PLoS Computational Biology Research Articles

Pilot study: Insights into the validity of Opencap to assess knee kinematics during the back squat

Introduction
 Advancements in technology have revolutionized the field of sports science, enabling researchers to gain deeper insights into the biomechanics of athletes' movements (Baca et al., 2022). Among these technological advancements, OpenCap has emerged as a powerful tool for biomechanical analysis (Uhlrich et al., 2023).  Integrating OpenCap with other innovative technologies, such as motion capture systems and data analytics, further enhances the understanding of human movement. However, the effective implementation of new technologies requires rigorous scientific validation and a nuanced approach to their comparison with already established techniques. The primary goal of this research is to establish basic characteristics for comparing biomechanical analysis results obtained from OpenCap and VICON.
 Methods
 A total of 3 healthy 23-29-year-old women with a minimum of one year of experience in strength training were recruited for the study. For OpenCap (opensimModel: LaiArnoldModified2017_poly_withArms_weldHand, posemodel: openpose, augmentermodel: v0.2), the system paired cameras of two iOS devices with a web app running on a standard laptop recording videos at 60Hz. A VICON system consisting of 10 cameras (200 Hz, Oxford Metrics Group, Oxford UK) was used for 3D motion analysis. The Plug-In Gait marker set (from the VICON system), comprising 42 markers with a diameter of 16mm, was employed along with two manual markers for tracking the barbell position. Ground reaction forces were measured using two force plates (1000 Hz, Kistler AG, Winterthur, CH). The collected data served as reference data for scaling the models and running OpenSim simulations. Barbell loads were adjusted based on body weight, with loads of 25% or 50% for the free-weight back squat. Each exercise consisted of three cycles of five repetitions, enabling subsequent calculation of average values for further analysis and evaluation.
 Results
 The analysis incorporated 22 valid squats. Statistical mapping revealed significant discrepancies in knee angles between Opencap and the OpenSim model throughout most of the back squat cycle, except from 10 to 35%. The average difference was 16.9 degrees (SD = 18.3 degrees). An RMSE of 24.9 and an ICC 3.1 of 0.503 (p = 0.006076) suggest moderate agreement between the models.
 Discussion/Conclusion
 Ongoing technological advancements are pushing the frontiers of sport biomechanics through groundbreaking innovations. To achieve a comprehensive assessment and comparison of new technologies, it is vital to perform correlation analyses on identical parameters produced by diverse models (Jing et al., 2023). The ICC results indicated a moderate agreement between the models, with the OpenCap model significantly underestimating knee angles. This lesser agreement, as compared to existing literature (Lima et al., 2023), may be attributed to the potential misinterpretation of the barbell by the model. Pending updates from the forthcoming augmenter model v0.3, we advise cautious application of Opencap technology in practical scenarios. However, we believe that with further technological advancement and continued refinement, it has the potential to greatly benefit the field of sports biomechanics.
 References
 Baca, A., Dabnichki, P., Hu, C. W., Kornfeind, P., & Exel, J. (2022). Ubiquitous computing in sports and physical activity—Recent trends and developments. Sensors, 22(21), Article 8370. https://www.mdpi.com/1424-8220/22/21/8370
 Jing, Z., Han, J., & Zhang, J. (2023). Comparison of biomechanical analysis results using different musculoskeletal models for children with cerebral palsy. Frontiers in Bioengineering and Biotechnology, 11, Article 1217918. https://doi.org/10.3389/fbioe.2023.1217918
 Lima, Y., Collings, T., Hall, M., Bourne, M., Diamond, L. (2023). Assessing lower-limb kinematics via OpenCap during dynamic tasks relevant to anterior cruciate ligament injury: A validity study. Journal of Science and Medicine in Sport, 26(Suppl2), S105. https://doi.org/10.1016/j.jsams.2023.08.123
 Uhlrich, S. D., Falisse, A., Kidziński, Ł., Muccini, J., Ko, M., Chaudhari, A. S., Hicks, J. L., & Delp, S. L. (2023). OpenCap: Human movement dynamics from smartphone videos. PLoS Computational Biology, 19(10), Article e1011462. https://doi.org/10.1371/journal.pcbi.1011462
 Acknowledgement
 This study was funded by the Swiss National Foundation (192289).

Critical evaluation of kinetic schemes for coagulation.

Two well-established numerical representations of the coagulation cascade either initiated by the intrinsic system (Chatterjee et al., PLOS Computational Biology 2010) or the extrinsic system (Butenas et al., Journal of Biological Chemistry, 2004) were compared with thrombin generation assays under realistic pathological conditions. Biochemical modifications such as the omission of reactions not relevant to the case studied, the modification of reactions related to factor XI activation and auto-activation, the adaptation of initial conditions to the thrombin assay system, and the adjustment of some of the model parameters were necessary to align in vitro and in silico data. The modified models are able to reproduce thrombin generation for a range of factor XII, XI, and VIII deficiencies, with the coagulation cascade initiated either extrinsically or intrinsically. The results emphasize that when existing models are extrapolated to experimental parameters for which they have not been calibrated, careful adjustments are required.

