Development of a cancer risk model and mobile health application to inform the public about cancer risks and risk factors.

OBJECTIVE: To develop and evaluate a mobile health application, the Cancer Risk Calculator (CRC), aimed at improving public health literacy by providing personalized information on cancer risks and preventive measures. MATERIALS AND METHODS: The CRC was developed through a comprehensive process involving the identification of necessary content, integration of average cancer risks using data from reliable sources, creation of a novel risk model emphasizing modifiable factors, and the application's development for easy access. The application covers 38 cancer types, 18 subtypes, and approximately 790 risk factors, utilizing data from the Surveillance, Epidemiology, and End Results Program and scientific literature. RESULTS: CRC offers users personalized risk assessments across a broad range of cancers, emphasizing modifiable risk factors to encourage preventive behaviors. It distinguishes itself by covering more cancer types and risk factors than existing tools, with preliminary user feedback indicating its utility in promoting health literacy and lifestyle changes. DISCUSSION: The CRC application stands out as an innovative tool in health informatics, significantly enhancing public understanding of cancer risks. Its development underscores the potential of digital health technologies to bolster preventive healthcare strategies through improved health literacy. CONCLUSION: The Cancer Risk Calculator is a pivotal development in mobile health technology, offering comprehensive and personalized insights into cancer risks and prevention. It serves as a valuable resource for public health education, facilitating informed decisions and lifestyle modifications for cancer prevention.

CPADS: a web tool for comprehensive pancancer analysis of drug sensitivity.

Drug therapy is vital in cancer treatment. Accurate analysis of drug sensitivity for specific cancers can guide healthcare professionals in prescribing drugs, leading to improved patient survival and quality of life. However, there is a lack of web-based tools that offer comprehensive visualization and analysis of pancancer drug sensitivity. We gathered cancer drug sensitivity data from publicly available databases (GEO, TCGA and GDSC) and developed a web tool called Comprehensive Pancancer Analysis of Drug Sensitivity (CPADS) using Shiny. CPADS currently includes transcriptomic data from over 29 000 samples, encompassing 44 types of cancer, 288 drugs and more than 9000 gene perturbations. It allows easy execution of various analyses related to cancer drug sensitivity. With its large sample size and diverse drug range, CPADS offers a range of analysis methods, such as differential gene expression, gene correlation, pathway analysis, drug analysis and gene perturbation analysis. Additionally, it provides several visualization approaches. CPADS significantly aids physicians and researchers in exploring primary and secondary drug resistance at both gene and pathway levels. The integration of drug resistance and gene perturbation data also presents novel perspectives for identifying pivotal genes influencing drug resistance. Access CPADS at https://smuonco.shinyapps.io/CPADS/ or https://robinl-lab.com/CPADS.

IHGA: An interactive web server for large-scale and comprehensive discovery of genes of interest in hepatocellular carcinoma.

Mining gene expression data is valuable for discovering novel biomarkers and therapeutic targets in hepatocellular carcinoma (HCC). Although emerging data mining tools are available for pan-cancer-related gene data analysis, few tools are dedicated to HCC. Moreover, tools specifically designed for HCC have restrictions such as small data scale and limited functionality. Therefore, we developed IHGA, a new interactive web server for discovering genes of interest in HCC on a large-scale and comprehensive basis. Integrative HCC Gene Analysis (IHGA) contains over 100 independent HCC patient-derived datasets (with over 10,000 tissue samples) and more than 90 cell models. IHGA allows users to conduct a series of large-scale and comprehensive analyses and data visualizations based on gene mRNA levels, including expression comparison, correlation analysis, clinical characteristics analysis, survival analysis, immune system interaction analysis, and drug sensitivity analysis. This method notably enhanced the richness of clinical data in IHGA. Additionally, IHGA integrates artificial intelligence (AI)-assisted gene screening based on natural language models. IHGA is free, user-friendly, and can effectively reduce time spent during data collection, organization, and analysis. In conclusion, IHGA is competitive in terms of data scale, data diversity, and functionality. It effectively alleviates the obstacles caused by HCC heterogeneity to data mining work and helps advance research on the molecular mechanisms of HCC.

Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors.

