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arXiv2021

Rosen's no-go theorem for regular categories

The famous biologist Robert Rosen argued for an intrinsic difference between biological and artificial life, supporting the claim that `living systems are not mechanisms'. This result, understood as the claim that life-like mechanisms are non-computable, can be phrased as the non-existence of an equivalence between a category of `static'/analytic elements and a category of `variable'/synthetic elements. The property of a system of being synthetic, understood as being the gluing of `variable families' of analytica, must imply that the latter class of objects does not retain sufficient information in order to describe said variability; we contribute to this thesis with an argument rooted in elementary category theory. Seen as such, Rosen's `proof' that no living system can be a mechanism arises from a tension between two contrapuntal needs: on one side, the necessity to consider (synthetically) variable families of systems; on the other, the necessity to describe a syntheticum via an universally chosen analyticum.

math.CT↗

arXiv2020

Eurythmic Dancing with Plants -- Measuring Plant Response to Human Body Movement in an Anthroposophic Environment

This paper describes three experiments measuring interaction of humans with garden plants. In particular, body movement of a human conducting eurythmic dances near the plants (beetroots, tomatoes, lettuce) is correlated with the action potential measured by a plant SpikerBox, a device measuring the electrical activity of plants, and the leaf movement of the plant, tracked with a camera. The first experiment shows that our measurement system captures external stimuli identically for different plants, validating the measurement system. The second experiment illustrates that the plants' response is correlated to the movements of the dancer. The third experiment indicates that plants that have been exposed for multiple weeks to eurythmic dancing might respond differently to plants which are exposed for the first time to eurythmic dancing.

eess.SP↗

arXiv2021

A Tutorial on the Mathematical Model of Single Cell Variational Inference

As the large amount of sequencing data accumulated in past decades and it is still accumulating, we need to handle the more and more sequencing data. As the fast development of the computing technologies, we now can handle a large amount of data by a reasonable of time using the neural network based model. This tutorial will introduce the the mathematical model of the single cell variational inference (scVI), which use the variational auto-encoder (building on the neural networks) to learn the distribution of the data to gain insights. It was written for beginners in the simple and intuitive way with many deduction details to encourage more researchers into this field.

q-bio.OT↗

arXiv2021

Extraction, isolation, structure elucidation and evaluation of toxicity, anti-inflammatory and analgesic activity of Pituranthos scoparius constituents

The present work aimed to investigate an ethnobotanical survey about Pituranthos scoparius and assess the toxicity, anti-inflammatory (in vitro, and in vivo) potential, in vitro antioxidant, and analgesic effects of stems and roots of Pituranthos scoparius. Furthermore; to isolate and elucidate the chemical constituents of the n-butanol stem extract of P. scoparius (ButE) and determine the toxicity and anti-inflammatory effects of these compounds added to the ButE. Data from an ethnopharmacological study showed that 24.47 % of people used this plant in folk medicine. Four compounds were isolated from ButE. These compounds were characterized by means of NMR and high-resolution mass spectral (HRMS) data.

q-bio.OT↗

arXiv2021

Continuous Glucose Monitoring Prediction

Diabetes is one of the deadliest diseases in the world and affects nearly 10 percent of the global adult population. Fortunately, powerful new technologies allow for a consistent and reliable treatment plan for people with diabetes. One major development is a system called continuous blood glucose monitoring (CGM). In this review, we look at three different continuous meal detection algorithms that were developed using given CGM data from patients with diabetes. From this analysis, an initial meal prediction algorithm was also developed utilizing these methods.

q-bio.OT↗

arXiv2021

Predicting Participation in Cancer Screening Programs with Machine Learning

In this paper, we present machine learning models based on random forest classifiers, support vector machines, gradient boosted decision trees, and artificial neural networks to predict participation in cancer screening programs in South Korea. The top performing model was based on gradient boosted decision trees and achieved an area under the receiver operating characteristic curve (AUC-ROC) of 0.8706 and average precision of 0.8776. The results of this study are encouraging and suggest that with further research, these models can be directly applied to Korea's healthcare system, thus increasing participation in Korea's National Cancer Screening Program.

