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1.
Regul Toxicol Pharmacol ; 153: 105713, 2024 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-39366517

RESUMO

The escalating challenge of New Psychoactive Substances (NPS) necessitates enhanced global monitoring and analysis capabilities. This study introduces an advanced interactive visualization tool that employs Geographic Information System (GIS) technologies to improve the functionality of the UNODC's Early Warning Advisory. The tool enables dynamic observation and analysis of NPS's geographical and temporal distribution, thereby facilitating a comprehensive understanding of their public health impacts. By incorporating detailed choropleth maps and annual and cumulative bar charts, the tool allows policymakers and researchers to visually track and analyze trends in NPS usage and control efforts across different regions. The results demonstrate the tool's effectiveness in providing actionable insights, which support the strategic development of public health policies and interventions to curb the global rise in NPS usage. This initiative illustrates the essential role of digital tools in enhancing public health strategies and responses to emerging drug trends. This rising challenge underscores the urgent need for innovative solutions in monitoring drug trends, a theme explored in this paper. The web tool is available at https://nps-vis.cmdm.tw, and the code is available at https://github.com/CMDM-Lab/nps-vis.

2.
BMJ Health Care Inform ; 31(1)2024 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-39389618

RESUMO

AIM: Interactions between patients and healthcare professionals (HCP) during hospital admissions are complex and difficult to interrogate using traditional analysis of electronic patient record (EPR) data. The objective of this study was to determine the feasibility of applying temporal network analytics to EPR data, focusing on HCP-patient interactions over time. METHOD: Network (graph) analysis was applied to routinely collected structured data from an EPR for HCP interactions with individual patients during admissions for patients undergoing renal transplantation between May 2019 and June 2023. Networks were constructed per day of admission within a session, defined by whether the patient was in the intensive care unit (ICU) or standard hospital ward. Connections between HCP were defined using a 60 min period. Reports were generated visualising daily interaction network structures, across individual admissions. RESULTS: 2300 individual networks were constructed from 127 hospital admissions for renal transplantation. The number of nodes or HCP per network varied from 2 to 45, and network metrics provided detail regarding variation in the density and transitivity, changes in structure with different diameters and radii, and variations in centralisation. Each network analysis metric has a contribution to play in describing the dynamics of a daily HCP network and the composite findings provide insights that cannot be determined with standard approaches. CONCLUSIONS: Network analysis provides a novel approach to investigate and visualise patterns of HCP-patient interactions which allow for a deeper understanding of the complex nature of hospital patient care and could have numerous practical operational applications.


Assuntos
Registros Eletrônicos de Saúde , Transplante de Rim , Humanos , Relações Profissional-Paciente , Estudos de Coortes , Pessoal de Saúde , Masculino , Unidades de Terapia Intensiva , Feminino , Hospitalização
3.
Int J Med Inform ; 192: 105646, 2024 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-39393126

RESUMO

BACKGROUND: Large-scale health data has significant potential for research and innovation, especially with longitudinal data offering insights into prevention, disease progression, and treatment effects. Yet, analyzing this data type is complex, as data points are repeatedly documented along the timeline. As a consequence, extracting cross-sectional tabular data suitable for statistical analysis and machine learning can be challenging for medical researchers and data scientists alike, with existing tools lacking balance between ease-of-use and comprehensiveness. OBJECTIVE: This paper introduces HERALD, a novel domain-specific query language designed to support the transformation of longitudinal health data into cross-sectional tables. We describe the basic concepts, the query syntax, a graphical user interface for constructing and executing HERALD queries, as well as an integration into Informatics for Integrating Biology and the Bedside (i2b2). METHODS: The syntax of HERALD mimics natural language and supports different query types for selection, aggregation, analysis of relationships, and searching for data points based on filter expressions and temporal constraints. Using a hierarchical concept model, queries are executed individually for the data of each patient, while constructing tabular output. HERALD is closed, meaning that queries process data points and generate data points. Queries can refer to data points that have been produced by previous queries, providing a simple, but powerful nesting mechanism. RESULTS: The open-source implementation consists of a HERALD query parser, an execution engine, as well as a web-based user interface for query construction and statistical analysis. The implementation can be deployed as a standalone component and integrated into self-service data analytics environments like i2b2 as a plugin. HERALD can be valuable tool for data scientists and machine learning experts, as it simplifies the process of transforming longitudinal health data into tables and data matrices. CONCLUSION: The construction of cross-sectional tables from longitudinal data can be supported through dedicated query languages that strike a reasonable balance between language complexity and transformation capabilities.