Computational approaches in immune-oncology therapies focus on using data-driven methods to identify potential immune targets and develop novel drug candidates. In particular, the search for PD-1/PD-L1 immune checkpoint inhibitors (ICIs) has enlivened the field, leveraging the use of cheminformatics and bioinformatics tools to analyze large datasets of molecules, gene expression and protein-protein interactions. Up to now, there is still an unmet clinical need for improved ICIs and reliable predictive biomarkers. In this review, we highlight the computational methodologies applied to discovering and developing PD-1/PD-L1 ICIs for improved cancer immunotherapies with a greater focus in the last five years. The use of computer-aided drug design structure- and ligand-based virtual screening processes, molecular docking, homology modeling and molecular dynamics simulations methodologies essential for successful drug discovery campaigns focusing on antibodies, peptides or small-molecule ICIs are addressed. A list of recent databases and web tools used in the context of cancer and immunotherapy has been compilated and made available, namely regarding a general scope, cancer and immunology. In summary, computational approaches have become valuable tools for discovering and developing ICIs. Despite significant progress, there is still a need for improved ICIs and biomarkers, and recent databases and web tools have been compiled to aid in this pursuit.

Web-tools for the genomic analysis of the 2022 Monkeypox virus global outbreak / Herramientas web para el análisis genómico del virus de la viruela símica durante el brote mundial de 2022

Abstract The resources and platforms available on the internet for collecting and sharing information and performing genomic sequence analysis have made it possible to follow closely the evolution the evolution of SARS-CoV-2. However, the current monkeypox outbreak in the world brings us back to the need to use these resources to appraise the extent of this outbreak. The objective of this work was an analysis of the information presented so far in the genomic database GISAID EpiPox™, using various tools available on the web. The results indicate that the monkeypox outbreak is referred as MPXV clade II B.1 lineage and sub-lineages, isolated from male patients mainly from the European and American continents. In the current scenario, the access to genomic sequences, epidemiological information, and tools available to the scientific community is of great importance for global public health in order to follow the evolution of pathogens.

Resumen Los recursos y plataformas disponibles en Internet para recopilar, compartir información y realizar análisis de secuencias genómicas han permitido seguir de cerca la evolución del SARS-CoV-2. El actual brote global de viruela del mono en el mundo, requiere de nuevo utilizar estos recursos para conocer el alcance de este brote. El objetivo de este trabajo fue un análisis de la información presentada hasta el momento en la base de datos genómica EpiPox™ de GISAID, utilizando diversas herramientas disponibles en la web. Los resultados indican que el brote de la viruela del mono o símica está referido al linaje y sub-linajes B.1 del clado II de MPXV, aislado principalmente de pacientes hombres de Europa y América. En el escenario actual, el acceso a las secuencias genómicas, la información epidemiológica, y las herramientas disponibles para la comunidad científica son de gran importancia para la salud pública mundial con el fin de seguir la evolución de los patógenos.

HPVTIMER: A shiny web application for tumor immune estimation in human papillomavirus-associated cancers.

The tumor immune microenvironment (TIME) is closely associated with tumor formation, particularly linked to the human papillomavirus (HPV), and regulates tumor initiation, proliferation, infiltration, and metastasis. With the rise of immunotherapy, an increasing amount of sample data used for TIME exploration is available in databases. However, no currently available web tool enables a comprehensive exploration of the TIME of HPV-associated cancers by leveraging these data. We have developed a web tool called HPV-associated Tumor Immune MicroEnvironment ExploreR (HPVTIMER), which provides a comprehensive analysis platform that integrates over 10,000 genes and 2290 tumor samples from 65 transcriptome data sets across 8 cancer types sourced from the Gene Expression Omnibus (GEO) database. The tool features four built-in analysis modules, namely, the differential expression analysis module, correlation analysis module, immune infiltration analysis module, and pathway analysis module. These modules enable users to perform systematic and vertical analyses. We used several analytical modules in HPVTIMER to briefly explore the role of CDKN2A in head and neck squamous cell carcinomas. We expect that HPVTIMER will help users explore the immune microenvironment of HPV-associated cancers and uncover potential immune regulatory mechanisms and immunotherapeutic targets. HPVTIMER is available at http://www.hpvtimer.com/.

CAMOIP: a web server for comprehensive analysis on multi-omics of immunotherapy in pan-cancer.

Immune checkpoint inhibitors (ICIs) have completely changed the approach pertaining to tumor diagnostics and treatment. Similarly, immunotherapy has also provided much needed data about mutation, expression and prognosis, affording an unprecedented opportunity for discovering candidate drug targets and screening for immunotherapy-relevant biomarkers. Although existing web tools enable biologists to analyze the expression, mutation and prognostic data of tumors, they are currently unable to facilitate data mining and mechanism analyses specifically related to immunotherapy. Thus, we effectively developed our own web-based tool, called Comprehensive Analysis on Multi-Omics of Immunotherapy in Pan-cancer (CAMOIP), in which we are able to successfully screen various prognostic markers and analyze the mechanisms involved in biomarker expression and function, as well as immunotherapy. The analyses include information relevant to survival analysis, expression analysis, mutational landscape analysis, immune infiltration analysis, immunogenicity analysis and pathway enrichment analysis. This comprehensive analysis of biomarkers for immunotherapy can be carried out by a click of CAMOIP, and the software should greatly encourage the further development of immunotherapy. CAMOIP provides invaluable evidence that bridges the information between the data of cancer genomics based on immunotherapy, providing comprehensive information to users and assisting in making the value of current ICI-treated data available to all users. CAMOIP is available at https://www.camoip.net.

