Revealing the hierarchical structure of microbial communities.

Measuring the dynamics of microbial communities results in high-dimensional measurements of taxa abundances over time and space, which is difficult to analyze due to complex changes in taxonomic compositions. This paper presents a new method to investigate and visualize the intrinsic hierarchical community structure implied by the measurements. The basic idea is to identify significant intersection sets, which can be seen as sub-communities making up the measured communities.

Computing all persistent subspaces of a reaction-diffusion system.

An algorithm is presented for computing a reaction-diffusion partial differential equation (PDE) system for all possible subspaces that can hold a persistent solution of the equation. For this, all possible sub-networks of the underlying reaction network that are distributed organizations (DOs) are identified. Recently it has been shown that a persistent subspace must be a DO.

COVID-19-associated pulmonary aspergillosis (CAPA): identification of Aspergillus species and determination of antifungal susceptibility profiles.

Among the co-infectious agents in COVID-19 patients, Aspergillus species cause invasive pulmonary aspergillosis (IPA). IPA is difficult to diagnose and is associated with high morbidity and mortality. This study is aimed at identifying Aspergillus spp.

Evaluation of amino acid profile in serum of patients with Covid-19 for providing a new treatment strategy.

Background: Amino acids have an important role in metabolism and may affect COVID-19-related outcomes. In our study, the amino acid serum level of hospitalized COVID19 patients was evaluated to determine a new treatment strategy.

Methods: The amino acid profile covering 43 amino acids in 68 subjects, comprising 30 (14 men and 16 women) controls and 38 (16 men and 22 women) COVID-19 patients, were examined.

Evaluation of the Relationship Between Aquaporin-1, Hepcidin, Zinc, Copper, and İron Levels and Oxidative Stress in the Serum of Critically Ill Patients with COVID-19.

Our study aims to determine the relationship between hepcidin, aquaporin (AQP-1), copper (Cu), zinc (Zn), iron (Fe) levels, and oxidative stress in the sera of seriously ill COVID-19 patients with invasive mechanical ventilation. Ninety persons with and without COVID-19 were taken up and separated into two groups. The first group included seriously COVID-19 inpatients having endotracheal intubation in the intensive care unit (n = 45).

Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure-Enumerating All Decompositions of Sequence Periods.

A coiled coil is a structural motif in proteins that consists of at least two α-helices wound around each other. For structural stabilization, these α-helices form interhelical contacts via their amino acid side chains. However, there are restrictions as to the distances along the amino acid sequence at which those contacts occur.

Coating indwelling urinary catheters with moxifloxacin prevents biofilm formation by Burkholderia cepacia.

Background: Burkholderia cepacia adhesion and biofilm formation onto abiotic surfaces is an important feature of clinically relevant isolates. The in vitro biofilm formation of B. cepacia onto coated indwelling urinary catheters (IDCs) with moxifloxacin has not been previously investigated.

Correction: Measuring attitudes towards biology major and non-major: Effect of students' gender, group composition, and learning environment.

[This corrects the article DOI: 10.1371/journal.pone.

Undiagnosed Chronic Obstructive Pulmonary Disease is Highly Prevalent in Patients Referred for Dobutamine Stress Echocardiography with Shortness of Breath.

Purpose: Shortness of breath (SOB) is a common symptom referral for dobutamine stress echocardiography (DSE). Patients with SOB and a normal DSE have worse long-term outcome than the general population. This suggests multiple aetiologies are involved.

Measuring attitudes towards biology major and non-major: Effect of students' gender, group composition, and learning environment.

This study examined the effect of collaborative learning (CL) versus traditional lecture-based learning (TL) pedagogies and gender group composition in effecting positive or negative attitudes of biology major and nonmajor men and women students. The experimental research method was administered in experimental and control groups to test the hypotheses. Students' attitudes refer to their positive or negative feelings and inclinations to learn biology.

