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Background: While sex-based differences in various health scenarios have been thoroughly acknowledged in the literature, we lack sufficient tools and methods that allow for an in-depth analysis of sex as a variable in biomedical research. To fill this knowledge gap, we created MetaFun as an easy-to-use web-based tool to meta-analyze multiple transcriptomic datasets with a sex-based perspective to gain major statistical power and biological soundness. Description: MetaFun is a complete suite that allows the analysis of transcriptomics data and the exploration of the results at all levels, performing single-dataset exploratory analysis, differential gene expression, gene set functional enrichment, and finally, combining results in a functional meta-analysis. Which biological processes, molecular functions or cellular components are altered in a common pattern in different transcriptomic studies when comparing male and female patients? This and other biological questions of interest can be answered with the use of MetaFun. This tool is available at https://bioinfo.cipf.es/metafun while additional help can be found at https://gitlab.com/ubb-cipf/metafunweb/-/wikis/Summary. Conclusions: Overall, Metafun is the first open-access web-based tool to identify consensus biological functions across multiple transcriptomic datasets, helping to elucidate sex differences in numerous diseases. Its use will facilitate the generation of novel biological knowledge that can be used in the research and application of Personalized Medicine considering the sex of patients. [ABSTRACT FROM AUTHOR]

Abstract Background While sex-based differences in various health scenarios have been thoroughly acknowledged in the literature, we lack sufficient tools and methods that allow for an in-depth analysis of sex as a variable in biomedical research. To fill this knowledge gap, we created MetaFun as an easy-to-use web-based tool to meta-analyze multiple transcriptomic datasets with a sex-based perspective to gain major statistical power and biological soundness. Description MetaFun is a complete suite that allows the analysis of transcriptomics data and the exploration of the results at all levels, performing single-dataset exploratory analysis, differential gene expression, gene set functional enrichment, and finally, combining results in a functional meta-analysis. Which biological processes, molecular functions or cellular components are altered in a common pattern in different transcriptomic studies when comparing male and female patients? This and other biological questions of interest can be answered with the use of MetaFun. This tool is available at https://bioinfo.cipf.es/metafun while additional help can be found at https://gitlab.com/ubb-cipf/metafunweb/-/wikis/Summary . Conclusions Overall, Metafun is the first open-access web-based tool to identify consensus biological functions across multiple transcriptomic datasets, helping to elucidate sex differences in numerous diseases. Its use will facilitate the generation of novel biological knowledge that can be used in the research and application of Personalized Medicine considering the sex of patients.

Abstract Background Reverse transcription quantitative PCR (RT-qPCR) with intercalating dyes is one of the main techniques to assess gene expression levels used in basic and applied research as well as in diagnostics. However, primer design for RT-qPCR can be complex due to the high demands on primer quality. Primers are best placed on exon junctions, should avoid polymorphic regions, be specific to the target transcripts and also prevent genomic amplification accurately, among others. Current software tools manage to meet all the necessary criteria only insufficiently. Here, we present ExonSurfer, a novel, user-friendly web-tool for qPCR primer design. Results ExonSurfer combines the different steps of the primer design process, encompassing target selection, specificity and self-complementarity assessment, and the avoidance of issues arising from polymorphisms. Amplification of potentially contaminating genomic DNA is avoided by designing primers on exon-exon junctions, moreover, a genomic alignment is performed to filter the primers accordingly and inform the user of any predicted interaction. In order to test the whole performance of the application, we designed primer pairs for 26 targets and checked both primer efficiency, amplicon melting temperature and length and confirmed the targeted amplicon by Sanger sequencing. Most of the tested primers accurately and selectively amplified the corresponding targets. Conclusion ExonSurfer offers a comprehensive end-to-end primer design, guaranteeing transcript-specific amplification. The user interface is intuitive, providing essential specificity and amplicon details. The tool can also be used by command line and the source code is available. Overall, we expect ExonSurfer to facilitate RT-qPCR set-up for researchers in many fields.

Chimeric antigen receptor (CAR) therapy has emerged as a ground-breaking advancement in cancer treatment, harnessing the power of engineered human immune cells to target and eliminate cancer cells. The escalating interest and investment in CAR therapy in recent years emphasize its profound significance in clinical research, positioning it as a rapidly expanding frontier in the field of personalized cancer therapies. A crucial step in CAR therapy design is choosing the right target as it determines the therapy's effectiveness, safety and specificity against cancer cells, while sparing healthy tissues. Herein, we propose a suite of tools for the identification and analysis of potential CAR targets leveraging expression data from The Cancer Genome Atlas and Genotype-Tissue Expression Project, which are implemented in CARTAR website. These tools focus on pinpointing tumor-associated antigens, ensuring target selectivity and assessing specificity to avoid off-tumor toxicities and can be used to rationally designing dual CARs. In addition, candidate target expression can be explored in cancer cell lines using the expression data for the Cancer Cell Line Encyclopedia. To our best knowledge, CARTAR is the first website dedicated to the systematic search of suitable candidate targets for CAR therapy. CARTAR is publicly accessible at https://gmxenomica.github.io/CARTAR/. [ABSTRACT FROM AUTHOR]

Abstract Recent studies have increasingly revealed the connection between metabolic reprogramming and tumor progression. However, the specific impact of metabolic reprogramming on inter-patient heterogeneity and prognosis in lung adenocarcinoma (LUAD) still requires further exploration. Here, we introduced a cellular hierarchy framework according to a malignant and metabolic gene set, named malignant & metabolism reprogramming (MMR), to reanalyze 178,739 single-cell reference profiles. Furthermore, we proposed a three-stage ensemble learning pipeline, aided by genetic algorithm (GA), for survival prediction across 9 LUAD cohorts (n = 2066). Throughout the pipeline of developing the three stage-MMR (3 S-MMR) score, double training sets were implemented to avoid over-fitting; the gene-pairing method was utilized to remove batch effect; GA was harnessed to pinpoint the optimal basic learner combination. The novel 3 S-MMR score reflects various aspects of LUAD biology, provides new insights into precision medicine for patients, and may serve as a generalizable predictor of prognosis and immunotherapy response. To facilitate the clinical adoption of the 3 S-MMR score, we developed an easy-to-use web tool for risk scoring as well as therapy stratification in LUAD patients. In summary, we have proposed and validated an ensemble learning model pipeline within the framework of metabolic reprogramming, offering potential insights for LUAD treatment and an effective approach for developing prognostic models for other diseases.