Virtual screening of potential anticancer drugs based on microbial products.

The development of microbial products for cancer treatment has been in the spotlight in recent years. In order to accelerate the lengthy and expensive drug development process, in silico screening tools are systematically employed, especially during the initial discovery phase. Moreover, considering the steadily increasing number of molecules approved by authorities for commercial use, there is a demand for faster methods to repurpose such drugs. Here we present a review on virtual screening web tools, such as publicly available databases of molecular targets and libraries of ligands, with the aim to facilitate the discovery of potential anticancer drugs based on microbial products. We provide an entry-level step-by-step description of the workflow for virtual screening of microbial metabolites with known protein targets, as well as two practical examples using freely available web tools. The first case presents a virtual screening study of drugs developed from microbial products using Caver Web, a web tool that performs docking along a tunnel. The second case comprises a comparative analysis between a wild type isocitrate dehydrogenase 1 and a mutant that results in cancer, using the recently developed web tool PredictSNPOnco. In summary, this review provides the basic and essential background information necessary for virtual screening experiments, which may accelerate the discovery of novel anticancer drugs.

Review of interactive digital solutions improving health literacy of personal cancer risks in the general public.

BACKGROUND: Health literacy is crucial in understanding the many risk factors for cancer. Low health literacy is associated with low adherence to medication, poor health status, and increased health care costs. Modern technology allows us to educate the general public on their risks. We focus herein on the available mobile applications and online web tools for the evaluation of cancer risk in the general public. METHODS: A systematic search was performed for cancer risk calculators mobile applications on both Google Play and the App Store and for online cancer risk calculators using Google, Bing, Yahoo! and Baidu. RESULTS: For mobile applications, out of 250 different apps found on GooglePlay, 16 Android applications were retained for evaluation in this review and for the AppStore, out of 10 different apps, 7 Android applications were retained for evaluation in this review. Only three apps were available for both Android and iOS systems. For web tools, a list of 20 tools was retained and evaluated. CONCLUSION: This review presents the most popular and prominent tools and their strengths and possible weaknesses are evaluated. We discuss not only its current state as it relates to general knowledge about cancer risks, but also barriers and future directions. It is imperative that as developers continue to create and improve such tools, health care providers remain aware of these efforts in order to properly guide patients towards appropriate resources and educate them on both their usefulness and limitations.

QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems.

The increasing role played by liquid chromatography-mass spectrometry (LC-MS)-based proteomics in biological discovery has led to a growing need for quality control (QC) on the LC-MS systems. While numerous quality control tools have been developed to track the performance of LC-MS systems based on a pre-defined set of performance factors (e.g., mass error, retention time), the precise influence and contribution of the performance factors and their generalization property to different biological samples are not as well characterized. Here, a web-based application (QCMAP) is developed for interactive diagnosis and prediction of the performance of LC-MS systems across different biological sample types. Leveraging on a standardized HeLa cell sample run as QC within a multi-user facility, predictive models are trained on a panel of commonly used performance factors to pinpoint the precise conditions to a (un)satisfactory performance in three LC-MS systems. It is demonstrated that the learned model can be applied to predict LC-MS system performance for brain samples generated from an independent study. By compiling these predictive models into our web-application, QCMAP allows users to benchmark the performance of their LC-MS systems using their own samples and identify key factors for instrument optimization. QCMAP is freely available from: http://shiny.maths.usyd.edu.au/QCMAP/.

Postgenomic Approaches and Bioinformatics Tools to Advance the Development of Vaccines against Bacteria of the Burkholderia cepacia Complex.

Bacteria of the Burkholderia cepacia complex (Bcc) remain an important cause of morbidity and mortality among patients suffering from cystic fibrosis. Eradication of these pathogens by antimicrobial therapy often fails, highlighting the need to develop novel strategies to eradicate infections. Vaccines are attractive since they can confer protection to particularly vulnerable patients, as is the case of cystic fibrosis patients. Several studies have identified specific virulence factors and proteins as potential subunit vaccine candidates. So far, no vaccine is available to protect from Bcc infections. In the present work, we review the most promising postgenomic approaches and selected web tools available to speed up the identification of immunogenic proteins with the potential of conferring protection against Bcc infections.