Female Dynamics in Authorship of Scientific Publications in the Public Library of Science: A 10-year Bibliometric Analysis of Biomedical Research

Women are generally underrepresented in science, technology, engineering, and mathematics (STEM). As scientific production reflects scholarly impact and participation in the scientific process, the number of journal publications forms a pertinent measure of academic productivity. This study examined the prevalence and evolution of female representation in prominent author positions across multidisciplinary biomedical research. Publications from seven exemplar cross-specialty journals of the Public Library of Science (PLoS Medicine, PLoS Biology, PLoS One, PLoS Computational Biology, PLoS Genetics, PLoS Pathogens, and PLoS Neglected Tropical Diseases) between January 2010 and December 2020 were extracted from Web of Science. Using Genderize.io, the gender of authors from their first names was estimated using a 75% threshold. The association between female prevalence in first and last authorship and journal was evaluated using a binary logistic regression, and odds ratios were estimated against a 50:50 reference on gender. In 266,739 publications, 43.3% of first authors and 26.7% of last authors were females. Across the ten-year period, female first authorship increased by 19.6% and last authorship by 3.2%. Among all journals, PLoS Neglected Tropical Diseases had the greatest total proportion of female first authors (45.7%) and PLoS Medicine of female last authors (32%), while PLoS Computational Biology had the lowest proportion in these categories (23.7% and 17.2%). First authors were less likely to be females in all PLoS journals (p < 0.05) except for PLoS Neglected Tropical Diseases (odds ratio: 0.84, 95% confidence interval: 0.71-1.00), where the odds of female authorship were not significantly different (p = 0.054). Last authors were not more likely to be females in all PLoS journals (p < 0.001). Overall, women still appear underrepresented as first authors in biomedical publications and their representation as last authors has severely lagged. Efforts towards gender equality in scholarly authorship will contribute to the representation of women in biomedical research and ensure that their potential is not lost.

Implementation of Bioinformatics Learning in Senior High School: A Systematic Review

This study aimed to analyze the implementation of bioinformatics learning in senior high school from research articles. A systematic review was conducted in this study and showed the findings of relevant studies about the implementation of bioinformatics learning in senior high school. Three journals used for a systematic review: PLOS Computational Biology, Briefing Bioinformatics, and CBE-Life Science Education. A total of nine papers were included in the systematic review from 166 articles screened by criteria; bioinformatics learning or bioinformatics education at the senior high school level, published from 2010 to 2019. The result of this study is the trend of learning outcomes of bioinformatics learning at senior high school is to increase cognitive or knowledge in the Biology field, especially molecular biology (67%). The trend for the type of assessment in bioinformatics learning at senior high school is the observation to assess the learning outcome (44%). The trend of contents in bioinformatics learning used Biology, computer science, and information technologies (100%). The trend of bioinformatics tools in bioinformatics learning at senior high school is BLAST (44%). The trend of teaching strategy to implement bioinformatics learning at senior high school is inquiry and problem-based learning (each teaching strategy is 22%). The last is the trend of the period in implementing bioinformatics learning at senior high school is three periods in each topic (33%). For further study, the trend of implementation of bioinformatics learning can be integrated to design the new framework for implementing bioinformatics learning at senior high school. These findings recommended that science teachers or science educators promote bioinformatics learning at senior high schools.

A survey of researchers' code sharing and code reuse practices, and assessment of interactive notebook prototypes.

This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing–linking articles to a code repository–was also the most useful method of accessing code from the reader’s perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools.

Preprint citation practice in PLOS

The role of preprints in the scientific production and their part in citations have been growing over the past 10 years. In this paper we study preprint citations in several different aspects: the progression of preprint citations over time, their relative frequencies in relation to the IMRaD structure of articles, their distributions over time, per preprint database and per PLOS journal. We have processed the PLOS corpus that covers 7 journals and a total of about 240,000 articles up to January 2021, and produced a dataset of 8460 preprint citation contexts that cite 12 different preprint databases. Our results show that preprint citations are found with the highest frequency in the Method section of articles, though small variations exist with respect to journals. The PLOS Computational Biology journal stands out as it contains more than three times more preprint citations than any other PLOS journal. The relative parts of the different preprint databases are also examined. While ArXiv and bioRxiv are the most frequent citation sources, bioRxiv’s disciplinary nature can be observed as it is the source of more than 70% of preprint citations in PLOS Biology, PLOS Genetics and PLOS Pathogens. We have also compared the lexical content of preprint citation contexts to the citation content to peer-reviewed publications. Finally, by performing a lexicometric analysis, we have shown that preprint citation contexts differ significantly from citation contexts of peer-reviewed publications. This confirms that authors make use of different lexical content when citing preprints compared to the rest of citations.

