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arXiv2021

Ultra Violet radiation from sunlight: A key moderating factor in the spread of SARS-CoV-2 during the pandemic of 2020

Lockdowns imposed in most of the countries were lifted following a decline in the COVID-19 cases towards May-June 2020. A recent surge (second wave) in the COVID-19 cases in Europe and other temperate countries as compared to the tropical regions suggests the likely role of solar radiation. We hypothesized that ultraviolet radiation's effect might be a significant factor moderating the spread of the COVID-19 across countries. Regression analysis was done for the UV radiation data for seven hotspot cities (New Delhi, Mumbai, Milan, Madrid, New York, Melbourne and Sydney) with the daily COVID-19 cases. Global erythemal UV radiation values were lower during winter and higher during summer. In general, the daily new COVID-19 cases registered were higher during the winter months having low UV radiation dose (0.5-3.7 kJ m-2). Cases began to decline with summer onset that corresponded to increased UV radiation (2.5-6.7 kJ m-2). Our studies suggest that the natural UV radiation could be a strong determining factor moderating the spread of COVID-19 cases. The importance of UV radiation in natural sunlight as a disinfectant for SARS-CoV-2 cannot be ignored since the lockdowns were lifted; further, it can be considered as a factor for COVID management.

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arXiv2021

Experimental and modeling methodologies for the analysis of water adsorption in food products. A review

The determination of the isothermal adsorption curves represents a mechanism that allows ob-taining information on the process of adsorption of water in organic and inorganic materials. In addition, it is a measure to be considered when characterizing the physicochemical and structural properties of the materials. We want to present an approach to the state of knowledge about the methods to characterize seeds and materials associated with food products physically and struc-turally, and to relate this knowledge to biophysical processes in these materials. This review considers the papers available since 2001 associated with water adsorption studies on seeds and other food products as well as the approach of different authors to to technical and experimental models and processes that are needed for the development of this topic. From these articles the applied experimental methodologies (obtaining samples, environmental conditions and labor-atory equipment) and the mathematical models used to give physical, chemical and biological meaning to the results were analyzed and discussed, concluding in the methodologies that have best adapted to the advance of the technology for obtaining isothermal curves in the last years.

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arXiv2021

Study of conduction, block and reflection at the excitable tissues boundary in terms of the interval model of action potential

Some mechanisms of cardiac arrhythmias can be presented as a composition of elementary acts of block and reflection on the contacts of homogeneous areas of the conducting tissue. For study this phenomena we use an axiomatic one-dimensional model of interaction of cells of excitable tissue. The model has four functional parameters that determine the functional states durations of the cell. We show that the cells of a homogeneous excitable tissue, depending on the ratio of the durations of the functional intervals, can operate in the mode of solitary waves conduction or in one of three modes of selfgeneration. It is proved that the propagation of a solitary wave through the boundary of homogeneous conducting tissues can be accompanied by a block or multiplex reflection. Block and reflection are unidirectional phenomena, and there are not compatible on the same boundary. Systematized rules of transmitting, block and reflection waves at the boundary of homogeneous conducting tissues open up new possibilities for design mechanisms of generation and analyzing complex heart rate patterns.

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arXiv2021

The Practice of Ensuring Repeatable and Reproducible Computational Models

Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how busy modern researchers are and the fact that no credit is given to authors for publishing repeatable work, it is inevitable that this will be the case. The situation can only be rectified when government agencies, universities and other research institutions change policies and that journals begin to insist that published work is in fact at least repeatable if not reproducible. In this chapter guidelines are described that can be used by researchers to help make sure their work is repeatable. A scoring system is suggested that authors can use to determine how well they are doing.

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arXiv2021

A Comparative Genomic Analysis of Coronavirus Families Using Chaos Game Representation and Fisher-Shannon Complexity

From its first emergence in Wuhan, China in December, 2019 the COVID-19 pandemic has caused unprecedented health crisis throughout the world. The novel coronavirus disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which belongs to the coronaviridae family. In this paper, a comparative genomic analysis of eight coronaviruses namely Human coronavirus OC43 (HCoV-OC43), Human coronavirus HKU1 (HCoV-HKU1), Human coronavirus 229E (HCoV-229E), Human coronavirus NL63 (HCoV-NL63), Severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome-related coronavirus (MERS-CoV), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Bat coronavirus RaTG13 has been carried out using Chaos Game Representation and Fisher-Shannon Complexity (CGR-FSC) measure. Chaos Game Representation (CGR) is a unique alignment-free method to visualize one dimensional DNA sequence in a two-dimensional fractal-like pattern. The two-dimensional CGR pattern is then quantified by Fisher-Shannon Complexity (FSC) measure. The CGR-FSC can effectively identify the viruses uniquely and their similarity/dissimilarity can be revealed in the Fisher-Shannon Information Plane (FSIP).

