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.

Sleep-Energy: An Energy Optimization Method to Sleep Stage Scoring.

Sleep is essential for physical and mental health. Polysomnography (PSG) procedures are labour-intensive and time-consuming, making diagnosing sleep disorders difficult. Automatic sleep staging using Machine Learning (ML) - based methods has been studied extensively, but frequently provides noisier predictions incompatible with typical manually annotated hypnograms.

Time for What? Dissociating Explicit Timing Tasks through Electrophysiological Signatures.

Estimating durations between hundreds of milliseconds and seconds is essential for several daily tasks. Explicit timing tasks, which require participants to estimate durations to make a comparison (time for perception) or to reproduce them (time for action), are often used to investigate psychological and neural timing mechanisms. Recent studies have proposed that mechanisms may depend on specific task requirements.

The Characteristics and Laboratory Findings of SARS-CoV-2 Infected Patients during the First Three COVID-19 Waves in Portugal-A Retrospective Single-Center Study.

: Given the wide spectrum of clinical and laboratory manifestations of the coronavirus disease 2019 (COVID-19), it is imperative to identify potential contributing factors to patients' outcomes. However, a limited number of studies have assessed how the different waves affected the progression of the disease, more so in Portugal. Therefore, our main purpose was to study the clinical and laboratory patterns of COVID-19 in an unvaccinated population admitted to the intensive care unit, identifying characteristics associated with death, in each of the first three waves of the pandemic.

Optimising HIV pre-exposure prophylaxis and testing strategies in men who have sex with men in Australia, Thailand, and China: a modelling study and cost-effectiveness analysis.

Background: Men who have sex with men (MSM) in the Asia-Pacific region have a disproportionately high burden of HIV infection compared with the general population. Although pre-exposure prophylaxis (PrEP) for HIV is highly effective at preventing new HIV infections, the cost-effectiveness of PrEP for MSM in different countries in the Asia-Pacific region with varying PrEP coverage and HIV testing frequencies remains unstudied. We aimed to analyse the economic and health benefits of long-acting injectable cabotegravir (CAB-LA) compared with oral PrEP in high-income countries and low-income and middle-income countries within the Asia-Pacific region.

Propagation of random excitations in the polar representation of strongly nonlinear four-wave systems of turbulence.

The present work is concerned with the uncertainty propagation of the wave turbulent system. In particular, we study the temporal development and long-term behavior of the probability with respect to the amplitude and phase of complex-valued waves constituting the generic four-wave system of turbulence. Our approach to approximating the target distribution function is via the three steps: (i) to grasp the physical process described by the true turbulence model as random process, (ii) to determine the stochastic differential equation whose solution exhibits statistically similar behavior with the underlying turbulent signal, and (iii) to solve the corresponding Kolmogorov forward equation.

Coupled chemical reactions: Effects of electric field, diffusion, and boundary control.

Chemical reactions involve the movement of charges, and this paper presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical thermodynamics principles. It encompasses both electrostatics and chemical reactions within consistently defined energetic and dissipative functionals.

scQA: A dual-perspective cell type identification model for single cell transcriptome data.

Single-cell RNA sequencing technologies have been pivotal in advancing the development of algorithms for clustering heterogeneous cell populations. Existing methods for utilizing scRNA-seq data to identify cell types tend to neglect the beneficial impact of dropout events and perform clustering focusing solely on quantitative perspective. Here, we introduce a novel method named scQA, notable for its ability to concurrently identify cell types and cell type-specific key genes from both qualitative and quantitative perspectives.

Structural characterization of the antimicrobial peptides myxinidin and WMR in bacterial membrane mimetic micelles and bicelles.

Antimicrobial peptides are a promising class of potential antibiotics that interact selectively with negatively charged lipid bilayers. This paper presents the structural characterization of the antimicrobial peptides myxinidin and WMR associated with bacterial membrane mimetic micelles and bicelles by NMR, CD spectroscopy, and molecular dynamics simulations. Both peptides adopt a different conformation in the lipidic environment than in aqueous solution.

