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arXiv2020

The case for algebraic biology: from research to education

Though it goes without saying that linear algebra is fundamental to mathematical biology, polynomial algebra is less visible. In this article, we will give a brief tour of four diverse biological problems where multivariate polynomials play a central role -- a subfield that is sometimes called "algebraic biology." Namely, these topics include biochemical reaction networks, Boolean models of gene regulatory networks, algebraic statistics and genomics, and place fields in neuroscience. After that, we will summarize the history of discrete and algebraic structures in mathematical biology, from their early appearances in the late 1960s to the current day. Finally, we will discuss the role of algebraic biology in the modern classroom and curriculum, including resources in the literature and relevant software. Our goal is to make this article widely accessible, reaching the mathematical biologist who knows no algebra, the algebraist who knows no biology, and especially the interested student who is curious about the synergy between these two seemingly unrelated fields.

q-bio.NC↗

arXiv2025

English dictionaries, gold and silver standard corpora for biomedical natural language processing related to SARS-CoV-2 and COVID-19

Automated information extraction with natural language processing (NLP) tools is required to gain systematic insights from the large number of COVID-19 publications, reports and social media posts, which far exceed human processing capabilities. A key challenge for NLP is the extensive variation in terminology used to describe medical entities, which was especially pronounced for this newly emergent disease. Here we present an NLP toolbox comprising very large English dictionaries of synonyms for SARS-CoV-2 (including variant names) and COVID-19, which can be used with dictionary-based NLP tools. We also present a silver standard corpus generated with the dictionaries, and a gold standard corpus, consisting of PubMed abstracts manually annotated for disease, virus, symptom, protein/gene, cell type, chemical and species terms, which can be used to train and evaluate COVID-19-related NLP tools. Code for annotation, which can be used to expand the silver standard corpus or for text mining is also included. This toolbox is freely available on GitHub (on https://github.com/Aitslab/corona) and zenodo (https://doi.org/10.5281/zenodo.6642275). The toolbox can be used for a variety of text analytics tasks related to the COVID-19 crisis and has already been used to create a COVID-19 knowledge graph, study the variability and evolution of COVID-19-related terminology and develop and benchmark text mining tools.

q-bio.OT↗

arXiv2020

Translational Knowledge Map of COVID-19

A translational knowledge map of COVID-19, based on the analysis of scientific papers and networks citation concurrence of terms and keywords of the terms: covid- 19, 2019-ncov and sars-cov-2 in leading databases (MEDLINE, web of Science and Scopus), was constructed. Some fields of the research on covid-19 are connected together, differing in structure, content and evolution.

cs.DL↗

arXiv2020

A Thermodynamic Approach towards the Question "What is Cellular Life?"

The question "What is life?" has been asked and studied by the researchers of various fields. Nevertheless, no global theory which unified various aspects of life has been proposed so far. Considering that the physical principle for the theory of birth should be the one known for the unanimated world, and that the life processes are irreversibly selective, we showed by a deductive inference that the maximum entropy production principle plays an essential role for the birth and the evolution of life in a fertile environment. In order to explain the survival strategy of life in a barren period of environment, we also proposed that life had simultaneously developed a reversible on and off switching mechanism of the chemical reactions by the dynamics of equilibrium thermodynamics. Thus, the birth and evolution of life have been achieved by the cooperation between the driving force due to the non-equilibrium thermodynamics and the protective force due to the equilibrium thermodynamics in the alternating environmental conditions.

physics.bio-ph↗

arXiv2020

SARS-CoV-2 (COVID-19) by the numbers

The current SARS-CoV-2 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers. In this snapshot, our aim is to provide a one-stop, curated graphical source for the key numbers that help us understand the virus driving our current global crisis. The discussion is framed around two broad themes: 1) the biology of the virus itself and 2) the characteristics of the infection of a single human host. Our one-page summary provides the key numbers pertaining to SARS-CoV-2, based mostly on peer-reviewed literature. The numbers reported in summary format are substantiated by the annotated references below. Readers are urged to remember that much uncertainty remains and knowledge of this pandemic and the virus driving it is rapidly evolving. In the paragraphs below we provide "back of the envelope" calculations that exemplify the insights that can be gained from knowing some key numbers and using quantitative logic. These calculations serve to improve our intuition through sanity checks, but do not replace detailed epidemiological analysis.