First year of open-access scientific journal publishing: our mishaps, our expectations, our plans for the bright future

In silico methods have become a versatile and effective tool for the studies of the natural phenomenon at multiple levels. However, unlike such fields as economics and physics, biology and physiology have always been slightly reluctant in acceptance of the novel systemic approaches. Since scientific articles are among the key metrics for the modern scientific society, the number of scientific journals, devoted to some topic, can be a good marker to evaluate the impact of this topic for the society. Indeed, there are esteemed journals, such as PLOS Computational Biology or Journal of Theoretical Biology, but they focus mainly on a common biological phenomenon, while questions of physiology and pathophysiology are often overlooked. On the other hand, the amount of work on computational biology is steadily growing with ~12000 works published in 2010 and ~28000 in 2020 with the keyword “computational model”, according to PubMed. With all this being said and our great experience in the different aspects of the field of computational physiology, our team has decided that it would be a mistake to lose an opportunity to cover this niche. Likewise, we, as a group of fellow scientists, at the end of 2019 decided to create our own venture and to launch our own scientific journal – Systems Biology and Physiology Reports (SBPReports) [1]. This publisher's would be an attempt to underline our first hectic year of the open access scientific publishing.

On testing structural identifiability by a simple scaling method: Relying on scaling symmetries can be misleading.

A recent paper published in PLOS Computational Biology [1] introduces the Scaling Invariance Method (SIM) for analysing structural local identifiability and observability. These two properties define mathematically the possibility of determining the values of the parameters (identifiability) and states (observability) of a dynamic model by observing its output. In this note we warn that SIM considers scaling symmetries as the only possible cause of non-identifiability and non-observability. We show that other types of symmetries can cause the same problems without being detected by SIM, and that in those cases the method may lead one to conclude that the model is identifiable and observable when it is actually not.

PLoS Computational Biology Issue Image | Vol. 17(9) October 2021

The tomato flowers are characterized by possessing poricidal anthers, which restrict the exit of the pollen to a tiny opening on the apex of the anther. To extract pollen efficiently, some visiting bees grasp the anthers and quickly contracting their flight muscles, producing vibrations and an audible sound. The vibrations are transferred to the anthers, shaking and stimulating the pollen inside them to leave by the pores, a phenomenon known as floral sonication or buzz-pollination. DOI: pcbi.1009426 Image Credit: Priscila de CE1;ssia Souza AraFA;jo (co-author of the manuscript) photographed this bee visiting flowers of tomato plants grown at the experimental fields of the Federal University of ViE7;osa (Minas Gerais State, Brazil). We confirm that the image can publish under the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). The authors own the copyright for the image and confirm that agree with open Access License of PLOS Computational Biology.

PLoS Computational Biology Issue Image | Vol. 1(9) October 2021.

The tomato flowers are characterized by possessing poricidal anthers, which restrict the exit of the pollen to a tiny opening on the apex of the anther. To extract pollen efficiently, some visiting bees grasp the anthers and quickly contracting their flight muscles, producing vibrations and an audible sound. The vibrations are transferred to the anthers, shaking and stimulating the pollen inside them to leave by the pores, a phenomenon known as floral sonication or buzz-pollination. DOI: pcbi.1009426 Image Credit: Priscila Souza AraFA;jo (co-author of the manuscript) photographed this bee visiting flowers of tomato plants grown at the experimental fields of the Federal University of ViE7;osa (Minas Gerais State, Brazil). We confirm that the image can publish under the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). The authors own the copyright for the image and confirm that agree with open Access License of PLOS Computational Biology.

Highlights of the 1st Latin American Conference of Women in Bioinformatics and Data Science

