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JUMPSTARTING THE HEART OF SCIENCE: HOW LABS AND VENDORS CAN WORK TOGETHER TO IMPROVE REPRODUCIBILITY
Reproducible experimental findings are fundamental to the quality and progress of scientific research. The ability to reproduce research emphasises the rigour and trustworthiness of the original data, building confidence in the veracity of an experimental observation.
Reproducibility also has important implications for success in research, encouraging publication and bolstering the reputations of researchers and their labs. Conducting reproducible research also enables scientists to repeat and modify experiments quickly and easily without doubting their validity, saving valuable time and money.
However, across scientific disciplines, many researchers are experiencing difficulty when trying to replicate previously observed experimental results. This ‘reproducibility crisis’ is reflected in many forms: a single scientist struggling to reproduce results across their own experiments, members of the same lab attempting to confirm the results of other lab members (sometimes years later) and independent research groups failing to obtain results published by other groups. In a recent poll, nearly 80% of biological scientists experienced failure to reproduce someone else’s results, citing “not replicated enough in the original lab” and “poor experimental design” as major contributors1 . Other inherent factors of scientific research, such as the discontinuation of certain reagents and equipment, significant gaps in published protocols and methodologies, and a competitive publishing culture that devalues negative results2, contribute to this issue. However, actionable steps toward research reproducibility can be made by providing sufficient education and validated research tools to
Jumpstarting the heart of science
How labs and vendors can work together to improve reproducibility
new users and empowering them to gather reliable and trustworthy data.
Prioritising new user education Aside from rare instances of malicious intent, inconsistent results are commonly rooted in an honest mistake due to a lack of proper training and sufficient education provided to new users. Even if a person has spent years in the lab, they are still new users to new methods and applications. Given that the culture of scientific publishing incentivises the speed of producing results to establish ownership of groundbreaking findings, researchers are often forced to cut corners in this first crucial training and education step. Even experienced researchers may assume that they can just ‘figure it out’ when performing a new technique and never pursue sufficient training.
Paradoxically, the emphasis on publishing only data that supports a research claim limits users’ access to literature on what methods or experiments don’t pan out as expected, extending the overall
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time to obtain positive results for groups unaware of the avenues that have yielded negative results for others. The combination of incentivised rushing and devalued negative publishing paves the way for users to make common mistakes when learning a new technique, particularly when that technique is new to the lab.
Often, the most significant mistakes are not running appropriate or sufficiently stringent controls and not optimising an assay. For example, techniques that require protein detection using primary and secondary antibodies, such as flow cytometry, immunohistochemistry and immunofluorescent microscopy, require finetuned optimisation to ensure that the ideal reagent concentrations and conditions are used. If users aren’t provided proper training on assay design and optimisation, they may use too low or too high a concentration of a particular reagent like a primary antibody, resulting in weak or absent signal and off-target binding, respectively3. And unfortunately, if the same concentrations are used over and over and give the same results, results that appear reproducible in that user’s hands are still inaccurate. While peer review in publishing attempts to catch and correct these common errors by suggesting orthogonal experimental approaches, this alone is insufficient to prevent the publication of unreliable results. Therefore, it’s important to identify additional sources of experimental education and expertise for new users to prevent these common — and often critical — technical mistakes.
Research product vendors can offer an underutilised reservoir of expertise. Most experiments require commercially available products and reagents, and these tools are developed by suppliers who often harbour an untapped breadth of knowledge on the scientific applications of their products. It’s valuable to choose product vendors that provide strong customer support and technical services. Working with an accessible and communicative vendor can bridge the education gap for a new user to learn the appropriate controls and optimisation steps required to ensure reproducible results. Vendors often have unique insights into the nuances of their products and established knowledge of other customers’ experiences, so seeking their guidance can foster success in the lab. Reshaping the connection with product vendors from transactional to relationship-based can significantly enhance new user education and, in turn, improve data reproducibility. Working with a vendor shouldn’t be a single transaction, like buying a pair of shoes, but rather a continuous relationship built on effective education and trust.