q-bio.OT↗

arXiv2020

Build-at-home UV-C disinfection system for healthcare settings

Significant research has shown that UV-C exposure is an effective disinfectant for a range of bacteria and viruses, including coronaviruses. As such, a UV-C treatment in combination with a chemical wipe, such as EPA hydrogen peroxide, is a common cleaning protocol in a medical setting, and such disinfection protocols have gained in importance during the current COVID-19 pandemic due to the need to reuse PPE. However, given the substantial increase in patient volume, the quantity of materials requiring disinfection exceeds the UV-C equipment throughput capabilities at many medical facilities. Therefore, there is a need for a UV-C disinfection system that can be rapidly deployed. In response to this demand, we designed, constructed, and validated a UV-C disinfection system from readily accessible components; specifically, a plastic bin, UV-C light bulb and conventional light housing. To further improve the performance, the interior of the tub was spray-painted with chrome paint, forming a low quality-factor (Q) Fabry-Perot optical cavity. As part of this work, a set of modular design criteria which allows for flexibility in component selection without degradation of UV-C dose performance is established. This flexibility is critical given the current fluctuating availability of source materials. The disinfection capabilities of the system are validated using Bacillus cereus, a gram-positive endospore-forming bacteria.

physics.med-ph↗

arXiv2020

Accelerated infection testing at scale: a proposal for inference with single test on multiple patients

In pandemics or epidemics, public health authorities need to rapidly test a large number of individuals, both to determine the line of treatment as well as to know the spread of infection to plan containment, mitigation and future responses. However, the lack of adequate testing kits could be a bottleneck, especially in the case of unanticipated new diseases, such as COVID-19, where the testing technology, manufacturing capability, distribution, human skills and laboratories might be unavailable or in short supply. In addition, the cost of the standard PCR test is approximately USD 48, which is prohibitive for poorer patients and most governments. We address this bottleneck by proposing a test methodology that pools the sample from two (or more) patients in a single test. The key insight is that a single negative result from a pooled sample likely implies negative infection of all the individual patients. and It thereby rules out further tests for the patients. This protocol, therefore, requires significantly fewer tests. This may, however, result in somewhat increased false negatives. Our simulations show that combining samples from two patients with 7% underlying likelihood of infection implies that 36% fewer test kits are required, with 14% additional units of time for testing.

q-bio.OT↗

arXiv2020

Modern alleles in archaic human Y chromosomes support origin of modern human paternal lineages in Asia rather than Africa

Recent studies have shown that hybridization between modern and archaic humans was commonplace in the history of our species. After admixture, some individuals with admixed autosomes carried the modern Homo Sapiens uniparental DNAs, while the rest carried the archaic versions. Coevolution of admixed autosomes and uniparental DNAs is expected to cause some of the sites in modern uniparental DNAs to revert back to archaic alleles, while the opposite process would occur (from archaic to modern) in some of the sites in archaic uniparental DNAs. This type of coevolution is one of the elements that differentiate the two different models of the Y phylogenetic tree of modern humans, rooting it either in Africa or East Asia. The expected reversion to archaic alleles is assumed to occur and is easily traceable in the Asia model, but is absent in the Africa model due to its infinite site assumption, which also precludes the independent or convergent mutation to modern alleles in archaic uniparental DNAs since mutations are assumed to occur randomly across a neutral genome, and convergent evolution is assumed not to occur. Here, we examined newly published high coverage Y chromosome sequencing data of two Denisovan and two Neanderthal samples to determine whether they carry modern-Homo Sapiens alleles in sites where they are not supposed to according to the Africa model. The results showed that a significant fraction of the sites that, according to the Asia model, should differentiate the original modern Y from the original archaic Y carried modern alleles in the archaic Y samples here. Some of these modern alleles were shared among all archaic humans while others could differentiate Denisovans from Neanderthals. The observation is best accounted for by coevolution of archaic Y and admixed modern autosomes, and hence supports the Asia model, since it takes such coevolution into account.

q-bio.OT↗

arXiv2020

Robust predictive model for Carriers, Infections and Recoveries (CIR): predicting death rates for CoVid-19 in Spain