Many efforts have been made to bridge the gender gaps in science and technology, but disparities still persist within academic, scientific, and technologic fields (1, 2). The United Nations Educational, Scientific and Cultural Organization (UNESCO) surveys conducted in June 2019 show that women represent only 30% of the population of researchers globally (3). Going deeper into the analysis, women are restricted in access to decision-making positions, even in countries in which the participation of women in science is higher than the global trend (4). The representation of women in science in Latin America is higher (∼40%), with differences within the region, but we believe that this also reveals a gender difference. Salaries in science are usually low and are even lower for women in the field (5), and they end up accepting them, while men do not (6). In science, technology, engineering, and mathematics areas, both horizontal and vertical barriers still persist for women, which is reflected in a reduced female presence in decision-making positions and the women struggling to reach senior leadership positions in various spheres of national scientific systems (7) or companies.In the bioinformatics field in particular, a survey published in PLOS Computational Biology (8) shows that there are fewer female authors in postgraduate levels in computational biology compared with biology in general. The imbalance is also evident with the author hierarchy and the impact factor of the journals. In both biology and computational biology, the presence of a woman as the last author of the work increases the probability that other authors in the article are also women. In addition, the majority of keynote speakers at conferences are men, giving women a secondary role. Although it has been observed that when women are on the organizing committee of a conference, the number of women speakers tends to increase (9). Another observation is that men are more prone to take part in question and answer sessions at meetings (10). Besides asking fewer questions, women make a disproportionate number of questions to women speakers, while men do the inverse (11), and their interactions are often more an explanation than a question, a kind of “mansplaining.” All of this highlights a reality in terms of gender representation, pointing out the potential role of female leaders to influence the balance and give young researchers confidence in their work.The Women in Bioinformatics and Data Science network in Latin America was created in 2019 with the aim of addressing some of these issues. This community has 3 main goals: (a) to promote and make visible women's research in the bioinformatics and data science fields; (b) to encourage women to establish collaborative research networks; and (c) to empower young scientists to be confident in work and capabilities.As a result of a joint effort of women from all over Latin America, the first conference was held virtually in September 2020 with excellent results. The conference not only increased the visibility of women's work in science, but it also generated networks and promoted alliances to enhance collaborations and scientific work.The 1st Latin American Conference of Women in Bioinformatics and Data Science was a virtual and nonprofit meeting aimed at promoting and making visible the research carried out by women in these fields. It was open to the entire community, but only with women as keynotes and speakers. This conference brought together researchers from Latin America in the public and private sectors working in systems biology, omics technologies, artificial intelligence, machine learning, data science, data mining, and high-performance computing with applications in biology.Over 800 participants from all over the world (Fig 1A) registered for the conference. The majority of participants came from South American countries, with Brazil, Argentina, Colombia, and Mexico accounting for 28%, 24.5%, 14.7%, and 7.4%, respectively. Most participants were women from academia and industry, followed by individuals who were identified as male (15.4%) and nonbinary (0.8%; Fig 1B). English was chosen as the official language, enabling students, academic researchers, and professionals from the industry to engage in thought exchange.The conference received 168 abstract submissions, with a total of 637 authors covering different topics (Table 1). The scientific committee that reviewed the abstracts was a group of 27 Latin American women researchers. On the basis of the reviews, the 18 best scored abstracts were selected for oral presentations. All accepted abstracts are available on the event website and are published in an abstract book (12). The majority of the abstracts' authors were from Argentina, Brazil, and Colombia, but some were also from Europe (Spain, Germany, France), the United Kingdom, North America (United States), Asia (India and Malaysia), and Oceania (Australia).Taking the list of authors that submitted abstracts and crosslinking with the information obtained from the registration, we analyzed the authorship with a gender perspective. We found, as expected, that although the conference was open to the entire community, the works received were mainly with women as first authors (87.5% compared with 7.1% men). However, we found the opposite tendency when looking at the last position. The last authors, an authorship position generally associated with higher reputation or senior researchers (13, 14), were predominantly male (57.7%; Fig 1C). In 55.4% of the cases, men were in the last author position, while women were the last authors in 44.6% of the cases.Twenty-four female speakers with experience in a broad range of topics were invited. With the exception of Professor Shoshana Wodak from Belgium, all other speakers were Latin American women researchers, mainly from Argentina (n = 10), but also Brazil and Mexico (n = 3), Chile and Colombia (n = 2), and Peru, Puerto Rico, and Uruguay (n = 1). On average, 180 people attended each day, and a total of 500 people participated in 3 days.Closing the conference, there was a discussion about gender and science, with the participation of specialists in gender from different areas: Diana Maffía (PhD and researcher in philosophy) and Valeria Edelsztein (researcher in chemistry and science promoter) from Argentina, Diana Farías (researcher in chemistry) from Colombia, and Márcia Barbosa (researcher in physics and winner of the L'Oréal UNESCO prize for women in science) from Brazil. We provided simultaneous translating (Portuguese and Spanish) to allow speakers to address the theme in their native languages.The last day consisted of 6 workshops on state-of-the-art topics, with 12 experienced women as teachers. This allowed knowledge exchange between scientists with different levels of expertise and different backgrounds. The hands-on courses covered genotyping-by-sequencing data analysis, molecular phylogenetics, machine learning applied to drug design, analysis of molecular dynamics simulations, introduction to machine learning with R language with tidymodels, and introduction to R language with tidyverse. The workshops had a total of 159 attendees: 93 were female; 23 were male; and 45 did not indicate a gender in the registration form.The 1st Latin American Conference of Women in Bioinformatics and Data Science initiative aimed at creating spaces for discussion and training in our community, not only in science and technology, but also from a gender perspective. As we discussed before, science and technology are masculinized environments in which gender disparities still remain as part of the structure. The data generated, even in this particular event created by women and especially for women, reinforced the evidence of the predominance of men in leadership roles. The glass ceiling effect with respect to differential access to leadership positions for women and men is still evident (15–18). In personal communication, the speakers and attendees expressed that they felt very comfortable and considered the conference venue to be a friendly environment to exchange, to learn, and to discuss ideas.In this report, we conclude from the great response of the community, evidenced by the large number of attendees, submitted abstracts and participating speakers, and the results obtained from our analysis, that there is a need for these types of spaces as provided through the 1st Latin American Conference of Women in Bioinformatics and Data Science. Women working in bioinformatics and data science are still waiting to be properly recognized. We need to create spaces that encourage participation and continuing education opportunities for women, and we need to analyze our research reality from a gender point of view, if we really want to contribute to reducing the gender disparity gap.This event was partially funded by Capacity Building for Bioinformatics in Latin America (CABANA), Argentinian Bioinformatics and Computational Biology Association, Mumuki, ATGenomics, EngineZyme, and Spyder.