q-bio.OT↗

arXiv2021

Tracking Short-Term Temporal Linguistic Dynamics to Characterize Candidate Therapeutics for COVID-19 in the CORD-19 Corpus

Scientific literature tends to grow as a function of funding and interest in a given field. Mining such literature can reveal trends that may not be immediately apparent. The CORD-19 corpus represents a growing corpus of scientific literature associated with COVID-19. We examined the intersection of a set of candidate therapeutics identified in a drug-repurposing study with temporal instances of the CORD-19 corpus to determine if it was possible to find and measure changes associated with them over time. We propose that the techniques we used could form the basis of a tool to pre-screen new candidate therapeutics early in the research process.

q-bio.OT↗

arXiv2021

Schrödinger's "What is Life?" at 75

2019 marked the 75th anniversary of the publication of Erwin Schrödinger's "What is Life?", a short book described by Roger Penrose in his preface to a reprint of this classic as "among the most influential scientific writings of the 20th century." In this article, I review the long argument made by Schrödinger as he mused on how the laws of physics could help us understand "the events in space and time which take place within the spatial boundary of a living organism." Though Schrödinger's book is often hailed for its influence on some of the titans who founded molecular biology, this article takes a different tack. Instead of exploring the way the book touched biologists such as James Watson and Francis Crick, as well as its critical reception by others such as Linus Pauling and Max Perutz, I argue that Schrödinger's classic is a timeless manifesto, rather than a dated historical curiosity. "What is Life?" is full of timely outlooks and approaches to understanding the mysterious living world that includes and surrounds us and can instead be viewed as a call to arms to tackle the great unanswered challenges in the study of living matter that remain for 21$^{st}$ century science.

q-bio.OT↗

arXiv2021

Towards Understanding the COVID-19 Case Fatality Rate

An important parameter for COVID-19 is the case fatality rate (CFR). It has been applied to wide applications, including the measure of the severity of the infection, the estimation of the number of infected cases, risk assessment etc. However, there remains a lack of understanding on several aspects of CFR, including population factors that are important to CFR, the apparent discrepancy of CFRs in different countries, and how the age effect comes into play. We analyze the CFRs at two different time snapshots, July 6 and Dec 28, 2020, with one during the first wave and the other a second wave of the COVID-19 pandemic. We consider two important population covariates, age and GDP as a proxy for the quality and abundance of public health. Extensive exploratory data analysis leads to some interesting findings. First, there is a clear exponential age effect among different age groups, and, more importantly, the exponential index is almost invariant across countries and time in the pandemic. Second, the roles played by the age and GDP are a little surprising: during the first wave, age is a more significant factor than GDP, while their roles have switched during the second wave of the pandemic, which may be partially explained by the delay in time for the quality and abundance of public health and medical research to factor in.

stat.AP↗

arXiv2021

Should the Endless Frontier of Federal Science be Expanded?

Scientific research in the United States could receive a large increase in federal funding--up to 100 billion dollars over five years -- if proposed legislation entitled the Endless Frontiers Act becomes law. This bipartisan and bicameral bill, introduced in May 2020 by Senators Chuck Schumer (D-NY) and Todd Young (R-IN) and Congressmen Ro Khanna (D-CA) and Mike Gallagher (R-WI), is intended to expand the funding of the physical sciences, engineering, and technology at the National Science Foundation (NSF) and create a new Technology Directorate focused on use-inspired research. In addition to provisions to protect the NSF's current missions, a minimum of 15\% of the newly appropriated funds would be used to enhance NSF's basic science portfolio. The Endless Frontier Act offers a rare opportunity to enhance the breadth and financial support of the American research enterprise. In this essay, we consider the benefits and the liabilities of the proposed legislation and recommend changes that would further strengthen it.

