyan in Doha Qatar (Project: Diversity of Bacteriophages in the ecology of Qatar, Figure 3), the project was continued to characterize and annotate it’s genome. The phage lysate was collected, isolated, purified and its DNA was extracted using a QIAamp MinElute Virus Kit ([3]Qiagen). The DNA was then sequenced as follows: SEQUENCING: The whole genome Ion Torrent S5 DNA sequencer[4] was used for this purpose which sequences DNA based on its synthesis of strands. It detects hydrogen ions which are released during the polymerization process and converts it into digital information ASSEMBLY: The resulting sequenced reads of the phage genome then need to be assembled into scaffolds using a variety of different assembly programs. These programs utilize complex algorithms to convert the de novo input into longer contiguity containing several genes. The program obtaining the best results was SPAdes 3.7. It used the optimal kmer of 127, the longest contig length of 43,683 nucleotides with a total of 67 genes with GC content 34.9%. ANNOTATION: A DNA Master program was used to compile the Basic Local Alignment Search Tool (BLAST) results from the National Centre for Biotechnology Information (NCBI’s) online database and to annotate each gene’s name and function. Finally this program was also used to export a genome map diagram (See Figure 4)

_______________________________________________________________________________

Analysis & Discussion

_________________________________________________________________________

In addition to some of the genes discussed above, almost half of the phage genes sequenced encode proteins of uncharacterized function. At present, we cannot determine the purpose of these proteins, as more proteomic and biochemical research would need to be conducted in order to determine their function. These initial findings prove that there is still a lot more to be learnt about these local bacteriophages. What is presented is simply a small part of a collection of novel genes and proteins. But we can learn a lot from studying the bacteriophage which is closest to this one in similarity, the Bacillus cereus BTCs33 phage. PROTEIN ANALYSIS AND MODELLING We are also finding the functions of the genes and the role the mutations play in allowing the phages to survive in the desert climate. Furthermore, we are trying to model some select proteins using programs such as Swiss-protein Modeller. In Figures 5 and 6, structural images of the proteins encoded by genes 52 and 3 are visualized. Figure 6; Gene 3 which encodes an HNH Endonuclease domain which is responsible for catalyzing the breaks between genomic DNA sequences and allows the movement of introns and inteins within the phage DNA also shared a sequence similarity with other endonuclease domains:

Figure 5: Gene 52, sharing similarity with a monomer of a bifunctional autolysin exhibiting Nacetylmuramoyl-lalanine amidase activity. It hydrolyzes the link between Nacetylmuramoyl residues and L-amino acid residues in bacterial cell-wall glycopeptides.[6]

____________________________________________________________

Conclusion

_______________________________________________________

Figure1: Diagram showing a summary of phage infection, replication and finally lysis of the bacterium Agar surface before pour plating

Agar surface with added top agar

Top agar surface with plaques

E-value

Figure 4: Genome Map diagram displaying the bacteriophage genes. This annota;on was done using an ACD/ Chemsketch program. This diagram displays the collec;on of protein-‐encoding genes within the phage genome., proteins that may help us counteract pathogenicity from the diﬀerent host bacteria species. Alterna;vely, it is possible that some of these proteins transfer their pathogenic proper;es to bacteria, only further study will allow us to determine this.

Figure 2: Diagram showing the process of plaque formation on an agar plate ____________________________________________________________

References

______________________________________________________

[1]World Health Organization. 2015. Antimicrobial Resistance. Available at: http://www.who.int/mediacentre/factsheets/fs194/en/. Accessed on 13 November 2015 [2] Howard Hughes Medical Institute. Science Education Alliance. Available at: http://www.hhmi.org/programs/science-educationalliance. Accessed on 13 November 2015. [3]Qiagen.com. 2015. QIAamp MinElute Virus Kit. Available at: https://www.qiagen.com/us/shop/sample-technologies/combinedsample-technologies/preparation/qiaamp-minelute-virus-spin-kit/. Accessed on 13 November 2015. [4] Thermo Fischer Scientific.2016. Ion Torrent. Available at: https://www.thermofisher.com/qa/en/home/brands/ion-torrent.html. Accessed on 18 March 2016 [5] UniProt.com. 2016.Available at: http://www.uniprot.org/uniprot/P32662. Accessed on 18 March 2016. [6]AmiGO.com. 2016. N-acetymuramoyl-L-alanine amidase activity. Available at: http://amigo.geneontology.org/amigo/term/GO: 0008745. Accessed on 18 March 2016.

The bacteriophage disovered in Qatar is unique in its genome and the protiens it makes. The mutations of the genome need to be studied further to understand how the phage has evolved unique functions and proteins to allow it to infect a range of bacteria species. Furthermore, phylogeny studies need to be carried out to determine the relationship between Arthrobacter and Bacillus bacteria to answer how the phage is able to infect both bacteria families.

___________________________________________________________________

Acknowledgements

__________________________________________________________________

The following people and corporations, without which this would not have been possible, deserve special thanks and recognition for their efforts: Weil Cornell Medical College, Howard Hughes Medical Institute, Aya Abd Elaal, Fatima Abdulaziz, Kranthi Sangishetty, Maya Kemaldean, Maria Navarro, Bernadette Bernales, Susmita Mate, Hasan Al Mana, Rayan Mahmoud, Omair Al-Nuaimi, Fatima Amir and Alaa Khader.

Microbiology-based Educational Kit for High School Students in Qatar Author Wadha Al-Marri

Advisor Annette Vincent

Category Biological Sciences

Abstract This project aims to help local Qatari high schools to incorporate scientific inquiry into their Biology curriculum through laboratory-based ready-to-use modular biology educational kits. This educational kit aims to teach high school students bacteria-related concepts such as antibiotic resistance and transformation. The first module of the kit uses transformation to show students how bacteria can take up DNA from the extracellular. The transformation rate was found to be 70% successful. For antibiotic sensitivity, the disc diffusion protocol was developed to test for Ampicillin resistance in transformed DH5-α. For comparison purposes, both transformed and untransformed DH5-α were treated with other antibiotics. For both transformed and untransformed DH5-α the sensitivity towards the other antibiotics remained constant. The third module on gene expression and the lactose operon, expression of β-galatosidase in transformed cells was induced by IPTG and its activity visualized by the presence of X-gal.

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Untransformed DH5-α lacks AmpR, and are sensitive to Ampicillin, suggesting poor growth if treated with Ampicillin. On the other hand, transformed DH5-α with pUC19 are Ampicillin resistance and can survive and show normal growth if treated with Ampicillin [10]. Because of convenience, efficiency and cost, the disk diffusion method is the most widely used method for determining antibiotic sensitivity in bacteria [8]. It uses a 5mm filter paper soaked with known concentration of antibiotic and placed into an agar plate plated with the culture [10]. If the culture is susceptible to a particular antibiotic, a clear area of “no growth” will be observed around that particular disk [8]. Instead, if the culture is resistance toward that antibiotic, an area of growth will be shown around the disk [8].The zone around an antibiotic disk that has no growth is referred to as the zone of inhibition [9].

Module Two: Developing Antibiotic Resistance

Bacteria are able to take up DNA from the extracellular environment that would result in an alteration to its phenotype. This results in phenotypes such as antibiotic resistance and increased pathogenicity. Students will use the E. coli strain DH5-α which is a non-pathogenic strain, developed for safe laboratory use [1,7]. When plasmid vector pUC19 that encodes for β-lactamase that results in ampicillin resistance in the bacterial strain.

Module One: Transformation

Learning Modules

The core curriculum of Biology focuses on the use of life science concepts in order to explain the intricacies and linkages between various life forms in nature. A laboratory based learning experience should be an essential part of the high school Biology curriculum as it encourages students to apply knowledge gained from the classroom and to establish skill in scientific inquiry. This project aims to help local Qatari high schools to incorporate scientific inquiry into their Biology curriculum through laboratory based ready-to-use modular Biology educational kits. This kit focuses on the concept of microbes, namely bacteria and the development of antibiotic resistance. Students will get a hands-on experience in essential molecular biology techniques, such transformation and spread plating. This will be taught in a modular approach. The kit was developed to facilitate easy delivery in a sparse laboratory setting and is accompanied by a manual that offers educators and students alike essential information for a successful learning experience.

Introduc6on

This project aims to help local Qatari high schools to incorporate scientific inquiry into their Biology curriculum through laboratory based ready-to-use modular Biology educational kits. This educational kit aims to teach high school students bacteria-related concepts such as antibiotic resistance and transformation. The first module of the kit uses transformation to show students how bacteria can take up DNA from the extracellular. The transformation rate was found to be 70% successful. For antibiotic sensitivity, the disc diffusion protocol was developed to test for Ampicillin resistance in transformed DH5-α. For comparison purposes, both transformed and untransformed DH5-α were treated with other antibiotics. For both transformed and untransformed DH5-α the sensitivity towards the other antibiotics remained constant. The third module on gene expression and the lactose operon, expression of β-galatosidase in transformed cells was induced by IPTG and its activity visualized by the presence of X-gal.

Abstract

The presence of IPTG, a lactose analog, activates expression of βgalactosidase.The activity of β-galactosidase allow for blue-white screening, a rapid and efficient technique for the identification of transformed bacteria [3]. To screen for cells transformed with pUC19, a chromogenic substrate known as X-gal is added to the agar plate. If βgalactosidase is produced, X-gal is hydrolyzed to form 5-bromo-4chloro-indoxyl, which spontaneously dimerizes to produce an insoluble blue pigment called 5,5’-dibromo-4,4’-dichloro-indigo [5]. Thus, transformed colonies will appear blue in color while the nontransformed ones appear white.

Gene expression – the Lac Operon

Students are provided with 1ml cultures of rehydrated bacteria (-pUC) and 1ml cultures of transformed bacteria (+pUC) from which they will spread plate onto LB plates. To test the development of antibiotic resistance, the disc diffusion protocol was used. To each quarter, three different antibiotics: 50mg/ml Ampicillin, 50mg/ml Carbenicillin, and 10mg/ml Penicillin/ streptomycin were tested. For control, a filter disc was immersed into sterile salt solution and placed at the center of the forth quarter. Plates were incubated at 37°C overnight. The diameter of the clearance zone was measured as an indicative of resistance.

Antibiotic Sensitivity

A filter paper strip spotted with the DH5-α cells will be provided. Educators can re-hydrate the strip with Luria Broth (LB) and streak the cells onto a LB plate. Cells can be made competent by inoculating a single colony from the freshly streaked LB into 500µl of ice-cold 0.1M CaCl2 as was done in this study. Transformed and untransformed cells were plated onto LB+amp plates Transformed (+pUC) = cells + pUC19 Untransformed (-pUC) = cells only

Transformation

All components mentioned will be provided in the kit except for equipment.

Methods

Figure.1 pUC19 plasmid containing lacZα genes and AmpR genes [11].

The plasmid also contains the lacZ gene (Figure.1). Transformation of the vector into DH5-α results in a functional expression of βgalatosidase enzyme. Regulation of lacZ expression is through the action of Isopropyl β-D-1-thiogalactopyranoside (IPTG). IPTG is a nonmetabolizable analog of galactose that induces the expression of lacZ gene [6] drawing a functional analogy to the Lac operon that students study in the textbooks.

Module Three: Gene Expression

Figure.4 Antibiotic resistance using disk-diffusion technique. LB plates of saturated cultures of untransformed (left) and transformed (right) DH5-α treated with different antibiotic, 50mg/ml Ampicillin (A), 50mg/ml Carbenicillin (C), and 10mg/ml Penicillin/ streptomycin (P/S), after incubation at 37°C overnight. Treatment with sterile saline solution served as a negative control.

Antibiotic Sensitivity:

Figure.3 Transformation following 37˚C heat-shock. A: LB plate showing competent DH5-α. B: LB+Amp plate showing colonies of DH5-α cells containing pUC19 plasmid. C: LB+Amp+Xgal+IPTG plate showing successful transformation of DH5-α with puUC19 plasmid and β-gal expression as indicated by the blue colored colonies More effective transformation result was observed after incubating the plates at 37°C for two nights.

Figure.2 Transformation following 42˚C heat-shock. A: LB plate showing competent DH5-α cells. B: LB+Amp plate showing colonies of DH5-α cells containing pUC19 plasmid. C: LB+Amp+Xgal+IPTG plate showing successful transformation of DH5-α with pUC19 plasmid and β-gal expression indicated by the blue colored colonies. More effective transformation result was observed after incubating the plates at 37°C for two nights.

Transformation/Gene expression:

Data Results

Wadha Al-‐Marri1, Dr. AnneGe Vincent1 Biological Sciences Program, Carnegie Mellon University in Qatar1

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References

Acknowledgements

BioLine Competent Cell Guide High Efficiency Cloning and Protein Expression. (n.d.). Retrieved from http:// www.bioline.com/us/downloads/dl/file/id/3087/ bioline_competent_cell_product_guide_high_efficiency_cloning_and_protein_expression.pdf Blue White Screening. (n.d.). Retrieved April 07, 2016, from http://oxfordgenetics.com/cloning-resources/cloning-guides/bluewhite-screening Introduction to Blue-White Screening. (n.d.). Retrieved April 07, 2016, from http://www.sigmaaldrich.com/technicaldocuments/articles/biology/blue-white-screening.html Invitrogen MAX Efficiency® DH5α Competent Cells. (n.d.). Retrieved from http://kirschner.med.harvard.edu/files/protocols/ Invitrogen_maxDH5.pdf MCLAB Dh5-Alpha Competent E. Coli. (n.d.). Retrieved from https://www.mclab.com/mclab_pages/Dh5AlphaUserManual.pdf Nakata, Y., Tang, X., & Yokoyama, K. K. (n.d.). Preparation of Competent Cells for High-Efficiency Plasmid Transformation of Escherichia coli. CDNA Library Protocols, 129-138. doi:10.1385/0-89603-383-x:129 Plasmids 101: Blue-white Screening. (n.d.). Retrieved April 07, 2016, from http://blog.addgene.org/plasmids-101-blue-whitescreening Abramson, I. J., & Smibert, R. M. (1972). Method of testing antibiotic sensitivity of spirochaetes, using antibiotic discs. Sexually Transmitted Infections, 48(4), 269-273. doi:10.1136/sti.48.4.269 Examples of Antibiotic Sensitivity Testing Methods. (n.d.). Retrieved April 08, 2016, from http://amrls.cvm.msu.edu/ microbiology/detecting-antimicrobial-resistance/test-methods/examples-of-antibiotic-sensitivity-tesing-methods Kirby-Bauer Disk Diffusion Susceptibility Test Protocol. (n.d.). Retrieved April 08, 2016, from http://www.microbelibrary.org/ component/resource/laboratory-test/3189-kirby-bauer-disk-diffusion-susceptibility-test-protocol PUC19 (OG590) High Copy Blue/White Cloning Plasmid. (n.d.). Retrieved April 08, 2016, from http://oxfordgenetics.com/ plasmid-products/antibiotic-selection/bacterial-selection/ampr/puc19-detail

I would like to thank Maya Kemaldean, and Bernadette C. Bernales for their endless support in the labs.

11.

10.