A model for the regulation of apoptosis intrinsic pathway: The potential role of the transcriptional regulator E2F in the point of no return

Apoptosis has been extensively characterized by both experimental approaches and model simulations. However, it is still not fully understood how the regulation occurs, especially in the intrinsic pathway, which can be activated by a great variety of signals. In addition, the conditions in which a point of no return could be reached remain elusive. In this work, we use differential equations models to approach these issues. Our starting point was the model for caspase activation of Legewie et al. (Legewie S, et al., PLoS Computational Biology 2006, 2(9): e120), which exhibits irreversible bistability. We added an activation module to this model, with the main events related to mitochondrial outer membrane permeabilization, which includes cytochrome C release by the mitochondria and its effects on caspase activation and respiratory chain disruption. This “Extended Legewie Model” (ELM) uses BAK as the apoptotic stimulus and active caspase 3 as a measure of apoptosis activation. Unexpectedly, in the extended model, BAK cannot trigger apoptosis activation using physiologically sound initial values of the variables, due to limitations in apoptosome concentration increase. Therefore, the next step was to find a regulatory mechanism, allowing apoptosis activation in the ELM, starting from physiological initial concentrations. For this aim, we performed a sensitivity analysis on the 61 parameters of the system, finding that those producing the most relevant changes in the qualitative behaviour were the rates of synthesis of caspase 3, caspase 9 and XIAP. Based on these results, the transcription factor E2F was included in the ELM because it directly regulates the rate of synthesis of caspase 3 and 9. Depending on the concentration of E2F, the ELM shows different qualitative behaviours. On one hand, for low E2F apoptosis is impossible and for high E2F apoptosis is inevitable. Therefore, if E2F is sufficiently increased, the point of no return is crossed. On the other hand, for intermediate values of E2F there is a bistable region where the fate of the system also depends on the concentration of BAK and other signalling species.

The C55 Peptide Portion of the Amyloid Precurosr Protein can Form Stable Dimers

Alzheimer's disease (AD) is a neurodegenerative disease of profound cost in terms of economic impact and human suffering that is becoming prevalent as life expectancy in the world's population rises. An important step in the pathology of Alzheimer's disease is the production of toxic amyloid β peptides (Aβ) by the processive cleavage of the amyloid precursor protein (APP). APP is cleaved by β-secretase producing C99 peptide which is processivity cleaved by γ-secretase to produce Aβ. There is no consensus on the effect APP dimerization has on γ-secretase cleavage and Aβ production, as studies have shown that APP dimers inhibits cleavage and others show APP dimers promote cleavage by γ-secretase. To further illuminate the effect of APP dimerization on its cleavage by γ-secretase, the structure of the APP dimer is needed. Using coarse grained enhanced sampling by the molecular dynamics engine, Upside (Jumper et. al. PLOS Computational Biology 2018), we created a large ensemble structure of C55 (the intermembrane and Aβ part of C99) dimers. After using principle component analysis (PCA) and k-means clustering we chose 10 starting conformations of the C55 dimer, which were then equilibrated for 100 nanoseconds in an explicit all-atom POPC membrane. PCA of these trajectories showed 7 possible stable dimer conformations. Dimers were mainly stabilized by interactions of hydrophobic residues and residues in the GxxxG zipper motif. The G37/38 helix kink and curvature of the helices observed experimentally in C99, were not observed in our conformations. initial binding free energy calculations for these dimers show strong interactions which are indicative of the viability, and stability, for these structures. These conformations can be used to assess the effect APP dimerization has on its cleavage mechanism of γ-secretase and the production of Aβ.