Relationship between Physicochemical and Cooking Quality Parameters with Estimated Glycaemic Index of Rice Varieties.

Rice is a significant staple food in the basic diet of the global population that is considered to have a high glycaemic index. The study of the physical and chemical parameters in rice that are related to the starch digestion process, which allows us to quickly predict the glycaemic index of varieties, is a major challenge, particularly in the classification and selection process. In this context, and with the goal of establishing a relationship between physicochemical properties and starch digestibility rates, thus shedding light on the connections between quality indicators and their glycaemic impact, we evaluated various commercial rice types based on their basic chemical composition, physicochemical properties, cooking parameters, and the correlations with digestibility rates.

Pharmacovigilance teaching and learning: a mixed cross-sectional analysis of the Portuguese public higher education system.

Pharmacovigilance stands out for its importance in obtaining existing knowledge about medicine and patient safety and should be recognized as a continuous line of study. It constitutes a highly relevant component in the activities of health professionals, with spontaneous notification of suspected adverse drug reactions being its main emphasis. The underreporting that persists can be overcome through continuous professional development programs, reinforcing theoretical and practical knowledge in the curricular plans of health courses.

Postural control of prolonged standing in people with Parkinson's disease.

People with Parkinson's disease (pwPD) have reduced adaptability to postural control during prolonged standing compared to neurologically healthy individuals (control). Objective. The study aimed to characterize postural changes during prolonged standing and their effect on postural control in pwPD compared to control.

Correction to: Identification of TAZ as the essential molecular switch in orchestrating SCLC phenotypic transition and metastasis.

[This corrects the article DOI: 10.1093/nsr/nwab232.].

On committor functions in milestoning.

As an optimal one-dimensional reaction coordinate, the committor function not only describes the probability of a trajectory initiated at a phase space point first reaching the product state before reaching the reactant state but also preserves the kinetics when utilized to run a reduced dynamics model. However, calculating the committor function in high-dimensional systems poses significant challenges. In this paper, within the framework of milestoning, exact expressions for committor functions at two levels of coarse graining are given, including committor functions of phase space point to point (CFPP) and milestone to milestone (CFMM).

Phase synchronization in a sparse network of randomly connected neurons under the effect of Poissonian spike inputs.

This article investigates the emergence of phase synchronization in a network of randomly connected neurons by chemical synapses. The study uses the classic Hodgkin-Huxley model to simulate the neuronal dynamics under the action of a train of Poissonian spikes. In such a scenario, we observed the emergence of irregular spikes for a specific range of conductances and also that the phase synchronization of the neurons is reached when the external current is strong enough to induce spiking activity but without overcoming the coupling current.

Increased Delta and Theta Power Density in Sickle Cell Disease Individuals with Chronic Pain Secondary to Hip Osteonecrosis: A Resting-State Eeg Study.

Purpose: Identify the presence of a dysfunctional electroencephalographic (EEG) pattern in individuals with sickle cell disease (SCD) and hip osteonecrosis, and assess its potential associations with depression, anxiety, pain severity, and serum levels of brain-derived neurotrophic factor (BDNF).

Methods: In this cross-sectional investigation, 24 SCD patients with hip osteonecrosis and chronic pain were matched by age and sex with 19 healthy controls. Resting-state EEG data were recorded using 32 electrodes for both groups.

Modeling early treatment response in AML from cell-free tumor DNA.

Monitoring disease response after intensive chemotherapy for acute myeloid leukemia (AML) currently requires invasive bone marrow biopsies, imposing a significant burden on patients. In contrast, cell-free tumor DNA (ctDNA) in peripheral blood, carrying tumor-specific mutations, offers a less-invasive assessment of residual disease. However, the relationship between ctDNA levels and bone marrow blast kinetics remains unclear.