Blue-pigmented colonies grown on LB+Amp+IPTG+Xgal plates are DH5-α cells transformed with puc19 plasmid as an indicative of successful transformation and activation of the lacZ gene.

Transformed DH5-α cells with puc19 plasmid showed resistance toward Ampicillin, indicated by the 44% decreased in diameter of the clearness zone (Figure.5 and Table.1). Both transformed and untransformed DH5-α showed a constant degree of susceptibility towards other antibiotics, such as Carbenicillin, Penicillin, and Streptomycin, indicated by the constant in the diameter measurements of the clearance zone. The resistancy towards Ampicillin found in DH5-α cells is an evidence for successful transformation of puc19 containing the AmpR gene.

The developed protocol showed a 70% successful transformation rate. DH5-α cells were effectively transformed with puc19 at heat shock temperatures ranging from 37˚C to 42˚C, suggesting that students will be able to safely observe this phenomenon without necessarily high temperatures. In addition, cells were able to show effective transformation when incubating/waiting times were shortened, allowing the students to conveniently perform the experiment in a single lab session.

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Table.1 Measurements of the diameter of the clearance zone for untransformed and transformed DH5-α cells with puc19 plasmid treated with 50mg/ml Ampicillin, 50mg/ml Carbenicillin (C), 10mg/ml Penicillin/streptomycin (P/S).

Microbiology-‐Based Educational Kit for High School Students in Qatar

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Computer Assisted Learning Using Foreign Language Material Author Alaa Khader

Advisors Francisco Guzmรกn (Qatar Computing Research Institute) Kemal Oflazer

Category Computer Science

Abstract Higher level science education in Qatar and other countries in the region is mostly taught in English. For Arabic-speaking ESL students, this adds obstacles to the experience of learning the sciences. Furthermore, there is a shortage of computer-assisted resources geared towards Arabic-speaking science students. This work aims to provide resources for non-proficient Arabic-speaking ESL students, to support their education in science. This is done using different strategies of detecting different possible sources of confusion that students may come across as they read Arabic subtitles on English videos, and to provide further support to alleviate said confusion. Confusion when reading text may arise from different possible sources: lexical (e.g. vocabulary), and other confusion that fall under the conceptual difficulty of the material. In our application we are focusing on lexical sources of confusion. Furthermore, we are using machine translated Arabic subtitles. This adds an extra layer of lexical confusion that we have to detect, as there is still plenty of room for improvement in machine translation. Based on the most likely source of confusion identified, appropriate feedback is provided to the student.

Computer Assisted Learning Using Foreign Language Material Alaa Khader Advisors : Francisco Guzmán & Kemal Oflazer

MOTIVATION

OBJECTIVES Use technology to support e-learning in the Arabic language. Specific objectives: • Use machine translation to make content accessible to Arabic speaking learners • Develop algorithms to predict sources of confusion for learners • Adapt computer assisted learning methods to support learning with machine translated subtitles

• Wide range of online education material in English. • Arabic online educational material is poorly covered • Educational material does not provide affective support based on behavior of learners

RELATED WORK over the square root of the difference

• Automatic video transcription of MOOCs (Brouns et al 2015) • Reading comprehension & Intelligent Tutoring Systems • Lexical features (Heilman et al, 2006) • Eye-tracking (Rayner et al, 2006)(Raney et al, 2014) • Readability of text • Lexical features (Selsky and Shen, 2014)(Dell’Orletta et al, 2014)

Using Machine Translation

‫ﻋﻠﻰ ﻣرﺑﻊ اﻟﻣﺳﺎﻓﺔ ﺑﯾﻧﮭﻣﺎ‬

Using existing system at QCRI (Moses)

Source:Khan Academy

APPROACH Source of Confusion: Machine translation error

Source of Confusion: Jargon EN subtitle because the most common isotope of hydrogen

EN subtitle It takes all the electrons from this covalent bond

Translated AR subtitle ‫ﻷن اﻟﻧظﺎﺋر اﻷﻛﺛر ﺷﯾوﻋﺎ ﻣن اﻟﮭﯾدروﺟﯾن‬

Translated AR subtitle ‫ﻓﺈﻧﮫ ﯾﺄﺧذ ﻛل اﻻﻟﻛﺗروﻧﺎت ﻣن ھذه اﻟﺳﻧدات اﻟﺗﺳﺎھﻣﯾﺔ‬

Feedback to user

Source of confusion: Jargon Definitions for: isotopes –‫اﻟﻧظﺎﺋر‬ *Recognition ‫ف‬ ‫ﺗﺧﺗﻠ‬con‫اﻟﻛﯾﻣﯾﺎﺋﻲ ﻟذرﺗﮭﺎ ﻧﻔس اﻟﻌدد اﻟذري وﻟﻛﻧﮭﺎ‬ -Anti

‫ﺷﻛﺎل ﻣن اﻟﻌﻧﺻر‬ . ‫ ﻓﻲ اﻟﻛﺗﻠﺔ اﻟذرﯾﺔ ﺑﺳﺑب اﺧﺗﻼف ﻋدد اﻟﻧﯾوﺗروﻧﺎت‬Z،

Alternatives for: ‫اﻟﺳﻧدات اﻟﺗﺳﺎھﻣﯾﺔ‬ 1. ‫اﻟﺳﻧدات اﻟﺗﺳﺎھﻣﯾﺔ‬ 2.‫اﻟراﺑطﺔ اﻟﺗﺳﺎھﻣﯾﺔ‬

Identifying jargon: results

Identifying machine translation error: results

Jargon

• Bilingual Word Embeddings Skip-Gram (BWESG) model (Vulie and Moens, 2015) used to compare original and translated phrases.

• AntConc version 3.4.4.0 keyword recognition used to predict jargon • Results: Figure 1

0.6 0.4

0.4

0 0

0 5

Threshold

Helpfulness of feeback to user

Other

Jargon

MTE 30.00%

40.00%

50.00%

60.00%

70.00%

Helpful

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

Bin range

400 300 200 100 0 0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

Bin ranges

CONCLUSION

• 16 participants tested framework in IRB approved study

20.00%

200

EXPERIMENTAL RESULTS

10.00%

300 100

Threshold

Identified confusions

400

0.2 0

500

Frequency

0.6

600

Frequency

1 0.8

Recall

Precision

1 0.8

Mismatched source-translation similarity scores

700

1.2

0.2

0.00%

Source-translation similarity scores

Figure 2

1.2

Not helpful

• Built initial Computer Assistive framework to make educational material more accessible to Arabic speakers • Recognized different lexical confusions and proposed feedback to users • Future work: • Improve performance of identification of confusions • Collect more data to improve classification of confusion

Device-to-Device Communication in the Internet of Things: Providing Development Guidelines for IoT Enthusiasts Author Aliaa Essameldin

Advisor Khaled Harras

Category Computer Science

Abstract The Internet we all know, or the network connecting computers all over the world, is slowly expanding and starting to include more physical objects, such as sensors and controllers. This can potentially allow it to provide smarter services without requiring human interference. This new computing paradigm is known as the Internet of Things. Fortunately, processors, communication modules and most electronic components are diminishing in size and price, which allows us to integrate them into more objects and systems. And now that they are being equipped with network interfaces, the IoT market has increased the demand for internet bandwidth that the current capacity will not meet. In this research, we focus on device-to-device (D2D) communication as a way to tackle this demand-capacity gap. We study mainstream IoT devicesâ&#x20AC;&#x2122; D2D communication capabilities over Wi-Fi and Bluetooth. Our work highlights some of the limitations of this approach and addresses the scarcity of practical data in this area. We also explore how device-to-device communication can be used to update existing systems by trying to deploy it on the Up & Away CPS test-bed being currently developed in Carnegie Mellon Qatarâ&#x20AC;&#x2122;s Networking Systems Lab.

Device-to-Device Communication in the Internet of Things

Providing Development Guidelines for IoT Enthusiasts Aliaa Essameldin and Khaled Harras Carnegie Mellon University Qatar

MOTIVATION Smaller and smarter devices permit revolutionary Internet of Things applications, such as wirelessly controlled refrigerators, to evolve. So motivated by: 1. the expected growth in the Internet of Things market Fig 3., 2. the role of device-to-device (d2d) communication in covering the need-capacity gap resulting from this growth Fig 4. and, 3. the scarcity of practically collected d2d data for IoT developers,

Wireless Spectral Efficiency Data Growth

This project aims to provide practical data on the d2d performance of mainstream IoT devices (Fig1, Fig2) over Wi-Fi and Bluetooth.

Fig 1. Raspberry-Pi Device

Fig 3. Growth in the Internet Of Things Market

Fig 2. Intel Edison Device

Fig 4. The expanding need-capacity gap in Internet bandwidth

II. D2D over Bluetooth

I. D2D over Wi-Fi RTT Measurements over UDP/IP

To accurately compare the performance of D2D communication over Wi-Fi between Raspberry-Pi devices and Intel Edison devices, we implemented a two threaded client that, along with a simple UDP echo server, can calculate average RTT at a given distance. Fig 5. shows the design of the experiment and the graph below shows the results.

Radio Frequency Communication Application Device A

Communication Segment

Application

Bluetooth Network Encapsulation

vs.

Device A

The RFCOMM protocol emulates the serial cable line settings and status of a serial port and is used for providing serial data transfer

Ethernet Header

Ethernet Payload

L2CAP Header BNEP Header

BNEP is used to transport common networking protocols over Bluetooth and is used for Personal Area Networking Profiles

RFCOMM’s Reliability issue

RFCOMM’s specification indicates that it should be reliability guarantees similar to TCP’s. however, while sending large files over it, we found out that at least a byte gets corrupted after sending more than 10MBytes of data (Fig 6) It is important to notice that, in an IoT, a single corrupted byte can compromise the entire system.

Fig 5. Methodology for measuring RTT over UDP

Throughput Measurements over TCP/IP Throughput is the amount of data that can be exchanged in a given time. In this experiment we used two Intel Edison Devices connected directly over Wi-Fi. We sent files of different sizes multiple times at a each given distance and used the average delay to calculate the throughput. The graph below shows the results.

As seen in the graph, throughput was completely lost after 200 meters.

III. APPLICATION: UP & AWAY To apply the concepts we’ve learnt in this study, we updated the Up & Away cyber-physical testbed from a centralized version (Fig 7) to a distributed version (Fig 8) by mounting an Intel Edison device on each node then establishing d2d communication between the Edison devices and the Central Node. By doing that, we could move most of the computation from the central node to the UAV Nodes, allowing higher scalability.

Fig 6. An example of a corrupted byte that was . . not caught by RFCOMM’s correctness check

Table. RFCOMM’s transmission bug tested across different devices

We could overcome this bug by simple error-check: stop-and-wait ARQ with checksum. As seen in the graph, the protocol resulted in a dramatic increase in delay.

1e+06

This increase could have been optimized by using a different protocol, but since TCP over BNEP performed almost as good as RFCOMM, we decided to use that instead.

3e+05

9e + 05 8e + 05 7e + 05 6e + 05 5e+05 4e + 05 2e + 05 1e+05 0

8 10 12 14 16 18 20

Throughput Measurements over TCP/BNEP

We used the same methodology for measuring throughput over Wi-Fi, but the Edison devices were connected over TCP/BNEP instead.

2.0 1.6 1.2 0.8 0.4 0.0

As seen in the graph, throughput was completely lost after 160 meters.

IV. CONCLUSION & FUTURE WORK Conclusions Bluetooth, we recommend the use of TCP/RFCOMM for applications that need reliability • For guarantees over the Intel Edison devices For Wi-Fi, Raspberry-Pi provides a lower RTT than Intel Edison devices. •

Fig 7. Centralized Up & Away Testbed architecture

Fig 8. Distributed Up & Away Testbed architecture

Future Work the energy consumption of bluetooth and Wifi communication • Study the Intel Edison’s low WiFi performance by disabling and/or controlling power • Overcome saving the network simulator to support multi-hop data transfer so it can be used to study • Update different Ad-Hoc protocols and techniques

Wireless Eruptions â&#x20AC;&#x201C; Reprogramming Wireless Sensor Networks: Challenges and Approaches Author Aliaa Essameldin

Advisors Saquib Razak Philip Gibbons (CMU-Pittsburgh)

Category Computer Science

Abstract Wireless reprogramming is a vital component in wireless sensor networks because nodes are often installed in hard-to-reach locations. Environmental Wireless Sensor Networks, in particular, are expected to scale to hundreds of thousands of nodes, to live for years without much human interference and to use cheap sensor nodes. These three expectations, scalability, durability and feasibility, motivate a list of reprogramming system requirements: efficient communication, complete-retasking, node safety guarantees, energy efficiency and memory efficiency. In this project, we studied how each of these requirements can be met in a single wireless reprogramming framework then we compared this theoretical framework against most popular existing reprogramming protocols. This allowed us to identify some performance gaps in existing systems that we can address in our future work.

Wireless Eruptions

Reprogramming Wireless Sensor Networks: Challenges and Approaches Aliaa Essameldin Saquib Razak, Philip Gibbons

Problem & Motivationâ&#x20AC;Ś Wireless reprogramming is a vital component in wireless sensor networks because nodes are often installed in hard-to-reach locations. Environmental Wireless Sensor Networks, in particular, are expected to scale to hundreds of thousands of nodes, to live for years without much human interference and to use cheap sensor nodes. These three expectations, scalability, durability and feasibility, motivate the system requirements listed below.

Sensor nodes used to collect volcanic data are hard to physically reach and update

In this project, we studied how each of these requirements can be met in a single wireless reprogramming framework then we compared this theoretical framework against most popular existing reprogramming protocols. This allowed us to identify some performance gaps in existing systems that we can address in our future work.

Durability, feasibility and scalability motivate our desired system features

The goal of this project is to develop a system for wireless reprogramming of sensor nodes with minimal energy and memory consumption

Desired System Features

State-of-the-art Framework Protocol

Scope Selection

Multi-hop Routing

Sends Updates only

Encoding/D ecoding

Pipelining Support NO

XNP

Trickle

YES

Deluge

YES

DiCode

YES

SenSeOP

YES

AdapCode

YES

Table 2. Different Wireless Reprogramming Protocols Supporting different features in the framework

Conclusion & Future Work

As a result to this result, we concluded that: 1. Despite the presence of a robust theoretical framework for efficient wireless reprogramming of sensor nodes, there are still multiple trade-offs that prevented a single protocol from fully implementing this framework 2. No system sends encoded updates, they all either encode entire image or send updates only, which reflects a big area of improvement in network usage and, thus, energy consumption 3. Writing a data-block to memory is almost 10 times more expensive than receiving a packet over wireless in stereotypical sensor node devices which indicates that using a bootloader is might be more costly than receiving bigger packets and writing them to application space directly.

