pwc-archive/papers-with-abstracts huggingface dataset:
Ontology-based annotation and analysis of COVID-19 phenotypes
Authors: Yang Wang, Fengwei Zhang, Hong Yu, Xianwei Ye, Yongqun He
Date: 2020-08-05 00:00:00
Tasks: Articles

The epidemic of COVID-19 has caused an unpredictable and devastated disaster to the public health in different territories around the world. Common phenotypes include fever, cough, shortness of breath, and chills. With more cases investigated, other clinical phenotypes are gradually recognized, for example, loss of smell, and loss of tastes. Compared with discharged or cured patients, severe or died patients often have one or more comorbidities, such as hypertension, diabetes, and cardiovascular disease. In this study, we systematically collected and analyzed COVID-19-related clinical phenotypes from 70 articles. The commonly occurring 17 phenotypes were classified into different groups based on the Human Phenotype Ontology (HPO). Based on the HP classification, we systematically analyze three nervous phenotypes (loss of smell, loss of taste, and headache) and four abdominal phenotypes (nausea, vomiting, abdominal pain, and diarrhea) identified in patients, and found that patients from Europe and USA turned to have higher nervous phenotypes and abdominal phenotypes than patients from Asia. A total of 23 comorbidities were found to commonly exist among COVID-19 patients. Patients with these comorbidities such as diabetes and kidney failure had worse outcomes compared with those without these comorbidities.
Quantitative clarification of key questions about COVID-19 epidemiology
Authors: Yinon M. Bar-On, Ron Sender, Avi I. Flamholz, Rob Phillips, Ron Milo
Date: 2020-07-09 00:00:00
Tasks: Epidemiology

Modeling the spread of COVID-19 is crucial for informing public health policy. All models for COVID-19 epidemiology rely on parameters describing the dynamics of the infection process. The meanings of epidemiological parameters like R_0, R_t, the "serial interval" and "generation interval" can be challenging to understand, especially as these and other parameters are conceptually overlapping and sometimes confusingly named. Moreover, the procedures used to estimate these parameters make various assumptions and use different mathematical approaches that should be understood and accounted for when relying on parameter values and reporting them to the public. Here, we offer several insights regarding the derivation of commonly-reported epidemiological parameters, and describe how mitigation measures like lockdown are expected to affect their values. We aim to present these quantitative relationships in a manner that is accessible to the widest audience possible. We hope that better communicating the intricacies of epidemiological models will improve our collective understanding of their strengths and weaknesses, and will help avoid possible pitfalls when using them.
A quantitative compendium of COVID-19 epidemiology
Authors: Yinon M. Bar-On, Ron Sender, Avi I. Flamholz, Rob Phillips, Ron Milo
Date: 2020-06-01 00:00:00
Tasks: Epidemiology

Accurate numbers are needed to understand and predict viral dynamics. Curation of high-quality literature values for the infectious period duration or household secondary attack rate, for example, is especially pressing currently because these numbers inform decisions about how and when to lockdown or reopen societies. We aim to provide a curated source for the key numbers that help us understand the virus driving our current global crisis. This compendium focuses solely on COVID-19 epidemiology. The numbers reported in summary format are substantiated by annotated references. For each property, we provide a concise definition, description of measurement and inference methods, and associated caveats. We hope this compendium will make essential numbers more accessible and avoid common sources of confusion for the many newcomers to the field such as using the incubation period to denote and quantify the latent period or using the hospitalization duration for the infectiousness period duration. This document will be repeatedly updated and the community is invited to participate in improving it.
Intermolecular Enzymatic Encoding of Nucleic Acid, Steroid Complexes: A New Theory on the Chemical Origin of Life Based on Evidence of Structural Symmetry
Authors: Charles D. Schaper
Date: 2020-06-09 00:00:00

