PLMSearch: Protein language model powers accurate and fast sequence search for remote homology.

Homologous protein search is one of the most commonly used methods for protein annotation and analysis. Compared to structure search, detecting distant evolutionary relationships from sequences alone remains challenging. Here we propose PLMSearch (Protein Language Model), a homologous protein search method with only sequences as input.

Post-weaning social isolation modifies neonatal anoxia-induced changes in energy metabolism and growth of rats.

Neonatal oxygen deficiency in rats may disturb growth and long-term metabolic homeostasis. In order to facilitate metabolic evaluation, the subjects are usually housed individually. However, social isolation associated with individually housed conditions alters animal behavior, which may influence the experimental results.

Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity.

The human microbiome, comprising microorganisms residing within and on the human body, plays a crucial role in various physiological processes and has been linked to numerous diseases. To analyze microbiome data, it is essential to account for inherent heterogeneity and variability across samples. Normalization methods have been proposed to mitigate these variations and enhance comparability.

Application of Data-Driven computing to patient-specific prediction of the viscoelastic response of human brain under transcranial ultrasound stimulation.

We present a class of model-free Data-Driven solvers that effectively enable the utilization of in situ and in vivo imaging data directly in full-scale calculations of the mechanical response of the human brain to sonic and ultrasonic stimulation, entirely bypassing the need for analytical modeling or regression of the data. The well-posedness of the approach and its convergence with respect to data are proven analytically. We demonstrate the approach, including its ability to make detailed spatially resolved patient-specific predictions of wave patterns, using public-domain MRI images, MRE data and commercially available solid-mechanics software.

Prior exposure to pathogens augments host heterogeneity in susceptibility and has key epidemiological consequences.

Pathogen epidemics are key threats to human and wildlife health. Across systems, host protection from pathogens following initial exposure is often incomplete, resulting in recurrent epidemics through partially-immune hosts. Variation in population-level protection has important consequences for epidemic dynamics, but how acquired protection influences inter-individual heterogeneity in susceptibility and its epidemiological consequences remains understudied.

Insular and prelimbic cortices control behavioral accuracy and precision in a temporal decision-making task in rats.

The anterior insular cortex (AIC) comprises a region of sensory integration. It appears to detect salient events in order to guide goal-directed behavior, code tracking errors, and estimate the passage of time. Temporal processing in the AIC may be instantiated by the integration of representations of interoception.

Plasma membrane calcium ATPase powered by glycolysis is the main mechanism for calcium clearance in the hippocampal pyramidal neuron.

Aims: This study sought to elucidate the primary ATP-dependent mechanisms involved in clearing cytosolic Ca in neurons and determine the predominant ATP-generating pathway-glycolysis or tricarboxylic acid cycle/oxidative phosphorylation (TCA/OxPhos)-associated with these mechanisms in hippocampal pyramidal neurons.

Main Methods: Our investigation involved evaluating basal Ca levels and analyzing the kinetic characteristics of evoked neuronal Ca transients after selectively combined the inhibition/blockade of key ATP-dependent mechanisms with the suppression of either TCA/OxPhos or glycolytic ATP sources.

Key Findings: Our findings unveiled that the plasma membrane Ca ATPase (PMCA) serves as the principal ATP-dependent mechanism for clearance cytosolic Ca in hippocampal pyramidal neurons, both during rest and neuronal activity.

Optimizing health resource allocation for improving timely HIV diagnosis in China.

Introduction: The Joint United Nations Programme on HIV/AIDS (UNAIDS) updated the 95-95-95 targets for the HIV endgame in 2030. To achieve the first target in a timely manner, we investigate the optimized strategy of resource allocation to maximize timely HIV diagnosis in 14 populations in China.

Methods: We developed a mathematical model by integrating epidemiological, demographical and behavioural data from 12 high-risk and two general populations to evaluate the impact of various resource allocation strategies of HIV testing on HIV incidence in China.

TGF-β specifies T versus T17 cell fates in murine CD4 T cells through c-Maf.

T follicular helper (T) cells are essential for effective antibody responses, but deciphering the intrinsic wiring of mouse T cells has long been hampered by the lack of a reliable protocol for their generation in vitro. We report that transforming growth factor-β (TGF-β) induces robust expression of T hallmark molecules CXCR5 and Bcl6 in activated mouse CD4 T cells in vitro. TGF-β-induced mouse CXCR5 T cells are phenotypically, transcriptionally, and functionally similar to in vivo-generated T cells and provide critical help to B cells.

VSG-GAN: A high-fidelity image synthesis method with semantic manipulation in retinal fundus image.

In recent years, advancements in retinal image analysis, driven by machine learning and deep learning techniques, have enhanced disease detection and diagnosis through automated feature extraction. However, challenges persist, including limited data set diversity due to privacy concerns and imbalanced sample pairs, hindering effective model training. To address these issues, we introduce the vessel and style guided generative adversarial network (VSG-GAN), an innovative algorithm building upon the foundational concept of GAN.

A wall-time minimizing parallelization strategy for approximate Bayesian computation.