Our next steps in this project will be: 1. Implement a framework that can combine all the features in Table 2. 2. Optimize memory consumption by studying memory-efficient ways to load the code without using a bootloader 3. Map the work done in this research to evolving Internet of Things applications

CheckMyStack Vulnerability Detection Tool for the Qatari Web Authors Aseel Ghazal Daanish Ali Khan

Advisor Thierry Sans

Category Computer Science

Abstract The goal of this project is to help administrators to audit and strengthen the security of their websites. Defense mechanisms exist but they are not widely adopted, especially by small businesses, small organizations, and individuals with presence on the web. To do so, we need to identify weaknesses, detect well-known vulnerabilities, and guide website owners to adopt good security practices. In this project, we intend to combine techniques from fingerprinting and data-mining to advance state-of-the-art passive scanning and vulnerability detection. First, we scan a website to collect all resources loaded either statically or dynamically. Thus, we use a probabilistic algorithm to infer the exact denomination and version of public libraries and frameworks. Finally, we match this information with existing Common Vulnerabilities and Exposure (CVE) bulletins to detect potential weaknesses. As an experiment, we have analyzed more than 1000 websites divided into two datasets: 1) the most popular websites in the world (according to Amazon Alexa) and 2) the most popular websites in Qatar with a .qa extension. Our results show that most popular websites contain on average 2.2 vulnerabilities. This number jumps to 3.9 when we consider Qatari websites only. As a future work, we plan to make our tool available as a browser extension and we want to build an automatic notification system to warn website owners about vulnerabilities affecting their websites.

CheckMyStack

Vulnerability Detection Tool For The Qatari Web Aseel Ghazal, Daanish Ali Khan & Thierry Sans

30,000 sites are hacked everyday

156 days to detect attacks

Data from 2012 Sophos Security Threat Report

Problem

The webstack is the collection of third-party applications and libraries that is used to build and run a website. Once a website is online, website owners tend not to update this webstack. Some of its components might get obsolete and even contain known vulnerabilities.

Scan the webpage

13 % of attacks are web based

$200,000 cost per attack

Solution

CheckMyStack detects obsolete and vulnerable applications and libraries by analyzing the webstack and reports known Common Vulnerabilities and Exposures (CVEs).

Detect applications and libraries

Generate CVE report

+24%

Using PhantomJS, we collect the javascript libraries and store their hashes

Dataset

Using Wappalyzer, we detect the name and version of the applications and libraries used by the website

Number of Websites

Number of CVEs

Average number of CVEs per website

Using the Apriori data mining algorithm, we match the results from Wappalyzer and PhantomJS to improve the detection rate of Javascript libraries Average severity of CVE (out of 10)

Vulnerable application type

Top 1000 Websites (Amazon Alexa Top Sites) 3%

Top 1000 most popular websites in the world

0% 6%

1000

2179

2.18

5.76

javascriptframeworks programminglanguages 91%

web-servers web-serverextensions

Qatar websites (.qa domains)

225

885

3.93

5.67

Using the CVE database, we retrieve the CVEs that match the product name and version

Top CVEs

1. CVE-2014-9427 : Severity 7.5 Allows remote attackers to obtain sensitive information from php-cgi process memory 2. CVE-2014-5459 : Severity 3.6 Allows local users to write to arbitrary files via a symlink attack in PHP 3. CVE-2014-0238 : Severity 5 allows remote attackers to cause a denial of service in PHP

As future work, we want to improve CheckMyStack by adding the following functionalities: Add a page crawler to scan multipage pages on a website

Make CheckMystack available as a browser extension for Chrome and Firefox

Build an automatic notification system to warn website owners about vulnerabilities affecting their websites

Software Defined Networking in Wireless Networks Using a Raspberry Pi Author Muhammad Ahmed Shah

Advisor Saquib Razak

Category Computer Science

Abstract Wireless networks share a common channel that is spatially reused. This gives rise to interesting and complex interference phenomena that have substantial effects on performance and fairness. The shared channel makes wireless networks a strongly coupled system where decisions by one node can have a substantial and cascading effect on other nodes in the system. Developing effective distributed protocols in such an environment is challenging since local decisions can have significant effect making it difficult to converge to effective operating points. SDN is establishing itself as a game changing technology in managing network infrastructure in a number of networking domains. SDNs makes it possible to carry out decisions that are globally effective and introduce the level of coordination not possible with distributed protocols. In addition, an SDN framework offers advantages with respect to service deployment, network monitoring and instrumentation as well as security. In this research project, we review some of the recent developments in wireless mobility, investigate the possibility of predicting paths to pre-empt access point handoff and investigate the feasibility of using Raspberry Pis â&#x20AC;&#x201C; a low cost credit card-sized single-board computer, as an SDN enabled wireless routers for a Wireless Mesh Network.

Applying Recurrent Neural Network for Arabic Named Entity Recognition Author Naassih Gopee

Advisors Kemal Oflazer Houda Bouamor Bhiksha Raj William Cohen (Carnegie Mellon University)

Category Computer Science

Abstract Named Entity Recognition (NER) (also known as entity identification) is a subtask of information extraction that seeks to locate and classify elements in text into predefined categories such as the names of persons, organizations, locations, etc. NER plays an important role in many NLP problems, such as Machine Translation as it helps improve their performance. In this work, we plan to tackle the Arabic NE recognition and classification task with a novel approach using Long Short Term Memory (LSTM) neural networks. We use LSTMsâ&#x20AC;&#x2122; ability to long memorize dependencies to train a model for Arabic NEs recognition, on a training dataset. The model is then used to predict the NEs for a sample of Arabic sentences in our testset. We tested our system on a pilot dataset. In its current version, it achieves a word level accuracy of 85%. More recently we trained our model on the more standard ACE 2007 dataset and achieved an F1 score of 51% for detecting boundaries and 16% for categorizing the named entity. We also compare it with different existing baselines, plan to identify a set of optimal feature set in order to study its impact on the accuracy of our predictor.

Applying Recurrent Neural Networks to Arabic Named Entity Recognition

Naassih Gopee Advisors: Kemal Oflazer, Houda Bouamor, Bhiksha Raj and William Cohen Named Entity Recognition and Neural Networks • Our task

• What is a Neural network?

• Identify proper names in texts, and classify them into a set of categories • Accepted categories: Person, Location, facilities and Organisation

Input sentences

NE tagged sentences

• Motivation:

• NER is important for many Natural Language Professing (NLP) applications: information extraction, machine translation

• Challenges:

• Neural networks (NN) have been shown to improve several NLP tasks

• NER for Arabic has not been extensively studied

• NER has two-components: NE Detection & NE Categorization

How can we automatically identify and categorize these entities using Neural Networks?

• Neural networks need numeric vector inputs (embeddings)

Our Approach

Experimental Design

Results Before POS

Dataset: • Automatic Content Extraction (ACE) 2007 dataset: Arabic corpus with NEs and their POS tags

After POS

Boundaries

Tags

Precision(%)

51.13

37.23

TBA

Evaluation:

Recall(%)

44.23

32.29

TBA

• Word-level accuracy as a metric

43.14

16.71

TBA

• 2,779 sentences (5-fold basis): 80% for training and 20% for testing

• Parameters tuning: Number of epochs, learning rate, embedding sizes

Percentage of correctly classified boundaries O

12871

1893

491

974

2183 0%

10%

20%

1961

30%

40%

50%

Correct

60%

70%

80%

90%

100%

Incorrect

Percentage of correctly classified named entities

Conclusion and Future Work

WEA

Conclusion

NNE

• LSTM is a promising model for such task

PER

• LSTM may not yet be at state of art: - Current state of the art solutions reported results are on other data

1813

1111

VEH

1460

FAC

• Optimal setting for paramenters not yet found (not optimized at all)

54 12871

78 78

LOC

227 64

143

Future Work

ORG

475

581

• Parameter exploration

GPE

594

728

• Are there other ways of factoring the problem? - As opposed to segmentation + classification

10%

20%

30%

40% Correct

• Adding other features: Currently only using the words & POS

50%

60%

Incorrect

70%

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An In-Car Speech-based Interactive Recitation Correction System Author Omar Shafie

Advisors Rita Singh Saquib Razak

Category Computer Science

Abstract In this work, we create a speech-based recitation correction system for use in automobile environments. Often, while driving, people may be reciting the Quran, or may want to practice their speech or other such activities. Therefore, they need to compile and set up an existing automatic speech recognition system which uses modern techniques and algorithms to do real-time processing of the input speech and then, collect different recitations of the Quran to make it recognize Arabic as a spoken language, but restricted to the vocabulary and grammar of the Quran.

AN IN-CAR SPEECH BASED INTERACTIVE RECITATION CORRECTION SYSTEM Omar Shafie, Rita Singh, Saquib Razak

Computer Science, Carnegie Mellon University in Qatar oshafie@cs.cmu.edu rsingh@cs.cmu.edu srazak@cs.cmu.edu

Abstract

Error determination

In this work, we create a speech-based recitation correction system for use in automobile environments. Often, while driving, people may be reciting the Quran, or may want to practice their speech or other such activities. Therefore, they need to compile and set up an existing automatic speech recognition system which uses modern techniques and algorithms to do realtime processing of the input speech. Then, collect different recitations of the Quran to make it recognize Arabic as a spoken language, but restricted to the vocabulary and grammar of the Quran. Then, we need to find the errors in the recitation and flag them at rum time.

The problem Many who want to memorize a texts (e.g. Quran) need a (human) partner to do the Speech-text Matching for them. Others, try to do self-matching by stealing a quick glance every couple of seconds at the text to make sure that they are on the right track. This becomes crucial when people started doing this while driving as it may jeopardize the driver’s life. To help people overcome this problem, we propose using a trained speech recognizer to match the recitation of the text and raise error flags at real-time for any detected mismatch between the text and speech.

The solution Schematic of the recitation correction system

Explanation of components The task of an Automatic Speech Recognition (ASR) engine is to take audio input and turn it into a written representation. The spoken phrase (possibly incorrectly) is recognized using a constrained grammar. Grammars are generated automatically within the code (or written by hand), and they describe the simple languages of the recognizer. More complicated languages require Statistical language models, which contain probabilities of the words and the word combinations. Those probabilities are estimated from a sample data, there are toolkits for this.

GRAMMAR

Speech in

Text out

Suggest the correction: the regions of the spoken input that were wrong • • • •

Identify the actual valid patterns that the person should have said.

Correction module

Next-Steps

In our problem, where people will be using the recognizer in car, there are some challenges that need to be considered. The car environment has lots of noise that interferes with good speech recognition performance (e.g. window opening, wind blowing, engine too noisy … etc.) Therefore, it is important to use small, affordable but good microphones for the clarity of the input speech in order to have better results. This is crucial for our application since we want to match the speech with the exact text. Also, this means that the system would have been trained on data that has car noise in it, to build models that are representative of the acoustic conditions in the car.

Many systems do not explicitly use semantic information in the recognizer, but leave that to a parser. Syntax can be weakly modelled with N-gram model in the engine that does not capture long distance relationships. A recognizer send the N-best decodes to the parser, and it can then find which ones are syntactically or semantically consistent.

Say “X” instead of “D” Say “Y” instead of “E” Say “Z” instead of “F” Don’t say “G”

References •

CMU Sphinx. (n.d.). Retrieved, from http://www.speech.cs.cmu.edu/sphinx/doc/Sphinx.html • Nymand, M. (n.d.). How to read Microphone specifications. Retrieved from http://www.otvpavlu.cz/_dataPublic/attachments/175a4b4f0eef6b2eec5c15d220ab30d6/12.p df

Tweets about Qatar: Who’s Setting the Agenda? Authors Shahan A. Memon Rohith K. Pillai

Advisors Ingmar Weber (Qatar Computing Research Institute) Yelena Mejova (Qatar Computing Research Institute) Susan Dun (Northwestern University in Qatar)

Category Computer Science

Abstract After winning the bid for the FIFA World Cup 2022, Qatar, albeit a small country in both size and population, has spurred significant international interest not just in the professional media but also on social media. Most of the recent coverage related to Qatar in public news channels and media portrays Qatar in a negative light, especially focusing on issues regarding migrant workers and allegations regarding improprieties in the FIFA bid. This recent trend in “Qatar bashing” in the media is damaging to the image of Qatar internationally. However, the extent to which these and other topics about Qatar are discussed by the general public on social media is unknown. Is the conversation dominated by a few sources such as in the traditional media? Or is there more diversity between residents of different countries on social media? To help answer this question we used Twitter to analyze public opinion about Qatar. Hence we collected tweets and mapped them to their country of origin, and then created tag clouds for each country. We also analyzed cited domain names pertaining to different URLs in the tweets, to provide insights about the key domains and figures that may have formed or influenced that perception. In our analysis, we found that largely similar topics such as “migrant workers”, “deaths” and “FIFA” are discussed around the world regarding Qatar, which is surprising given linguistic and cultural differences. The key insight of the data analyzed is how different public sentiment in different countries stacks up against each other regarding issues relating to Qatar. For example, the tag clouds indicate that in Nepal, the leading sentiment on the issue of migrant workers is relatively grim featuring uni-grams like “funerals”. On the other hand, the tag cloud for France does not show much attention to the migrant workers. Interestingly, we also found that few professional media sources dominate the international conversation on Twitter. Though our study revolves around Qatar specifically, we believe this methodology can be used to track “nation branding” via social media, providing key insights to stake holders about how their nation is discussed across the world.

Tweets about Qatar: Who’s setting the agenda? Shahan A. Memon Rohith K. Pillai

Dr. Ingmar Weber Dr. Yelena Mejova

Methodology

High-level Observations POSSIBLE AGENDA SETTERS:

DATA COLLECTION :

The following article in Washington post regarding migrant workers was amongst the top 10 citations across many countries..

Collected 4,458,914 tweets about Qatar in 35 different languages during a 6-month period from 3rd of May 2015 to 15th of November 2015. Out of the initial 4,458,914 tweets, 1,837,280 (41.2%) tweets could be mapped to a country using the user defined locations. Our analysis includes data for 660,006 distinct users, covering 173 countries.

•

Distribution of citation for the article "The toll of human casualties in Qatar" 2500 2000 1500 1000 500 0

Motivation

• What do individuals themselves find interesting about and discuss about Qatar? Understanding the answer to this question allows us to evaluate Qatar’s attempts to brand itself as a global leader via its soft power strategy. • What are the key sources that are setting the agenda about Qatar on Twitter? • How do different counties stack up against each other regarding issues discussed about Qatar?

Findings TOP HASHTAGS: Number of “#fifa” Mentions

The graph (left) shows the top hashtag “FIFA” across 5 countries. The radius depicts the intensity. Normalized count of "bbc.co.uk" mentions

France

Australia 8 7 6 5 4 3 2 1 0

United Kingdom

TOP DOMAINS: The following graphs illustrate the top 10 regional distribution of citations of different news sources reporting about Qatar. The radius depicts the intensity of appearances possibly defining the public opinion of that region. Normalized count of "theguardian.com" mentions Chile

Qatar 0.6 0.5

Ghana

0.3 0.2

Thailand

Kenya

Laos

Ireland Nigeria

Normalized count of "washingtonpost.com" mentions

Colombia

Ireland

Turkey New Zealand

0.1 0 Mexico

Czech Republic

Uganda

0.4 Honduras

Uruguay

Denmark 9 8 7 6 5 4 3 2 1 0

United States of America

Australia

India

• PUBLIC DEMO:

No. of tweets

400000 350000 300000 250000 200000 150000 100000 50000 0

The graph shows the distribution of tweets about Qatar skewed towards May and June 2015 probably because of the Prominence of the FIFA corruption case in those months.