Abstract Background Oral inflammatory diseases are localized infectious diseases primarily caused by oral pathogens with the potential for serious systemic complications. However, publicly available datasets for these diseases are underutilized. To address this issue, a web tool called OralExplorer was developed. This tool integrates the available data and provides comprehensive online bioinformatic analysis. Methods Human oral inflammatory disease-related datasets were obtained from the GEO database and normalized using a standardized process. Transcriptome data were then subjected to differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis, and visualization. The single-cell sequencing data was visualized as cluster plot, feature plot, and heatmaps. The web platform was primarily built using Shiny. The biomarkers identified in OralExplorer were validated using local clinical samples through qPCR and IHC. Results A total of 35 human oral inflammatory disease-related datasets, covering 6 main disease types and 901 samples, were included in the study to identify potential molecular signatures of the mechanisms of oral diseases. OralExplorer consists of 5 main analysis modules (differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis and single-cell analysis), with multiple visualization options. The platform offers a simple and intuitive interface, high-quality images for visualization, and detailed analysis results tables for easy access by users. Six markers (IL1β, SRGN, CXCR1, FGR, ARHGEF2, and PTAFR) were identified by OralExplorer. qPCR- and IHC-based experimental validation showed significantly higher levels of these genes in the periodontitis group. Conclusions OralExplorer is a comprehensive analytical platform for oral inflammatory diseases. It allows users to interactively explore the molecular mechanisms underlying the action and regression of these diseases. It also aids dental researchers in unlocking the potential value of transcriptomics data related to oral diseases. OralExplorer can be accessed at https://smuonco.shinyapps.io/OralExplorer/ (Alternate URL: http://robinl-lab.com/OralExplorer ).

Recent studies have increasingly revealed the connection between metabolic reprogramming and tumor progression. However, the specific impact of metabolic reprogramming on inter-patient heterogeneity and prognosis in lung adenocarcinoma (LUAD) still requires further exploration. Here, we introduced a cellular hierarchy framework according to a malignant and metabolic gene set, named malignant & metabolism reprogramming (MMR), to reanalyze 178,739 single-cell reference profiles. Furthermore, we proposed a three-stage ensemble learning pipeline, aided by genetic algorithm (GA), for survival prediction across 9 LUAD cohorts (n = 2066). Throughout the pipeline of developing the three stage-MMR (3 S-MMR) score, double training sets were implemented to avoid over-fitting; the gene-pairing method was utilized to remove batch effect; GA was harnessed to pinpoint the optimal basic learner combination. The novel 3 S-MMR score reflects various aspects of LUAD biology, provides new insights into precision medicine for patients, and may serve as a generalizable predictor of prognosis and immunotherapy response. To facilitate the clinical adoption of the 3 S-MMR score, we developed an easy-to-use web tool for risk scoring as well as therapy stratification in LUAD patients. In summary, we have proposed and validated an ensemble learning model pipeline within the framework of metabolic reprogramming, offering potential insights for LUAD treatment and an effective approach for developing prognostic models for other diseases. [ABSTRACT FROM AUTHOR]

Embedding environmental concepts in the minds of young students within a traditional classroom setting poses challenges due to the abstract nature of these concepts and the temporal dilemma associated with environmental change, as students are unable to observe the immediate consequences of their actions directly. To address this, innovative instructional methods incorporating technology were explored. Based on socio-constructivism, a quasi-experimental study employed a web tool to teach environmental concepts. The experimental group utilized the 7E constructivist learning model, while the control group followed traditional instruction. The results of the data analysis indicated a statistically significant disparity in students' motivation levels to learn about environmental challenges, with active learning strategies receiving the highest scores due to engaging students in online discussions and collaborative tasks. The active and constructive learning techniques encouraged collaboration and cooperation and also embraced the students' autonomy. Furthermore, students felt motivated to act and solve community issues, fostering civic responsibility for long-term growth and a sustainable future. The learning performance in the posttest significantly increased for the experimental group. These findings suggest the importance of integrating technology and active learning approaches to enhance environmental education among young students. [ABSTRACT FROM AUTHOR]