Selecting validated tools While it may seem obvious, it’s important to use research products and tools that have been validated by the vendor/manufacturer for the specific application to reduce the potential for unreliable results. Similar reagents, such as targetspecific detection reagents, can be used in many applications, but blocking reagents, diluents, concentrations and incubation times may vary greatly depending on the assay and sample type. The art of determining where to purchase validated tools is not a common lesson taught to scientific researchers. The key is to select vendors with experience and expertise in specific applications and who make the intended, validated use of their product readily available to the user.
Scientific expertise within a specific application space allows a vendor or manufacturer to anticipate certain shortcomings and pitfalls of a new product during development, well before it becomes available to researchers. If a company is attuned to how a product is likely to be used in inexperienced hands, it can incorporate mechanisms to prevent these mistakes. Robust product development processes incorporate many tools, one of which is a ‘failure modes and effects analysis’ (FMEA). This analysis, typically employed to ensure safety and reproducibility in diagnostic tool development, can also be applied to research use only (RUO) product development. In terms of product performance, FMEA effectively considers how a product can fail due to incorrect use. FMEA also identifies steps in the manufacturing process that require tightly controlled parameters and takes steps to eliminate or mitigate the points of potential failure. Ultimately, this assessment aims to limit the parameters and variables that the end user must optimise and consider, thereby reducing the possibility of erroneous results and enhancing the likelihood of reproducible data4. For example, if a biological reagent will not function optimally if used in an imperfect buffer, the manufacturer can remove this possibility by providing the ideal buffer along with the reagent. This requires the manufacturer to test the reagent in a variety of commonly used buffers to understand their impact to product performance. Moreover, in areas that can’t be addressed by product design, a manufacturer can include accompanying education in instructions and user guides, bridging the education gap between the user’s experience in a technique and the experiment’s requirements for success.
Each company and manufacturer differs in the level of investment given to this stage of product development. In general, the more stringent the FMEA, the higher the reliability and quality of the product. It’s essential to consider a supplier’s dedication to this critical step of product development to bolster the chance of producing reliable and reproducible results. Setting yourself up for success To foster a community of reliable research, it’s important to partner with suppliers that provide both continuous education and well-validated products. My experience in research has informed my priorities working on the supply side: I have seen the value of a vendor’s upfront investment in product development (or lack of it) to an end user’s success. Developing products using a team of in-house experts and striving to establish extended relationships with researchers can support their scientific endeavours from experimental design to manuscript publication. By fostering communication, education and diligence, researchers and product vendors can work together to increase research reproducibility and ensure the reliability of future scientific discoveries.
*Pamela James is VP of Product at Vector Laboratories.
1. Baker, M. 1,500 scientists lift the lid on reproducibility.
Nature 533, 452–454 (2016). https://doi. org/10.1038/533452a 2. https://kosheeka.com/factors-affecting-researchreproducibility-in-biomedical-research/ 3. https://www.ncbi.nlm.nih.gov/pmc/articles/
PMC4985043/ 4. https://link.springer.com/article/10.1007/s00769020-01441-9
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Rapid identification of food poisoning bacteria
Scientists from Osaka Metropolitan University have developed a simple, rapid method to simultaneously identify multiple food poisoning bacteria, based on colour differences in scattered light by nanometre-scaled organic metal nanohybrid structures (NHs) that bind via antibodies to those bacteria. Published in the journal Analytical Chemistry, their method is a promising tool for rapidly detecting bacteria at food manufacturing sites and thereby improving food safety.