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arXiv2021

Lattice-based simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology

Yeasts exist in communities that expand over space and time to form complex structures and patterns. We developed a computational lattice-based framework to perform spatial-temporal simulations of budding yeast colonies exposed to different nutrient and magnetic field conditions. The budding patterns of haploid and diploid yeast cells were incorporated into the framework, as well as the filamentous growth that occurs in yeast colonies under nutrient limiting conditions. Simulation of the lattice-based model predicted that magnetic fields decrease colony growth rate, density, and roundness. Magnetic field simulations further predicted that colony elongation and boundary fluctuations increase in a nutrient- and ploidy-dependent manner. These in-silico predictions are an important step towards understanding the effects of the physico-chemical environment on microbial colonies and for informing bioelectromagnetic experiments on yeast colony biofilms and fungal pathogens.

physics.bio-ph↗

arXiv2021

The mystery of energy compensation

The received wisdom on how activity affects energy expenditure is that the more activity is undertaken, the more calories will have been burned by the end of the day. Yet traditional hunter-gatherers, who lead physically hard lives, burn no more calories each day than western populations living in labour-saving environments. Indeed, there is now a wealth of data, both for humans and other animals, demonstrating that long-term lifestyle changes involving increases in exercise or other physical activities do not result in commensurate increases in daily energy expenditure (DEE). This is because humans and other animals exhibit a degree of energy compensation at the organismal level, ameliorating some of the increases in DEE that would occur from the increased activity by decreasing the energy expended on other biological processes. And energy compensation can be sizable, reaching many hundreds of calories in humans. But the processes that are downregulated in the long-term to achieve energy compensation are far from clear, particularly in humans. We do not know how energy compensation is achieved. My review here of the literature on relevant exercise intervention studies, for both humans and other species, indicates conflict regarding the role that basal metabolic rate (BMR) or low level activity such as fidgeting play, if any, particularly once changes in body composition are factored out. In situations where BMR and low-level activity are not major components of energy compensation, what then drives it? I discuss how changes in mitochondrial efficiency and changes in circadian fluctuations in BMR may contribute to our understanding of energy management. Currently unexplored, these mechanisms and others may provide important insights into the mystery of how energy compensation is achieved.

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arXiv2021

ricu: R's Interface to Intensive Care Data

Providing computational infrastructure for handling diverse intensive care unit (ICU) datasets, the R package 'ricu' enables writing dataset-agnostic analysis code, thereby facilitating multi-center training and validation of machine learning models. The package is designed with an emphasis on extensibility both to new datasets as well as clinical data concepts, and currently supports the loading of around 100 patient variables corresponding to a total of 319,402 ICU admissions from 4 data sources collected in Europe and the United States. By allowing for the addition of user-specified medical concepts and data sources the aim of 'ricu' is to foster robust, data-based intensive care research, allowing the user to externally validate their method or conclusion with relative ease, and in turn facilitating reproducible and therefore transparent work in this field.

stat.AP↗

arXiv2021

Periodontitis and preeclampsia in pregnancy: A systematic review and meta-analysis

Objectives: A conflicting body of evidence suggests localized periodontal inflammation to spread systemically during pregnancy inducing adverse pregnancy outcomes. This systematic review and meta-analysis aimed to specifically evaluate the relationship between periodontitis and preeclampsia. Methods: Electronic searches were carried out in Medline, Pubmed, Cochrane Controlled Clinical Trial Register to identify and select observational case-control and cohort studies that analyzed the association between periodontal disease and preeclampsia. Prisma guidelines and Moose checklist were followed. Results: Thirty studies including six cohorts and twenty-four case-control studies were selected. Periodontitis was significantly associated with increased risk for preeclampsia, especially in a subgroup analysis including cohort studies and subgroup analysis with lower-middle-income countries. Conclusion: Periodontitis appears as a significant risk factor for preeclampsia, which might be even more pronounced in lower-middle-income countries.

