Risk factors for Covid-19 severity and fatality: a structured literature review.

Purpose: Covid-19 is a global threat that pushes health care to its limits. Since there is neither a vaccine nor a drug for Covid-19, people with an increased risk for severe and fatal courses of disease particularly need protection. Furthermore, factors increasing these risks are of interest in the search of potential treatments.

Basins of Attraction, Commitment Sets, and Phenotypes of Boolean Networks.

The attractors of Boolean networks and their basins have been shown to be highly relevant for model validation and predictive modeling, e.g., in systems biology.

Survival and weak chaos.

Survival analysis in biology and reliability theory in engineering concern the dynamical functioning of bio/electro/mechanical units. Here we incorporate effects of chaotic dynamics into the classical theory. Dynamical systems theory now distinguishes strong and weak chaos.

The evolutionary ecology of molecular replicators.

By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise.

Decomposition of Jones and Mueller matrices in terms of four basic polarization responses.

A simple new method is introduced to analyze the polarization of light by media. This method decomposes a Jones matrix into a linear combination of four basic matrices that represent different polarization responses. The Mueller matrix expressed in terms of the response coefficients of the basic matrices demonstrates a highly symmetric form that spells out the physical origins of each matrix element.

Controlling for non-independence in comparative analysis of patterns across populations within species.

How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow).

Genome-wide association studies in Plasmodium species.

Genome-wide association studies (GWAS) look for correlations between traits of interest and genetic markers spread throughout the genome. A recent study in BMC Genetics has found that populations of the malaria parasite Plasmodium vivax should be amenable to GWAS searching for a genetic basis of parasite pathogenicity. Geographical substructure in populations may, however, prove a problem in interpreting the results.

Optical scattering depolarization in a biomedium with anisotropic biomolecules.

The depolarization property of a biomedium with anisotropic biomolecule optical scattering is investigated theoretically. By using a simple ellipsoid model of a single biomolecule, the scattering fields and Mueller matrices are derived from fundamental electromagnetism theory. The biomedium is modeled as a system of uncorrelated anisotropic molecules.

Degrees of polarization and coherence of paired linear polarized laser beam by scattering glass plates measured using optical coherent ellipsometer.

An accurate optical coherent ellipsometer (OCE) is proposed and setup in which a two-frequency paired linear polarized laser beam is integrated with a common-path heterodyne interferometer. This OCE is able to precisely measure the optical properties of scattering specimen by measuring ellipsometric parameters (Psi, Delta). In the mean time the degree of polarization P, and degree of coherence Chi of incident two-frequency linear polarized laser beam are measured too.

Scattering polarization by anisotropic biomolecules.

The full polarization properties of anisotropic biomolecule optical scattering are investigated theoretically. By using a simple ellipsoid model of a single biomolecule, the scattering fields and Mueller matrices are derived from fundamental electromagnetism theory. The energy of scattered photons is not necessarily equal to that of the incident laser beam.

Depolarization and principal mueller matrix measured by null ellipsometry.

Methods for accurately measuring depolarization and principal Mueller matrix by null ellipsometry are devised. The measurement errors obtained with these methods are analyzed, and methods to correct for the errors are devised. The depolarization spectrum measured directly by null ellipsometry for a sapphire slab agrees excellently with the depolarization spectrum reduced indirectly from the retardance spectrum measured by rotating analyzer ellipsometry and the depolarization spectrum simulated for the retardance spread caused by a finite bandwidth of monochromator [J.

Slope distribution of a rough surface measured by transmission scattering and polarization.

Transmission scattering from medium to air was used to measure the slope distribution of the rough plane surface of a transparent glass hemisphere. A facet model successfully explained the measured results of refraction, scattering, and polarization: Transmission scattering existed for incident angles greater than the critical angle, all measured curves for the normalized scattered intensity versus the facet slope angle for different detection directions overlapped, and the measured polarization of scattering was approximately constant for >99% of the facets. The slope distribution obtained by transmission scattering agrees with those of the surface profiles in the valid range of the profiler and can represent the slope distribution of the rough surface.

Error analysis of null ellipsometry with depolarization.

Null ellipsometry is analyzed for components with depolarizations for unpolarized incident light. Serious imperfections include sample depolarization D < 0.2, misalignment (deltaC < 2 degrees) and off-quarter-wave retardance (deltatau < 5 degrees) of the compensator.

Characterization for imperfect polarizers under imperfect conditions.

The principles for measuring the extinction ratio and transmittance of a polarizer are formulated by use of the principal Mueller matrix, which includes both polarization and depolarization. The extinction ratio is about half of the depolarization, and the contrast is the inverse of the extinction ratio. Errors in the extinction ratio caused by partially polarized incident light and the misalignment of polarizers can be corrected by the devised zone average method and the null method.

The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types.

It is commonly believed that influenza epidemics arise through the incremental accumulation of viral mutations, culminating in a novel antigenic type that is able to escape host immunity. Successive epidemic strains therefore become increasingly antigenically distant from a founding strain. Here, we present an alternative explanation where, because of functional constraints on the defining epitopes, the virus population is characterized by a limited set of antigenic types, all of which may be continuously generated by mutation from preexisting strains and other processes.

Errors of Mueller matrix measurements with a partially polarized light source.

The linear errors of Mueller matrix measurements, using a partially polarized light source, have been formulated for imperfections of misalignment, depolarization, and nonideal ellipsometric parameters of the polarimetric components. The error matrices for a source-polarizer system and a source-polarizer-compensator system are derived. A polarized light source, when used with an imperfect polarizer, generates extra errors in addition to those for an unpolarized source.

Quantifying the roles of immigration and chance in shaping prokaryote community structure.

Naturally occurring populations of bacteria and archaea are vital to life on the earth and are of enormous practical significance in medicine, engineering and agriculture. However, the rules governing the formation of such communities are still poorly understood, and there is a need for a usable mathematical description of this process. Typically, microbial community structure is thought to be shaped mainly by deterministic factors such as competition and niche differentiation.

The illusion of invariant quantities in life histories.

Life-history theory attempts to provide evolutionary explanations for variations in the ways in which animal species live their lives. Recent analyses have suggested that the dimensionless ratios of several key life-history parameters are the same for different species, even across distant taxa. However, we show here that previous analyses may have given a false picture and created an illusion of invariants, which do not necessarily exist; essentially, this is because life-history variables have been regressed against themselves.

A grid-enabled lightweight computational steering client: a .NET PDA implementation.

The grid has been developed to support large-scale computer simulations in a diverse range of scientific and engineering fields. Consequently, the increasing availability of powerful distributed computing resources is changing how scientists undertake large-scale modelling/simulation. Instead of being limited to local computing resources, scientists are now able to make use of supercomputing facilities around the world.

Polarization of transmission scattering simulated by using a multiple-facets model.

A Mueller matrix for scattering by a rough plane surface of a glass hemisphere was simulated by using a micro-facet model. The algorithms are formulated in vector representation in terms of the input and output directions. The single-facet scattering simulation used the results of the Kirchhoff integral for medium rough surfaces with exponential height distribution.

Extinction, slime, and bottoms.

Is biodiversity decreasing or is it being replaced by a splendid profusion of microbes -- and does this matter?