Background: Oral inflammatory diseases are localized infectious diseases primarily caused by oral pathogens with the potential for serious systemic complications. However, publicly available datasets for these diseases are underutilized. To address this issue, a web tool called OralExplorer was developed. This tool integrates the available data and provides comprehensive online bioinformatic analysis. Methods: Human oral inflammatory disease-related datasets were obtained from the GEO database and normalized using a standardized process. Transcriptome data were then subjected to differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis, and visualization. The single-cell sequencing data was visualized as cluster plot, feature plot, and heatmaps. The web platform was primarily built using Shiny. The biomarkers identified in OralExplorer were validated using local clinical samples through qPCR and IHC. Results: A total of 35 human oral inflammatory disease-related datasets, covering 6 main disease types and 901 samples, were included in the study to identify potential molecular signatures of the mechanisms of oral diseases. OralExplorer consists of 5 main analysis modules (differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis and single-cell analysis), with multiple visualization options. The platform offers a simple and intuitive interface, high-quality images for visualization, and detailed analysis results tables for easy access by users. Six markers (IL1β, SRGN, CXCR1, FGR, ARHGEF2, and PTAFR) were identified by OralExplorer. qPCR- and IHC-based experimental validation showed significantly higher levels of these genes in the periodontitis group. Conclusions: OralExplorer is a comprehensive analytical platform for oral inflammatory diseases. It allows users to interactively explore the molecular mechanisms underlying the action and regression of these diseases. It also aids dental researchers in unlocking the potential value of transcriptomics data related to oral diseases. OralExplorer can be accessed at https://smuonco.shinyapps.io/OralExplorer/ (Alternate URL: http://robinl-lab.com/OralExplorer). [ABSTRACT FROM AUTHOR]

Decision support systems (DSSs) enable the optimisation of pesticide application timing to increase pesticide efficacy and thus reduce pesticide use without compromising yield quality and quantity. Limited access to information about available DSSs for use in integrated pest management (IPM) is a major barrier to the uptake of DSSs for IPM across Europe. To overcome this barrier, a typology for DSSs for IPM in Europe was developed, introducing a systematic approach to describe the ever-growing number of DSSs for IPM. The developed IPM-DSS typology was implemented in the free web tool "IPM Adviser", where currently 79 IPM DSSs are described with over 50 attributes describing their structural and performance characteristics. The information about IPM DSSs, which was previously scattered on different websites and difficult to compare, is now standardised and presented in a uniform way, so that it is possible to compare different IPM DSSs on the basis of all the attributes described. The presented IPM-DSS typology implemented in the web tool IPM Adviser facilitates the dissemination and uptake of DSSs for IPM and thus contributes to the achievement of the EU targets for the sustainable use of pesticides. [ABSTRACT FROM AUTHOR]

One challenge in creating commercial solutions with supervised deep learning is acquiring large, customized labeled datasets. These datasets must often fit within commercial industries’ production times and budgets. There is still a need for target data that allows the model to learn specific characteristics of the target domain. The construction of customized datasets is relevant in imaging waste identification to improve the accuracy and efficiency of models, allowing adaptation to specific conditions. To address this challenge, we propose the EcoMind open-source tool. This tool facilitates waste labeling from user-provided images and empowers local dataset creation and collaborative building with users.

The study has as its original database the decarbonization process initiated in Mexico by the National Commission for the Efficient Use of Energy (CONUEE) as part of its "Savings Program of Electric Power in Buildings of the Federal Public Administration" (PAEIAPF) of 1999. The primary purpose of PAEIAPF was to reduce the levels of electric power consumption in Federal Government buildings. The program has operated for 20 years; however, its scope only reaches operational carbon. Since 90% of existing buildings will be in use by 2050, the Retrofit Models will be the base to determine solutions for a more resilient living environment that fortifies and extends the grid's capacity and meets climate change mitigation targets. Secondly, significant socioeconomic and profound environmental impacts are not calculated explicitly in existing tools and are often referred to as "secondary" or Non-Energy Benefits (NEB). "The goal is to give them a measurement value to be considered in the decision-making calculus. It is assumed that soon; such factors will enter the general climate change economy, not unlike carbon in the past decade." In this context, the proposed research aims to develop a value-based framework that will support a Building Stock Model and subsequent Retrofit Models, documented in a web-tool platform. The framework has three main steps: A) Building Stock Model: Mapping of selected buildings of the program PAEIAPF in a GIS system. Documentation of the baseline energy consumption and embodied CO2-eq of the existing building. B) Retrofit Models: Involving a Whole Life Cycle Assessment (WLCA) and Non-Energy Benefits (resilience coefficient, health, productivity). C) Web Tool Platform: Application and toolset that allows for consistent documentation, environmental impact evaluation of existing building stock, and solution design in identifying energy reduction concepts. [ABSTRACT FROM AUTHOR]

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Simple Summary: Neurofibromatosis 1 (NF1) is a genetic disorder that predisposes patients to developing nerve sheath tumors that are difficult to treat. There is currently just one drug approved for the treatment of NF1-related inoperable plexiform neurofibromas (for a limited patient population), highlighting the need for further drug discovery in this field. High-throughput screening data are used to guide drug development, but identifying and selecting promising targets can be complex. The aim of our study is to improve the value of high-throughput screening data by combining potency and effectiveness into single-value indices (S, ΔS, and ΔS mean), which are used to assess and rank drug sensitivity and drug resistance in cells exposed to potential therapeutic drugs. Our approach with S indices was applied to cell lines derived from plexiform neurofibromas of patients with NF1 gene mutations. The use of S indices provides valuable additional and independent information for discriminating among candidate compounds for follow-up pre-clinical evaluations. Background: Neurofibromatosis type 1 (NF1) is a genetic disorder characterized by heterozygous germline NF1 gene mutations that predispose patients to developing plexiform neurofibromas, which are benign but often disfiguring tumors of the peripheral nerve sheath induced by loss of heterozygosity at the NF1 locus. These can progress to malignant peripheral nerve sheath tumors (MPNSTs). There are no approved drug treatments for adults with NF1-related inoperable plexiform neurofibromas, and only one drug (selumetinib), which is an FDA-approved targeted therapy for the treatment of symptomatic pediatric plexiform neurofibromas, highlighting the need for additional drug screening and development. In high-throughput screening, the effectiveness of drugs against cell lines is often assessed by measuring in vitro potency (AC50) or the area under the curve (AUC). However, the variability of dose–response curves across drugs and cell lines and the frequency of partial effectiveness suggest that these measures alone fail to provide a full picture of overall efficacy. Methods: Using concentration–response data, we combined response effectiveness (EFF) and potency (AC50) into (a) a score characterizing the effect of a compound on a single cell line, S = log[EFF/AC50], and (b) a relative score, ΔS, characterizing the relative difference between a reference (e.g., non-tumor) and test (tumor) cell line. ΔS was applied to data from high-throughput screening (HTS) of a drug panel tested on NF1−/− tumor cells, using immortalized non-tumor NF1+/− cells as a reference. Results: We identified drugs with sensitivity, targeting expected pathways, such as MAPK-ERK and PI3K-AKT, as well as serotonin-related targets, among others. The ΔS technique used here, in tandem with a supplemental ΔS web tool, simplifies HTS analysis and may provide a springboard for further investigations into drug response in NF1-related cancers. The tool may also prove useful for drug development in a variety of other cancers. [ABSTRACT FROM AUTHOR]