4.
Am J Biol Anthropol ; : e25020, 2024 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-39222382

RESUMO

A central goal of biological anthropology is connecting environmental variation to differences in host physiology, biology, health, and evolution. The microbiome represents a valuable pathway for studying how variation in host environments impacts health outcomes. While there are many resources for learning about methods related to microbiome sample collection, laboratory analyses, and genetic sequencing, there are fewer dedicated to helping researchers navigate the dense portfolio of bioinformatics and statistical approaches for analyzing microbiome data. Those that do exist are rarely related to questions in biological anthropology and instead are often focused on human biomedicine. To address this gap, we expand on existing tutorials and provide a "road map" to aid biological anthropologists in understanding, selecting, and deploying the data analysis and visualization methods that are most appropriate for their specific research questions. Leveraging an existing dataset of fecal samples and survey data collected from wild geladas living in Simien Mountains National Park in Ethiopia (Baniel et al., 2021), this paper guides researchers toward answering three questions related to variation in the gut microbiome across host and environmental factors. By providing explanations, examples, and a reproducible workflow for different analytic methods, we move beyond the theoretical benefits of considering the microbiome within anthropological research and instead present researchers with a guide for applying microbiome science to their work. This paper makes microbiome science more accessible to biological anthropologists and paves the way for continued research into the microbiome's role in the ecology, evolution, and health of human and non-human primates.

5.
Heliyon ; 10(16): e35979, 2024 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-39247267

RESUMO

We analyze leading journals in behavioral finance to identify the most-used keywords in the area and how they have evolved. Using keyword analysis of data between 2000 and 2020 as well as data mapping and visualization tools, a dynamic map of the discipline was constructed. This study assesses the state-of-the-art of the field, main topics of discussion, relationships that arise between the concepts discussed, and emerging issues of interest. The sample comprises 3876 pieces, including 15859 keywords from journals responsible for the growth of the discipline, namely the Journal of Behavioral and Experimental Economics, Journal of Behavioral and Experimental Finance, Journal of Economic Psychology, Journal of Behavioral Finance, and Review of Behavioral Finance. During the period analyzed, our results depict a lively area and highlight the prominent role that experiments play in the field. Two related but different streams of behavioral finance research are revealed.

6.
Heliyon ; 10(16): e36127, 2024 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-39224260

RESUMO

Extensive research has made significant progress in exploring the potential application of extracellular vesicles (EV) in the diagnosis and treatment of osteoarthritis (OA). However, there is current a lack of study on bibliometrics. In this study, we completed a novel bibliometric analysis of EV research in OA over the past two decades. Specifically, we identified a total of 354 relevant publications obtained between January 1, 2003 and December 31, 2022. We also provided a description of the distribution information regarding the countries or regions of publication, institutions involved, journals, authors, citations, and keywords. The primary research focuses encompassed the role of extracellular vesicles in the diagnosis of OA, delivery of active ingredients, treatment strategies, and cartilage repair. These findings highlight the latest research frontiers and emerging areas, providing valuable insights for further investigations on the application of extracellular vesicles in the context of osteoarthritis.