physics.soc-ph↗

arXiv2021

Defining the lead time of wastewater-based epidemiology for COVID-19

Individuals infected with SARS-CoV-2, the virus that causes COVID-19, may shed the virus in stool before developing symptoms, suggesting that measurements of SARS-CoV-2 concentrations in wastewater could be a "leading indicator" of COVID-19 prevalence. Multiple studies have corroborated the leading indicator concept by showing that the correlation between wastewater measurements and COVID-19 case counts is maximized when case counts are lagged. However, the meaning of "leading indicator" will depend on the specific application of wastewater-based epidemiology, and the correlation analysis is not relevant for all applications. In fact, the quantification of a leading indicator will depend on epidemiological, biological, and health systems factors. Thus, there is no single "lead time" for wastewater-based COVID-19 monitoring. To illustrate this complexity, we enumerate three different applications of wastewater-based epidemiology for COVID-19: a qualitative "early warning" system; an independent, quantitative estimate of disease prevalence; and a quantitative alert of bursts of disease incidence. The leading indicator concept has different definitions and utility in each application.

q-bio.OT↗

arXiv2021

Theoretical Modeling of Structure-Toxicity Relationship of Cyanides

The global descriptors of chemical activity:ionization potential IP, electron affinity EA, chemical potential mu, absolute electronegativity chi, molecular hardness eta and softness S,electrophilicity index omega for cyanides X(CN)k with X=H, Na, K, Ag, Cu, Ca, Hg, Cd, Zn in the gas phase and water medium have been determined by taking advantage of the quantum-chemical computations.To this aim, the HOMO and LUMO energy levels were calculated using DFT B3LYP method and QZVP (Valence Quadruple-Zeta Polarization) basis set, which enables precise calculations for hydrogen cyanide and its salts containing both light (H, Na, Ca) and heavy (K, Ag, Cu, Cd, Hg, Zn) atoms.The results obtained indicate that while the EA-parameter roughly determines the LD50 values for the cyanides considered, the omega-descriptor is related rather to the product of cyanide LD50 and hydrolysis n-degree.Hence,the theoretical LD50CN(omega) function proposed is interconnected with the nLD50 collective variable, whereas LD50(EA)directly approximates LD50 indicating that the toxicity of cyanides decreases with increasing EA, omega-values.The calculations carried out suggest that some of the LD50(Exp)experimentally determined are incorrect (AgCN) or inaccurate (Cd(CN)2) and require revision.Comparison of the theoretically estimated LD50(omega) with NOAEL toxicity parameters indicates that they are well correlated in contrast to LD50(EA) and LD50(Exp), exhibiting lower and marginal degrees of correlation, respectively.

physics.chem-ph↗

arXiv2021

A field guide to cultivating computational biology

Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered in an era of data-driven discovery which requires moving beyond the traditional individual, single-discipline investigator research model. This interdisciplinary niche is where computational biology thrives. It has matured over the past three decades and made major contributions to scientific knowledge and human health, yet researchers in the field often languish in career advancement, publication, and grant review. We propose solutions for individual scientists, institutions, journal publishers, funding agencies, and educators.

q-bio.OT↗

arXiv2021

A Gentle Introduction to Scaling Laws in Biological Systems

This paper investigates the role of size in biological organisms. More specifically, how the energy demand, expressed by the metabolic rate, changes according to the mass of an organism. Empirical evidence suggests a power-law relation between mass and metabolic rate, namely allometric law. For vascular organisms, the exponent $β$ of this power-law is smaller than one, which implies scaling economy; that is, the greater the organism is, the lesser energy per cell it demands. However, the numerical value of this exponent is a theme of an extensive debate and a central issue in comparative physiology. It is presented in this work some empirical data and a detailed discussion about the most successful theories to explain these issues. A historical perspective is also shown, beginning with the first empirical insights in the sec. 19 about scaling properties in biology, passing through the two more important theories that explain the scaling properties quantitatively. Firstly, the Rubner model, that consider organism surface area and heat dissipation to derive $β= 2/3$. Secondly, the West-Brown-Enquist theory, that explains such scaling properties as a consequence of the hierarchical and fractal nutrient distribution network, deriving $β= 3/4$.