Cracks indicates the real time deformity in concrete structures. It is characterized as discontinuity in terms of shape and size of the concrete structures. To ensure the structural health and safety, crack detection is an important task. The traditional methods of crack detection include visual introspection, ultrasonic and hand-held testing of crack. These methods require a high human intervention along with an experienced and skilled inspector. Moreover, these methods are subjective and time-consuming process which fails to identify the crack of the complex concrete structures properly. To overcome these issues, a GrabCut with improved Sobel has been proposed for automatic crack detection from the concrete structures. The proposed method works as a two-step model where cracks regions are segmented in the first step and a precise crack assessment is performed in the second step. Furthermore, to improve the efficacy of Sobel, the mask is modified with the aid of local variance of the image instead of using conventional mask of the filter. For the experimentation study, the images of self-prepared concrete sample have been acquired. The effectiveness of the proposed method has been compared with respect to various pre-existing methods like Sobel, Prewitt, Robert, LoG, Zero Cross, and Canny. The comparative qualitative result exhibits that the proposed method surpasses the outcomes of the other pre-existing methods. Additionally, for easy implementation and application point of view a web tool of the proposed method has been developed. The web tool can be utilised by the civil infrastructure maintenance agency and construction engineers in the task of structure maintenance. [ABSTRACT FROM AUTHOR]

The study has as its original database the decarbonization process initiated in Mexico by the National Commission for the Efficient Use of Energy (CONUEE) as part of its “Savings Program of Electric Power in Buildings of the Federal Public Administration” (PAEIAPF) of 1999. The primary purpose of PAEIAPF was to reduce the levels of electric power consumption in Federal Government buildings. The program has operated for 20 years; however, its scope only reaches operational carbon. Since 90% of existing buildings will be in use by 2050, the Retrofit Models will be the base to determine solutions for a more resilient living environment that fortifies and extends the grid’s capacity and meets climate change mitigation targets. Secondly, significant socioeconomic and profound environmental impacts are not calculated explicitly in existing tools and are often referred to as “secondary” or Non-Energy Benefits (NEB). “The goal is to give them a measurement value to be considered in the decision-making calculus. It is assumed that soon; such factors will enter the general climate change economy, not unlike carbon in the past decade.” In this context, the proposed research aims to develop a value-based framework that will support a Building Stock Model and subsequent Retrofit Models, documented in a web-tool platform. The framework has three main steps: A) Building Stock Model: Mapping of selected buildings of the program PAEIAPF in a GIS system. Documentation of the baseline energy consumption and embodied CO2-eq of the existing building. B) Retrofit Models: Involving a Whole Life Cycle Assessment (WLCA) and Non-Energy Benefits (resilience coefficient, health, productivity). C) Web Tool Platform: Application and toolset that allows for consistent documentation, environmental impact evaluation of existing building stock, and solution design in identifying energy reduction concepts.

ABSTRACTEnterococcus faecium (Efm) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the Efm clade B was assigned as Enterococcus lactis (Elts), which usually lack HA-Efm infection markers. Available databases for extracting PVM are incomplete and/or present an intermix of genes from Efm and Enterococcus faecalis, with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20 (pili gene cluster 1, PGC-1), fms14-fms17-fms13 (PGC-2), empA-empB-empC (PGC-3), fms11-fms19-fms16 (PGC-4), ccpA, bepA, gls20-glsB1, and gls33-glsB] from nine reference genomes (seven Efm + two Elts). The database was validated against these reference genomes and further evaluated using a collection of well-characterized Efm (n = 43) and Elts (n = 7) control strains, by assessing PVM presence/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and in silico findings of the PVM, with Elts clustering separately and mostly carrying Elts-specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of Efm and Elts based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.IMPORTANCEThe newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives.

This paper showcases some of the main contributions from the research project Switch2Steel, in which a web application is developed for the calculation and optimization of the cost of steel industrial sheds. Unprotected steel structures, compared to other construction materials, possess relatively low fire resistance. To enhance their fire performance, adequate fire protection is required. Simplified fire design, without considering the real influence of the main parameters on the development and propagation of natural fires, often leads to excessive amounts of costly protective material. On the other hand, the use of advanced software tools may be impractical because of iterative time‐consuming computational processes such as structural optimization. Hence, this work presents a simple user‐friendly calculation tool that allows users to define the characteristics of the sheds to be built and based on a set of metrics, weights, and advanced algorithms, to minimize their cost by reducing the consumption of steel and fire protection material. To illustrate the use of the tool, a reference case of a steel industrial shed is selected and the results obtained by the tool are compared with those obtained by FEM tools. The tool gives more optimized results than the use of prescriptive rules, and the results are obtained considerably faster than by advanced expensive computational tools. [ABSTRACT FROM AUTHOR]