7.
Stud Health Technol Inform ; 317: 314-323, 2024 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-39234736

RESUMO

INTRODUCTION: User-centered data visualizations can reduce physician cognitive load and support clinical decision making. To facilitate the selection of appropriate visualizations for single patient health data summaries, this scoping review provides a literature overview of possible visualization techniques and the corresponding reported user-centered design phases. METHODS: The publication databases PubMed, Web of Science, IEEE Xplore and ACM Digital Library were searched for relevant articles from 2017 to 2022. RESULTS: Of the 777 articles screened, 78 articles were included in the final analysis. The most commonly used visualization techniques are table, scatterplot-line timeline, text and event timelines, with 24 other visualization techniques identified. The testing phase of the user centered design process is reported most frequently. CONCLUSION: This scoping review can support developers in the selection of suitable visualizations for single patient health data by revealing the design space of possible visualization techniques.


Assuntos
Sistemas de Apoio a Decisões Clínicas , Humanos , Visualização de Dados , Tomada de Decisão Clínica , Registros Eletrônicos de Saúde , Interface Usuário-Computador , Design Centrado no Usuário
8.
Health Informatics J ; 30(3): 14604582241279720, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39224960

RESUMO

The analysis of large sets of spatio-temporal data is a fundamental challenge in epidemiological research. As the quantity and the complexity of such kind of data increases, automatic analysis approaches, such as statistics, data mining, machine learning, etc., can be used to extract useful information. While these approaches have proven effective, they require a priori knowledge of the information being sought, and some interesting insights into the data may be missed. To bridge this gap, information visualization offers a set of techniques for not only presenting known information, but also exploring data without having a hypothesis formulated beforehand. In this paper, we introduce Epid Data Explorer (EDE), a visualization tool that enables exploration of spatio-temporal epidemiological data. EDE allows easy comparisons of indicators and trends across different geographical areas and times. It facilitates this exploration through ready-to-use pre-loaded datasets as well as user-chosen datasets. The tool also provides a secure architecture for easily importing new datasets while ensuring confidentiality. In two use cases using data associated with the COVID-19 epidemic, we demonstrate the substantial impact of implemented lockdown measures on mobility and how EDE allows assessing correlations between the spread of COVID-19 and weather conditions.


Assuntos
COVID-19 , Análise Espaço-Temporal , Humanos , COVID-19/epidemiologia , Mineração de Dados/métodos , Visualização de Dados , SARS-CoV-2 , Software
9.
Bioinformatics ; 2024 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-39348165

RESUMO

SUMMARY: Computational metabolomics workflows have revolutionized the untargeted metabolomics field. However, the organization and prioritization of metabolite features remains a laborious process. Organizing metabolomics data is often done through mass fragmentation-based spectral similarity grouping, resulting in feature sets that also represent an intuitive and scientifically meaningful first stage of analysis in untargeted metabolomics. Exploiting such feature sets, feature-set testing has emerged as an approach that is widely used in genomics and targeted metabolomics pathway enrichment analyses. It allows for formally combining groupings with statistical testing into more meaningful pathway enrichment conclusions. Here, we present msFeaST (mass spectral Feature Set Testing), a feature-set testing and visualization workflow for LC-MS/MS untargeted metabolomics data. Feature-set testing involves statistically assessing differential abundance patterns for groups of features across experimental conditions. We developed msFeaST to make use of spectral similarity-based feature groupings generated using k-medoids clustering, where the resulting clusters serve as a proxy for grouping structurally similar features with potential biosynthesis pathway relationships. Spectral clustering done in this way allows for feature group-wise statistical testing using the globaltest package, which provides high power to detect small concordant effects via joint modeling and reduced multiplicity adjustment penalties. Hence, msFeaST provides interactive integration of the semi-quantitative experimental information with mass-spectral structural similarity information, enhancing the prioritization of features and feature sets during exploratory data analysis. AVAILABILITY AND IMPLEMENTATION: The msFeaST workflow is freely available through https://github.com/kevinmildau/msFeaST and built to work on MacOS and Linux systems. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