Structure and Hierarchy of SARS-CoV-2 Infection Dynamics Models Revealed by Reaction Network Analysis.

This work provides a mathematical technique for analyzing and comparing infection dynamics models with respect to their potential long-term behavior, resulting in a hierarchy integrating all models. We apply our technique to coupled ordinary and partial differential equation models of SARS-CoV-2 infection dynamics operating on different scales, that is, within a single organism and between several hosts. The structure of a model is assessed by the theory of chemical organizations, not requiring quantitative kinetic information.

The International Virus Bioinformatics Meeting 2020.

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online.

A novel method for achieving an optimal classification of the proteinogenic amino acids.

The classification of proteinogenic amino acids is crucial for understanding their commonalities as well as their differences to provide a hint for why life settled on the usage of precisely those amino acids. It is also crucial for predicting electrostatic, hydrophobic, stacking and other interactions, for assessing conservation in multiple alignments and many other applications. While several methods have been proposed to find "the" optimal classification, they have several shortcomings, such as the lack of efficiency and interpretability or an unnecessarily high number of discriminating features.

Differential equation-based minimal model describing metabolic oscillations in biofilms.

Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995.

Extending the minimal model of metabolic oscillations in Bacillus subtilis biofilms.

Biofilms are composed of microorganisms attached to a solid surface or floating on top of a liquid surface. They pose challenges in the field of medicine but can also have useful applications in industry. Regulation of biofilm growth is complex and still largely elusive.

Combining evolution and self-organization to find natural Boolean representations in unconventional computational media.

Designing novel unconventional computing systems often requires the selection of the computational structure as well as choosing the right symbol encoding. Several approaches apply heuristic search and evolutionary algorithms to find both computational structure and symbol encoding, which is time consuming because they depend on each other. Here, we present a novel approach that combines evolution with self-organization, in particular we evolve the computational structure but let the symbol encoding emerge through self-organization.

Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis.

Influenza A virus is recognized today as one of the most challenging viruses that threatens both human and animal health worldwide. Understanding the control mechanisms of influenza infection and dynamics is crucial and could result in effective future treatment strategies. Many kinetic models based on differential equations have been developed in recent decades to capture viral dynamics within a host.

The Third Annual Meeting of the European Virus Bioinformatics Center.

The Third Annual Meeting of the European Virus Bioinformatics Center (EVBC) took place in Glasgow, United Kingdom, 28-29 March 2019. Virus bioinformatics has become central to virology research, and advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks, being successfully used to detect, control, and treat infections of humans and animals. This active field of research has attracted approximately 110 experts in virology and bioinformatics/computational biology from Europe and other parts of the world to attend the two-day meeting in Glasgow to increase scientific exchange between laboratory- and computer-based researchers.

Spatial Rule-Based Simulations: The SRSim Software.

SRSim combines rule-based reaction network models with spatial particle simulations allowing to simulate the dynamics of large molecular complexes changing according to a set of chemical reaction rules. As the rule can contain patterns of molecular complexes and specific states of certain binding sites, a combinatorially complex or even infinitely sized reaction network can be defined. Particles move in a three-dimensional space according to molecular dynamics implemented by LAMMPS, while the BioNetGen language is used to formulate reaction rules.

Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint.

The complexity of biological models makes methods for their analysis and understanding highly desirable. Here, we demonstrate the orchestration of various novel coarse-graining methods by applying them to the mitotic spindle assembly checkpoint. We begin with a detailed fine-grained spatial model in which individual molecules are simulated moving and reacting in a three-dimensional space.

SilentMutations (SIM): A tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs.

A single nucleotide change in the coding region can alter the amino acid sequence of a protein. In consequence, natural or artificial sequence changes in viral RNAs may have various effects not only on protein stability, function and structure but also on viral replication. In recent decades, several tools have been developed to predict the effect of mutations in structured RNAs such as viral genomes or non-coding RNAs.