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arXiv2021

Biologists need modern data infrastructure on campus

Modern tools for biological research, especially microscopy, have rapidly advanced in recent years, which has led to the generation of increasingly large amounts of data on a regular basis. The result is that scientists desperately need state-of-the-art technical infrastructure for raw data storage, transfer, and processing. These scientists currently rely on outdated ways to move and store data, costing valuable time and risking loss of valuable data. While the community is aware of modern approaches to data management and high-level principles (including FAIR), highly-trained and highly-paid scientists are forced to spend time dealing with technical problems, which can ultimately costs more than providing storage and a fast network on campus. Here we provide concise arguments for better infrastructure, blueprints of possible solutions, and advice in navigating the political process of solving this issue. We suggest, as a broad solution, separate NIH-managed fund for supporting universities and institutes in deployment of data storage and long-term data sharing for all funded projects. This position statement is open for more contributors from imaging, life sciences, and other disciplines. Please contact us with your experience and perspective.

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arXiv2021

Recommendations on the use and reporting of race, ethnicity, and ancestry in genetic research: experiences from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program

The ways in which race, ethnicity, and ancestry are used and reported in human genomics research has wide-ranging implications for how research is translated into clinical care, incorporated into public understanding, and implemented in public policy. Genetics researchers play an essential role in proactively dismantling genetic conceptions of race and in recognizing the social and structural factors that drive health disparities. Here, we offer commentary and concrete recommendations on the use and reporting of race, ethnicity, and ancestry across the arc of genetic research, including terminology, data harmonization, analysis, and reporting. While informed by our experiences as researchers in the NHLBI Trans-Omics for Precision Medicine (TOPMed) program, the recommendations are broadly applicable to basic and translational genomic research in diverse populations. To fully realize the benefit of diversifying genetics research beyond primarily European ancestry populations, we as genetics researchers need to make structural changes to the research process and within the research community. Considerable collaborative effort and ongoing reflection will be required to root out elements of racism from the field and generate scientific knowledge that yields broad and equitable benefit.

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arXiv2022

MITI Minimum Information guidelines for highly multiplexed tissue images

The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.

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arXiv2021

Characterizing interdisciplinarity in drug research: a translational science perspective

Despite the significant advances in life science, it still takes decades to translate a basic drug discovery into a cure for human disease. To accelerate the process from bench to bedside, interdisciplinary research (especially research involving both basic research and clinical research) has been strongly recommend by many previous studies. However, the patterns and the roles of the interdisciplinary characteristics in drug research have not been deeply examined in extant studies. The purpose of this study was to characterize interdisciplinary characteristics in drug research from the perspective of translational science, and to examine the role of different kinds of interdisciplinary characteristics in translational research for drugs.

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arXiv2021

Incorporating Computational Challenges into a Multidisciplinary Course on Stochastic Processes

Quantitative methods and mathematical modeling are playing an increasingly important role across disciplines. As a result, interdisciplinary mathematics courses are increasing in popularity. However, teaching such courses at an advanced level can be challenging. Students often arrive with different mathematical backgrounds, different interests, and divergent reasons for wanting to learn the material. Here we describe a course on stochastic processes in biology, delivered between September and December 2020 to a mixed audience of mathematicians and biologists. In addition to traditional lectures and homeworks, we incorporated a series of weekly computational challenges into the course. These challenges served to familiarize students with the main modeling concepts, and provide them with an introduction on how to implement them in a research-like setting. In order to account for the different academic backgrounds of the students, they worked on the challenges in small groups, and presented their results and code in a dedicated discussion class each week. We discuss our experience designing and implementing an element of problem-based learning in an applied mathematics course through computational challenges. We also discuss feedback from students, and describe the content of the challenges presented in the course. We provide all materials, along with example code for a number of challenges.

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arXiv2021

Feedback patterns in simulating intestinal wall motions: interdisciplinary approach to the motility mechanisms

Ability of smooth muscles to contract in response to distension plays a crucial role in motor function of intestine. Qualitative analysis of dynamical models using myogenic active property of smooth muscles has shown well agreement with physiologic data. Considered as a self-regulatory unit, function of gastrointestinal (GI) segment is assumed to be regulated by integration of basis patterns providing accumulation and propagation of intestinal content. By implementing external, depending on neural system, variable to the previous model, and considering two attaches to one another reservoirs as a physical analogue of the segmental partition of intestine, a system of six ODE equations, three for each reservoir, describes coordinated wall motions and propagation of the content from one reservoir to another. It was shown that besides negative feedback (NFB), other functional patterns, namely positive feedback (PFB) and reciprocal links (RL) are involved in regulations of filling-emptying cycle. Being integrated in a whole functional system these three patterns expressed in a matrix form represent basis elements of imaginary part of coquaternion which with identity basis component is an algebraically closed structure under addition and multiplication of its elements. A coquaternion ring may be considered as a model of inner self-regulatory functional structure providing coordinated wall motions of GI tract portions.