10.
Appl Spectrosc ; : 37028241280669, 2024 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-39340333

RESUMO

Modern developments in autonomous chemometric machine learning technology strive to relinquish the need for human intervention. However, such algorithms developed and used in chemometric multivariate calibration and classification applications exclude crucial expert insight when difficult and safety-critical analysis situations arise, e.g., spectral-based medical decisions such as noninvasively determining if a biopsy is cancerous. The prediction accuracy and interpolation capabilities of autonomous methods for new samples depend on the quality and scope of their training (calibration) data. Specifically, analysis patterns within target data not captured by the training data will produce undesirable outcomes. Alternatively, using an immersive analytic approach allows insertion of human expert judgment at key machine learning algorithm junctures forming a sensemaking process performed in cooperation with a computer. The capacity of immersive virtual reality (IVR) environments to render human comprehensible three-dimensional space simulating real-world encounters, suggests its suitability as a hybrid immersive human-computer interface for data analysis tasks. Using IVR maximizes human senses to capitalize on our instinctual perception of the physical environment, thereby leveraging our innate ability to recognize patterns and visualize thresholds crucial to reducing erroneous outcomes. In this first use of IVR as an immersive analytic tool for spectral data, we examine an integrated IVR real-time model selection algorithm for a recent model updating method that adapts a model from the original calibration domain to predict samples from shifted target domains. Using near-infrared data, analyte prediction errors from IVR-selected models are reduced compared to errors using an established autonomous model selection approach. Results demonstrate the viability of IVR as a human data analysis interface for spectral data analysis including classification problems.

11.
J Med Internet Res ; 26: e56804, 2024 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-39288409

RESUMO

BACKGROUND: Data dashboards have become more widely used for the public communication of health-related data, including in maternal health. OBJECTIVE: We aimed to evaluate the content and features of existing publicly available maternal health dashboards in the United States. METHODS: Through systematic searches, we identified 80 publicly available, interactive dashboards presenting US maternal health data. We abstracted and descriptively analyzed the technical features and content of identified dashboards across four areas: (1) scope and origins, (2) technical capabilities, (3) data sources and indicators, and (4) disaggregation capabilities. Where present, we abstracted and qualitatively analyzed dashboard text describing the purpose and intended audience. RESULTS: Most reviewed dashboards reported state-level data (58/80, 72%) and were hosted on a state health department website (48/80, 60%). Most dashboards reported data from only 1 (33/80, 41%) or 2 (23/80, 29%) data sources. Key indicators, such as the maternal mortality rate (10/80, 12%) and severe maternal morbidity rate (12/80, 15%), were absent from most dashboards. Included dashboards used a range of data visualizations, and most allowed some disaggregation by time (65/80, 81%), geography (65/80, 81%), and race or ethnicity (55/80, 69%). Among dashboards that identified their audience (30/80, 38%), legislators or policy makers and public health agencies or organizations were the most common audiences. CONCLUSIONS: While maternal health dashboards have proliferated, their designs and features are not standard. This assessment of maternal health dashboards in the United States found substantial variation among dashboards, including inconsistent data sources, health indicators, and disaggregation capabilities. Opportunities to strengthen dashboards include integrating a greater number of data sources, increasing disaggregation capabilities, and considering end-user needs in dashboard design.


Assuntos
Saúde Materna , Estados Unidos , Humanos , Saúde Materna/estatística & dados numéricos , Feminino , Saúde Pública , Gravidez , Sistemas de Painéis
12.
Life (Basel) ; 14(9)2024 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-39337979

RESUMO

Type 2 diabetes, prediabetes, and insulin resistance (IR) are widespread yet often undetected in their early stages, contributing to a silent epidemic. Metabolic Syndrome (MetS) is also highly prevalent, increasing the chronic disease burden. Annual check-ups are inadequate for early detection due to conventional result formats that lack specific markers and comprehensive visualization. The aim of this study was to evaluate low-budget biochemical and hematological parameters, with data visualization, for identifying IR and MetS in a community-based laboratory. In a cross-sectional study with 1870 participants in Patras, Greece, blood samples were analyzed for key cardiovascular and inflammatory markers. IR diagnostic markers (TyG-Index, TyG-BMI, Triglycerides/HDL ratio, NLR) were compared with HOMA-IR. Innovative data visualization techniques were used to present metabolic profiles. Notable differences in parameters of cardiovascular risk and inflammation were observed between normal-weight and obese people, highlighting BMI as a significant risk factor. Also, the inflammation marker NHR (Neutrophils to HDL-Cholesterol Ratio) Index was successful at distinguishing the obese individuals and those with MetS from normal individuals. Additionally, a new diagnostic index of IR, combining BMI (Body Mass Index) and NHR Index, demonstrated better performance than other well-known indices. Lastly, data visualization significantly helped individuals understand their metabolic health patterns more clearly. BMI and NHR Index could play an essential role in assessing metabolic health patterns. Integrating specific markers and data visualization in routine check-ups enhances the early detection of IR and MetS, aiding in better patient awareness and adherence.