Microsatellites, also known as SSRs or STRs, are polymorphic DNA regions with tandem repetitions of a nucleotide motif of size 1-6 base pairs with a broad range of applications in many fields, such as comparative genomics, molecular biology, and forensics. However, the majority of researchers do not have computational training and struggle while running command-line tools or very limited web tools for their SSR research, spending a considerable amount of time learning how to execute the software and conducting the post-processing data tabulation in other tools or manually--time that could be used directly in data analysis. We present EasySSR, a user-friendly web tool with command-line full functionality, designed for practical use in batch identifying and comparing SSRs in sequences, draft, or complete genomes, not requiring previous bioinformatic skills to run. EasySSR requires only a FASTA and an optional GENBANK file of one or more genomes to identify and compare STRs. The tool can automatically analyze and compare SSRs in whole genomes, convert GenBank to PTT files, identify perfect and imperfect SSRs and coding and non-coding regions, compare their frequencies, abundancy, motifs, flanking sequences, and iterations, producing many outputs ready for download such as PTT files, interactive charts, and Excel tables, giving the user the data ready for further analysis in minutes. EasySSR was implemented as a web application, which can be executed from any browser and is available for free at https://computationalbiology.ufpa.br/easyssr/. Tutorials, usage notes, and download links to the source code can be found at https://github.com/engbiopct/EasySSR. [ABSTRACT FROM AUTHOR]

Decision support systems (DSSs) enable the optimisation of pesticide application timing to increase pesticide efficacy and thus reduce pesticide use without compromising yield quality and quantity. Limited access to information about available DSSs for use in integrated pest management (IPM) is a major barrier to the uptake of DSSs for IPM across Europe. To overcome this barrier, a typology for DSSs for IPM in Europe was developed, introducing a systematic approach to describe the ever-growing number of DSSs for IPM. The developed IPM-DSS typology was implemented in the free web tool “IPM Adviser”, where currently 79 IPM DSSs are described with over 50 attributes describing their structural and performance characteristics. The information about IPM DSSs, which was previously scattered on different websites and difficult to compare, is now standardised and presented in a uniform way, so that it is possible to compare different IPM DSSs on the basis of all the attributes described. The presented IPM-DSS typology implemented in the web tool IPM Adviser facilitates the dissemination and uptake of DSSs for IPM and thus contributes to the achievement of the EU targets for the sustainable use of pesticides.

Visual observation of the seafloor is invaluable in understanding deep-sea biogeography, uncovering and expanding key global geological, oceanographic, and climate processes. And yet, due to the expense, inefficiency, and inequitable distribution of deep-sea tools, we have barely explored a small, biased fraction of it. Systematic and efficient exploration of the entire deep sea will require a concerted global effort. The current study uses global-coverage geospatial data to develop an interactive online tool for deep seafloor observation planning (i.e., depths below 200 m). The Seafloor Observation Scenario Exploration Tool integrates stakeholder goals and constraints into a dynamic modeling process that combines information about seafloor depth, seafloor geomorphology features, sites of past seafloor observation, Exclusive Economic Zones, and vessel traffic density. With the tool, users can identify maximally suitable areas for seafloor observation, which we envision supporting seafloor expedition planning and marine conservation action.

The outbreak of Covid-19 has caused a global health crisis, presenting numerous challenges to the healthcare system with its severe respiratory symptoms and variable presentation. Early and accurate diagnosis of the virus is critical in controlling its spread and reducing the burden on healthcare facilities. To address this issue and relieve the strain on the healthcare system, this paper proposes a machine learning-based approach for Covid-19 diagnosis. Four algorithms were used for analyzing early Covid-19 detection, i.e., logistic regression, random forest, decision tree, and naive Bayes, using a data set of basic symptoms such as fever, shortness of breath, etc. for predicting positive and negative Covid-19 cases. Furthermore, development of a web portal that provides information on global vaccine distribution and the most widely used vaccines by country along with Covid-19 predictions. Our evaluation results demonstrate that the decision tree model outperformed the other models, achieving an accuracy of 97.69%. This study provides a practical solution to the ongoing Covid-19 crisis through an improved diagnosis method and access to vaccination information.

Microsatellites, also known as SSRs or STRs, are polymorphic DNA regions with tandem repetitions of a nucleotide motif of size 1–6 base pairs with a broad range of applications in many fields, such as comparative genomics, molecular biology, and forensics. However, the majority of researchers do not have computational training and struggle while running command-line tools or very limited web tools for their SSR research, spending a considerable amount of time learning how to execute the software and conducting the post-processing data tabulation in other tools or manually—time that could be used directly in data analysis. We present EasySSR, a user-friendly web tool with command-line full functionality, designed for practical use in batch identifying and comparing SSRs in sequences, draft, or complete genomes, not requiring previous bioinformatic skills to run. EasySSR requires only a FASTA and an optional GENBANK file of one or more genomes to identify and compare STRs. The tool can automatically analyze and compare SSRs in whole genomes, convert GenBank to PTT files, identify perfect and imperfect SSRs and coding and non-coding regions, compare their frequencies, abundancy, motifs, flanking sequences, and iterations, producing many outputs ready for download such as PTT files, interactive charts, and Excel tables, giving the user the data ready for further analysis in minutes. EasySSR was implemented as a web application, which can be executed from any browser and is available for free at https://computationalbiology.ufpa.br/easyssr/. Tutorials, usage notes, and download links to the source code can be found at https://github.com/engbiopct/EasySSR.