REGIONAL DIFFERENCES IN PUBLIC DISCUSSION ABOUT TOPICS:

The topics around different regions may have vast similarities (migrant workers, FIFA, etc.). However, there were differences in intensity of discussion of those topics. Tag clouds showing variance in the intensity of discussion on migrant workers.

Future Work

Create an interactive web demo showing heat map, tag clouds, etc.

• TOPIC MODELING: Discovering the widelydiscussed topics regarding Qatar around the world

• SENTIMENT ANALYSIS:

How positive/negative do people from different This figure shows the heat map depicting the intensity of tweets parts of the world feel about Qatar around the world.

Japan

Australia Kuwait

Canada

The discussion about Qatar on social media varied across different periods.

• Created tag-clouds • Created heat map • Determined top domains, hashtags, URLs, etc.

Germany

United Kingdom

TWEETS ACROSS 7 MONTHS:

DATA VISUALIZATION:

United States of America

No. of URL citations

United States

• Using ‘Nominatim’, we geo-tagged the tweets as per their user-defined location..

Canada

The graph shows the distribution of citations amongst the top few countries

3000

GEO TAGGING:

United Kingdom 7000 6000 5000 4000 3000 2000 1000 0

Dr. Susan Dun

Finland

Paraguay Guatemala

Republic of Serbia

Sweden

Norway Canada

TOP RETWEETED USERS: USA

LokmanKarki (4479) Adel__Almalki (4317) GNRD_NGO (2680) SportsCenter (1563) VicesAdulation (1449)

United Kingdom

Adel__Almalki (2067) laplandes (1714) prodnose (1651) thereaIbanksy (1542) jonsnowC4 (1037)

Germany

Adel__Almalki (316) laplandes (144) Tim_Roehn (120) thereaIbanksy (108) boedefeld_ (81)

REFERENCES: Dun, S., Memon, S. A., Pillai, R. K., Mejova, Y., & Weber, I. (2016). Branding a Nation: The Global Discussion about Qatar on Twitter [abstract]. Retrieved April 10, 2016. TOOLS USED:

Twitter Streaming API ,Twitter Inc. CartoDB Open Street Maps Nominatim draw.io

Social Media Image Analysis for Public Health Author AbdulRahman Alfayad

Advisors V.R. Kiran Garimella (Aalto University) Ingmar Weber (Qatar Computing Research Institute)

Category Computer Science

Abstract: Several projects have shown the feasibility to use textual social media data to track public health concerns, such as temporal influenza patterns or geographical obesity patterns. In this paper, we look at whether geotagged images from Instagram also provide a viable data source. Especially for “lifestyle” diseases, such as obesity, drinking or smoking, images of social gatherings could provide information that is not necessarily shared in, say, tweets. In this study, we explore whether (i) tags provided by the users and (ii) annotations obtained via automatic image tagging are indeed valuable for studying public health. We find that both user-provided and machine-generated tags provide information that can be used to infer a country’s health statistics. Whereas for most statistics user-provided tags are better features, for predicting excessive drinking machine-generated tags such as “liquid” and “glass” yield better models. This hints at the potential of using machine-generated tags to study substance abuse.

Social Media Image Analysis for Public Health Motivation Over the last couple of years, social media has emerged as a viable data source to use for large-scale public health studies. People have been using mostly text for these studies, but one type of social media data that, to the best of our knowledge, has not been tapped into for large-scale public health studies is images. More than 1.8 billion images are shared online every day (compared to 500M tweets per day), making rich media content a prolific data source. In addition to its huge amount, social media image data might contain complementary data that is not shared in textual status updates.

Research Question

Figure 1: Example food image with the tags predicted by Imagga on the right.

● Can public images from social media be used to track public health issues such as obesity, smoking or excessive drinking? ● Does state-of-the-art automatic image classification provide a stronger signal than human-provided image annotations?

Methodology ● We obtained 200,000 geo-tagged Instagram images from the 100 most populous U.S. counties. ● For these images, we obtained (i) Machine generated tags using Imagga.com (see Figure 1), and (ii) Human provided textual tags (hashtags). ● The image features obtained above were augmented with other county-level demographic variables such as, age, gender, and race distributions. ● We used Ridge regression with the above image features to predict public health variables, such as Excessive drinking, Obesity, and Smoking.

Figure 2: Example image with the automatically detected alcohol-related tags highlighted.

Try it yourself: http://imagga.com/auto-tagging-demo

Pearson’s r Correlation

Results ● Data from social media provides a strong signal for modeling regional variation in health statistics, especially combined with demographic data (see Table 1). ● Though human-provided tags are usually more informative than machine-derived tags, the opposite holds for modeling variation in statistics for “excessive drinking”. ● Automatic image analysis might hold potential for tracking population-level substance abuse (see Figure 2).

Human Tags

Imagga Tags

Demographics (baseline)

Human+Demog.

Imagga+Demog .

Hum.+Im.+Dem.

Smokers

0.55

0.53

0.72

0.73

0.75

0.73

Obese

0.42

0.48

0.81

0.84

0.82

0.84

Food Env. Index

0.54

0.45

0.87

0.91

0.87

0.90

Physically Active

0.46

0.58

0.70

0.79

0.74

0.79

Excessive Drinking

0.22

0.49

0.38

0.33

0.48

0.38

Alcohol Impaired

0.51

0.26

0.25

0.43

0.28

0.44

Diabetic

0.34

0.40

0.77

0.83

0.78

0.82

Food Insecure

0.37

0.38

0.84

0.86

0.84

0.87

Limited Access

0.61

0.40

0.46

0.58

0.48

0.58

Key References http://tinyurl.com/jl234ko

AbdulRahman Alfayad | Carnegie Mellon University V. R. Kiran Garimella | Aalto University Ingmar Weber | Qatar Computing Research Institute

Table 1: Prediction performance for nine health statistics using different feature sets.

Graceful Trees and Parking Functions Author Qasim Nadeem

Advisor Niraj Khare

Category General Education

Abstract: A tree is a type of graph that is connected (there is a path between every pair of vertices) and is acyclic (no cycles in the graph). The Graceful Tree Conjecture which states that there exists a special labelling (called a graceful labelling) for every tree, remains an unsolved problem in graph theory despite continued efforts over the last 50 years. It has applications in coding theory and network communication addressing. This past summer, we explored the one-to-one correspondence between parking functions and labelled trees in order to find connections that can further our understanding of the elusive GTC.

Graceful Trees and Parking Functions .

Name: Qasim Nadeem

Advisor: Niraj Khare

Abstract

Their relationship

A math problem (Graceful Tree Conjecture) asks 'whether all trees have a graceful labeling'. Posed in the 1960s by Rosa [1], it remains unsolved. Besides being an elegant problem, graceful labellings have applications in coding theory and communication network addressing (MPLS multi-casting using gracefully labeled caterpillar trees [2]). We explore the connection between labeled trees and parking functions, hoping to get insight into the elusive GTC.

Cayley's formula is a proved result that tells us that there are n

( n−2 )

different trees on n labeled vertices.

We know that the set of all labeled trees on n vertices has the same size as the set of all Prufer sequences of size (n-2). Heinz Prufer used these sequences to prove Cayley's formula.

Graceful Trees A tree is a an undirected graph that is acyclic and connected:

Quite similarly, parking functions of length (n-1) are in bijection with all labeled trees of length n. The number of parking functions of length (n-1) is also n

A Labeled Tree A: Its vertices are arbitrarily labeled 1 to 7.

( n−2 )

If two sets have the same size, bijections exist between them. We considered a particular known bijection (call it f()) between parking functions and labeled trees. Details of the bijection are omitted here, but below are two examples of that bijection mapping a parking function to a labeled tree:

We can get an edge-labeling (difference between endpoints) from the given vertex labels..

Is it possible to get better edge labels for this tree: one where each edge label is unique?

Yes; the new vertex labels on the left allow us to get unique edge labels!

This vertex labeling is a graceful labeling of the (unlabeled) tree.

Our Contribution 1) We gave our own proof for why f() is a bijection.

An unlabeled tree is a graceful tree if it has a graceful labeling. Thus, Tree A (with labels removed) is a graceful tree.

Rosa conjectured that all trees are graceful (1967)

Parking Functions

2) Our aim was to look at all labeled trees on n vertices, get corresponding parking functions (PF) of length (n-1) for each of them, and study these. We wrote a python program that partitioned the set of PFs into those that mapped to graceful trees and otherwise. We were able to do this for values of n up to 10. We wanted to (a) form the concept of what makes a PF graceful, and (b) find concretely the number of graceful parking functions on n. Some patterns we found that may help in the future: (i) PFs of the form (2,1,1,1,...) are graceful (ii) The non-decreasing PFs (1,1,1,1, …) with even length are always graceful, and always non-graceful with odd length (iii) Replacing vertex label ‘i’ (for all) with the label ‘n-i' preserves gracefulness, as edge labels remain the same

Taken from [3]

We have n cars that want to park in a parking lot of size n. For each car, C i , it's preferred parking space is enter the parking lot one after another.

ai . The cars

ai is occupied, then C i parks in the first empty space after ai . If there is none, then it is unable to park. If

We call ( a1, a 2, .. . ,a n ) a parking function (of length n) if all the n cars are able to park in the n-sized parking lot. Some examples are (1,1), (1,2), (2,1), (1,1,1), (1,1,2), (1,2,1).

(iv) A PF and its permutation have the same tree structure (v) It is not the case that you can always take a bad (no permutation graceful), non-decreasing PF and get a graceful, non-decreasing PF by switching children's ordering at some node in the tree representation. A counter-example is (1,1,2,2,3) We could not make significant progress towards our main aim. Further exploration of this and other bijections can be done to improve our understanding of PF and gracefulness.

References [1] A. Rosa, On Certain Valuations of the Vertices of a Graph, Theory of Graphs, Gordong and Breach, N. Y. and Dunod Paris 1967, 349-355 [2] Basak A. 2004. MPLS multicasting using caterpillars and a graceful labelling scheme. Proceedings: Eighth International Conference on Information Visualisation. [3] R. P. Stanley, MIT, available at http://www-math.mit.edu/~rstan

Helping Qatarâ&#x20AC;&#x2122;s Disabled: Identifying Our Web Accessibility Problems Author Dana Al-Muftah

Advisor Divakaran Liginlalh.D.

Category Information Systemsnformation Systems

Abstract Research has been undertaken in many countries to examine and study website accessibility and implement standardized Web accessibility guidelines to allow disabled users to have equal access to the Web. However, there appears to be hardly any research on this topic related to Qatar. Thus, this thesis aims to study the state of Web accessibility and related regulations in Qatar. A thorough literature review aimed at understanding the topic of web accessibility and its importance to the Gulf region and specifically the State of Qatar was first undertaken. It was found that not much work has been done to analyze Web accessibility in Qatar. The next phase involved a study of 30 websites of a selected set of organizations based in the State of Qatar. The homepages of the selected sites were evaluated using WCAG guidelines. The auditing results confirmed that none of the selected Qatari websites were fully compliant with Web accessibility standards. Specifically, retail business websites exhibited the highest number of accessibility violations and university websites exhibited the least number of violations. The auditing results suggest the need to raise awareness among executives and other key stakeholders regarding Web accessibility, and to develop best practices and improved policy framework to facilitate universal access to Web information and online resources in the State of Qatar. Based on these findings, interviews with thirty CIOs and senior IT managers of different organizations in Qatar were conducted. The results suggest developing best practices and an improved policy framework to facilitate universal access to Web information and online resources in the State of Qatar.

Helping Qatar’s Disabled: Identifying Our Web Accessibility Problems Dana Al-Muftah | Advised By Divakaran Liginlal

While disability prevalence in Qatar is lower than international levels, “it is growing significantly”1 Qatar

0.4% which is approximately 12% of

Disability prevalence: the population2

Saudi Arabia

0.8%

OBJECTIVE & RESEARCH QUESTIONS Web accessibility implies ‘universal access to websites regardless of disability.’ The proposed study analyzes the state of Web accessibility in Qatar and recommends improvements. To achieve this objective the following questions had to be answered: • What is the current state of Web accessibility in Qatar? • What standardization efforts are needed to increase compliance? • What gaps exist in current e-accessibility policies in Qatar? • What action is needed to address these gaps?

LITERATURE REVIEW

My work in this area focused on:

UAE 0.8% 2

• Defining Web Accessibility and its Importance • Exploring Regional Approaches • Analyzing Accessibility Studies in the Middle East

Little research has been reported on Web accessibility in Qatar, leaving a gap that this research studies using the following methodologies: Studied 30 websites from 6 categories: Education, Retail, Tourism, Healthcare, News, & Universities

Conducted interviews with key stakeholders including CIOs and IT managers

Utilized the WAVE Toolbar as well as manual checking to audit the homepages of those sites

1. Website Auditing Result The graphs to the left show that none of the 30 websites studied completely passed all accessibility tests (AAA Compliance). The results suggest that people with disabilities do not have equal access to Qatari-based Internet sites and essential online resources. Recommendation: To begin solving this problem, we must raise awareness among executives and other key stakeholders regarding Web accessibility.

2. Interview Results

RESULTS are of Interest to: Interviews revealed that without government enforcement, organizations will not comply due to cost issues and the concern that accessibility standards undermine website design. Recommendations: We suggest developing best practices, standards and policies to facilitate universal access to Web information and online resources in the state of Qatar.

Carnegie Mellon University Qatar

• MADA (Provider of the ICT related technology needs of people with disabilities in the state of Qatar) • Businesses and organizations in Qatar • The research community

REFERENCES MADA Qatar assistive technology center. 2012. An Open Call for the development of assistive technologies to support the needs of Arabic speaking disabled people. Retrieved from http://mada.org.qa/ en/wp-content/uploads/2012/02/call-for-assistive-technologies-to-support-disabled-people-in-Qatar.pdf Dr. William H. Foege, Senior Fellow, Bill and Melinda Gates Foundation. 2014. Disability in the Arab Region. Retrieved from https://www.unescwa.org/sites/www.unescwa.org/files/page_attachments/disability_in_the_arab_region-_an_overview_-_en_1.pdf

Designing Services in Healthcare: A Research Collaboration with Hamad General Hospital Author Shaika Al-Thani

Advisor Alexander Cheekmoud, Ph.D.

Category Information Systemst-Graduate

Abstract The healthcare industry is currently undergoing significant shifts in its form of delivery, particularly in the realm of patient care. In the last decade, the framework of healthcare moved from a mass production model to one of more individual care or, “mass customization”. Today, an ‘open innovation’ movement seeks to advance patient care through the co-creation of services. The fledging discipline of Service Design is playing a significant role in bringing a human-centered approach to healthcare services. Service design engages many stakeholders in the design process and ultimately leads to better care for patients, and better relationships amongst all stakeholders. In this thesis project, I am conducting design research with the goal of improving services and patient care at Hamad General Hospital’s Emergency Department, one of the busiest in the State of Qatar. It is important to note that this is an ongoing project and research is still being conducted at Hamad General Hospital. Deliverables will include design blueprints, journey maps, and frameworks for change and recommendation for environmental, operational, interpersonal, and service changes. We are currently collecting qualitative and quantitative data; collaborating and co-designing with the staff and patient to design an improved experience for the emergency care facility at the hospital.