Profil Mikrobiota Saluran Cerna Pada Anak, Dewasa, Berbagai Suku dan Ras

Background and Purpose: Microbiota is defined as a collection of microorganisms that live in the host's body, which can consist of bacteria, archae, viruses, and other eukaryotes. Microbiota in humans is also found in the skin, lungs, urinary tract, oral cavity, although the digestive tract plays a role in contributing to the highest number of microbiota in humans. The purpose of this article is to provide an overview of the various profiles of the gastrointestinal microbiota in children, adults, various ethnicities and races. Methods: This study uses a narrative review method. The data sources of this study come from literature obtained via the internet in the form of research results from national and international journals in 2010-2020 such as Elsevier, Clinical Key, Pubmed, Biomed Research International, Nature Journal, PLOS Computational Biology, PNAS Journal dan American Society For Microbiology. Results: From several collections of journals related to microbiota, many studies reveal that the two bacterial phyla Firmicutes and Bacteroidetes are found in a higher proportion in humans in general followed by Prevotella, Actinobacteria and Bifidobacterium. Whereas in children the microbiota is more dominated by Bacteroidetes / Bifidobacterium and not a few studies have found Clostridium in children. It is no different from ethnicities and races from other countries in that the findings of general microbiota are almost the same. Various microbiota also can be built from the environment, geography, ethnicity and culture. Conclusion: The variability of the microbiota in the human tract is very diverse, it is related to various factors, namely age, genetics, metabolic, diet, diet, lifestyle, environment, geography, ethnicity, culture and socio-economy.

Getting started on twitter as a scientist

“Using Twitter can be more than just a social media activity. It can be a real career incubator in which researchers can develop their professional circles, launch new research projects and get helped by the community at various stages of the projects”. In a PLOS Computational Biology paper experienced scientific Twitter users share ‘Ten simple rules for getting started on Twitter as a scientists’ [1].

On the choice of metric in gradient-based theories of brain function.

This is a PLOS Computational Biology Education paper.The idea that the brain functions so as to minimize certain costs pervades theoretical neuroscience. Because a cost function by itself does not predict how the brain finds its minima, additional assumptions about the optimization method need to be made to predict the dynamics of physiological quantities. In this context, steepest descent (also called gradient descent) is often suggested as an algorithmic principle of optimization potentially implemented by the brain. In practice, researchers often consider the vector of partial derivatives as the gradient. However, the definition of the gradient and the notion of a steepest direction depend on the choice of a metric. Because the choice of the metric involves a large number of degrees of freedom, the predictive power of models that are based on gradient descent must be called into question, unless there are strong constraints on the choice of the metric. Here, we provide a didactic review of the mathematics of gradient descent, illustrate common pitfalls of using gradient descent as a principle of brain function with examples from the literature, and propose ways forward to constrain the metric.

Computational Design and Interpretation of Single-RNA Translation Experiments

Translation is an essential step in which ribosomes decipher mRNA sequences to manufacture proteins. Recent advances in super-resolution fluorescence microscopy allow live-cell quantification of ribosome kinetics at single-molecule resolution. Here, we integrate single-molecule data and stochastic models to investigate canonical and non-canonical translation processes. Recent findings by our group using these modern methodologies allowed us to observe, for the first time, ribosomal frameshifting at single-molecule resolution. Our results corroborate that frameshifting is a bursty process, where the RNA stochastically switch between non-frameshifting and frameshifting states in which either 0% or 100% of ribosomes produce frameshifted proteins. We predicted that ribosomal traffic jams contribute to the persistence of the frameshifting state for long periods of time (Lyon, K., et al., 2019. Molecular cell). Additionally, we simulate single-molecule experiments under multiple imaging conditions and for thousands of human genes, and we evaluate which experiments are most likely to provide accurate estimates of elongation kinetics. In this study, we provide an interpretation for the well-established experimental procedures, such as Fluorescence Correlation Spectroscopy (FCS), ribosome Run-Off Assays (ROA) after Harringtonine application, and Fluorescence Recovery After Photobleaching (FRAP) (Aguilera, L.U., et al., 2019, Plos Computational Biology). Our results show previously unknown mechanisms taking place during translation at single-molecule resolution in living cells.