13.
J Clin Transl Sci ; 8(1): e121, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39345710

RESUMO

Multisector stakeholders, including, community-based organizations, health systems, researchers, policymakers, and commerce, increasingly seek to address health inequities that persist due to structural racism. They require accessible tools to visualize and quantify the prevalence of social drivers of health (SDOH) and correlate them with health to facilitate dialog and action. We developed and deployed a web-based data visualization platform to make health and SDOH data available to the community. We conducted interviews and focus groups among end users of the platform to establish needs and desired platform functionality. The platform displays curated SDOH and de-identified and aggregated local electronic health record data. The resulting Social, Environmental, and Equity Drivers (SEED) Health Atlas integrates SDOH data across multiple constructs, including socioeconomic status, environmental pollution, and built environment. Aggregated health prevalence data on multiple conditions can be visualized in interactive maps. Data can be visualized and downloaded without coding knowledge. Visualizations facilitate an understanding of community health priorities and local health inequities. SEED could facilitate future discussions on improving community health and health equity. SEED provides a promising tool that members of the community and researchers may use in their efforts to improve health equity.

14.
J Am Soc Mass Spectrom ; 35(10): 2315-2323, 2024 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-39221961

RESUMO

Mass spectrometry imaging (MSI) provides information about the spatial localization of molecules in complex samples with high sensitivity and molecular selectivity. Although point-wise data acquisition, in which mass spectra are acquired at predefined points in a grid pattern, is common in MSI, several MSI techniques use line-wise data acquisition. In line-wise mode, the imaged surface is continuously sampled along consecutive parallel lines and MSI data are acquired as a collection of line scans across the sample. Furthermore, aside from the standard imaging mode in which full mass spectra are acquired, other acquisition modes have been developed to enhance molecular specificity, enable separation of isobaric and isomeric species, and improve sensitivity to facilitate the imaging of low abundance species. These methods, including MS/MS-MSI in both MS2 and MS3 modes, multiple-reaction monitoring (MRM)-MSI, and ion mobility spectrometry (IMS)-MSI have all demonstrated their capabilities, but their broader implementation is limited by the existing MSI analysis software. Here, we present MSIGen, an open-source Python package for the visualization of MSI experiments performed in line-wise acquisition mode containing MS1, MS2, MRM, and IMS data, which is available at https://github.com/LabLaskin/MSIGen. The package supports multiple vendor-specific and open-source data formats and contains tools for targeted extraction of ion images, normalization, and exportation as images, arrays, or publication-style images. MSIGen offers multiple interfaces, allowing for accessibility and easy integration with other workflows. Considering its support for a wide variety of MSI imaging modes and vendor formats, MSIGen is a valuable tool for the visualization and analysis of MSI data.