The outbreak of Covid-19 has caused a global health crisis, presenting numerous challenges to the healthcare system with its severe respiratory symptoms and variable presentation. Early and accurate diagnosis of the virus is critical in controlling its spread and reducing the burden on healthcare facilities. To address this issue and relieve the strain on the healthcare system, this paper proposes a machine learning-based approach for Covid-19 diagnosis. Four algorithms were used for analyzing early Covid-19 detection, i.e., logistic regression, random forest, decision tree, and naive Bayes, using a data set of basic symptoms such as fever, shortness of breath, etc. for predicting positive and negative Covid-19 cases. Furthermore, development of a web portal that provides information on global vaccine distribution and the most widely used vaccines by country along with Covid-19 predictions. Our evaluation results demonstrate that the decision tree model outperformed the other models, achieving an accuracy of 97.69%. This study provides a practical solution to the ongoing Covid-19 crisis through an improved diagnosis method and access to vaccination information. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has had a global impact, transforming how we manage infectious diseases and interact socially. Researchers from various fields have worked tirelessly to develop vaccines on an unprecedented scale, while different countries have developed various sanitary protocols to deal with more contagious variants. Machine learning-assisted diagnosis has emerged as a powerful tool that can help health professionals deliver faster and more accurate outcomes. However, medical systems that rely on deep learning often require extensive data, which may be impractical for real-world applications. This paper compares lightweight neural architectures for COVID-19 identification using chest X-rays, highlighting the strengths and weaknesses of each approach. Additionally, a web tool has been developed that accepts chest computer tomography images and outputs the probability of COVID-19 infection along with a heatmap of the regions used by the intelligent system to make this determination. The experiments indicate that most lightweight architectures considered in the study can identify COVID-19 correctly, but further investigation is necessary. Lightweight neural architectures show promise in computer-aided COVID-19 diagnosis using chest X-rays, but they did not reach accuracy rates above 88%, which is necessary for medical applications. These findings suggest that additional research is necessary to improve the accuracy of lightweight models and make them practical for real-world use.

Research on food-derived bioactive peptides is expanding and the need for a convenient online platform that combines a foolproof and intuitive user interface with a reliable database and tools for prediction and analysis is rising. In this regard, this paper presents an open-access web-based platform PepLab (Peptides Laboratory). The database contains 2764 peptide sequence entries, grouped into sixteen classes according to their biological activity and into seven classes according to the source from which they were derived. Moreover, it includes bioinformatic tools for their processing and analysis. The DMpep tool allows extracting information about a number of physicochemical characteristics of a peptide or a set of peptides, including those that are not recorded in the database. The main advantages of PepLab are a user-friendly interface, a responsive design, and optimized search engines for better visibility on the Internet. Prediction of non-reported activity is available based on amino acid sequence analysis. In addition, users can download data and results in a convenient format (text and/or graphic) that was limited in the existing platforms. In this way, the presented PepLab platform will be helpful for researchers from various fields—bioinformatics, pharmaceuticals, food sciences, dietetics, biotechnology, analytical chemistry, etc. [ABSTRACT FROM AUTHOR]

Selection of differentially expressed genes (DEGs) is a vital process to discover the causes of diseases. It has been shown that modelling of genomics data by considering relation among genes increases the predictive performance of methods compared to univariate analysis. However, there exist serious differences among most studies analyzing the same dataset for the reasons arising from the methods. Therefore, there is a strong need for easily accessible, user-friendly, and interactive tool to perform gene selection for RNA-seq data via machine learning algorithms simultaneously not to miss DEGs. We develop an open-source and freely available web-based tool for gene selection via machine learning algorithms that can deal with high performance computation. This tool includes six machine learning algorithms having different aspects. Moreover, the tool involves classical pre-processing steps; filtering, normalization, transformation, and univariate analysis. It also offers well-arranged graphical approaches; network plot, heatmap, venn diagram, and box-and-whisker plot. Gene ontology analysis is provided for both mRNA and miRNA DEGs. The implementation is carried out on Alzheimer RNA-seq data to demonstrate the use of this web-based tool. Eleven genes are suggested by at least two out of six methods. One of these genes, hsa-miR-148a-3p, might be considered as a new biomarker for Alzheimer's disease diagnosis. Kidney Chromophobe dataset is also analyzed to demonstrate the validity of GeneSelectML web tool on a different dataset. GeneSelectML is distinguished in that it simultaneously uses different machine learning algorithms for gene selection and can perform pre-processing, graphical representation, and gene ontology analyses on the same tool. This tool is freely available at www.softmed.hacettepe.edu.tr/GeneSelectML. [ABSTRACT FROM AUTHOR]

Grape (Vitis vinifera L.) transcriptomes have been extensively profiled in different tissues, at various developmental stages, under biotic or abiotic stresses, and other conditions. However, there is still no user-friendly tool to explore these precious data. A total of 1 019 microarray sample data were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database (NCBI GEO). Weighted gene correlation network analysis (WGCNA) was conducted. Forty-one gene co-expression modules were identified. Module functional annotation suggested that these modules performed different functions and were associated with experimental conditions ／ phenotypes. Hub genes, which bear important functions, were screened based on intramodule connectivity. Module genes with unknown functions were annotated according to the "guilt-by-association" rationale. Finally, a web tool VitisMod was developed as a new resource for grape gene function investigation. VitisMod is freely available at http: ／ ／ bioinformatics.fafu. edu.cn ／ grape. [ABSTRACT FROM AUTHOR]

The molecular landscape in breast cancer is characterized by large biological heterogeneity and variable clinical outcomes. Here, we performed an integrative multi-omics analysis of patients diagnosed with breast cancer. Using transcriptomic analysis, we identified three subtypes (cluster A, cluster B and cluster C) of breast cancer with distinct prognosis, clinical features, and genomic alterations: Cluster A was associated with higher genomic instability, immune suppression and worst prognosis outcome; cluster B was associated with high activation of immune-pathway, increased mutations and middle prognosis outcome; cluster C was linked to Luminal A subtype patients, moderate immune cell infiltration and best prognosis outcome. Combination of the three newly identified clusters with PAM50 subtypes, we proposed potential new precision strategies for 15 subtypes using L1000 database. Then, we developed a robust gene pair (RGP) score for prognosis outcome prediction of patients with breast cancer. The RGP score is based on a novel gene-pairing approach to eliminate batch effects caused by differences in heterogeneous patient cohorts and transcriptomic data distributions, and it was validated in ten cohorts of patients with breast cancer. Finally, we developed a user-friendly web-tool (https://sujiezhulab.shinyapps.io/BRCA/) to predict subtype, treatment strategies and prognosis states for patients with breast cancer.