Empathy; They must imagine the world by taking the firsthand approach. Integrative thinking; by being able to see all areas of a problem. Optimism; that allows designers to consider at least one solution which is better than existing alternatives. Experimentalism; by exploring ways that take designers to new directions. Collaboration; by being able to get input from different perspectives and different discplines.

Design sits between two forms of thinking: analytical thinking and exploration.This form of thinking has the ability to compliment the originality associated with exploration and the reasoning within the concept of analytical thinking. Design thinking can allow for organizations to use existing knowledge and can develop it through a specific logic and process; a creative process. Although this may be less certain than analytical thinking, it can allow us to advance even further the knowledge organizations have with much greater consistency.

Patients are just numbers in this model.

mass production

value creation

The concept of co-production in service design comes from the fact that many people have diverse backgrounds. These diverse backgrounds should be used to mitigate and enhance the complex systems in healthcare. Amongst opportunities in Service Design, experience-based deisgn methods or EBD is a thiriving field for co-production. EBD “is a user-focused design process with the goal of making user experience accessible to the designers in order to design experiences rather than services”. It allows us to pinpont moments of truth between patients and staff members, find emotional ‘hot spots’’ and ‘big moments’ to analyze and improve upon them.

co-production with service design

Patients are included in the decision making and cocreation of patient experience.

The design process is most often divided into phases, starting with the explanatory phase then moves to the synthesis phase, the ideation phase, the realization phase and validation phase respectively.This design process allow us to observe, analyze and generate new design ideas for services that we could then bring back to the stakeholders in order to test and validate the new design ideas.

what are design methods?

observational research

UPMC Visit

surveys

patient journey maps

service blueprints

co-design sessions

Brown, T. (2008). Design Thinking. Harvard Business Review. | Freire,!K.,!&!Sangiorgi,!D.!(2010).SERVICE!DESIGN!&!HEALTHCARE!INNOVATION:!From!consumption!to!coD! |

Martin, R. L. (2009). The design of business: Why design thinking is the next competitive advantage. Boston, MA: Harvard Business Press.Martin, R. L. (2009). The design of business: Why design thinking is the next competitive advantage. Boston, MA: Harvard Business Press.

Shaika Al-Thani, Information Systems ‘16; Advised by Professor Alexander R. Wilcox Cheek, M.Des. A research collaboration with Hamad General Hospital.

directed storytelling & interviews

affinity diagraming

storyboarding improvements and solutions

I am studying how service design could be applied at Qatar’s busiest emergency care facility in this shift to co-production. This will allow HGH to deliver services and enhanced experiences for all stakeholders. Design research methods provide new perspectives and approaches in complex environments and have the ability to advance change in human-centered ways.

In the last decade, changes in healthcare came with a shift from mass production to mass customization and now to the ‘open innovation’ movement of mass collaboration in which service can be co-produced and users are involved in the value creation of services. Since the challenges of healthcare is more complex, with diseases becoming less acute and more chronic, studies suggest that there are a number of factors that interact in complex ways. As a result, healthcare professionals can’t work by themselves to solve or mitigate these problems. It needs more integrative thinking, support and a keen eye on the needs of the users to understand how to move forward. Thus, co-production and patient’s engagement through collaboration becomes the ideal way to mitigate the complex problems of healthcare services today.

‘open innovation’ movement in healthcare co-production

The discipline of design in services takes the formal approach of Service Design. Service Design aims to look at the people, process, resources of an organization and purpose and develop methods that could allow for these entities to work together through a user centered approach.

what is service design?

designing services in healthcare: a research collaboration with hamad general hospital

a design thinker must have..

why design?

A Leg in the Future of Hive Mind Programming Authors Edmund Lam Ali Elgazar Iliano Cervesato

Category Postgraduate

Abstract Traditionally, distributed applications are implemented by writing a separate program for each (class of) device(s). Each program manages communication with other programs and handles concurrency. This nodecentric approach is tedious to use and extremely error-prone. Instead, CoMingle allows the programmer to write a single declarative program that describes what the entire distributed application is doing. This ensemble-centric approach eliminates the hassle of dealing with communication and concurrency. Ensemblecentric programs are compiled automatically into the node-centric code that runs on the actual devices.

Edmund Lam

Ali Elgazar

aee@andrew.cmu.edu

Iliano Cervesato iliano@cmu.edu

sllam@andrew.cmu.edu

INTRODUCTION

CoMingle is a programming language created at CMU-Qatar, which enables programmers to seamlessly create distributed and decentralized applications over android based devices. Distributed applications generally require separate communication codes (Commonly known as message passing interfaces or M.P.I.s for short), which are extremely tedious to write, run and synchronize due to them being node-centric. Using CoMingle, you can write a single declarative application, eliminating the hassle of traditional node-centric distributed approaches, and without the need of implementing a MPI yourself. The easier it is for a programmer to create a distributed application, the better the product, and here at CMU-Qatar we believe that CoMingle allows programmers to effortlessly produce distributed applications, that would be beneficial to all spectrums of the Qatari industry.

OLD SCHOOL CONCURRENT / DISTRIBUTED PROGRAMMING Human Development Activities

HIGH-EXPERTISE DEVELOPMENT

What we EXPECT from COMPUTURIZED ENSEMBLES

HIGH-EXPERTISE DEVELOPMENT

WHAT IS CoMingle? Human Development Activities

Machine Automated Procedures

HAND-WRITTEN Node-centric Code (Process A)

Machine Automated Procedures

HANDWRITTEN Node-centric Code (Process A)

COMPILE

HAND-WRITTEN Node-centric Code (Process B)

COMPILE

HAND-WRITTEN Node-centric Code (Process C)

COMPILE

What we EXPECT from COMPUTURIZED ENSEMBLES

MODERATE EXPERTISE DEVELOPMENT

ENSEMBLE-CENTRIC COORDINATION SPECS + Local Computations ( Java + Android SDK )

HANDWRITTEN Node-centric Code (Process B)

HANDWRITTEN Node-centric Code (Process C)

DRAG RACING •

rule init :: [I]initRace(Ps) --o { [A]next (B)|(A,B) <-Cs}, [E]last( ), { [P]all(Ps),[P]at(I)|P<-Ps} {[P] renderTrack (Ls),[I] has (P)|P<-Ps} where (Cs,E) = makeChain(I,Ps).

•

rule start ::

[X]all(Ps) \ [X]stRace( ) --o { [P] release ( )|P<-Ps}.

•

rule tap

[X]at(Y) \ [X]sendTap( ) --o [Y] recvTap (X).

•

rule exit

•

rule win ::

[X]next(Z) \ [X]exit(Y), [Y]at(X) --o [Z] has (Y), [Y]at(Z). [X]last() \ [X]all(Ps), [X]exit(Y) --o {[P] decWinner (Y)|P<-Ps}.

FUTURE APPLICATIONS

OTHER APPLICATIONS CoDoodle: A screen sharing application which is used as a presentation assistant tool.

•

CoMingle music orchestrator: An application which synchronizes phones to play musical notes in harmony.

•

CoMingle BattleShips: A family fun game in which many players have to battle each other’s fleet of ships.

•

CoMingle Mafia: A party game in which citizens band together against conniving Mafia members.

Supported by QNRF grant JSREP 4-003-2-001 and NPRP 09-667-1-100

COMPILE

• Ensemble-centric: Write distributed computation code as a whole. • Declarative: Easy to verify with state-of-the-art verification tools and theorem provers. • Concise: Less lines of code and more human readable.

Compile. Run, and Pray. Normally Works. But it’s hard, tedious and error-prone

•

COMPILE

SYNCHRONIZING DRONES

SMART HOMES

A Web-based Framework For Arabic Text Diacritization Annotation Authors Ossama Obeid Wajdi Zaghouani Houda Bouamor Kemal Oflazer Mona Diab (George Washington University) Mahmoud Ghoneim (George Washington University) Abdelati Hawwari (George Washington University)

Category Postgraduate

Abstract

Modern Standard Arabic (MSA) script employs a writing system that typically omits diacritical marks and uses symbols to represent only a sequence of consonants. However, diacritics are useful for several applications and for text readability and understanding. Their absence in text adds another layer of lexical and morphological ambiguity. From an NLP perspective, the two universal problems for processing language that affect the performance of (usually statistically motivated) NLP tools and tasks are: (1) sparseness in the data where not enough instances of a word type is observed in a corpus, and (2) ambiguity where a word has multiple readings or interpretations. Designing and implementing methods to assign diacritics to each letter in a word requires a large amount of manually-created gold standard annotated training data. However, building such datasets is tedious and time-consuming for the NLP research efforts, as it places heavy demands on human annotators for maintaining annotation quality and consistency. We describe the design and implementation of our web-based annotation system, developed to help expedite the diacritization task. Our framework provides intuitive interfaces for both managing the annotation process and performing the annotations. As opposed to raw text editors, our system provides facilities for managing thousands of documents, distributing tasks to tens of annotators and evaluating inter-annotator agreement (IAA). In these aspects, our system is similar to QAWI a token-based editor that was developed to correct manually spelling errors in Arabic text. However, instead of performing corrections on text directly, we instead use MADAMIRA to compute a ranked list of diacritizations for each token to display as options for annotators. An option to manually edit a token is available in the cases where none of the precomputed options are correct. Our system is a web application composed of four major components: the back-end server, MADAMIRA, the annotation interface, and the management interface. The back-end server provides an HTTP REST API with which the management and annotation interfaces interact with the server. The back-end server also uses HTTP requests to obtain precomputed diacritizations from MADAMIRA. To evaluate the efficiency of our system, we assigned to five annotators around 1500 words extracted from the Penn Arabic Treebank. Half of the words were completed using a text editor while the other half were completed using our system. The results obtained show that our system allows annotators to double their annotation speed.

A Web-based Framework For Arabic Text Diacritization Annotation Ossama Obeid oobeid@cmu.edu

Houda Bouamor hbouamor@cmu.edu

Wajdi Zaghouani wajdiz@cmu.edu

Abdelati Hawwari abhawwari@gwu.edu

Mahmoud Ghoneim ghoneim@gwu.edu

Mona Diab mdiab@gwu.edu

Kemal Oflazer ko@cs.cmu.edu

2. Automatic Diacritization: Challenges

1. Motivation

• Diacritics are usually absent from Arabic texts. • Texts are typically a sequence of consonants. o Leads to lexical and morphological ambiguity.

• Ambiguity negatively affects NLP tasks and text readability [Zitouni et al., 2006; Belinkov and Glass, 2015].

• Lack of large scale manually-created gold standard datasets. • Lack of text genre coverage (annotated text is mostly news). • Tediousness and time-consumption of task. An efficient annotation system is required.

4. MANDIAC: Our Annotation Framework

3. Existing Annotation Systems

• Large-scale manual diacritization annotation tools are unavailable. • Existing text-editor-like interface are inefficient. o Allow for modification of the consonants as well.

• No tools can manage multiple annotators working simultaneously in different regions.

• MANDIAC is a web-based system that is easy to learn and use. • It is a tool for: o Managing a large number of documents. o Distributing tasks to tens of annotators . o Evaluating inter-annotator agreement (IAA).

• It is a follow up to QAWI, a token-based editor for manually correcting spelling errors in Arabic text [Obeid et al., 2013].

Fig 2. Pre-computed diacritizations.

Fig 1. The annotation interface.

Fig 3. The token editor for manual diacritization.

5. Annotation Features

• Undo and redo buttons. • Link to annotation guidelines. • A counter that tracks the number of words that are yet to be annotated. • A timer to track the annotation speed. • Pre-computed diacritization options to reduce typing using MADAMIRA. • Restriction of edits to diacritics only.

6. Management Features

• • • •

Manage users. Upload documents. Assign tasks to an individual or to a group (for IAA). Download annotations for analysis.

7. Design and Implementation

Fig 4. System architecture diagram.

8. System Evaluation

• System is composed of a HTTP REST API at the back-end • We extracted 1,500 words from the Penn Arabic and two web interfaces (annotation and management) at Treebank and assigned to five annotators. the front-end. • Half of the words were annotated using a text editor • Data is stored in a flexible JSON object. while the other half were annotated using our system. • Results show that our system doubles annotation o This allows for quick implementation of new features. speed. • MADAMIRA is used to pre-compute diacritizations.

Acknowledgements

This research was supported by Qatar National Research Fund (QNRF), NPRP grant 6-1020-1-199

Alice in the Middle East: Computing Curriculum for K-12 Authors Hanan Alshikhabobakr Huda Gedawy Saquib Razak Nour Tabet (Alarqam Middle School) Divakaran Liginlal, Ph.D.

Category Postgraduateory Information Syste

Abstract Alice is a visualization software for introducing computational thinking and programming concepts in the context of creating 3D animations. Our research aims to introduce computational thinking and problem solving skills in the middle schools in Qatar. To make this aim accessible, we have adapted the Alice software for a conservative Middle Eastern culture, developed curricular materials, and provided professional development workshops for teachers and students in the Middle East. There is a trend for countries to evaluate curriculum from other cultures, and then try to bring the successful curriculum to their own school systems. This culture is a result of societies beginning to realize the importance of education and knowledge. Qatarâ&#x20AC;&#x2122;s efforts towards building knowledge-based society and upgrading their higher education infrastructure are proofs of this realization. The challenge is to recognize that although a strong curriculum is necessary, simply porting a successful curriculum to a different environment is not sufficient to guarantee success. Here we share our attempt to customize a tool with associated curriculum that has been very successful in several countries in the West, and apply it in an environment with very different cultures and social values. We have piloted the curriculum, instructional materials, and the customized version of Alice for middle school students in one private English school and two public Arabic schools. The pilot test involved more than 400 students in the three schools combined. During the pilot testing, we conducted a survey to obtain initial feedback regarding the 3D models from the Middle East gallery. This academic year (2015-2016), Alice based curriculum is being used in Arabic in six independent schools and in English in four private English schools. There are more than 1400 students currently studying this content.

Cumulus: A Distributed Flexible Computing Testbed for Edge Cloud Computational Offloading Authors Hend Gedawy Sannan Tariq Abderrahmen Mtibaa (Texas A&M University at Qatar) Khaled A. Harras

Category Postgraduate

Abstract Mobile devices are becoming increasingly capable computing platforms with significant processor power and memory. However, mobile compute capabilities are often underutilized. In this work we consider how a collection of co-located devices can be orchestrated to provide a cloud service at the edge. Scenarios with co-located devices include, but are not limited to, passengers with mobile devices using public transit services, students in classrooms, smart home settings, and groups of people sitting in a coffee shop. We introduce a testbed called â&#x20AC;&#x153;Cumulusâ&#x20AC;? for edge cloud computational offloading, and a visualization tool that allows real time monitoring of resources usage at the IoT devices running on the testbed. Cumulus is designed to be scalable by allowing IoT clouds, managed by controller devices, to join the workforce. A Tasks dispatcher is responsible for generating and offloading tasks to worker IoT devices or clouds. The dispatcher generates matrix multiplication tasks which resemble real applications, like chess and video processing, in terms of computing load and input/output sizes. The dispatcher is built with two scheduling algorithms to distribute tasks at workers. The testbed is flexible and open to adding more scheduling algorithms and new types of tasks.