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arXiv2021

Fetal oxygen delivery and consumption and blood gases in relation to gestational age

Fetal oxygen delivery and consumption and blood gases in relation to gestational age. Oxygen crosses the placenta by diffusion and placental permeability to O$_2$ is high. Thus, the fetus receives adequate amounts, but vascular Po$_2$ is much lower than after birth. Studies of sustained fetal hypoxemia and acute 40-45% hemorrhage show that hypoxemia is not tolerated whereas hemorrhage is. This suggests that if fetal Po$_2$ falls markedly, O$_2$ diffusion from blood to tissue is impaired. Uterine blood and umbilical blood flows/fetal weight fall progressively with advancing gestation. This results in fetal hypoxemia, an increase in Pco$_2$, and decrease in pH. This decreases fetal O$_2$ delivery, and in fetal lambs and horses there is a decrease in fetal O$_2$ consumption. The decrease in O$_2$ demands is linked to a decrease in fetal breathing and body movements and growth rate. The decrease in fetal motility is due to an increase in fetal plasma PGE2 concentration, which begins at ~120 days GA in sheep and is due to the prepartum rise in fetal cortisol. Also, adenosine administration to fetal lambs decreases fetal breathing and REM sleep and the plasma adenosine concentration increases in late gestation. The fetal plasma levels of neurosteroids, which suppress fetal motility, increase with advancing gestation. The prepartum cortisol rise also inhibits fetal growth. In normal pregnancies, these mechanisms operate effectively to maintain an appropriate balance between fetal oxygen consumption and delivery. However, in pregnancies with either further reduce O$_2$ delivery or increase fetal O$_2$ demands, the mismatch between O$_2$ delivery and consumption may worsen leading to IUGR, hypoxic organ damage or stillbirth.

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arXiv2022

Study of Drug Assimilation in Human System using Physics Informed Neural Networks

Differential equations play a pivotal role in modern world ranging from science, engineering, ecology, economics and finance where these can be used to model many physical systems and processes. In this paper, we study two mathematical models of a drug assimilation in the human system using Physics Informed Neural Networks (PINNs). In the first model, we consider the case of single dose of drug in the human system and in the second case, we consider the course of this drug taken at regular intervals. We have used the compartment diagram to model these cases. The resulting differential equations are solved using PINN, where we employ a feed forward multilayer perceptron as function approximator and the network parameters are tuned for minimum error. Further, the network is trained by finding the gradient of the error function with respect to the network parameters. We have employed DeepXDE, a python library for PINNs, to solve the simultaneous first order differential equations describing the two models of drug assimilation. The results show high degree of accuracy between the exact solution and the predicted solution as much as the resulting error reaches10^(-11) for the first model and 10^(-8) for the second model. This validates the use of PINN in solving any dynamical system.

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arXiv2021

Lewontin (1972)

Richard C. Lewontin is arguably the most influential evolutionary biologist of the second half of the 20th century. In this chapter, I provide two windows on his influential 1972 article "The Apportionment of Human Diversity": First, I show how the fourteen publications that he cites influenced him and framed his exploration; second, I present close readings of the five sections of the article: "Introduction," "The Genes," "The Samples," "The Measure of Diversity," and "The Results." I hope to illuminate the article's basic anatomy and argumentative arc, and why it became such a historically important document. In particular, I make explicit all of the mathematics (e.g., six Shannon information measures) and the general population genetic theory underlying this mathematics (e.g., the Wahlund effect). Lewontin did not make this explicit in his article. Furthermore, in redoing all of his calculations, I find that Lewontin made calculation errors (including rounding errors or omitting diversity component values) for all the genes he analyzed except one (P), and understated the among races diversity component, according to even just his own calculations. In reproducing the original computation, I find that the values of, respectively, within populations, among populations but within races, and among races diversity apportionments shift slightly (86%, 7%, 7%); here, in this "field guide" to Lewontin (1972), as well as in Winther (2022), I discuss this change in light of the values produced in subsequent replications of Lewontin's calculation with other statistics and data sets.

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