This article presents a new model to predict the evolution of infective diseases under uncertainty or low-quality information, just as it has happened in the initial scenario during the CoVid-19 spread in China and Europe. The model has been used to predict the death rate in Spain but can be used to predict the demand of ICUs or mechanical ventilators under different restraint policies. The main novelty of the model is that it keeps track of the date of infection of a single individual and uses stochastic distributions to aggregate individuals who share the same date of infection. In addition, it uses two types of infections, mild and serious, with a different recovery time. These features are implemented in a set of differential equations which determine the number of Carriers, Infections, Recoveries, Hospitalized and Deaths. Comparison with real data shows good agreement.

q-bio.OT↗

arXiv2020

History of Onychophorology, 1826-2020

Velvet worms, or onychophorans, are animals of extraordinary importance in the study of evolution. This is the first history of their study. They were described by Lansdown Guilding (1797-1831). This paper identifies the landmarks of their study, in a worldwide level, for almost 200 years. The beginning, 1826-1879, was based on describing their anatomy with light miscroscopy, mostly by famous French naturalists such as Milne-Edwards and Blanchard. In 1880-1929 peiord, work concentrated in anatomy, physiology, behavior, biogeography and ecology, but the most important work was Bouvier`s mammoth monograph. The next period, 1930-1979, was important for the discovery of Cambrian species; Vachons explanation of how ancient distribution defined the existence of two families; Pioneer DNA and electron microscopy from Brazil; and primitive attempts at systematics using embryology or isolated anatomical characteristics. Finally, the 1980-2020 period, with research centered in Australia, Brazil, Costa Rica and Germany, is marked by an evolutionary approach to everything, from body and behavior to distribution; for the solution of the old problem of how they form their adhesive net and how the glue works; the reconstruction of Cambrian onychophoran communities, the first experimental taphonomy; the first countrywide map of conservation status (from Costa Rica); the first model of why they survive in cities; the discovery of new phenomena like food hiding, parental feeding investment and ontogenetic diet shift; and for the birth of a new research branh, Onychophoran Etnobiology, founded in 2015,

q-bio.OT↗

arXiv2020

A Bayesian approach to recover the theoretical temperature-dependent hatch date distribution from biased samples: the case of the common dolphinfish (Coryphaena hippurus)

Reproductive phenology, growth and mortality rates are key ecological parameters that determine population dynamics and are therefore of vital importance to stock assessment models for fisheries management. In many fish species, the spawning phenology is sensitive to environmental factors that modulate or trigger the spawning event, which differ between regions and seasons. In addition, climate change may also alter patterns of reproductive phenology at the community level. Usually, hatch-date distributions are determined back-calculating the age estimated on calcified structures from the capture date. However, these estimated distributions could be biased due to mortality processes or time spaced samplings derived from fishery. Here, we present a Bayesian approach that functions as a predictive model for the hatching date of individuals from a fishery-dependent sampling with temporal biases. We show that the shape and shift of the observed distribution is corrected. This model can be applied in fisheries with multiple cohorts, for species with a wide geographical distribution and living under contrasting environmental regimes and individuals with different life histories such as thermo-dependent growth, length-dependent mortality rates, etc.

q-bio.OT↗

arXiv2020

The pandemic of viruses with a long incubation phase in the small world

A model of the spread of viruses in selected city and in a network of cities is considered, taking into account the delay caused by the long incubation period of the virus. The effect of delay effects is shown in comparison with pandemics without such delay. A temporary asymmetry of the spread of infection has been identified, which means that the time for a pandemic to develop significantly exceeds the time for its completion. Model calculations of the spread of viruses in a network of interconnected large and small cities were carried out, and dynamics features were revealed in comparison with the spread of viruses in a single city, including the possibility of reinfection of megalopolis.

q-bio.OT↗

arXiv2020

Open Data Resources for Fighting COVID-19

We provide an insight into the open data resources pertinent to the study of the spread of Covid-19 pandemic and its control. We identify the variables required to analyze fundamental aspects like seasonal behaviour, regional mortality rates, and effectiveness of government measures. Open data resources, along with data-driven methodologies, provide many opportunities to improve the response of the different administrations to the virus. We describe the present limitations and difficulties encountered in most of the open-data resources. To facilitate the access to the main open-data portals and resources, we identify the most relevant institutions, at a world scale, providing Covid-19 information and/or auxiliary variables (demographics, mobility, etc.). We also describe several open resources to access Covid-19 data-sets at a country-wide level (i.e. China, Italy, Spain, France, Germany, U.S., etc.). In an attempt to facilitate the rapid response to the study of the seasonal behaviour of Covid-19, we enumerate the main open resources in terms of weather and climate variables. CONCO-Team: The authors of this paper belong to the CONtrol COvid-19 Team, which is composed of different researches from universities of Spain, Italy, France, Germany, United Kingdom and Argentina. The main goal of CONCO-Team is to develop data-driven methods for the better understanding and control of the pandemic.