Cumulus: A Distributed Flexible Computing Testbed for Edge Cloud Computational Offloading Hend Gedawy, Sannan Tariq, Abderrahmen Mtibaa, and Khaled A. Harras Carnegie Mellon University in Qatar I. MOTIVATION • Smart Devices' increase in numbers, computing power, resources, and communication capabilities

II. TESTBED ARCHITECTURE

• Wasted Computing Energy in these Devices (e.g. Smart Phones):

III. VISUALIZER

IV. CUMULUS IN OPERATION Hardware & Set Up

Architecture One device

Multiple Devices

Line Plotting

Computational Tasks [1] CPU HeatMap

Heat Map

V. RESULTS • 2000 tasks assigned • Tasks types are a combination of the four application types • Completion time= time last task’s result was received – time first task was assigned • Workers Scheduling: first available • Testbed Mode of Operation: Standalone Workers (No Controllers) • Results averaged over 10 runs

• 500 Tasks assigned to devices • Tasks Types are a combination of the four application Types • 5 standalone worker devices • Results averaged over 88 seconds

Varying Parameters

VI. CONCLUSION & FUTURE WORK • Adding the controller and mobile clouds to the architecture enabled hierarchy • Allow Generic Tasks implementation/Execution in the system • Run the System with multiple controllers and multiple IOT clouds • Make the System’s Source Code available in GitHub • Add a smart scheduler which is able to decide when to forward tasks to standalone devices and when to forward them to IOT clouds

References

Acknowledgements

[1] Habak, Karim, et al. "Femto Clouds: Leveraging Mobile Devices to Provide Cloud Service at the Edge." Cloud Computing (CLOUD), 2015 IEEE 8th International Conference on. IEEE, 2015. [2] D. Etherington. Htc wants to harness your smartphones idle power to make the world a better place. February 2014. [3] T. Lee. Americans spend an average of 4.7 hours a day on their smartphones. February 2015.

This work was made possible by the QF ARC Award for best national project in computing and ICT. The statements made herein are solely the responsibility of the authors.

Detecting and Tracking Attacks in Mobile Edge Computing Platforms Authors Abderrahmen Mtibaa (Texas A&M University at Qatar) Khaled A. Harras Hussein Alnuweiri (Texas A&M University at Qatar)

Category Postgraduatelty Advisor Divakaran Liginlal, Ph.D.CategoryInformation System

Abstract The evolution of mobile devices into highly capable computing platforms that sense, store, and execute complex tasks is making them attractive candidates for edge computational micro-cloud settings. Such solutions are creating novel security challenges due to the increased push for more seamless computational cyber-foraging that leverages the exploding proliferation of mobile devices. A major concern is that security challenges stemming from these trends, are growing at a rate exceeding the evolution of security solutions. In this work, we consider an environment in which computational offloading is performed among a set of mobile devices. We propose HoneyBot, a defense technique for device-to-device (d2d) malicious communication. While classical honeypots designed to isolate distributed denial of service (DDoS) botnet attacks fail to detect d2d insider attacks, HoneyBot nodes detect, track, and isolate such attacks. We propose and investigate detection and tracking algorithms that leverage insecure d2d infected communication channels to accurately and efficiently identify suspect malicious nodes and isolate them. Our data driven evaluation and analysis, based on 3 real world mobility traces, show that the number and placement of HoneyBot nodes in the network considerably impact the tracking delay and the detection accuracy.

Detecting And Tracking Attacks in Mobile Edge Computing Platforms Abderrahmen Mtibaa*, Khaled Harras+, and Hussein Alnuweiri* *Texas A&M University Qatar and +Carnegie Mellon University Qatar

Computational Offloading Evolution

I. INTRODUCTION

Resulting Security Threats

Classical Botnets Capable Edge devices enable d2d offloading paradigm ď&#x192;¨ Enabling novel security & privacy challenges

MobiBots

vs.

Easy to identify/isolate e.g., Firewalls, Intrusion detection

Mobility increases propagation Difficult to identify/isolate

Objective: Detecting, Tracking, and Isolating Malicious Nodes in Mobile Edge Computing Platforms (MobiBots)

II. HONEYBOT HoneyBot is a novel defense technique for malicious device to device (d2d) communication

IV. EVALUATION Infection Phase (Vulnerable mode)

- We measure detection delay vs. number of HBs - Use state-of-the-art detection mechanisms

Tracking Phase (Crowdsourcing)

Step1: Cure infected nodes - Identify the infected interface (i) - Broadcast purge_msg Step2: Cured nodes help track - Update suspect list - Forward purge_msg, Step3: HoneyBot identifies a set of suspect nodes - After a Time To Track (TTT)

Isolation phase (Localization)

a) Malicious code propagation via d2d communication b) HoneyBot nodes detect malicious communication

c) Tracking messages are propagated to identify suspects d) Localizing a set of suspects within an indoor environment

(1) Real Experiment Lab environment (5 nodes: 1 attacker) Accuracy:1 to 2.5 meters

a) Sigcomm09

b) Infocom06

Sigcomm09 (2) Large Scale Evaluation SF Cab trace: 500 taxis, 10 days

Questions How/Where do we place HoneyBot nodes? How many HoneyBots (HB)?

III. EVALUATION METHODOLOGY - Three HoneyBot Placements - Random - Static/Landmarks (e.g., elevators, reception) - Social Awareness (Betweeness, PeopleRank[infocomâ&#x20AC;&#x2122;10]) - Mobility based on datasets collected in conference environments (see Table) - Computation & Communication based on experimental testbed (See Fig.)

Acknowledgments

*This work was made possible by the NPRP award [NPRP 5-648-2-264] from the Qatar National Research Fund (a member of The Qatar Foundation). The statements made herein are solely the responsibility of the author[s]

VI. CONCLUSION & FUTURE WORK - HoneyBot is a novel defense technique for malicious device to device (d2d) communication - Detection, tracking, and isolation - Placement and number of HoneyBot nodes matters - Future Work - Real world deployment - Evaluation based on a set of attack models

References

[1] A. Mtibaa, and K. Harras, and H. Alnuweiri. From Botnets To MobiBots: A Novel Malicious Communication Paradigm For Mobile Botnets. IEEE Communications Magazine, April, 2015. [2] A. Mtibaa, K.A. Harras, and H. Alnuweiri. Malicious Attacks in Mobile Device Clouds: A Data Driven Risk Assessment. IEEE ICCCN 2014

Drone-Be-Gone: Agile Low-Cost Vision-Based UAV Cyber Physical Testbed Authors Mouhyemen Khan (Qatar University) Sidra Alam Amr Mohamed (Qatar University) Khaled A. Harras

Category PostgraduateFaculty Advisor Divakaran Liginlal, Ph.D.egorormation Systems

Abstract Unmanned Aerial Vehicles (UAVs) continue to be the most dynamic sector of the aerospace industry as sensor and automation technologies mature. Due to the growth in potential UAV applications such as military, aerial survey, disaster recovery, and search & rescue, the need for more realistic testbeds has risen. Prior efforts dealing with UAV testbeds typically have a large barrier of entry due to high-cost and extreme customization. In this work, we present Drone-Be-Gone (DbeG): an agile, inexpensive and, general-purpose Cyber-Physical System (CPS) testbed using off-the-shelf UAV with centralized or distributed control and/or processing. Our testbed in its initial stages has 2-D localization within 5 cm precision, controllability of multiple UAVs, a simulation environment of the testbed, external processing units, and switching between centralized or distributed control and/or processing. To demonstrate the ease of use and potential behind our testbed, we subject our testbed to three case studies to determine its applicability in real-time.

Drone-Be-Gone: Agile Low-Cost Vision-based UAV Cyber Physical Testbed Mouhyemen Khan*+, Sidra Alam*+, Amr Mohamed* and Khaled A. Harras+ *Qatar University and +Carnegie Mellon University Qatar

I. MOTIVATION -

II. DRONE-BE-GONE ARCHITECTURE Central Module:

Exponential UAV growth: $4B to $14B annually for next 10 years Many challenges: Localization, Navigation, Communication Realistic solutions beyond simulation needed Problem: High barrier of entrance due to expensive non-customizable solutions and/or testbeds Solution: Drone-Be-Gone: A Low cost, agile, distributed testbed for UAV CPS applications

Mandatory task is localization of UAVs and targets.

Client Module:

Mandatory task is sensory data acquisition from UAVs.

Multi-Homed Module:

III. DRONE-BE-GONE FEATURES 1. Vision-Based Localization UAV Localization uses intensity detection (1.a) & contour detection (1.b) techniques. Adaptive Tracking Window distinguishes UAVs by placing a window on each UAV (1.c) and tracking its flight trajectory.

Figure (1.a)

Figure (1.b)

Figure (1.c)

Drone occlusion (2.a) is plausible when multiple UAVs are deployed. Currently, we handle cases where a moving UAV is identified from a non-moving UAV (2.b) and then re-localized (2.c).

Figure (2.a)

Figure (2.b)

Figure (2.c)

3. External Processing Unit

Contains sub-modules which serve as Desired task(s) for Central or Client module. Desired tasks are algorithmic processing (e.g. facial detection) and UAV navigation.

2. UAV Autonomous Navigation The UAV Control Flow is shown on the right.

A rotation matrix maps UAV-frame velocities to global-frame velocities: [x, y, z] [x’, y’, z’] ф

- PD output speeds - Global-frame mapped speeds - Yaw angle in z-axis.

IV. CASE STUDIES Scenario 1: Target coverage in visual sensor networks

Algorithm: Predictive Fuzzy Algorithm Input: Target locations Output: UAV destination Central Module: Localization UAV Navigation Client Module: IMU sensor - UAV destination locations & orientations generated (3.a) - Partial coverage of respective clusters (3.b) - Targets fall in field-of-view of UAVs in next step (3.c)

Figure (3.a)

Algorithm: Facial detection on EPU Central Module: Localization Client Module: IMU sensor -

Checkpoint 1: EPU does not detect human face (4.a)

Checkpoint 2: EPU detects human face (4.b)

We explore three systems and choose Intel Edison as our EPU. It is smaller & computationally stronger than Arduino and Raspberry Pi.

Raspberry-Pi Setup: - IMU sensor & Wi-Fi dongle attached - Raspbian Linux OS - UAV + Indoor Hull + R-Pi system = 536 g

Facial Detection

Figure (4.b)

Scenario 3: Realistic dimensional target coverage

Algorithm: Oriented Line Segment Coverage Input: Target locations Output: UAV destination Central Module: Localization UAV Navigation Client Module: IMU sensor Facial Detection We build a simulator: Testbed Simulation with Localization & Autonomy (TeSLA). TeSLA allows:- Safety testing & integration with CPS application - Parameter tuning - Placement of targets - UAV trajectories

UAVs fly to cover targets (5.a)

Faces detected by EPU on target’s interested dimension (5.b) Figure (5.a)

Figure (5.b)

V. CONCLUSION & FUTURE WORK

Intel Edison Setup: - IMU sensor attached - Built-in Wi-Fi - Yocto Linux OS - UAV + Indoor Hull + Edi system = 501 g TeSLA Architecture

References

UAV Navigation

Figure (4.a)

EPUs enable distributed control, extra processing power and added flexibility.

Arduino-Setup: - IMU sensor attached - Xbee radio used to communicate with Central Module - No Wi-Fi & OS

Input: UAV destination Output: Human face

Drone-Be-Gone in Action

4. Testbed Simulator - TeSLA

Figure (3.c)

Figure (3.b)

Scenario 2: Distributed search & rescue operation

[1] http://www.tealgroup.com/index.php/teal-group-news-media/item/press-release-uav-production-will-total-93-billion. [2] N. Michael, D. Mellinger, Q. Lindsey, and V. Kumar, “The grasp multiple micro-uav testbed,” IEEE, 2010. [3] S. Lupashin, A. Schollig, M. Sherback, and R. D’Andrea, “A simple learning strategy for high-speed quadrocopter multi-flips,” (ICRA), 2010

Drone-Be-Gone is an agile, low-cost, general-purpose CPS testbed for UAVs with: • Easy migration between centralized and distributed platform • Ability to implement wide-variety of applications in 2-D cost-effectively Future directions: • Implement 3-D localization and Extended Kalman Filter for better navigation

Acknowledgements

This work was made possible by NPRP award [NPRP 4-463-2-172] from the Qatar National Research Fund (a member of Qatar Foundation). The statements made herein are solely the responsibility of the authors.

Extending the Range via Ad-hoc Communication for Cooperative Robotic Watercraft Authors Ahmed Emam Abderrahmen Mtibaa (Texas A&M University at Qatar) Khaled A. Harras Nathan Brooks (Carnegie Mellon University) Paul Scerri (Carnegie Mellon University)

Category PostgraduateFaculty Advisor DivakarDivakaran Liginlal, Ph.D.

Abstract In this project, we outline a low-cost, easy-to-deploy, mobile, autonomous marina sensor that can support a broad set of applications including water PH sensing, water-depth sensing, and oil spill detection. By working cooperatively, fleets of boats (sensor nodes) can cover large areas that would be impractical otherwise. We start with describing the boatâ&#x20AC;&#x2122;s design, hardware and communication architecture. Then, we focus more on the communication architecture and discuss its limited coverage range, which stops the boats from going farther in their exploration quest. We propose a solution for such limitation via device-2-device ad-hoc communication methodologies in both multi-hop and DTN settings. We discuss our evaluation of single-hop device-2-device WiFi ad-hoc communication on-water with regards to horizontal and vertical distances. At the end we discuss experiments performed on-land to validate and evaluate our multi-hop and DTN ad-hoc prototypes. In the future, we plan to evaluate our prototypes on-water using the boats, also use appropriate routing algorithms to support real-world topologies.