Angiogenic gene overexpression has been the main strategy in numerous vascular regenerative gene therapy projects. However, most have failed in clinical trials. CRISPRa technology enhances gene overexpression levels based on the identification of sgRNAs with maximum efficiency and safety. CRISPick and CHOP CHOP are the most widely used web tools for the prediction of sgRNAs. The objective of our study was to analyze the performance of both platforms for the sgRNA design to angiogenic genes (VEGFA, KDR, EPO, HIF-1A, HGF, FGF, PGF, FGF1) involving different human reference genomes (GRCH 37 and GRCH 38). The top 20 ranked sgRNAs proposed by the two tools were analyzed in different aspects. No significant differences were found on the DNA curvature associated with the sgRNA binding sites but the sgRNA predicted on-target efficiency was significantly greater when CRISPick was used. Moreover, the mean ranking variation was greater for the same platform in EPO, EGF, HIF-1A, PGF and HGF, whereas it did not reach statistical significance in KDR, FGF-1 and VEGFA. The rearrangement analysis of the ranking positions was also different between platforms. CRISPick proved to be more accurate in establishing the best sgRNAs in relation to a more complete genome, whereas CHOP CHOP showed a narrower classification reordering.

In the present study, an online web tool (http://www.iaees.org/publications/software/netJa/netGen.htm) for generating user-interface interactive networks was presented. In the network, the user can mouse-press any of the nodes to drag the network, examine network topology, evaluate node centrality, etc. It can be freely used and run on popular web browsers as Chrome, etc.

Abstract Background Multi-state models are used in complex disease pathways to describe a process where an individual moves from one state to the next, taking into account competing states during each transition. In a multi-state setting, there are various measures to be estimated that are of great epidemiological importance. However, increased complexity of the multi-state setting and predictions over time for individuals with different covariate patterns may lead to increased difficulty in communicating the estimated measures. The need for easy and meaningful communication of the analysis results motivated the development of a web tool to address these issues. Results MSMplus is a publicly available web tool, developed via the Shiny R package, with the aim of enhancing the understanding of multi-state model analyses results. The results from any multi-state model analysis are uploaded to the application in a pre-specified format. Through a variety of user-tailored interactive graphs, the application contributes to an improvement in communication, reporting and interpretation of multi-state analysis results as well as comparison between different approaches. The predicted measures that can be supported by MSMplus include, among others, the transition probabilities, the transition intensity rates, the length of stay in each state, the probability of ever visiting a state and user defined measures. Representation of differences, ratios and confidence intervals of the aforementioned measures are also supported. MSMplus is a useful tool that enhances communication and understanding of multi-state model analyses results. Conclusions Further use and development of web tools should be encouraged in the future as a means to communicate scientific research.

Tipping points or critical transitions widely exist during the progression of many biological processes. It is of great importance to detect the tipping point with the measured omics data, which may be a key to achieving predictive or preventive medicine. We present the tipping point detector (TPD), a web tool for the detection of the tipping point during the dynamic process of biological systems, and further its leading molecules or network, based on the input high-dimensional time series or stage course data. With the solid theoretical background of dynamic network biomarker (DNB) and a series of computational methods for DNB detection, TPD detects the potential tipping point/critical state from the input omics data and outputs multifarious visualized results, including a suggested tipping point with a statistically significant P value, the identified key genes and their functional biological information, the dynamic change in the DNB/leading network that may drive the critical transition and the survival analysis based on DNB scores that may help to identify 'dark' genes (nondifferential in terms of expression but differential in terms of DNB scores). TPD fits all current browsers, such as Chrome, Firefox, Edge, Opera, Safari and Internet Explorer. TPD is freely accessible at http://www.rpcomputationalbiology.cn/TPD. [ABSTRACT FROM AUTHOR]

Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences. [ABSTRACT FROM AUTHOR]

Background: Cross-platform or cross-experiment transcriptome data is hard to compare as the original gene expression values from different platforms cannot be compared directly. The inherent gene expression ranking information is rarely utilized. Objective: Use of reduced vector to represent transcriptome data independent of platforms. Methods: Thus, we turned the expression profile into a rank vector, where a higher expression has a higher rank value, then applied Latent semantic analysis (LSA) to get compact and continuous 100-dimensional vector representations for samples. Results: Results showed that the reconstructed vector has a precision of 96.7% in recovering tissue labels from an independent dataset. A user-friendly tool TissueSpace was developed, which provides users the following functionalities: (1) convert different gene ID types to Ensembl gene IDs; (2) project any human transcriptome profile to get vector representation for downstream analysis; (3) functional enrichment for each of the 100-dimensional vector features. Case studies for its applications in human common diseases indicate its usefulness. Conclusions: TissueSpace could be used to generate testable hypotheses for translational medicine. The TissueSpace tool is available at http://bioinformatics.fafu.edu.cn/tissuespace/. [ABSTRACT FROM AUTHOR]