Bacterial tests are regularly conducted to detect food poisoning bacteria at food manufacturing factories, but it takes more than 48 hours to obtain results due to the time required for a bacteria incubation process called culturing; therefore, there remains a demand for rapid testing methods to eliminate food poisoning accidents. Responding to this need, the researchers utilised the optical properties of organic metal NHs — composites consisting of polyaniline particles that encapsulate a large number of metal nanoparticles — to rapidly and simultaneously identify food poisoning-inducing bacteria called enterohaemorrhagic Escherichia coli (E. coli O26 and E. coli O157) and Staphylococcus aureus.
The team first found that organic metal NHs produced stronger scattered light than metal nanoparticles of the same size. Since the scattered light of these NHs is stable in the air for a long period of time, they are expected to function as stable and highly sensitive labelling materials. Furthermore, it has been revealed that these NHs exhibit different colours of scattered light (white, red and blue) depending on the metal elements of the nanoparticles (gold, silver and copper).
Then the team introduced antibodies that bind specifically to E. coli O26, E. coli O157 and S. aureus into the organic metal NHs and used these NHs as labels to evaluate the binding properties of the antibodyconjugated NHs to specific bacterial species. As a result, E. coli O26, E. coli O157 and S. aureus were observed as white, red and blue scattered light, respectively, under the microscope. Furthermore, when adding predetermined amounts of E. coli O26, E. coli O157 and S. aureus to rotten meat samples containing various species of bacteria, the team succeeded in using these labels to simultaneously identify each bacterial species added.
This method can identify various types of bacteria by changing the antibodies to be introduced. In addition, since it does not require culturing, bacteria can be rapidly detected within one hour, increasing its practicality as a new testing method.
Retinal damage a marker of MS severity
It is essential to assess the severity of multiple sclerosis (MS) in order to choose appropriate therapeutic measures, but this cannot be reliably done using existing methods. Researchers at the Medical University of Vienna have now shown that the retina can be used as a prognostic marker, with retinal layer thinning as a result of an MS relapse predicting the severity of future relapses and, hence, the likelihood of disability.
Multiple sclerosis is a chronic inflammatory autoimmune disease that leads to the loss of axons and neurons throughout the entire nervous system. Although this damage often goes unnoticed by patients at first, its extent determines the prognosis for the severity of the disease. Since predictions about the course of the disease are important in MS for selecting the appropriate treatment, medical research has long been searching for reliable prognostic tools.
The Vienna researchers studied 167 MS patients over a period of more than three years, hypothesising that retinal damage due to relapse reflects the extent of damage in the brain. The researchers measure retinal layer thickness using optical coherence tomography (OCT) — an imaging technique that uses infrared light to produce high-resolution threedimensional images of very thin layers of tissue in the micrometre range. It is already used as a tool for diagnosing eye diseases such as glaucoma and for evaluating disease progression. “The technique for predicting the course of MS is therefore already available to us,” said Gabriel Bsteh, first author of the study.
As the scientific analyses confirmed, the loss of approximately 5 µm of retinal layer thickness after optic neuritis equates to a doubling of the risk of permanent disability after the next relapse. The results of the study, published in the journal Neurology, suggest that more aggressive treatment is indicated where there is significant retinal layer thinning than would be the case for a smaller degree of thinning. This is true even if the patient has no disability or only slight disability at the time of measurement.
“As we discovered in the course of our clinical trial, measurements should be taken at initial diagnosis, directly when optic neuritis occurs in relapsing MS and six months thereafter,” Bsteh said.
“In retinal layer thickness, we have found a new biomarker that represents a window to the brain, as it were,” Bsteh concluded. If the results are confirmed in larger follow-up studies, the technique could also be applied in routine clinical practice.
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Scientists and engineers at the University of Minnesota have found a way to improve the performance of traditional magnetic resonance imaging (MRI) reconstruction techniques, allowing for faster MRIs to improve health care. Their breakthrough has been published in Proceedings of the National Academy of Sciences (PNAS). “MRIs take a long time because you’re acquiring the data in a sequential manner,” explained Mehmet Akçakaya, an associate professor at U of M and senior author on the paper. “We want to make MRIs faster so that patients are there for shorter times and so that we can increase the efficiency in the healthcare system.”