Approximate Bayesian Computation (ABC) is a widely applicable and popular approach to estimating unknown parameters of mechanistic models. As ABC analyses are computationally expensive, parallelization on high-performance infrastructure is often necessary. However, the existing parallelization strategies leave computing resources unused at times and thus do not optimally leverage them yet.

Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features.

Advances in cryo-electron microscopy (cryo-EM) imaging technologies have led to a rapidly increasing number of cryo-EM density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational heterogeneity analysis using global alignment and atomic model assembly through local alignment. Here, we present a fast and accurate global and local cryo-EM density map alignment method called CryoAlign, that leverages local density feature descriptors to capture spatial structure similarities.

Are vehicle tires major contributors to microplastic emissions into the China seas? A simple model perspective.

Microplastics pose a substantial threat to our environment. Given China's large population and rapid economic growth, it is urgent to estimate the annual emissions of microplastics into its marine environment. The microplastics show a significant variation in their source emissions as well as in their physical and chemical properties, leading to differences in their transport and fate in aquatic environments.

Distinct patterns of metabolic motor cortex activity for phantom and residual limb pain in people with amputations: A functional near-infrared spectroscopy study.

Background: Phantom pain limb (PLP) has gained more attention due to the large number of people with amputations around the world and growing knowledge of the pain process, although its mechanisms are not completely understood.

Objectives: The aim of this study was to understand, in patients with amputations, the association between PLP and residual limb pain (RLP), and the brain metabolic response in cortical motor circuits, using functional near-infrared spectroscopy (fNIRS).

Methods: Sixty participants were recruited from the rehabilitation program in São Paulo, Brazil.

Neurotoxicity of Pyrethroids in neurodegenerative diseases: From animals' models to humans' studies.

Neurodegenerative diseases are associated with diverse symptoms, both motor and mental. Genetic and environmental factors can trigger neurodegenerative diseases. Chemicals as pesticides are constantly used in agriculture and also domestically.

Activation of M1 muscarinic acetylcholine receptors by proline-rich oligopeptide 7a (

Background: The bioactive peptides derived from snake venoms of the Viperidae family species have been promising as therapeutic candidates for neuroprotection due to their ability to prevent neuronal cell loss, injury, and death. Therefore, this study aimed to evaluate the cytoprotective effects of a synthetic proline-rich oligopeptide 7a (PRO-7a;
Methods: Both cells were pre-treated for four hours with different concentrations of PRO-7a, submitted to HO-induced damage for 20 h, and then the oxidative stress markers were analyzed.

The Impact of Interdisciplinary, Gender and Geographic Distributions on the Citation Patterns of the Journal of Chemical Information and Modeling.

There has been a growing recognition of the need for diversity and inclusion in scientific fields. This trend is reflected in the Journal of Chemical Information and Modeling (JCIM), where there has been a gradual increase in the number of papers that embrace this diversity. In this viewpoint, we analyze the evolution of the profile of papers published in JCIM from 1996 to 2022 addressing three diversity criteria, namely interdisciplinarity, geographic and gender distributions, and their impact on citation patterns.

Adaptive exponential integrate-and-fire model with fractal extension.

The description of neuronal activity has been of great importance in neuroscience. In this field, mathematical models are useful to describe the electrophysical behavior of neurons. One successful model used for this purpose is the Adaptive Exponential Integrate-and-Fire (Adex), which is composed of two ordinary differential equations.

RNA threading with secondary structure and sequence profile.

Motivation: RNA threading aims to identify remote homologies for template-based modeling of RNA 3D structure. Existing RNA alignment methods primarily rely on secondary structure alignment. They are often time- and memory-consuming, limiting large-scale applications.

Impact of Transcranial Direct Current Stimulation in Pain, Fatigue, and Health Quality of Life of Patients with Idiopathic Inflammatory Myopathies: A Randomized, Double-Blind, Sham-Controlled Crossover Clinical Trial.

Objectives: To assess the effectiveness of transcranial direct current stimulation (tDCS) for pain, fatigue, physical function, and health-related quality of life in patients with idiopathic inflammatory myopathy (IIM).

Methods: This randomized, double-blind, sham-controlled, crossover clinical trial enrolled IIM patients with fatigue and pain who received tDCS (20 min, 2 mA) or sham stimulation for 10 daily sessions. Electrodes were placed according to the 10/20 EEG system.

Genomic prediction using machine learning: a comparison of the performance of regularized regression, ensemble, instance-based and deep learning methods on synthetic and empirical data.

Background: The accurate prediction of genomic breeding values is central to genomic selection in both plant and animal breeding studies. Genomic prediction involves the use of thousands of molecular markers spanning the entire genome and therefore requires methods able to efficiently handle high dimensional data. Not surprisingly, machine learning methods are becoming widely advocated for and used in genomic prediction studies.

Sequential activity of CA1 hippocampal cells constitutes a temporal memory map for associative learning in mice.

Sequential neural dynamics encoded by time cells play a crucial role in hippocampal function. However, the role of hippocampal sequential neural dynamics in associative learning is an open question. We used two-photon Ca imaging of dorsal CA1 (dCA1) neurons in the stratum pyramidale (SP) in head-fixed mice performing a go-no go associative learning task to investigate how odor valence is temporally encoded in this area of the brain.