The origin of life is one of the greatest mysteries. The mechanism for the synthesis of DNA is synonymous with the chemical origin of life, and theories have been developed along many lines of reasoning, but resolving all requirements remains a challenge, such as defining an objective path to produce sequences of encoded nucleotides paired as adenine to thymine and guanine to cytosine. Here, a new theory for the origin of DNA is presented. The theory is based upon three lines of experimental evidence and agreement of structural symmetry between DNA nucleotides and steroid hormones, and introduces a new concept of synthesizing both structural and functional characteristics of DNA at the same time within a single unified complex of interleaved tetra-ringed structures, steroid molecules which form reaction vessels that serve as co-enzymatic building blocks. The new theory indicates that the establishment of the DNA nucleotide code is among the very first synthesis steps. Moreover, as a consequence of the intermolecular synthesis of both structural and functional characteristics within a unified complex, there is a culminating process step that sets forth in motion both DNA and the steroid structures that subsequently trigger replication and transcription, as well as protein translation, thereby resulting in the instantaneous release of life function.
Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry
Authors: Alexander Leitner, Alexandre M. J. J. Bonvin, Christoph H. Borchers, Robert J. Chalkley, Julia Chamot-Rooke, Colin W. Combe, Jürgen Cox, Meng-Qiu Dong, Lutz Fischer, Michael Götze, Fabio C. Gozzo, Albert J. R. Heck, Michael R. Hoopmann, Lan Huang, Yasushi Ishihama, Andrew R. Jones, Nir Kalisman, Oliver Kohlbacher, Karl Mechtler, Robert L. Moritz, Eugen Netz, Petr Novak, Evgeniy Petrotchenko, Andrej Sali, Richard A. Scheltema, Carla Schmidt, David Schriemer, Andrea Sinz, Frank Sobott, Florian Stengel, Konstantinos Thalassinos, Henning Urlaub, Rosa Viner, Juan A. Vizcaino, Marc R. Wilkins, Juri Rappsilber
Date: 2020-07-01 00:00:00

Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformation analysis and mapping protein interactions in complex mixtures. Crosslinking MS has become a much-appreciated and routinely applied tool especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Crosslinking MS for which guidelines should be developed as part of a Crosslinking MS standards initiative.
Clinical Trial Drug Safety Assessment for Studies and Submissions Impacted by COVID-19
Authors: Mary Nilsson, Brenda Crowe, Greg Anglin, Greg Ball, Melvin Munsaka, Seta Shahin, Wei Wang
Date: 2020-06-05 00:00:00

In this paper, we provide guidance on how standard safety analyses and reporting of clinical trial safety data may need to be modified, given the potential impact of the COVID-19 pandemic. The impact could include missed visits, alternative methods for assessments (such as virtual visits), alternative locations for assessments (such as local labs), and study drug interruptions. We focus on safety planning for Phase 2-4 clinical trials and integrated summaries for submissions. Starting from the recommended safety analyses proposed in white papers and a workshop, created as part of an FDA/PHUSE collaboration (PHUSE 2013, 2015, 2017, 2019), we assess what modifications might be needed. Impact from COVID-19 will likely affect treatment arms equally, so analyses of adverse events from controlled data can, to a large extent, remain unchanged. However, interpretation of summaries from uncontrolled data (summaries that include open-label extension data) will require even more caution than usual. Special consideration will be needed for safety topics of interest, especially events expected to have a higher incidence due to a COVID-19 infection or due to quarantine or travel restrictions (e.g., depression). Analyses of laboratory measurements may need to be modified to account for the combination of measurements from local and central laboratories.
Analysis of Compression Techniques for DNA Sequence Data
Authors: Shakeela Bibi, Javed Iqbal, Adnan Iftekhar, Mir Hassan
Date: 2020-06-01 00:00:00

Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic material that exist in all breathingcreatures. This biomolecule (DNA) comprehends the genetic material obligatory for the operational and expansion of all personified lives. To save DNA data of single person we require 10CD-ROMs.Moreover, this size is increasing constantly, and more and more sequences are adding in the public databases. This abundant increase in the sequence data arise challenges in the precise information extraction from this data. Since many data analyzing and visualization tools do not support processing of this huge amount of data. To reduce the size of DNA and protein sequence, many scientists introduced various types of sequence compression algorithms such as compress or gzip, Context Tree Weighting (CTW), Lampel Ziv Welch (LZW), arithmetic coding, run-length encoding and substitution method etc. These techniques have sufficiently contributed to minimizing the volume of the biological datasets. On the other hand, traditional compression techniques are also not much suitable for the compression of these types of sequential data. In this paper, we have explored diverse types of techniques for compression of large amounts of DNA Sequence Data. In this paper, the analysis of techniques reveals that efficient techniques not only reduce the size of the sequence but also avoid any information loss. The review of existing studies also shows that compression of a DNA sequence is significant for understanding the critical characteristics of DNA data in addition to improving storage efficiency and data transmission. In addition, the compression of the protein sequence is a challenge for the research community. The major parameters for evaluation of these compression algorithms include compression ratio, running time complexity etc.
In-silico nucleotide and protein analyses of S-gene region in selected zoonotic coronaviruses reveal conserved domains and evolutionary emergence with trajectory course of viral entry from SARS-CoV2 genomic data
Authors: Adejoke Olukayode Obajuluwa, Pius Abimbola Okiki, Tiwalola Madoc Obajuluwa, Olakunle Bamikole Afolabi
Date: 2020-05-06 00:00:00
Tasks: Management