Vegetative status of children as a territorial bio-indicator of ecological safety

The quantity of environment contaminators (pollutants) and their combinations cannot be counted and specified. Consequently, the current situation needs a change of principles of ecological control. In our case, the indicators of functional health of child population and levels of its vegetative disorders appear as integral bioindicators of individual health (dynamic stability of functional-vegetative homeostasis) and characterize the ecological dynamics in regions of compact settlement. Environmental certification of children functional health could define the region with a pre-crisis or crisis state of the environment. Vegetative levels (vegetative coefficients, k-V of functional-vegetative homeostasis testify to vegetative health (norm), or prevalence of sympathetic and parasympathetic activity. Permanent functional voltage distorts the pathogenesis of functional-vegetative adaptation and requires specific monitoring in the form of "Functional-ecological expertise" (FEE) of selected staff. The basis of the FEE methodology developed by us is "Functional-vegetative diagnostics" (FVD) by the method of V.G. Makats. The diagnostic complex "BIOTEST-12M" (Diagnostic complexes VITA-01-M and computerized system VITA-01-Biotest) serves as the technical tool of the FVD. Indicators of - vegetative coefficients (k-V = ΣSA: ΣPSA; (levels of vegetative balance, sympathetic, or parasympathetic activity) act as integral bioindicators of internal homeostasis and its dependence on the conditions of the environment. The criterion of FEE is a systemically dependent comparison of inhibition of the functional activity of the organism (parasympathetic activity (PA), vegetative equilibrium (VE) and sympathetic activity (SA) and can be calculated for children in particular region. This, we suggested the integral characteristic of territorial ecological state and the levels (zones) of ecological pressure. Key words: Vegetology; Vegetative Nervous System (VNS); Functional-vegetative homeostasis; Functional-vegetative diagnostics (FVD); Children   References Goralczyk, K., & Majcher, A. (2019). Are the civilization diseases the result of organohalogen environmental pollution? Acta biochimica Polonica, 66(2), 123–127. Henderson, K., & Loreau, M. (2018). How ecological feedbacks between human population and land cover influence sustainability. PLoS computational biology, 14(8), e1006389.  Hennig, B., Petriello, M.C., Gamble, M.V., Surh, Y.J., Kresty, L.A., Frank, N., Rangkadilok, N., Ruchirawat, M., & Suk, W.A. (2018). The role of nutrition in influencing mechanisms involved in environmentally mediated diseases. Reviews on environmental health, 33(1), 87–97. 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Vinnytsia (in Ukrainian). Mudrak, O., Sobchyk, V., Nahorniuk, O., Mudrak, H., Yashnik, S., Tarasenko H. (2019). Environmental literacy of the leaders of the new formation in an open society. Mechanisms of stimulation of socio-economic development of regions in conditions of transformation. Opole: The Academy of Management and Administration in Opole  (Poland). Mudrak, O.V., Mudrak, G.V. (2019). The system of continuous environmental education as a basis for sustainable development of Ukraine/Psychological principles of development, psychodiagnostics and personality correction in the system of continuing education. Proceedings of the IV Podolsk scientific-practical conference. 107–113 (in Ukrainian). Prescott, S.L., & Logan, A.C. (2019). Planetary Health: From the Wellspring of Holistic Medicine to Personal and Public Health Imperative. Explore (New York, N.Y.), 15(2), 98–106.  Rezende, E.L., & Bozinovic, F. (2019). Thermal performance across levels of biological organization. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 374(1778), 20180549.  Russ, K., & Howard, S. (2016). Developmental Exposure to Environmental Chemicals and Metabolic Changes in Children. Current problems in pediatric and adolescent health care, 46(8), 255–285.  Serrano, H.C., Oliveira, M.A., Barros, C., Augusto, A.S., Pereira, M.J., Pinho, P., & Branquinho, C. (2019). Measuring and mapping the effectiveness of the European Air Quality Directive in reducing N and S deposition at the ecosystem level. The Science of the total environment, 647, 1531–1538.  Spicer, J.I., Morley, S.A., & Bozinovic, F. (2019). Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 374(1778), 20190032. Zheng, T., Zhang, J., Sommer, K., Bassig, B. A., Zhang, X., Braun, J., Xu, S., Boyle, P., Zhang, B., Shi, K., Buka, S., Liu, S., Li, Y., Qian, Z., Dai, M., Romano, M., Zou, A., & Kelsey, K. (2016). Effects of Environmental Exposures on Fetal and Childhood Growth Trajectories. Annals of global health, 82(1), 41–99.  Van den Brink, P.J., Boxall, A., Maltby, L., Brooks, B.W., Rudd, M.A., Backhaus, T., Spurgeon, D., Verougstraete, V., Ajao, C., Ankley, G.T., Apitz, S.E., Arnold, K., Brodin, T., Canedo-Arguelles, M., Chapman, J., Corrales, J., Coutellec, M. A., Fernandes, T. F., Fick, J., Ford, A.T., van Wensem, J. (2018). Toward sustainable environmental quality: Priority research questions for Europe. Environmental toxicology and chemistry, 37(9), 2281–2295.  Vrijheid, M., Casas, M., Gascon, M., Valvi, D., & Nieuwenhuijsen, M. (2016). Environmental pollutants and child health-A review of recent concerns. International journal of hygiene and environmental health, 219(4-5), 331–342.  World Health Organization (2016). Preventing disease through healthy environments: towards an estimate of the environmental burden of disease.  Yermishev, O.V. (2018). The levels of functional-vegetative homeostasis as criteria for magnetotherapy efficacy. International Journal of Medicine and Medical Research, 4(1), 13-20. Yermishev, O. (2019). Peculiarities of functional-vegetative homeostasis of preschool-age females (first childhood). Biologija, 65(1), 56–65.  Yermishev, O.V., Makats, V.G., Petruk, V.G. (2017). The functional health of children as an environmental bio-indicator of Ukraine. Vinnytsia: Nilan-LTD (in Ukrainian).