q-bio.OT↗

arXiv2020

Role of a Habitat's Air Humidity in Covid-19 Mortality

Transient local over-dry environment might be a contributor and an explanation for the observed asynchronous local rises in Covid-19 mortality. We propose that a habitat's air humidity negatively correlate with Covid-19 morbidity and mortality, and support this hypothesis on the example of publicly available data from German federal states.

q-bio.OT↗

arXiv2020

A new method for life table and life expectancy calculation

The existing life table method needs to calculate the age-specific mortality first, not only has too many and complicated calculation steps, but also introduces the multiple approximation to bring error. This paper redefines the probability of death for the life table as the average probability of death of a group of people born in a certain period at a later time. Based on this definition, a new method for the life table is proposed to obtain the life expectancy, which has the same meaning to that from the traditional life table. Using the Japanese population data to verify the method, the results show that it is consistent with the life expectancy of the birth of the baby, the maximum relative difference is no more than 0.1%, and average relative difference is less than 0.03%. The theory and method of life table described in this paper are simple and easy to understand. The needed data are easy to obtained from statistics, and the calculation is easy, the results obtained are accurate and reliable. It should be a very valuable demographic method for application.

q-bio.OT↗

arXiv2020

On the origin of the standard genetic code as a fusion of prebiotic single-base-pair codes

The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal approach explains the number of the proteinogenic amino acids and the codon assignment in the resulting standard genetic code. It shows how norleucine, pyrrolysine, selenocysteine and two other unknown amino acids, included into the prebiotic codes, disappeared after the fusion. The properties of these two missing amino acids were described. The ambiguous translation observed in mitochondria is explained. The internal structure of the codes allows a more detailed insights into molecular evolution in prebiotic time. In particular, the structure of the oldest single base-pair code is presented. The fusion concept reveals the appearance of the DNA machinery on the level of the single dominant AU-code. The time before the appearance of standard genetic code is divided into four epochs: pre-DNA, 2-code, pre-fusion, and after-fusion epochs. The prebiotic single-base-pair codes may help design novel peptide-based catalysts.

q-bio.OT↗

arXiv2020

Information and order of genomic sequences within chromosomes as identified by complexity theory. An integrated methodology

Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose of the study was to assess information and order that may be concealed within the size distribution of these sequences. For this purpose, we developed an innovative integrated methodology. Our analysis is based upon the reconstructed phase space theorem, the non-extensive statistical theory of Tsallis, ML techniques and a new technical index, integrating the generated information, which we introduce and named it Complexity Factor (COFA). The low-dimensional deterministic nonlinear chaotic and non-extensive statistical character of the DNA sequences was verified with strong multifractal characteristics and long-range correlations with significant variations per genomic entity and per chromosome. The results of the analysis reveal changes in complexity behavior per genomic entity and chromosome regarding the size distribution of individual genomic segment. The lengths of intron regions show greater complexity behavior in all metrics than the exonic ones, with longer range correlations, and stronger memory effects, for all chromosomes. We conclude from our analysis, that the size distribution of the genomic regions within chromosomes, are not random, but follow a specific pattern with characteristic features, that have been seen here through its complexity character, and it is part of the dynamics of the whole genome according to complexity theory. This picture of dynamics of the redundancy of information in DNA recognized from ML tools for clustering, classification and prediction.

physics.bio-ph↗

arXiv2020

Callas or the trajectory of the meteor

The lyric career of Maria Callas, though exceptional, is also noteworthy for its brevity. The first signs of downturn appeared at the age of 36 and her voice fell silent at only 40. Though the literature has massively commented on this premature worsening, few analyses of its characteristics have been made public so far. The purpose of our study was to realise a perceptual and acoustical analysis of recorded arias by the artist at the climax to the fall. The audible impairments were first verbally described, and then compared to acoustical observations based on spectrographic analyses and fundamental-frequency measurements.

q-bio.OT↗