BACKGROUND: Alignment of reads to a reference genome sequence is one of the key steps in the analysis of human whole-genome sequencing data obtained through Next-generation sequencing (NGS) technologies. The quality of the subsequent steps of the analysis, such as the results of clinical interpretation of genetic variants or the results of a genome-wide association study, depends on the correct identification of the position of the read as a result of its alignment. The amount of human NGS whole-genome sequencing data is constantly growing. There are a number of human genome sequencing projects worldwide that have resulted in the creation of large-scale databases of genetic variants of sequenced human genomes. Such information about known genetic variants can be used to improve the quality of alignment at the read alignment stage when analysing sequencing data obtained for a new individual, for example, by creating a genomic graph. While existing methods for aligning reads to a linear reference genome have high alignment speed, methods for aligning reads to a genomic graph have greater accuracy in variable regions of the genome. The development of a read alignment method that takes into account known genetic variants in the linear reference sequence index allows combining the advantages of both sets of methods.
RESULTS: In this paper, we present the minimap2_index_modifier tool, which enables the construction of a modified index of a reference genome using known single nucleotide variants and insertions/deletions (indels) specific to a given human population. The use of the modified minimap2 index improves variant calling quality without modifying the bioinformatics pipeline and without significant additional computational overhead. Using the PrecisionFDA Truth Challenge V2 benchmark data (for HG002 short-read data aligned to the GRCh38 linear reference (GCA_000001405.15) with parameters k = 27 and w = 14) it was demonstrated that the number of false negative genetic variants decreased by more than 9500, and the number of false positives decreased by more than 7000 when modifying the index with genetic variants from the Human Pangenome Reference Consortium.

Brugada Syndrome (BrS) is a primary electrical epicardial disease characterized by ST-segment elevation followed by a negative T-wave in the right precordial leads on the surface electrocardiogram (ECG), also known as the \'type 1\' ECG pattern. The risk stratification of asymptomatic individuals with spontaneous type 1 ECG pattern remains challenging. Clinical and electrocardiographic prognostic markers are known. As none of these predictors alone is highly reliable in terms of arrhythmic prognosis, several multi-factor risk scores have been proposed for this purpose. This article presents a new workflow for processing endocardial signals acquired with high-density RV electro-anatomical mapping (HDEAM) from BrS patients. The workflow, which relies solely on Matlab software, calculates various electrical parameters and creates multi-parametric maps of the right ventricle. The workflow, but it has already been employed in several research studies involving patients carried out by our group, showing its potential positive impact in clinical studies. Here, we will provide a technical description of its functionalities, along with the results obtained on a BrS patient who underwent an endocardial HDEAM.

In today\'s digital landscape, organizations face significant challenges, including sensitive data leaks and the proliferation of hate speech, both of which can lead to severe consequences such as financial losses, reputational damage, and psychological impacts on employees. This work considers a comprehensive solution using a microservices architecture to monitor computer usage within organizations effectively. The approach incorporates spyware techniques to capture data from employee computers and a web application for alert management. The system detects data leaks, suspicious behaviors, and hate speech through efficient data capture and predictive modeling. Therefore, this paper presents a comparative performance analysis between Spring Boot and Quarkus, focusing on objective metrics and quantitative statistics. By utilizing recognized tools and benchmarks in the computer science community, the study provides an in-depth understanding of the performance differences between these two platforms. The implementation of Quarkus over Spring Boot demonstrated substantial improvements: memory usage was reduced by up to 80% and CPU usage by 95%, and system uptime decreased by 119%. This solution offers a robust framework for enhancing organizational security and mitigating potential threats through proactive monitoring and predictive analysis while also guiding developers and software architects in making informed technological choices.

Background: Previous studies have assessed the capability of PRAAT for acoustic voice analysis in total laryngectomized (TL) patients, although this software was designed for acoustic analysis of laryngeal voice. Recently, we have witnessed the development of specialized acoustic analysis software, Tracheoesophageal Voice Analysis (TEVA). This study aims to compare the analysis with both programs in TL patients. Methods: Observational analytical study of 34 TL patients where a quantitative acoustic analysis was performed for stable phonation with vowels [a] and [i] as well as spectrographic characterization using the TEVA and PRAAT software. Results: The Voice Handicap Index (VHI-10) showed a mean score of 11.29 ± 11.16 points, categorized as a moderate handicap. TEVA analysis found lower values in the fundamental frequency vs. PRAAT (p < 0.05). A significant increase in shimmer values was observed with TEVA (>20%). No significant differences were found between spectrographic analysis with TEVA and PRAAT. Conclusions: Tracheoesophageal speech is an alaryngeal voice, characterized by a higher degree of irregularity and noise compared to laryngeal speech. Consequently, it necessitates a more tailored approach using objective assessment tools adapted to these distinct features, like TEVA, that are designed specifically for TL patients. This study provides statistical evidence supporting its reliability and suitability for the evaluation and tracking of tracheoesophageal speakers.