Bioinformatics for the Masses: The Need for Practical Data Science in Undergraduate Biology.

OMICS: A Journal of Integrative BiologyVol. 23, No. 6 CommentaryBioinformatics for the Masses: The Need for Practical Data Science in Undergraduate BiologySandra G. Porter and Todd M. SmithSandra G. PorterAddress correspondence to: Sandra G. Porter, PhD, Digital World Biology, LLC, 2442 NW Market Street, Seattle, WA 98107 E-mail Address: sandra@digitalworldbiology.comDigital World Biology, LLC, Seattle, Washington.Austin Community College Bio-Link Regional Center, Austin, Texas.Search for more papers by this author and Todd M. SmithTodd M. Smith, PhD, Digital World Biology, LLC, 2442 NW Market Street, Seattle, WA 98107 E-mail Address: todd@digitalworldbiology.comDigital World Biology, LLC, Seattle, Washington.Search for more papers by this authorPublished Online:5 Jun 2019https://doi.org/10.1089/omi.2019.0080AboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetailsCited byEarly Undergraduate Biostatistics & Data Science Introduction Using R, R Studio & the TidyverseThe American Biology Teacher, Vol. 84, No. 3Bringing bioinformatics to schools with the 4273pi project20 January 2022 | PLOS Computational Biology, Vol. 18, No. 1Undergraduate Education in Bioinformatics—Progress and Lessons Learnt from an Engineering Degree17 February 2021Rethinking Omics Education in Brazil and South America: From Genomics to Multiomics and Critical Policy Studies Alberto M.R. Dávila6 July 2020 | OMICS: A Journal of Integrative Biology, Vol. 24, No. 7 Volume 23Issue 6Jun 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Sandra G. Porter and Todd M. Smith.Bioinformatics for the Masses: The Need for Practical Data Science in Undergraduate Biology.OMICS: A Journal of Integrative Biology.Jun 2019.297-299.http://doi.org/10.1089/omi.2019.0080Published in Volume: 23 Issue 6: June 5, 2019Online Ahead of Print:May 20, 2019Keywordsbioinformaticsdata sciencebiology educationcurriculum developmentscience 2.0data science internshipPDF download

Reliable Biomolecular Structural Modelling with Small-Angle Scattering

The small-angle scattering (SAS) of X-rays or neutrons from biomolecules in solution can provide (1) unique structural insights, (2) information on the range of potential conformations present, (3) and powerful restraints for integrative/hybrid structural modelling (IHM). The rotational and ensemble averaging of the signal presents multiple challenges to the reliable utilisation of SAS data: (1) demonstrating SAS profile represents the species of interest, (2) reliably evaluating model fits, and (3) over-interpretation and over-fitting of data. A community driven project has been underway for more than a decade now to define the information that should be made available regarding sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular SAS experiments. These guidelines (Trewhella et al. (2017) Acta D73, 710) provide a reporting framework so that “readers can independently assess the quality of the data and the basis for any interpretations presented” concerning the results of bimolecular SAS experiments, including the generation or testing of 3D models. The validation task forces for SAS (Trewhella et al. (2013) Structure 21, 875) and for IHM (Sali et al. (2015) Structure 23, 1156) of the world-wide Protein Data Bank are additionally addressing the complex issues concerning the archiving and validation of IHM models that depend upon computational methods and disparate data from multiple techniques (Burley et al. (2017) Structure 25, 1317). Finally, the question of how many parameters are justified by the model evidence inherent in the SAS profile is an important question to answer when modelling conformational ensembles (Potrzebowski, Trewhella and Andr⌈ (2018) in review PLOS Computational Biology). This presentation will address the recommended reporting framework and its rationale, the reliable incorporation of SAS data in IHM, and the strengths and limits of SAS in ensemble modelling.