Every year, marine scientists around the world read thousands of otolith or scale images to determine the age structure of commercial fish stocks. This knowledge is important for fisheries and conservation management. However, the age-reading procedure is time-consuming and costly to perform due to the specialized expertise and labor needed to identify annual growth zones in otoliths. Effective automated systems are needed to increase throughput and reduce cost. DeepOtolith is an open-source artificial intelligence (AI) platform that addresses this issue by providing a web system with a simple interface that automatically estimates fish age by combining otolith images with convolutional neural networks (CNNs), a class of deep neural networks that has been a dominant method in computer vision tasks. Users can upload otolith image data for selective fish species, and the platform returns age estimates. The estimates of multiple images can be exported to conduct conclusions or further age-related research. DeepOtolith currently contains classifiers/regressors for three fish species; however, more species will be included as related work on ageing will be tested and published soon. Herein, the architecture and functionality of the platform are presented. Current limitations and future directions are also discussed. Overall, DeepOtolith should be considered as the first step towards building a community of marine ecologists, machine learning experts, and stakeholders that will collaborate to support the conservation of fishery resources. [ABSTRACT FROM AUTHOR]

Homorepeat sequences, consecutive runs of identical amino acids, are prevalent in eukaryotic proteins. It has become necessary to annotate and evaluate this feature in entire proteomes. The definition of what constitutes a homorepeat is not fixed, and different research approaches may require different definitions; therefore, flexible approaches to analyze homorepeats in complete proteomes are needed. Here, we present polyX2, a fast, simple but tunable script to scan protein datasets for all possible homorepeats. The user can modify the length of the window to scan, the minimum number of identical residues that must be found in the window, and the types of homorepeats to be found. [ABSTRACT FROM AUTHOR]

The Membranome database provides comprehensive structural information on single‐pass (i.e., bitopic) membrane proteins from six evolutionarily distant organisms, including protein–protein interactions, complexes, mutations, experimental structures, and models of transmembrane α‐helical dimers. We present a new version of this database, Membranome 3.0, which was significantly updated by revising the set of 5,758 bitopic proteins and incorporating models generated by AlphaFold 2 in the database. The AlphaFold models were parsed into structural domains located at the different membrane sides, modified to exclude low‐confidence unstructured terminal regions and signal sequences, validated through comparison with available experimental structures, and positioned with respect to membrane boundaries. Membranome 3.0 was re‐developed to facilitate visualization and comparative analysis of multiple 3D structures of proteins that belong to a specified family, complex, biological pathway, or membrane type. New tools for advanced search and analysis of proteins, their interactions, complexes, and mutations were included. The database is freely accessible at https://membranome.org. [ABSTRACT FROM AUTHOR]

Biological interpretation of a large amount of gene or protein data is complex. Ontology analysis tools are imperative in finding functional similarities through overrepresentation or enrichment of terms associated with the input gene or protein lists. However, most tools are limited by their ability to do ontology-specific and species-limited analyses. Furthermore, some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data. Here, we present MOET or the Multi-Ontology Enrichment Tool (v.1 released in April 2019 and v.2 released in May 2021), an ontology analysis tool leveraging data that the Rat Genome Database (RGD) integrated from in-house expert curation and external databases including the National Center for Biotechnology Information (NCBI), Mouse Genome Informatics (MGI), The Kyoto Encyclopedia of Genes and Genomes (KEGG), The Gene Ontology Resource, UniProt-GOA, and others. Given a gene or protein list, MOET analysis identifies significantly overrepresented ontology terms using a hypergeometric test and provides nominal and Bonferroni corrected P-values and odds ratios for the overrepresented terms. The results are shown as a downloadable list of terms with and without Bonferroni correction, and a graph of the P-values and number of annotated genes for each term in the list. MOET can be accessed freely from https://rgd.mcw.edu/rgdweb/enrichment/start.html. [ABSTRACT FROM AUTHOR]

Statistical methods for enrichment analysis are important tools to extract biological information from omics experiments. Although these methods have been widely used for the analysis of gene and protein lists, the development of high-throughput technologies for regulatory elements demands dedicated statistical and bioinformatics tools. Here, we present a set of enrichment analysis methods for regulatory elements, including CpG sites, miRNAs, and transcription factors. Statistical significance is determined via a power weighting function for target genes and tested by the Wallenius noncentral hypergeometric distribution model to avoid selection bias. These new methodologies have been applied to the analysis of a set of miRNAs associated with arrhythmia, showing the potential of this tool to extract biological information from a list of regulatory elements. These new methods are available in GeneCodis 4, a web tool able to perform singular and modular enrichment analysis that allows the integration of heterogeneous information. [ABSTRACT FROM AUTHOR]

Background: The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein. Methods: Hence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions. Results: The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds. Discussion: Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop a1'/ß1', as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the SARSCoV-2 complexes, marking a major step in the real-time tracking of the virus mutant lineages. E-Volve is available at http://bioinfo.dcc.ufmg.br/evolve. [ABSTRACT FROM AUTHOR]

Virtual learning environments have become a tool to acquire knowledge and avoid limiting access to education. This research study aims at diagnosing, in the context of the COVID-19 pandemic, the performance of elementary school third grade students in Physical Education (PE) at a school of Montería, through the LUDOS platform with the use of ICT. This was a quantitative descriptive correlational study with a single control group composed of 28 students. A survey was applied and two pedagogical workshops were held to determine the correlation between learning mediated by information and communication technologies and the students’ academic performance. The findings show that all participants had access to electronic devices with Internet access. As a result of the virtual workshops, academic performance was found to be higher in 36% of students and it remained stable in 43% of students. Additionally, students’ technological skills, capacities and physical condition were found to be improved.