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Новости за 05.08.2024

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Attentional selection and communication through coherence: Scope and limitations

Plos.org 
En

by Priscilla E. Greenwood, Lawrence M. Ward

Synchronous neural oscillations are strongly associated with a variety of perceptual, cognitive, and behavioural processes. It has been proposed that the role of the synchronous oscillations in these processes is to facilitate information transmission between brain areas, the ‘communication through coherence,’ or CTC hypothesis. The details of how this mechanism would work, however, and its causal status, are still unclear. Here we investigate computationally... Читать дальше...

Rhythmidia: A modern tool for circadian period analysis of filamentous fungi

Plos.org 
En

by Alex T. Keeley, Jeffrey M. Lotthammer, Jacqueline F. Pelham

Circadian rhythms are ubiquitous across the kingdoms of life and serve important roles in regulating physiology and behavior at many levels. These rhythms occur in ~24-hour cycles and are driven by a core molecular oscillator. Circadian timekeeping enables organisms to anticipate daily changes by timing their growth and internal processes. Neurospora crassa is a model organism with a long history in circadian biology, having conserved... Читать дальше...

Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning

Plos.org 
En

by The CRyPTIC consortium

There remains a clinical need for better approaches to rapid drug susceptibility testing in view of the increasing burden of multidrug resistant tuberculosis. Binary susceptibility phenotypes only capture changes in minimum inhibitory concentration when these cross the critical concentration, even though other changes may be clinically relevant. We developed a machine learning system to predict minimum inhibitory concentration from unassembled whole-genome sequencing data for 13 anti-tuberculosis drugs. Читать дальше...

COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms

Plos.org 
En

by Teemu J. Rintala, Vittorio Fortino

Recent research on multi-view clustering algorithms for complex disease subtyping often overlooks aspects like clustering stability and critical assessment of prognostic relevance. Furthermore, current frameworks do not allow for a comparison between data-driven and pathway-driven clustering, highlighting a significant gap in the methodology. We present the COPS R-package, tailored for robust evaluation of single and multi-omics clustering results. COPS features advanced methods... Читать дальше...

A quantitative description of light-limited cyanobacterial growth using flux balance analysis

Plos.org 
En

by Rune Höper, Daria Komkova, Tomáš Zavřel, Ralf Steuer

The metabolism of phototrophic cyanobacteria is an integral part of global biogeochemical cycles, and the capability of cyanobacteria to assimilate atmospheric CO2 into organic carbon has manifold potential applications for a sustainable biotechnology. To elucidate the properties of cyanobacterial metabolism and growth, computational reconstructions of genome-scale metabolic networks play an increasingly important role. Here, we present... Читать дальше...

Diffusion model predicts the geometry of actin cytoskeleton from cell morphology

Plos.org 
En

by Honghan Li, Shiyou Liu, Shinji Deguchi, Daiki Matsunaga

Cells exhibit various morphological characteristics due to their physiological activities, and changes in cell morphology are inherently accompanied by the assembly and disassembly of the actin cytoskeleton. Stress fibers are a prominent component of the actin-based intracellular structure and are highly involved in numerous physiological processes, e.g., mechanotransduction and maintenance of cell morphology. Although it is widely... Читать дальше...



A novel kinetic model to demonstrate the independent effects of ATP and ADP/Pi concentrations on sarcomere function

Plos.org 
En

by Andrew A. Schmidt, Alexander Y. Grosberg, Anna Grosberg

Understanding muscle contraction mechanisms is a standing challenge, and one of the approaches has been to create models of the sarcomere–the basic contractile unit of striated muscle. While these models have been successful in elucidating many aspects of muscle contraction, they fall short in explaining the energetics of functional phenomena, such as rigor, and in particular, their dependence on the concentrations of the biomolecules involved in the cross-bridge cycle. Читать дальше...

Upper bounds for integrated information

Plos.org 
En

by Alireza Zaeemzadeh, Giulio Tononi

Originally developed as a theory of consciousness, integrated information theory provides a mathematical framework to quantify the causal irreducibility of systems and subsets of units in the system. Specifically, mechanism integrated information quantifies how much of the causal powers of a subset of units in a state, also referred to as a mechanism, cannot be accounted for by its parts. If the causal powers of the mechanism can be fully explained by its parts... Читать дальше...

Reliable estimation of tree branch lengths using deep neural networks

Plos.org 
En

by Anton Suvorov, Daniel R. Schrider

A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the tree, which include extant taxa (external nodes) and their last common ancestors (internal nodes). During phylogenetic tree inference, the branch lengths are typically co-estimated along with other phylogenetic... Читать дальше...

An optimal normalization method for high sparse compositional microbiome data

Plos.org 
En

by Michael B. Sohn, Cynthia Monaco, Steven R. Gill

In many omics data, including microbiome sequencing data, we are only able to measure relative information. Various computational or statistical methods have been proposed to extract absolute (or biologically relevant) information from this relative information; however, these methods are under rather strong assumptions that may not be suitable for multigroup (more than two groups) and/or longitudinal outcome data. In this article, we first... Читать дальше...

Elephant Rumblings: Beane reminisces, praises Athletics Nation

Athletics Nation 
En

Brad Penner-USA TODAY Sports

MLB news roundup

Happy Monday, Athletics Nation!

The A’s lost their first series since July 11 yesterday as the Dodgers prevailed in a hard-fought third and decisive game. Their homestand continues today against a historically bad Chicago White Sox team that has lost 20 straight, thus providing Oakland a golden opportunity to right the ship and continue the winning ways they’ve exhibited since right before the All-Star Break.

Yesterday’s... Читать дальше...

Gabrial Arias carries Clippers offense in victory, Jervis Alfaro dominates in full-season pitching debut

Let's Go Tribe 
En

Cleveland Guardians minor league recap for Monday, Aug. 5, 2024

Columbus Clippers 4, Syracuse Mets 1

Box Score · Clippers improve to 54-52

Will Dion entered the 2024 season as one of the next men up with a potential to help Cleveland’s rotation at MLB. He has struggled mightily this season at Triple-A, but that wasn’t the case Sunday when he had by far his best start of the season.

Dion tossed six shutout frames on four hits with four strikeouts and just one walk allowed... Читать дальше...

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