15.
Imaging Neurosci (Camb) ; 2: 1-39, 2024 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-39257641

RESUMO

Quality control (QC) assessment is a vital part of FMRI processing and analysis, and a typically underdiscussed aspect of reproducibility. This includes checking datasets at their very earliest stages (acquisition and conversion) through their processing steps (e.g., alignment and motion correction) to regression modeling (correct stimuli, no collinearity, valid fits, enough degrees of freedom, etc.) for each subject. There are a wide variety of features to verify throughout any single-subject processing pipeline, both quantitatively and qualitatively. We present several FMRI preprocessing QC features available in the AFNI toolbox, many of which are automatically generated by the pipeline-creation tool, afni_proc.py. These items include a modular HTML document that covers full single-subject processing from the raw data through statistical modeling, several review scripts in the results directory of processed data, and command line tools for identifying subjects with one or more quantitative properties across a group (such as triaging warnings, making exclusion criteria, or creating informational tables). The HTML itself contains several buttons that efficiently facilitate interactive investigations into the data, when deeper checks are needed beyond the systematic images. The pages are linkable, so that users can evaluate individual items across a group, for increased sensitivity to differences (e.g., in alignment or regression modeling images). Finally, the QC document contains rating buttons for each "QC block," as well as comment fields for each, to facilitate both saving and sharing the evaluations. This increases the specificity of QC, as well as its shareability, as these files can be shared with others and potentially uploaded into repositories, promoting transparency and open science. We describe the features and applications of these QC tools for FMRI.

16.
Artigo em Inglês | MEDLINE | ID: mdl-39348270

RESUMO

OBJECTIVES: This article describes the design and evaluation of MS Pattern Explorer, a novel visual tool that uses interactive machine learning to analyze fitness wearables' data. Applied to a clinical study of multiple sclerosis (MS) patients, the tool addresses key challenges: managing activity signals, accelerating insight generation, and rapidly contextualizing identified patterns. By analyzing sensor measurements, it aims to enhance understanding of MS symptomatology and improve the broader problem of clinical exploratory sensor data analysis. MATERIALS AND METHODS: Following a user-centered design approach, we learned that clinicians have 3 priorities for generating insights for the Barka-MS study data: exploration and search for, and contextualization of, sequences and patterns in patient sleep and activity. We compute meaningful sequences for patients using clustering and proximity search, displaying these with an interactive visual interface composed of coordinated views. Our evaluation posed both closed and open-ended tasks to participants, utilizing a scoring system to gauge the tool's usability, and effectiveness in supporting insight generation across 15 clinicians, data scientists, and non-experts. RESULTS AND DISCUSSION: We present MS Pattern Explorer, a visual analytics system that helps clinicians better address complex data-centric challenges by facilitating the understanding of activity patterns. It enables innovative analysis that leads to rapid insight generation and contextualization of temporal activity data, both within and between patients of a cohort. Our evaluation results indicate consistent performance across participant groups and effective support for insight generation in MS patient fitness tracker data. Our implementation offers broad applicability in clinical research, allowing for potential expansion into cohort-wide comparisons or studies of other chronic conditions. CONCLUSION: MS Pattern Explorer successfully reduces the signal overload clinicians currently experience with activity data, introducing novel opportunities for data exploration, sense-making, and hypothesis generation.

17.
Front Bioinform ; 4: 1349205, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39286643

RESUMO

Rvisdiff is an R/Bioconductor package that generates an interactive interface for the interpretation of differential expression results. It creates a local web page that enables the exploration of statistical analysis results through the generation of auto-analytical visualizations. Users can explore the differential expression results and the source expression data interactively in the same view. As input, the package supports the results of popular differential expression packages such as DESeq2, edgeR, and limma. As output, the package generates a local HTML page that can be easily viewed in a web browser. Rvisdiff is freely available at https://bioconductor.org/packages/Rvisdiff/.

18.
Heliyon ; 10(18): e37439, 2024 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-39315188

RESUMO

The emergence of artificial intelligence (AI) technology has presented new challenges and opportunities for Traditional Chinese Medicine (TCM), aiming to provide objective assessments and improve clinical effectiveness. However, there is a lack of comprehensive analyses on the research trajectory, key directions, current trends, and future perspectives in this field. This research aims to comprehensively update the progress of AI in TCM over the past 24 years, based on data from the Web of Science database covering January 1, 2000, to March 1, 2024. Using advanced analytical tools, we conducted detailed bibliometric and visual analyses. The results highlight China's predominant influence, contributing 54.35 % of the total publications and playing a key role in shaping research in this field. Significant productivity was observed at institutions such as the China Academy of Chinese Medical Sciences, Beijing University of Chinese Medicine, and Shanghai University of Traditional Chinese Medicine, with Wang Yu being the most prolific contributor. The journal Molecules contributed the most publications in this field. This study identified hepatocellular carcinoma, chemical and drug-induced liver injury, Papillon-Lefèvre disease, Parkinson's disease, and anorexia as the most significant disorders researched. This comprehensive bibliometric assessment benefits both seasoned researchers and newcomers, offering quick access to essential information and fostering the generation of innovative ideas in this field.