q-bio.OT↗

arXiv2021

A Digital Twin of a Compartmental Epidemiological Model based on a Stieltjes Differential Equation

We introduce a digital twin of the classical compartmental SIR (Susceptible, Infected, Recovered) epidemic model and study the interrelation between the digital twin and the system. In doing so, we use Stieltjes derivatives to feed the data from the real system to the virtual model which, in return, improves it in real time. As a byproduct of the model, we present a precise mathematical definition of solution to the problem. We also analyze the existence and uniqueness of solutions, introduce the concept of Main Digital Twin and present some numerical simulations with real data of the COVID-19 epidemic, showing the accuracy of the proposed ideas.

q-bio.OT↗

arXiv2021

Assessing ecosystem services for evidence-based nature-based solutions

The term nature-based solutions has often been used to refer to adequate green infrastructure, which is cost-effective and simultaneously provides environmental, social and economic benefits, through the delivery of ecosystem services, and contributes to build resilience. This paper provides an overview of the recent work mapping and assessing ecosystem services in Malta and the implications for decision-making. Research has focused on the identification and mapping of ecosystems, and ecosystem condition, the capacity to deliver key ecosystem services and the actual use (flow) of these services by local communities leading to benefits to human well-being. The integration of results from these different assessments demonstrates several significant synergies between ecosystem services, indicating multifunctionality in the provision of ecosystem services leading to human well-being. This is considered as key criterion in the identification of green infrastructure in the Maltese Islands. A gradient in green infrastructure cover and ecosystem services capacity is observed between rural and urban areas but ecosystem services flow per unit area was in some cases higher in urban environments. These results indicate a potential mismatch between ecosystem service demand and capacity but also provide a scientific baseline for evidence-based policy which fosters the development of green infrastructure through nature-based innovation promoting more specific and novel solutions for landscape and urban planning.

q-bio.OT↗

arXiv2021

Essential Metadata for 3D BRAIN Microscopy

Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments' images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native context, leading to a better understanding of normal development and disease etiology. Consistent annotation of metadata is needed to provide the context necessary to understand, reuse, and integrate these data. This report describes an effort to establish metadata standards for 3D microscopy datasets for use by the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative and the neuroscience research community. These standards were built on existing efforts and developed with input from the brain microscopy community to promote adoption. The resulting Essential Metadata for 3D BRAIN Microscopy includes 91 fields organized into seven categories: Contributors, Funders, Publication, Instrument, Dataset, Specimen, and Image. Adoption of these metadata standards will ensure that investigators receive credit for their work, promote data reuse, facilitate downstream analysis of shared data, and encourage collaboration.

q-bio.OT↗

arXiv2021

Blessing or Curse of Democracy?: Current Evidence from the Covid-19 Pandemic

Background: A major question in Covid-19 research is whether democracies handled the Covid-19 pandemic crisis better or worse than authoritarian countries. However, it is important to consider the issues of democracy versus authoritarianism, and state fragility, when examining official Covid-19 death counts in research, because these factors can influence the accurate reporting of pandemic deaths by governments. In contrast, excess deaths are less prone to variability in differences in definitions of Covid-19 deaths and testing capacities across countries. Here we use excess pandemic deaths to explore potential relationships between political systems and public health outcomes. Methods: We address these issues by comparing the official government Covid-19 death counts in a well-established John Hopkins database to the generally more reliable excess mortality measure of Covid-19 deaths, taken from the recently released World Mortality Dataset. We put the comparison in the context of the political and fragile state dimensions. Findings: We find (1) significant potential underreporting of Covid-19 deaths by authoritarian governments and governments with high state fragility and (2) substantial geographic variation among countries and regions with regard to standard democracy indices. Additionally, we find that more authoritarian governments are (weakly) associated with more excess deaths during the pandemic than democratic governments. Interpretations: The inhibition and censorship of information flows, inherent to authoritarian states, likely results in major inaccuracies in pandemic statistics that confound global public health analyses. Thus, both excess pandemic deaths and official Covid-19 death counts should be examined in studies using death as an outcome variable.

econ.GN↗