Improving the efficacy-safety balance of polypharmacology in multi-target drug discovery.

INTRODUCTION: Polypharmacology has emerged as an essential paradigm for modern drug discovery process. Multiple lines of evidence suggest that agents capable of modulating multiple targets in a selective manner may offer also improved balance between therapeutic efficacy and safety compared to single-targeted agents. Areas covered: Herein, the authors review the recent progress made in experimental and computational strategies for addressing the critical challenges with rational discovery of selective multi-targeted agents within the context of polypharmacological modelling. Specific focus is placed on multi-targeted mono-therapies, although examples of combinatorial polytherapies are also covered as an important part of the polypharmacology paradigm. The authors focus mainly on anti-cancer treatment applications, where polypharmacology is playing a key role in determining the efficacy-toxicity trade-off of multi-targeting strategies. Expert opinion: Even though it is widely appreciated that complex polypharmacological interactions can contribute both to therapeutic and adverse side-effects, systematic approaches for improving this balance by means of integrated experimental-computational strategies are still lacking. Future developments will be needed for comprehensive collection and harmonization of systems-wide target selectivity data, enabling better utilization and control for multi-targeted activities in the drug development process. Additional areas of future developments include model-based strategies for drug combination screening and improved pre-clinical validation options with animal models.

Herramientas web e informáticas en el ámbito laboral de nutrición / The use of informatics and web tools in the work field of nutrition

Actualmente es casi indispensable el uso y conocimiento de la tecnología en cualquier área de desempeño profesional. En el sector salud se ha visto un marcado incremento en el uso de herramientas, tanto web como informáticas. Éstas son importantes ya que facilitan el desempeño laboral y la comunicación con los otros. Objetivos: determinar cuáles son las herramientas web e informáticas que los nutricionistas conocen y usan durante el año 2013. Materiales y métodos: estudio descriptivo, retrospectivo y de corte transversal realizado en profesionales del área de nutrición sector público y privado. Se creó un cuestionario para este estudio que se aplicó a través de la plataforma SurveyMonkey para que los participantes completaran online. Resultados: el 50% de la población tiene un nivel de conocimiento básico sobre las herramientas web evaluadas. Sólo el 10% tiene un nivel avanzado. En cuanto al nivel de uso de las mismas, fue aún menor.Conclusiones: es necesario fomentar la creación, selección, transferencia y difusión del conocimiento de las herramientas web e informáticas en el área de Nutrición, y aprovechar las facilidades que éstas brindan.

Introduction: currently, it is almost essential to use the science of technology in every professional area. In the area of Health, we have seen a steep rise in the use of web tools, and of informatics. These are very important tools since they facilitate professional labor and a good communication with others. Objectives: to determine which web and informatics tools nutritionists best knew and used during 2013. Material and methods: descriptive and retrospective study with cross sectional design performed in Professionals of the Nutritional Public Health area and also the private sector. A questionnaire for this study was created and applied through the Survey Monkey platform for participants to complete online. Results: according to results, 50% of the population has a basic knowledge of tools that was presented. But only 10% has the knowledge and ability to use it at a higher level. Regarding the level of their use, the percentage was even lower.Conclusions:it is necessary to promote the creation, selection, transfer and publicity of knowledge in the area of nutrition, and take advantage of facilities offered by web and software tools.

Usabilidad de los sitios Web, los métodos y las técnicas para la evaluación / Usability of Web sites, methods and evaluation techniques

En la sociedad actual es incuestionable la relevancia de la Web, y existe una gran variedad de sitios web que brindan servicio a los usuarios. En este contexto, la usabilidad juega un papel primordial en el proceso de desarrollo de sitios web de éxito. En este artículo se revisan diferentes definiciones sobre la disciplina usabilidad, su incorporación en el proceso de ingeniería (ingeniería de la usabilidad) y su relación con la ingeniería de software, sus atributos y métodos de evaluación. Se presentan las consideraciones sobre el sistema de evaluación de la usabilidad Web orientado al usuario y basado en la determinación de tareas críticas (SIRIUS revisado por las autoras)

In the present society, the relevance of the Web is unquestionable and there is a great variety of Web sites that offer services to users. In this context, usability plays a fundamental role in the process of developing successful Web sites. In this article we review different definitions about the discipline of usability, its incorporation in the engineering process (usability engineering) and its relation to software engineer, as well as its attributes and evaluation methods. The considerations about the evaluation system of the Web usability are also presented, advising the user and basing it in the establishment of critical tasks (SIRIUS, reviewed by the authors)