Extending The Range Via Ad-hoc Communication For Cooperative Robotic Watercraft Ahmed Emam +, Abderrahmen Mtibaa*, Khaled A. Harras+ , Nathan Brooks+ and Paul Scerri+ +Carnegie Mellon University and *Texas A&M University Qatar I. INTRODUCTION & BACKGROUND A) Application

B) Marina sensor node design

C) Architecture • Hardware

• Communication

Need a low-cost, easy-to-deploy, mobile, autonomous marina sensor network

On-board Navigator & Communicator

Current design of Lutra Prop

Command Center

II. PROBLEM & PROPOSED SOLUTION Problem

• Boat 1 achieves 2-way comm. Command center  Boat Boat  Command Center • Boat 2 achieves one-way communication, no live feedback from the boats Command Center  Boat

Method 1: Multi-hop

Method 2: DTN

- A route has to exist from end-to-end - Data is sent in real-time from one end to other via intermediate nodes - Appropriate routing algorithms are needed

Boats opportunistically communicate Each boat stores and forwards data Data must be delay tolerant No guaranteed data delivery

• No communication coverage in green-shaded area

Solution

• Extend communication coverage via Boat-2-Boat communication

Exploration and coverage

IV. EXPERIMENTS ON-LAND

III. EXPERIMENTS ON-WATER • •

Single-hop

Building block for any Boat-2-Boat communication Investigate communication properties on water surface (Prior works are onland or under-water)

Distance d: Horizontal distance between two phones Altitude h: Distance from phone to water surface

Time elapsing

DTN Scenario

- Sender sends data to Sink Opportunistically via Proxy - Proxy moves to blue circles, adjacent to Sender’s movement to red circles

Effective Throughput

Multi-hop

h = 5 cm

Scenario

h = 20 cm

h = 50 cm

- Sender sends data to Sink via Proxy - Proxy moves to blue circles, parallel to Sender’s movement to red circles

Effective Throughput

V. CONCLUSION & FUTURE WORK Conclusion

• Investigated single-hop ad-hoc Wi-Fi communication on-water • Built prototype for multi-hop and DTN Boat-2-Boat communication

Future Work • Better understanding of Wi-Fi performance at sea-level • Fast degradation in quality of communication because of refraction and refraction of EM waves caused by sea waves

References

[1] Valada, Abhinav, et al. "Development of a low cost multi-robot autonomous marine surface platform." Field and Service Robotics. Springer Berlin Heidelberg, 2014. [2] Scerri, Paul, et al. "Real-world testing of a multi-robot team." Proceedings of the 11th International Conference on Autonomous Agents and Multiagent Systems-Volume 3. International Foundation for Autonomous Agents and Multiagent Systems, 2012.

• Perform multi-hop and DTN experiment on-water using boats • Investigate trade-offs between DTN and multi-hop in terms of explored-area size, time and number of boats used • Use appropriate routing algorithm

Acknowledgements

This work was made possible by NPRP award [NPRP 4-1330-1-213] from the Qatar National Research Fund (a member of Qatar Foundation). The statements made herein are solely the responsibility of the authors.

GraphSim: A Distributed and Adaptive Graph Simulation System Authors Pooja Nilangekar Mohammad Hammoud

Category PostgraduateFaculty Advisor DivakarFaculty AdvisorDivakaran Liginlal, Ph.D.ategornformation System

Abstract Large-scale graph processing is becoming central to our modern life. For instance, graph pattern matching (GPM) can be utilized to search and analyze social graphs, biological data and road networks, to mention a few. Conceptually, a GPM algorithm is typically defined in terms of subgraph isomorphism, whereby it seeks to find subgraphs in an input data graph, G, which are similar to a given query graph, Q. Although subgraph isomorphism forms a uniquely important class of graph queries, it is NP-complete and very restrictive in capturing sensible matches for emerging applications like software plagiarism detection, protein interaction networks, and intelligence analysis, among others. Consequently, GPM has been recently relaxed and defined in terms of graph simulation. As opposed to subgraph isomorphism, graph simulation can run in quadratic time, return more intuitive matches, and scale well with modern big graphs (i.e., graphs with billions of vertices and edges). Nonetheless, the current state-of-the-art distributed graph simulation systems still rely on graph partitioning (which is also NP-complete), induce significant communication overhead between worker machines to resolve local matches, and fail to adapt to various complexities of query graphs. In this work, we observe that big graphs are not big data. That is, the largest big graph that we know of can still fit on a single physical or virtual disk (e.g., 6TB physical disks are cheaply available nowadays and AWS EC2 instances can offer up to 24 × 2048GB virtual disks). However, since graph simulation requires exploring the entire input big graph, G, and naturally lacks data locality, existing memory capacities can get significantly dwarfed by G’s size. As such, we propose GraphSim, a novel distributed and adaptive system for efficient and scalable graph simulation. GraphSim precludes graph partitioning altogether, yet still exploits parallel processing across cluster machines. In particular, GraphSim stores G at each machine but only matches an interval of G’s vertices at the machine. All machines are run in parallel and each machine simulates its interval locally. Nevertheless, if necessary, a machine can inspect remaining dependent vertices in G to fully resolve its local matches without communicating with any other machine. Hence, GraphSim does not shuffle intermediate data whatsoever. In addition, it attempts not to overwhelm the memory of any machine via employing a mathematical model to predict the best number of machines for any given query graph, Q, based on Q’s complexity, G’s size and the memory capacity of each machine. Subsequently, GraphSim renders adaptive as well. We experimentally verified the efficiency and the scalability of GraphSim over private and public clouds using real-life and synthetic big graphs. Results show that GraphSim can outperform the current fastest distributed graph simulation system by several orders of magnitude.

GraphSim:

A Distributed and Adaptive Graph Simulation System Pooja Nilangekar and Mohammad Hammoud

Graph Simulation Professional Social Network G

Query Graph Q

Graph Simulation: q is a less restrictive Graph Pattern Matching (GPM) technique q captures meaningful matches in realworld applications (e.g., social community detection, network traffic analysis) q runs in quadratic time

I2 I1

O PM

RS1

RS2

RS3

PM1

PM2

RS4

GPM Technique Subgraph Isomorphism Graph Simulation

Matches O RS PM P

0 0

2 3

2 4

Legend O

Organisation

Research Scientist

Project Manager

Project

Unmatched

Interval i

Computation Model Centralized

Distributed

GraphSim

S I1 I2

S S

(+) No intermediate communication (-) Centralized computation

(+) Distributed computation (-) Intermediate data communication

I1 I2 I3

(+) No intermediate communication (+) Distributed computation

Adaptive Nature GraphSim employs a mathematical model, which predicts a number of workers for each query to ensure:

Smem â&#x2030;¤ (Î˛+Îł)

đ?&#x2018;&#x2020;đ?&#x2018;&#x2020;đ?&#x2018;&#x161;đ?&#x2018;&#x161;đ?&#x2018;&#x161;đ?&#x2018;&#x161;đ?&#x2018;&#x161;đ?&#x2018;&#x161; đ?&#x203A;˝đ?&#x203A;˝ đ?&#x203A;žđ?&#x203A;ž

= Memory at each machine = Engine data induced by the storage & processing engine = Application data induced by GraphSim

Experimental Results

GS-PowerGraph

10000 8000 6000 4000 2000 0

C-Q(4, 8)

A-Q(6, 12)

C-Q(8,16)

Query Graph

C-Q(10, 20)

GS-PowerGraph

200

Time in Seconds

8000 6000

150

4000 0

1 Machine

2 Machines

Sweet Spot & Predicted

100

2000

A-Q(4, 6)

A-Q(6, 10) A-Q(8, 12) A-Q(10, 20) Query Graph

GS-PowerGraph

GraphSim

12000

DGS

Accuracy

50 0

A-Q(4, 6)

3 Machines

GraphSim

60000

Time in Seconds

GraphSim

A-Q(4, 6) A-Q(6, 10) A-Q(8, 12) A-Q(10, 20) Query Graph

GS-GraphChi

Yahoo!

GS-PowerGraph

Network Traffic in MBs

1000000 100000 10000 1000 100 10 1

DGS

Network Traffic in MBs

Time in Seconds (Log-Scale)

GS-GraphChi

Citation

Network Traffic

Runtime

Dataset

50000 40000 30000 20000 10000 0

C-Q(4, 8)

A-Q(6, 12)

C-Q(8,16)

Query Graph

C-Q(10, 20)

1600 1400 1200 1000 800 600 400 200 0

A-Q(6, 10)

A-Q(8, 12)

Query Graph

4 Machines

5 Machines

A-Q(10, 20)

6 Machines

Sweet Spot & Predicted

C-Q(4, 8)

A-Q(6, 12) C-Q(8,16) Query Graph

C-Q(10, 20)

Work Supported by QNRF, NPRP Grant No.: 7-1330-2-483

NEXCEL: A Deductive Spreadsheet Authors Iliano Cervesato Askerali Maruthullathil Afroz Aziz

Category PostgraduateFaculty AdvisorDivakarFacDivakaran Liginlal, Ph.D.ategorInformation Systems

Abstract We live in a world today with more data than we know how to deal with. We are unable to easily derive interesting consequences from this base data with existing technologies as they often tend to be too technical or overly priced. While millions of users use spreadsheets on a daily basis, they are not equipped with the necessary tools on this to perform more advanced tasks without a lot of formal training. Even then, these softwares are unable to perform tasks that require recursive relational calculations needed for many types of common data correlational problems. Yet, their simple user interface, ease of use and gentle learning curves make them extremely commonly used. Database tools on the other hand, require a lot of technical training and are usually very expensive to acquire. NEXCEL successfully marries the power of database tools with the design and interface of a common spreadsheet by extending the spreadsheet paradigm with support for deductive reasoning, thus equipping a novice user with the ability to define useful forms of correlation in the data that they have. NEXCELâ&#x20AC;&#x2122;s design exploits techniques from logic programming and database theory in its core while retaining the cognitive simplicity of todayâ&#x20AC;&#x2122;s spreadsheets. NEXCEL is intended to be used as common spreadsheets are: as an assistant for daily decision making needs of its users added to the ability to define logical rules and relations with their data.

NEXCEL

nexcel.qatar.cmu.edu This work was funded by the Qatar National Research Fund as project NPRP 4-341-1-059

Iliano Cervesato <iliano@cmu.edu> Askerali Maruthullathil <askerm@qatar.cmu.edu> Afroz Aziz <afrozulhaq@cmu.edu>

a deductive spreadsheet Wh y N E XC E L

Motivation

Current Spreadsheets

Spreadsheets are one of the most ubiquitous computer applications. They allow users with very little computer science training to perform complex computations and make decisions based on nu-

NEXCEL

Lack support for manipulating relations as

Native support for manipulating data as

first-class objects -- only commands on tab-

relations. New relations are calculated as

ular areas of the spreadsheet.

formulas over existing relations.

No facilities for drawing interesting conse-

Full integration with traditional spread-

quences of symbolic data.

sheet functionalities.

Limited support for reasoning about

Retains the cognitive simplicity, ease of

non-numerical data, via commands not for-

use and gentle learning curve of today’s

mulas.

spreadsheet applications.

merical data. However, a large percentage the decisions we make every day depends on information that is not numerical, for example deciding on what course to take next semester, exploring one’s portfolio’s exposure to a given industry, or scheduling the details of a trip. Nexcel extends traditional spreadsheet applications with supports for combining numeric and symbolic decisions. It does so while retaining the cognitive simplicity of current products.

What ca n we do w i t h N E XC E L ? 1. Define relations

2. Compute relations

3. Perform analysis

4. Get explanations

Designate tabular regions of the spreadsheet as relations.

Write formulas inside some groups that evaluate to relations.

Show dependencies among relations graphically.

Explain why an unexpected result was returned.

Give symbolic names to relations and columns, and specify attributes.

Support for constraints, recursion, negation, and much more.

Help ensure results are in accordance to user intentions.

Explain why an expected result was not returned.

How do e s N E XC E L w o rk ? Theory

Application

Programming language

Built on open source JavaScript library

Integrates constraint programming and forward logic programming within the basic functional programming paradigm of traditional spreadsheets.

require.js used to dynamically load module-based JavaScript files

Databases Combines the expressive power of recursive SQL with traditional spreadsheet calculations.

Web programming Natively designed as an interactive, client-based, web application.

Cognitive psychology Designed to retain the intuitive appeal and gentle learning curve of traditional spreadsheet applications.

JQuery and Bootstrap to make it browser independent WebWorker to dynamically load and process workbook data in parallel Raphaël to generate graphs (evaluation, explanation and dependency graphs)

NEXCEL used to develop NEXCEL Formula evaluation process uses projection and difference to find independent variables and ranges to complete evaluation and to find circular dependencies. Cell and group dependencies updates are calculated using NEXCEL evaluation process to find the best order of execution.

Technologies used JQuery

JavaScript

PHP 5.0

QUnit

HTML 5

CSS3

MySQL

Raphaël

The OptDiac Project: Guidelines and Framework for a Large Scale Arabic Diacritized Corpus Authors Wajdi Zaghouani Houda Bouamor Ossama Obeid Kemal Oflazer Mona Diab (George Washington University) Sawsan Alqahtani (George Washington University) Mahmoud Ghoneim (George Washington University)

Category PostgraduateFaculty AdvisorDivakarFacDivakaran Liginlal, Ph.D.ategorInformation Systems

Abstract We present the annotation guidelines developed as part of an effort to create a large scale manually diacritized corpus for various Arabic text genres. The target size of the annotated corpus is 2 million words. We summarize the guidelines and describe issues encountered during the training of the annotators. We also discuss the challenges posed by the complexity of the Arabic language and how they are addressed. Finally, we present the diacritization annotation procedure and detail the quality of the resulting annotations.

The OptDiac Project: Guidelines and Framework for a Large Scale Arabic Diacritized Corpus Wajdi Zaghouani wajdiz@cmu.edu

Houda Bouamor hbouamor@cmu.edu

Abdelati Hawwari abhawwari@gwu.edu

Mona Diab mdiab@gwu.edu

Ossama Obeid oobeid@cmu.edu

Mahmoud Ghoneim ghoneim@gwu.edu

Sawsan Alqahtani sawsanq@gwu.edu

Kemal Oflazer ko@cs.cmu.edu

1. Problem Statement • Modern Standard Arabic script typically omits diacritics and only represents a sequence of consonants. • The lack of diacritics leads usually to considerable lexical and morphological ambiguity. • What is the optimal level of minimal diacritization?

2. Solution

3. The OptDiac Project

• Build annotated resources with added diacritics.

The project has produced two components:

• Build systems for automatic diacritization of Arabic text.

• Multi genre Diacritized Corpus (2 million words). • Automatic diacritization tool for Arabic at different diacritization level.

4. OptDiac Annotation Guidelines

5. Annotation Tool

• Comprehensive and simplified annotation guidelines

• Provides Pre-computed diacritization options to reduce typing. • Limits token edits to diacritics only. • Link to annotation guidelines. • Tracks the number of words that are yet to be annotated.

• Several annotated examples to illustrate the specified rules

Fig 2. Pre-computed diacritization

Fig 3. The token editor for manual diacritization

Fig 1. The annotation interface

6. Evaluation

7. Error Analysis

• We assigned around 3100 words extracted from the Corpus of Contemporary Arabic (CCA) to five annotators. • We conducted three annotation evaluation using the Word Error Rate (WER)-(lower is better).

• • • • • • •

Sentence interpretation disagreement. Proper noun diacritics disagreement. Misspelled words diacritization disagreement. Case endings disagreement. Shadda diacritization disagreement. Soukoun diacritization disagreement. Dialectal Arabic expressions diacritization.

Acknowledgements

This research was supported by Qatar National Research Fund (QNRF), NPRP grant 6-1020-1-199

Effect of Wave Interference on Richtmyer-Meshkov Instability Authors Arun Pandian Mohamed Hassan Robert Stellingwerf (Stellingwerf Consulting) Snejana Abarji

Category PostgraduateFaculty AdvisorDivakarFacDivakaran Liginlal, Ph.D.ategorInformation Systems

Abstract We study the dynamics of structures that formed due to Richtmyerâ&#x20AC;&#x201C;Meshkov instability (RMI) at the interface between two fluids with different densities when a strong shock wave refracts it. While previous research in this field was focused on the effects of the wavelength and amplitude of the interface perturbation, the information was largely ignored on the influence on RMI evolution of the relative phase of a multi-wave perturbation and the interference of the perturbation waves. Based on group theory analysis and by applying the Smooth Particle Hydrodynamics (SPH) simulations, we study the effects of the relative phase between the interfacial sinusoidal waves on the structure of bubbles and spikes that is formed at the interface after the shock passage. A number of new qualitative and quantitative effects are found, a strong effect of the wave interference on RMI evolution is observed. Our results indicate that the symmetry of the interface is an important factor of the dynamics of RM flows. In particular, evidences so far indicate that the symmetry of the interface leads to faster growing spikes as compared to asymmetric cases. We also discuss how to control the growth of RMI by controlling the phases of waves of the initial perturbation.