For the last decade, scientists have been making MRIs faster using a technique called compressed sensing, which uses the idea that images can be compressed into smaller sizes, akin to zipping a JPEG on a computer. More recently, researchers have been looking into using deep learning, a
Respected molecular biologist Professor Frank Gannon has been selected to oversee the implementation of interim recommendations arising from an inquiry into forensic DNA testing in Queensland, after a report found there was potential for the miscarriage of justice.
State Minister for Health and Ambulance Services Yvette D’Ath said Gannon would provide independent oversight of the implementation of the interim recommendations from the ongoing Commission of Inquiry into Forensic DNA Testing in Queensland. The Commission of Inquiry was sparked by concerns about the DNA testing thresholds used by Queensland Health Forensic and Scientific Services between February 2018 and June 2022.
“Commissioner Walter Sofronoff KC’s interim findings and recommendations, which the government will implement, relate to the issue of how some DNA testing results were reported by Forensic and Scientific Services (FSS),” D’Ath said.
“The Commissioner found that between February 2018 and June 2022, FSS scientists provided untrue or misleading information regarding the detection of DNA in some sworn witness statements relating to samples with very small amounts of DNA.
“He has recommended that the relevant statements be withdrawn and corrective statements issued.”
While Sofronoff did not find that previous DNA testing was inaccurate, he did find that, due to the possibility that additional processing of DNA samples could lead to partial or full DNA being detected in some cases, statements issued stating “DNA insufficient for further processing” or “no DNA detected” were not factually correct.
To rectify this potential injustice, Sofronoff has recommended: • that all witness statements issued by FSS since 2018 that stated “DNA
insufficient for further processing” or “No DNA detected” have new statements issued stating that the original statement was incorrect; and • that the government appropriately fund any bodies required to investigate, consider and resolve these issues.
Although no recommendation was made regarding further analysis of samples the subject of the incorrect statements, the government will now undertake a full audit of all samples relating to major crime taken between 2018 and June 2022 that resulted in witness statements stating “DNA insufficient for further processing” or “No DNA detected” that did not progress to further testing due to DNA results falling between 0.001 ng/µL and 0.0088 ng/µL. This will help identify whether any partial or full DNA can be detected; where DNA is found, such results will be provided to the Queensland Police Service for further consideration. Furthermore, a taskforce has been established to implement the recommendations and to support work coming out of the ongoing Commission of Inquiry.
type of machine learning, to speed up MRI image reconstruction. Instead of capturing every frequency during the MRI procedure, this process skips over frequencies and uses a trained machine learning algorithm to predict the results and fill in those gaps.
While deep learning can be a more effective alternative than traditional compressed sensing, there are concerns with using deep learning as well. For example, having insufficient training data could create a bias in the algorithm that might cause it to misinterpret the MRI results. Using a combination of modern data science tools and machine learning ideas, the U of M researchers have found a way to fine-tune the traditional compressing method to make it nearly as high quality as deep learning — a process that would eliminate some of the concerns related to overdependence on deep learning exclusively.
“There’s a lot of hype surrounding deep learning in MRIs, but maybe that gap between new and traditional methods isn’t as big as previously reported,” Akçakaya said. “We found that if you tune the classical methods, they can perform very well. So maybe we should go back and look at the classical methods and see if we can get better results. There is a lot of great research surrounding deep learning as well, but we’re trying to look at both sides of the picture to see where we can find the best performance, theoretical guarantees and stability.”
Qld forensic scientists provided misleading information: report
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Cellular ‘waste product’ helps immune cells to fight cancer
Scientists from the University of Texas Southwestern Medical Center have found that lactate, a metabolic by-product produced by cells during strenuous exercise, can rejuvenate immune cells that fight cancer. Their finding, published in the journal Nature Communications, could eventually be used to develop new strategies to augment the anti-tumour effect of cancer immunotherapies.