19.
J Med Internet Res ; 26: e58502, 2024 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-39178032

RESUMO

As digital phenotyping, the capture of active and passive data from consumer devices such as smartphones, becomes more common, the need to properly process the data and derive replicable features from it has become paramount. Cortex is an open-source data processing pipeline for digital phenotyping data, optimized for use with the mindLAMP apps, which is used by nearly 100 research teams across the world. Cortex is designed to help teams (1) assess digital phenotyping data quality in real time, (2) derive replicable clinical features from the data, and (3) enable easy-to-share data visualizations. Cortex offers many options to work with digital phenotyping data, although some common approaches are likely of value to all teams using it. This paper highlights the reasoning, code, and example steps necessary to fully work with digital phenotyping data in a streamlined manner. Covering how to work with the data, assess its quality, derive features, and visualize findings, this paper is designed to offer the reader the knowledge and skills to apply toward analyzing any digital phenotyping data set. More specifically, the paper will teach the reader the ins and outs of the Cortex Python package. This includes background information on its interaction with the mindLAMP platform, some basic commands to learn what data can be pulled and how, and more advanced use of the package mixed with basic Python with the goal of creating a correlation matrix. After the tutorial, different use cases of Cortex are discussed, along with limitations. Toward highlighting clinical applications, this paper also provides 3 easy ways to implement examples of Cortex use in real-world settings. By understanding how to work with digital phenotyping data and providing ready-to-deploy code with Cortex, the paper aims to show how the new field of digital phenotyping can be both accessible to all and rigorous in methodology.


Assuntos
Fenótipo , Software , Humanos , Biomarcadores , Visualização de Dados
20.
J Cheminform ; 16(1): 101, 2024 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-39152469

RESUMO

With the increased availability of chemical data in public databases, innovative techniques and algorithms have emerged for the analysis, exploration, visualization, and extraction of information from these data. One such technique is chemical grouping, where chemicals with common characteristics are categorized into distinct groups based on physicochemical properties, use, biological activity, or a combination. However, existing tools for chemical grouping often require specialized programming skills or the use of commercial software packages. To address these challenges, we developed a user-friendly chemical grouping workflow implemented in KNIME, a free, open-source, low/no-code, data analytics platform. The workflow serves as an all-encompassing tool, expertly incorporating a range of processes such as molecular descriptor calculation, feature selection, dimensionality reduction, hyperparameter search, and supervised and unsupervised machine learning methods, enabling effective chemical grouping and visualization of results. Furthermore, we implemented tools for interpretation, identifying key molecular descriptors for the chemical groups, and using natural language summaries to clarify the rationale behind these groupings. The workflow was designed to run seamlessly in both the KNIME local desktop version and KNIME Server WebPortal as a web application. It incorporates interactive interfaces and guides to assist users in a step-by-step manner. We demonstrate the utility of this workflow through a case study using an eye irritation and corrosion dataset.Scientific contributionsThis work presents a novel, comprehensive chemical grouping workflow in KNIME, enhancing accessibility by integrating a user-friendly graphical interface that eliminates the need for extensive programming skills. This workflow uniquely combines several features such as automated molecular descriptor calculation, feature selection, dimensionality reduction, and machine learning algorithms (both supervised and unsupervised), with hyperparameter optimization to refine chemical grouping accuracy. Moreover, we have introduced an innovative interpretative step and natural language summaries to elucidate the underlying reasons for chemical groupings, significantly advancing the usability of the tool and interpretability of the results.

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