Eﬀect of Wave Interference on Richtmyer-Meshkov instability Arun Pandian, Carnegie Mellon University – Qatar Mohamed Hassan, Carnegie Mellon University – Qatar Robert F. Stellingwerf, Stellingwerf ConsulIng, Inc., USA Snejana I. Abarji, Carnegie Mellon University – Qatar;

RMI occurs when a shock passes through a perturbed interface between two ﬂuids with different values of acoustic impedance (ﬂuid densities).!

We studied Richtmyer-Meshkov instability (RMI) induced by strong shocks by means of Smooth Particle Hydrodynamic Simulations (SPH) to determine the effect of the initial conditions on RMI evolution.!

We determine how wave interference of multimode initial perturbation affects RMI evolution.!

RMI plays an important role in various phenomena, from inertial conﬁnement fusion and explosion of supernova to scramjets and material mixing.! !

RMI EvoluIon

After the shock refracts the interface, a structure of bubbles (red) and spikes (blue) appear. At late times the bubble fronts ﬂatten due to their effective deceleration (Abarzhi 2002.)! Single Mode case

Initial growth rate of Spikes(Single Mode)!

Conclusions!

•  When secondary amplitude is low, relative phase does not affect growth rate of RMI structures. ! •  When secondary amplitude is low, relative phase does not affect growth rate of RMI structures. ! •  RMI growth rate depends on an interplay between phase and secondary amplitude. !

Double Mode case

Initial growth rate of Spikes(Double Mode)!

Implications! •  Can explain the generation of heavy mass elements in supernova.! •  Can be used for mitigation and control of mixing in internal conﬁnement fusion.! •  Can generate more efﬁcient combustion in scram jets.!

Teacher Development for Student Reading Author Dudley Reynolds

Category PostgraduateFaculty AdvisorDivakarFacDivakaran Liginlal, Ph.D.ategorInformation Systems

Abstract On multiple international assessments of student science and reading ability including the IEA’s TIMSS and the OECD’s PISA, Qatar students have performed poorly in comparison to international peers. Addressing this academic and societal challenge, Qatar National Research Fund grant NPRP 4 - 1172 - 5 – 172 “Improving Reading Skills in the Middle School Science Classroom” trialed an innovative model for professional development of teachers in order to impact how reading is taught as part of both science and English instruction at the preparatory level. This poster showcases findings from the three-year project highlighting in particular the curriculum created, the development of participating teachers, and a case study of what happens when teachers use both Arabic and English (translanguaging) while teaching.

Teacher Development for Student Reading Dudley Reynolds

Student Performance

Human Capacity Challenges

Professional Development

International Tests of Science and Reading Project Reading Assessments (Bilingual)

43.2 hours of PD / year (SEC, 2012-2013) Banking, not Liberating, model (Freire, 1970)

Difficulties with science in Arabic, science in English

Intervention

Method

Results

Year 1. What was being taught and how?

1. Performance reading emphasized

Year 2. Pilot Program (2 schools)

2. Teacher development

textbook review, teacher survey, class observations

(not the process of reading)

5 Lesson Study cycles – “Strategic Reading” interviews, class observations

understanding of reading process, instructional strategies, value of reflective practice

Year 3. Scaled Program (12 schools)

3. Teacher development trainers ↑; teachers ?

school representatives trained, interviews, class observations, students assessed

Student reading

more valid assessment instrument; no clear improvement in 10 weeks

Curricular Content

Significance and Impact Teacher Development

Instructional Methodology

collaborative planning

translanguaging case study (García & Wei, 2014)

lesson study it was useful and very helpful program . . . when we gather we have many ideas and many opinions and we can select at the end from what we brainstormed . . . it was very important for as one teacher he is going to deliver the lesson and many options around him giving him support ...

effective instruction

it was very helpful for students . . . it develops their reading in different ways ... it's like continuous like a circle ... if you start ... make them know how to identify and recognize and develop their interest then they move on to find a purpose and then it will be very easy for them to check or select the appropriate . . strategy . . . So I believe this is the most important program that I have had in Qatar related to something that directly helps the students CMUQ Meeting of the Minds 2016

Traditional Instruction (Arabic or English) Translingual Instruction (Arabic and English)

Supported by Qatar National Research Fund Grant, NPRP 4 - 1172 - 5 - 172

A Study of Visual Metaphors on Arab e-Commerce Websites Authors Maryam Al-Fehani Divakaran Liginlal

Category PostgraduateFaculty AdvisorDivakarFacDivakaran Liginlal, Ph.D.ategorInformation Systems

Abstract The last two decades have witnessed a rapid increase in the adoption of e-commerce by businesses worldwide. This has been accompanied by its slow but steady diffusion to the Arab world. Many researchers have documented the influence of national cultures on the design of e-commerce websites and the resulting impact on consumer behavior. This thesis focuses on the creation of culturally attuned visual metaphors for e-commerce website design and a study of how their use enhances the experience of Arab online shoppers. The first phase of the research, consisting of a survey of related research literature and an exhaustive search of Arab e-commerce websites, helped to conclude that website designers mostly adopt existing Westerninfluenced interface metaphors giving scant attention to creating Arab culture-specific visual metaphors. The research, therefore, focused on the discovery process accompanying the creation of culturally attuned visual metaphors as Web interface elements. Such creative design was reinforced through the collection and content analysis of Arabic stories to extract design themes and study of an existing corpus of Arabic linguistic metaphors to generate design ideas. The resulting collection of visual metaphors is documented in this thesis. A selected set of interface icons derived from these metaphors were then included in an eye-tracking experiment designed to study their influence on Arab shopper behavior. Because of the small sample size of 32 native Arabic speaking participants, the results from the experiment are not conclusive. Qualitative analysis of the interview data and heat maps from the eye-tracking data, however, indicate culturally attuned visual metaphors have a positive influence on shopper behavior. The results address a gap in the literature related to the study of Arab culture specific visual metaphors and their use in Arab e-commerce websites. Most importantly, other researchers in this area stand to gain from the methodological insights gained, and website designers of Arab countries will benefit from the design ideas and metaphor examples generated from this thesis.

MOTIVATION

Many research studies have looked into the influence of Arab culture on e-commerce websites. These studies predominantly used Hofstede’s cultural dimensions. They analyzed the different features of websites whether they were linguistic, visual or structural features.

HYPOTHESIS

The use of visual metaphors that relate to Arab culture in Arab e-commerce websites will enhance user experience for an Arab audience.

OBJECTIVES

Examine different multimodal metaphors and analyze their use in existing e-commerce websites to understand their culture significance To achieve this research objectives the following questions were answered: •Do culturally attuned visual metaphors capture the attention of shoppers on Arab e-commerce websites? •Do Arab shoppers react differently to websites designed for other cultures? •Do culturally attuned sites influence perceived usefulness and perceived enjoyment of Arab shoppers, in turn influencing their urge to buy?

Visual Metaphors on Arab e-commerce Websites

A Study of

Maryam Al-Fehani | Advisor: Divakaran Liginlal

RESEARCH METHODOLOGY 1. Exploratory Research

• Analyzed results of prior study of 500 Arab e-commerce websites • Analyzed metaphorical expressions in 50 advertisements

Resulted In

Visual metaphors in ads

Visual metaphors in icons

(Only around 15 ads and 4 icons were found after extensive search)

2. Design Research

• Creative Research: Created 40 visual metaphors tuned to Arab culture • Synthesized metaphorical themes from Arab folklore • Translated textual metaphors to visual metaphors

3. Experiment

• Designed three websites portraying different cultures as shown below. • Conducted eye-tracking experiment that included a questionnaire and an interview Resulted In

Resulted in 40 visual metaphors, an example is shown below:

Western Website Design

Arab Website Design

FINDINGS

The results provide deeper insights into how culture shapes the design of websites: • Participants paid more attention to the localized elements of website design. • A questionnaire-based study provided further evidence that localization of site design in general and the use of culturally attuned visual metaphors in particular, positively influences e-shopper behavior. • The mean fixation duration for the wishlist icon is much greater at 1.01secs for the Arab website while it is 47 secs for the Western website. This shows that the participants noticed the Arab wishlist more. • In the interviews the participants stated that the western websites’ design and icons were “international” and “regular” and that they needed to be improved. • The participants stated that the following about the Arab website “it reflects our culture” and “the wish list and other culturally attuned icons aids us.” • These results indicate that participants reacted positively to culturally attuned visual metaphors.

Western Website Heatmap

Arab Website Heatmap

This research work was partially supported by NPRP Grant 5-1393-6-044 from the Qatar National Research Fund (A Member of the Qatar Foundation). The statements made herein are solely the responsibility of the authors.

Websites as Cultural Expressions: A Multimodal Analysis of Arabic e-Commerce Websites Authors Divakaran Liginlal Preetha Gopinath Robert Meeds (Qatar University) Rizwan Ahmad (Qatar University)

Category PostgraduateFaculty AdvisorDivakarFacDivakaran Liginlal, Ph.D.ategorInformation Systems

Abstract

This project examines the use of metaphors in Arabic language e-commerce websites and shows that metaphorical language plays an important role in enhancing the effectiveness of websites and e-commerce businesses in general. Arabic text was extracted from 3,065 websites across 22 Arab countries and 10 types of e-commerce domains. More than 14,000 metaphors were annotated in a sample of 1,208 rhetorical clusters (cohesive text units). Metaphor usage was highest in fashion, restaurant, and retail websites and lowest in e-banking, airline, and tourism websites. Colloquial figurative language was rare, suggesting e-commerce businesses could do more linguistically to localize their websites. Based on an analysis of a corpus of Arabic ecommerce websites, the project further investigated the use of figurative language in e-business texts. The empirical analysis demonstrates that the metaphor of “companies are living organisms” is the most prevailing one and provides the cognitive framework within which the e-commerce texts are constructed. Despite the fact that the e-commerce text is in Arabic, the cognitive framework underlying the texts is not much different from that in other languages. The second phase of this project involved an eye-tracking study, a first of its kind, to use Arabic language website stimuli to experimentally examine how cultural design style and information richness variables such as metaphors influence consumers’ visual attention, comprehension and attitudes toward the website. Results show both design style and information richness induce differential persuasive effects. In particular, participants exhibited higher trust and more favorable attitudes toward Arabic e-commerce websites using an Arabic design style compared to a Western design style. Also, participants who read Arabic language web pages with higher levels of figurative language spent more time reading the text, resulting in both better comprehension of the content and better attitudes toward the website. Finally, based on the results of the prior studies and a careful analysis of the corpus, general guidelines for the use of metaphors in the context of Arabic e-commerce sites were formulated. These guidelines are deliberately phrased in such a way as to be intelligible to non-linguists, such as PR staff. A set of common metaphors in the corpus drawn from different domains were generated and grouped around common themes, such as ‘touch’, ‘richness’, and ‘magic’. The result can be considered the core of content patterns for metaphoric language in Arabic e-commerce. In conclusion, the results suggest that e-commerce web content managers should use well qualified Arabic translators for their web content and use localized rather than standardized communications approaches where possible.

WEBSITES AS CULTURAL EXPRESSIONS: A MULTIMODAL ANALYSIS OF ARABIC E‐COMMERCE WEBSITES

MOTIVATION Many studies of global ecommerce have treated cultures as monolithic entities and resorted to evaluating websites against the five cultural dimensions proposed by Hofstede.

Think globally but act locally

OBJECTIVES  Build a corpus of textual and multimedia content gleaned from 3065 Arab e-commerce websites.  Study how cultural design & information richness influences Arab consumer perceptions.  Build best practices and content patterns for e-commerce websites targeted at Arab customers.

CENTRAL HYPOTHESIS Deconstructing websites as cultural expressions provides insights into the ideologies and practices of the contentproducers that can be harnessed to enrich customer’s overall e-commerce experience.

KEY FINDINGS Sparse use of interface icons which are culturally expressive.  Figurative language use is richest in restaurant and fashion domains.  Use of metaphors is key to persuading consumers and enhancing their trust.  Cultural design style has no significant effect on visual attention; however it influences trust and persuasion/liking. 

RESEARCH METHODOLOGY Crawl E-Commerce Websites

Pre-Process

Filter

Select

Generate

Analyze

CORPUS ANALYSIS ‐SUMMARY STATISTICS

LINGUISTIC & PICTORIAL METAPHORS

Rate of Metaphor Average Metaphor Count Occurrence Per 100 Words Per Document Average Maximum 24

EXAMPLES OF MANY PICTORIAL METAPHORS WE FOUND

DOMAIN‐WISE METAPHOR DISTRIBUTION

A.HOTSPOT ANALYSIS

EYE TRACKING EXPERIMENT RESULTS

Shows the 10 most attention grabbing spots in the design B.ATTENTION MAP

Gives an indication of how much attention is commanded (hot spots) C.PERCEPTION MAP

CULTURAL DESIGN STYLE AND INFORMATION RICHNESS Do They Influence Consumer Perceptions?

Effect of design style on visual attention

Effect of information richness on visual Effect of design style on trust

attention

Shows what the participant sees in the first 3 seconds COVERT ATTENTION ANALYSIS

- Cultural design style has no significant effect on visual attention - Cultural design style influences trust and persuasion/liking

- Information richness contributes significantly to higher trust and better comprehension; but has weak correlation with visual attention.

Authors: Divakaran Liginlal, Preetha Gopinath (Carnegie Mellon University in Qatar), Robert Meeds, Rizwan Ahmad (Qatar University)

Funding for this project: NPRP 5-1393-6-044

For more than a century, Carnegie Mellon University has been an innovator in education, with programs that inspire creativity, collaborate across disciplines and educate some of the worldâ&#x20AC;&#x2122;s most influential thinkers. Consistently top ranked, Carnegie Mellon has more than 13,000 students, 100,000 alumni and 5,000 faculty and staff globally. Nineteen Nobel Laureates and 12 Turing Award winners have called CMU home. At the invitation of Qatar Foundation, Carnegie Mellon joined Education City in 2004. Education City is a groundbreaking center for scholarship and research that is the ideal complement to Carnegie Mellonâ&#x20AC;&#x2122;s mission and vision. Carnegie Mellon Qatar offers undergraduate programs in biological sciences, business administration, computational biology, computer science, and information systems. Students from 37 countries enroll at our world-class campus. To learn more, visit qatar.cmu.edu and follow us on: Twitter: @CarnegieMellonQ Instagram: @carnegiemellonq Facebook: CarnegieMellonQ YouTube: Youtube.com/CarnegieMellonQatar