The recent zoonotic coronavirus virus outbreak of a novel type [COVID 19] has necessitated the adequate understanding of the evolutionary pathway of zoonotic viruses which adversely affects human populations for therapeutic constructs to combat the pandemic now and in the future. We analyzed conserved domains of the severe acute respiratory coronavirus 2 [SARS-CoV2] for possible targets of viral entry inhibition in host cells, evolutionary relationship of human coronavirus [229E] and zoonotic coronaviruses with SAR-CoV2 as well as evolutionary relationship between selected SARS-CoV 2 genomic data. Conserved domains with antagonistic action on host innate antiviral cellular mechanisms in SARS-CoV 2 include nsp 11, nsp 13 etc. Also, multiple sequence alignments of the spike [S] gene protein of selected candidate zoonotic coronaviruses alongside the S gene protein of the SARs-CoV2 revealed closest evolutionary relationship [95.6%] with pangolin coronaviruses [S] gene. Clades formed between Wuhan SARS-CoV2 phylogeny data and five others suggests viral entry trajectory while revealing genomic and protein SARS CoV 2 data from Philippines as early ancestors. Therefore, phylogeny of SARS-CoV 2 genomic data suggests profiling in diverse populations with and without the outbreak alongside migration history and racial background for mutation tracking and dating of viral subtype divergence which is essential for effective management of present and future zoonotic coronavirus outbreaks.
The pandemic of viruses with a long incubation phase in the small world
Authors: P. A. Golovinski
Date: 2020-04-08 00:00:00

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.
The Chiral Puzzle of Life
Authors: Noemie Globus, Roger D. Blandford
Date: 2020-02-23 00:00:00

Biological molecules chose one of two structurally, chiral systems which are related by reflection in a mirror. It is proposed that this choice was made, causally, by magnetically polarized and physically chiral cosmic-rays, which are known to have a large role in mutagenesis. It is shown that the cosmic rays can impose a small, but persistent, chiral bias in the rate at which they induce structural changes in simple, chiral monomers that are the building blocks of biopolymers. A much larger effect should be present with helical biopolymers, in particular, those that may have been the progenitors of RNA and DNA. It is shown that the interaction can be both electrostatic, just involving the molecular electric field, and electromagnetic, also involving a magnetic field. It is argued that this bias can lead to the emergence of a single, chiral life form over an evolutionary timescale. If this mechanism dominates, then the handedness of living systems should be universal. Experiments are proposed to assess the efficacy of this process.
Predation by Atractosteus tropicus on Bufo marinus and its possible affect on population in a lowland tropical wet rainforest
Authors: Todd R Lewis, Colin Ryall, Thomas C Laduke, Paul B C Grant
Date: 2020-05-01 00:00:00

Fish predation can affect amphibian populations. Most examples report invasive fish species and their negative effect on specific amphibians. Here we provide an occurrence of natural fish predation by the tropical gar Atractosteus tropicus on the cane toad Bufo marinus. We observed physical damage caused by A. tropicus attacking B. marinus. When adult B. marinus were removed from the population subadult toads refilled the adults niche, resupplementing the population. Local observations of predation by fish on amphibians are important to differentiate natural population fluctuations from amphibian population declines.
Pathogen Infection Recovery Probability (PIRP) Versus Proinflammatory Anti-Pathogen Species (PIAPS) Levels: Modelling and Therapeutic Strategies
Authors: Sam-Shajing Sun
Date: 2020-03-11 00:00:00
Tasks: Math

Current CoVID-19 pandemic is spreading rapidly worldwide, and it may become one of the largest pandemic events in modern history if out of control. It appears most of the SARS-CoV2 virus infection resulted deaths are mainly due to dysfunctions or failures of the lung or multiple organs that could be attributed to hosts immunodysfunctions particularly hyperinflammatory type disorders. In this brief review and study, a math model is proposed to correlate the Pathogen Infection Recovery Probability (PIRP) versus Proinflammatory Anti-Pathogen Species (PIAPS) levels within a host unit, where a maximum PIRP is exhibited when the PIAPS levels are equal to or around PIAPS equilibrium levels at the pathogen elimination or clearance onset. Based on this model, rational or effective therapeutic strategies at right stages or timing, with right type of agents (immuno-stimulators or immuno-suppressors), and right dosages, may be designed and implemented that are expected to effectively achieve maximum PIRP or reduce the mortality.
On the Inhibition of COVID-19 Protease by Indian Herbal Plants: An In Silico Investigation
Authors: Ambrish Kumar Srivastava, Abhishek Kumar, Neeraj Misra
Date: 2020-04-05 00:00:00