Lactate is commonly used in Ringer’s solution, administered intravenously to replace fluids after blood loss (due to trauma, surgery or severe burns) or to treat a condition called metabolic acidosis. While lactic acid (lactate with an additional proton) has been associated with cancer growth and immune suppression, the effects of lactate on cancer and immunity have been unclear.
To investigate this question, Dr Jimmy Gao and his colleagues gave lactate injections to mice with colon cancer or melanoma; other tumour-bearing mice received glucose injections. While glucose had little effect, tumour growth was significantly reduced in mice treated with lactate. When the researchers tried the same experiment in mice genetically engineered to lack T cells, this anti-tumour benefit was blocked, suggesting that lactate appeared to be exerting its effects through this immune cell population.
Administering lactate alone didn’t completely eliminate the tumours. But when the researchers added a commonly used immune checkpoint inhibitor — a type of cancer immunotherapy that releases the brakes that prevent T cells from fighting malignancies — about half the mice became completely tumour-free. Lactate also significantly improved the effects of a cancerfighting vaccine and improved the anti-cancer response of cultured T cells that were injected into tumour-bearing mice.
Further single-cell RNA sequencing analysis showed that more T cells infiltrated the tumours of the lactate-treated mice. Compared to animals that didn’t receive this treatment, T cells from the mice that received lactate expressed more genes associated with stem-like T cells and a smaller number of genes associated with exhaustion markers, making them more fit to effectively fight cancer.
“The lactate that we usually think of as a waste product appears to have a previously unrecognised role in fighting cancer,” Gao said.
Gao said the data suggest that lactate could be used to supplement existing immunotherapies, such as immune checkpoint inhibitors, cancer vaccines and CAR-T cell therapy — a cancer treatment in which T cells engineered to fight specific tumour types are expanded in the laboratory and then injected into patients. It also suggests that exercise, which naturally raises lactate levels, may be protective against cancer or may augment the immune system to fight cancer as well. Gao and his colleagues plan to investigate these topics in future studies.
Dogs can smell when people are stressed
The physiological processes associated with an acute psychological stress response produce changes in human breath and sweat that dogs can detect with an accuracy of 93.75%, according to a new study from Queen’s University Belfast.
Odours emitted by the body constitute chemical signals that have evolved for communication, primarily within species. Given dogs’ remarkable sense of smell, their close domestication history with humans and their use to support various human psychological conditions, researchers wondered whether dogs could be sensing chemical signals to respond to their owners’ psychological states.
In the new study, the researchers collected samples of breath and sweat from non-smokers who had not recently eaten or drunk. Samples were collected both before and after a fast-paced arithmetic task, along with self-reported stress levels and objective physiological measures: heart rate (HR) and blood pressure (BP). Samples from 36 participants who reported an increase in stress because of the task, and experienced an increase in HR and BP during the task, were shown to trained dogs within three hours of being collected. Four dogs of different breeds and breed mixes had been trained, using a clicker as well as kibble, to match odours in a discrimination task. At testing, dogs were asked to find the participant’s stress sample (taken at the end of the task) while the same person’s relaxed sample (taken only minutes before, prior to the task starting) was also in the sample line-up.
Overall, dogs could detect and perform their alert behaviour on the sample taken during stress in 675 out of 720 trials, or 93.75% of the time — much greater than expected by chance. The first time they were exposed to a participant’s stressed and relaxed samples, the dogs correctly alerted to the stress sample 94.44% of the time. Individual dogs ranged in performance from 90% to 96.88% accuracy.
Reporting their results in the journal PLOS ONE, the study authors concluded that dogs can detect an odour associated with the change in volatile organic compounds produced by humans in response to stress — a finding that tells us more about the human–dog relationship and could have applications to the training of anxiety and PTSD service dogs that are currently trained to respond predominantly to visual cues.
Image has been cropped from the original, courtesy of Kerry Campbell under CC-BY 4.0