B-cell epitope prediction is key to developing peptide-based vaccines and immunodiagnostics along with antibodies for prophylactic, therapeutic and/or diagnostic use. This entails estimating paratope binding affinity for variable-length peptidic sequences subject to constraints on both paratope accessibility and antigen conformational flexibility, as described herein for the HAPTIC2/HEPTAD User Toolkit (HUT). HUT comprises the Heuristic Affinity Prediction Tool for Immune Complexes 2 (HAPTIC2), the HAPTIC2-like Epitope Prediction Tool for Antigen with Disulfide (HEPTAD) and the HAPTIC2/HEPTAD Input Preprocessor (HIP). HIP enables tagging of residues (e.g., in hydrophobic blobs, ordered regions and glycosylation motifs) for exclusion from downstream analyses by HAPTIC2 and HEPTAD. HAPTIC2 estimates paratope binding affinity for disulfide-free disordered peptidic antigens (by analogy between flexible-ligand docking and protein folding), from terms attributed to compaction (in view of sequence length, charge and temperature-dependent polyproline-II helical propensity), collapse (disfavored by residue bulkiness) and contact (with glycine and proline regarded as polar residues that hydrogen bond with paratopes). HEPTAD analyzes antigen sequences that each contain two cysteine residues for which the impact of disulfide pairing is estimated as a correction to the free-energy penalty of compaction. All of HUT is freely accessible online ( https://freeshell.de/~badong/hut.htm ).

This manuscript describes the development of a resource module that is part of a learning platform named \"NIGMS Sandbox for Cloud-based Learning\" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on RNA sequencing (RNAseq) data analysis in an interactive format that uses appropriate cloud resources for data access and analyses. Biomedical research is increasingly data-driven, and dependent upon data management and analysis methods that facilitate rigorous, robust, and reproducible research. Cloud-based computing resources provide opportunities to broaden the application of bioinformatics and data science in research. Two obstacles for researchers, particularly those at small institutions, are: (i) access to bioinformatics analysis environments tailored to their research; and (ii) training in how to use Cloud-based computing resources. We developed five reusable tutorials for bulk RNAseq data analysis to address these obstacles. Using Jupyter notebooks run on the Google Cloud Platform, the tutorials guide the user through a workflow featuring an RNAseq dataset from a study of prophage altered drug resistance in Mycobacterium chelonae. The first tutorial uses a subset of the data so users can learn analysis steps rapidly, and the second uses the entire dataset. Next, a tutorial demonstrates how to analyze the read count data to generate lists of differentially expressed genes using R/DESeq2. Additional tutorials generate read counts using the Snakemake workflow manager and Nextflow with Google Batch. All tutorials are open-source and can be used as templates for other analysis.

The rapid advances in Generative AI tools have produced both excitement and worry about how AI will impact academic writing. However, little is known about what norms are emerging around AI use in manuscript preparation or how these norms might be enforced. We address both gaps in the literature by conducting a survey of 271 academics about whether it is necessary to report ChatGPT use in manuscript preparation and by running GPT-modified abstracts from 2,716 published papers through a leading AI detection software to see if these detectors can detect different AI uses in manuscript preparation. We find that most academics do not think that using ChatGPT to fix grammar needs to be reported, but detection software did not always draw this distinction, as abstracts for which GPT was used to fix grammar were often flagged as having a high chance of being written by AI. We also find disagreements among academics on whether more substantial use of ChatGPT to rewrite text needs to be reported, and these differences were related to perceptions of ethics, academic role, and English language background. Finally, we found little difference in their perceptions about reporting ChatGPT and research assistant help, but significant differences in reporting perceptions between these sources of assistance and paid proofreading and other AI assistant tools (Grammarly and Word). Our results suggest that there might be challenges in getting authors to report AI use in manuscript preparation because (i) there is not uniform agreement about what uses of AI should be reported and (ii) journals might have trouble enforcing nuanced reporting requirements using AI detection tools.

SignalP ( https://services.healthtech.dtu.dk/services/SignalP-6.0/ ) is a very popular prediction method for signal peptides, the intrinsic signals that make proteins secretory. The SignalP web server has existed since 1995 and is now in its sixth major version. In this historical account, we (three authors who have taken part in the entire journey plus the first author of the latest version) describe the differences between the versions and discuss the various decisions taken along the way.

Carbohydrates are chemically and structurally diverse, composed of a wide array of monosaccharides, stereochemical linkages, substituent groups, and intermolecular associations with other biological molecules. A large repertoire of carbohydrate-active enzymes (CAZymes) and enzymatic activities are required to form, dismantle, and metabolize these complex molecules. The software SACCHARIS (Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity) provides a rapid, easy-to-use pipeline for the prediction of potential CAZyme function in new datasets. We have updated SACCHARIS to (i) simplify its installation by re-writing in Python and packaging for Conda; (ii) enhance its usability through a new (optional) interactive GUI; and (iii) enable semi-automated annotation of phylogenetic tree output via a new R package or the commonly-used webserver iTOL. Significantly, SACCHARIS v2 has been developed with high-throughput omics in mind, with pipeline automation geared toward complex (meta)genome and (meta)transcriptome datasets to reveal the total CAZyme content (\"CAZome\") of an organism or community. Here, we outline the development and use of SACCHARIS v2 to discover and annotate CAZymes and provide insight into complex carbohydrate metabolisms in individual organisms and communities.

The Gene Ontology (GO) project describes the functions of the gene products of organisms from all kingdoms of life in a standardized way, enabling powerful analyses of experiments involving genome-wide analysis. The scientific literature is used to convert experimental results into GO annotations that systematically classify gene products\' functions. However, to address the fact that only a minor fraction of all genes has been characterized experimentally, multiple predictive methods to assign GO annotations have been developed since the inception of GO. Sequence homologies between novel genes and genes with known functions help to approximate the roles of these non-characterized genes. Here we describe the main sequence homology methods to produce annotations: pairwise comparison (BLAST), protein profile models (InterPro), and phylogenetic-based annotation (PAINT). Some of these methods can be implemented with genome analysis pipelines (BLAST and InterPro2GO), while PAINT is curated by the GO consortium.