COVID-19 has quickly spread across the globe, becoming a pandemic. This disease has a variable impact in different countries depending on their cultural norms, mitigation efforts and health infrastructure. In India, a majority of people rely upon traditional Indian medicine to treat human maladies due to less-cost, easier availability and without any side-effect. These medicines are made by herbal plants. This study aims to assess the Indian herbal plants in the pursuit of potential COVID-19 inhibitors using in silico approaches. We have considered 18 extracted compounds of 11 different species of these plants. Our calculated lipophilicity, aqueous solubility and binding affinity of the extracted compounds suggest that the inhibition potentials in the order; harsingar > aloe vera > giloy > turmeric > neem > ashwagandha > red onion > tulsi > cannabis > black pepper. On comparing the binding affinity with hydroxychloroquine, we note that the inhibition potentials of the extracts of harsingar, aloe vera and giloy are very promising. Therefore, we believe that these findings will open further possibilities and accelerate the works towards finding an antidote for this malady.
History of Onychophorology, 1826-2020
Authors: Julian Monge-Najera
Date: 2020-04-01 00:00:00
Tasks: Anatomy

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,
A framework for parsing heritable information
Authors: Antony M Jose
Date: 2019-12-19 00:00:00

Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here I develop a framework for heredity and development that includes the cycling regulators parsed in terms of what an organism can sense about itself and its environment by defining entities, their sensors, and the sensed properties. Entities include small molecules (ATP, ions, metabolites, etc.), macromolecules (individual proteins, RNAs, polysaccharides, etc.), and assemblies of molecules. While concentration may be the only relevant property measured by sensors for small molecules, multiple properties that include concentration, sequence, conformation, and modification may all be measured for macromolecules and assemblies. Each configuration of these entities and sensors that is recreated in successive generations in a given environment thus specifies a potentially vast amount of information driving complex development in each generation. This Entity-Sensor-Property framework explains how sensors limit the number of distinguishable states, how distinct molecular configurations can be functionally equivalent, and how regulation of sensors prevents detection of some perturbations. Overall, this framework is a useful guide for understanding how life evolves and how the storage of information has itself evolved with complexity since before the origin of life.
Did Sequence Dependent Geometry Influence the Evolution of the Genetic Code?
Authors: Alex Kasman, Brenton LeMesurier
Date: 2020-03-01 00:00:00

The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also has a separate geometric interpretation. A question then arises: How well-duplexed are these two "codes"? In other words, in choosing a genetic sequence to encode a particular protein, how much freedom does one still have to vary the geometry (or vice versa). A recent paper by the first author addressed this question using two different methods. After reviewing those results, this paper addresses the same question with a third method: the use of Monte Carlo and Gaussian sampling methods to approximate a multi-integral representing the mutual information of a variety of possible genetic codes. Once again, it is found that the genetic code used in nuclear DNA has a slightly lower than average duplexing efficiency as compared with other hypothetical genetic codes. A concluding section discusses the significance of these surprising results.
Natural intelligence and anthropic reasoning
Authors: P Slijepcevic
Date: 2020-01-04 00:00:00

This paper aims to justify the concept of natural intelligence, the type of intelligence wider than human intelligence and its derivative, AI. I will argue that the process of life is a cognitive process and that organisms, from bacteria to animals, are cognitive agents. To justify these arguments, the neural intelligence represented by the form of reasoning known as anthropic reasoning will be compared and contrasted with types of intelligence explicated by four disciplines of biology, relational biology, evolutionary epistemology, biosemiotics and the systems view of life, not biased towards neural intelligence. The comparison will be achieved by asking several questions that probe the concepts of observers and true observers. To answer the questions I will rely on a range of established concepts including SETI, Fermi's paradox, bacterial cognition, versions of the panspermia theory, and some newly introduced concepts including biocivilisations, cognitive universes, and the cognitive multiverse. The key point emerging from the answers is that the process of cognition, the essence of natural intelligence, is a biological universal.