SEAOP: a statistical ensemble approach for outlier detection in quantitative proteomics data.

Quality control in quantitative proteomics is a persistent challenge, particularly in identifying and managing outliers. Unsupervised learning models, which rely on data structure rather than predefined labels, offer potential solutions. However, without clear labels, their effectiveness might be compromised. Single models are susceptible to the randomness of parameters and initialization, which can result in a high rate of false positives. Ensemble models, on the other hand, have shown capabilities in effectively mitigating the impacts of such randomness and assisting in accurately detecting true outliers. Therefore, we introduced SEAOP, a Python toolbox that utilizes an ensemble mechanism by integrating multi-round data management and a statistics-based decision pipeline with multiple models. Specifically, SEAOP uses multi-round resampling to create diverse sub-data spaces and employs outlier detection methods to identify candidate outliers in each space. Candidates are then aggregated as confirmed outliers via a chi-square test, adhering to a 95% confidence level, to ensure the precision of the unsupervised approaches. Additionally, SEAOP introduces a visualization strategy, specifically designed to intuitively and effectively display the distribution of both outlier and non-outlier samples. Optimal hyperparameter models of SEAOP for outlier detection were identified by using a gradient-simulated standard dataset and Mann-Kendall trend test. The performance of the SEAOP toolbox was evaluated using three experimental datasets, confirming its reliability and accuracy in handling quantitative proteomics.

An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management.

In this chapter, we explore the application of high-throughput crop phenotyping facilities for phenotype data acquisition and the extraction of significant information from the collected data through image processing and data mining methods. Additionally, the construction and outlook of crop phenotype databases are introduced and the need for global cooperation and data sharing is emphasized. High-throughput crop phenotyping significantly improves accuracy and efficiency compared to traditional measurements, making significant contributions to overcoming bottlenecks in the phenotyping field and advancing crop genetics.

Whole-cycle management of women with epilepsy of child-bearing age: ontology construction and application.

BACKGROUND: The effective management of epilepsy in women of child-bearing age necessitates a concerted effort from multidisciplinary teams. Nevertheless, there exists an inadequacy in the seamless exchange of knowledge among healthcare providers within this context. Consequently, it is imperative to enhance the availability of informatics resources and the development of decision support tools to address this issue comprehensively. MATERIALS AND METHODS: The development of the Women with Epilepsy of Child-Bearing Age Ontology (WWECA) adhered to established ontology construction principles. The ontology's scope and universal terminology were initially established by the development team and subsequently subjected to external evaluation through a rapid Delphi consensus exercise involving domain experts. Additional entities and attribute annotation data were sourced from authoritative guideline documents and specialized terminology databases within the respective field. Furthermore, the ontology has played a pivotal role in steering the creation of an online question-and-answer system, which is actively employed and assessed by a diverse group of multidisciplinary healthcare providers. RESULTS: WWECA successfully integrated a total of 609 entities encompassing various facets related to the diagnosis and medication for women of child-bearing age afflicted with epilepsy. The ontology exhibited a maximum depth of 8 within its hierarchical structure. Each of these entities featured three fundamental attributes, namely Chinese labels, definitions, and synonyms. The evaluation of WWECA involved 35 experts from 10 different hospitals across China, resulting in a favorable consensus among the experts. Furthermore, the ontology-driven online question and answer system underwent evaluation by a panel of 10 experts, including neurologists, obstetricians, and gynecologists. This evaluation yielded an average rating of 4.2, signifying a positive reception and endorsement of the system's utility and effectiveness. CONCLUSIONS: Our ontology and the associated online question and answer system hold the potential to serve as a scalable assistant for healthcare providers engaged in the management of women with epilepsy (WWE). In the future, this developmental framework has the potential for broader application in the context of long-term management of more intricate chronic health conditions.

GPDminer: a tool for extracting named entities and analyzing relations in biological literature.

PURPOSE: The expansion of research across various disciplines has led to a substantial increase in published papers and journals, highlighting the necessity for reliable text mining platforms for database construction and knowledge acquisition. This abstract introduces GPDMiner(Gene, Protein, and Disease Miner), a platform designed for the biomedical domain, addressing the challenges posed by the growing volume of academic papers. METHODS: GPDMiner is a text mining platform that utilizes advanced information retrieval techniques. It operates by searching PubMed for specific queries, extracting and analyzing information relevant to the biomedical field. This system is designed to discern and illustrate relationships between biomedical entities obtained from automated information extraction. RESULTS: The implementation of GPDMiner demonstrates its efficacy in navigating the extensive corpus of biomedical literature. It efficiently retrieves, extracts, and analyzes information, highlighting significant connections between genes, proteins, and diseases. The platform also allows users to save their analytical outcomes in various formats, including Excel and images. CONCLUSION: GPDMiner offers a notable additional functionality among the array of text mining tools available for the biomedical field. This tool presents an effective solution for researchers to navigate and extract relevant information from the vast unstructured texts found in biomedical literature, thereby providing distinctive capabilities that set it apart from existing methodologies. Its application is expected to greatly benefit researchers in this domain, enhancing their capacity for knowledge discovery and data management.

The evolutionary dynamics of how languages signal who does what to whom.

Languages vary in how they signal "who does what to whom". Three main strategies to indicate the participant roles of "who" and "whom" are case, verbal indexing, and rigid word order. Languages that disambiguate these roles with case tend to have either verb-final or flexible word order. Most previous studies that found these patterns used limited language samples and overlooked the causal mechanisms that could jointly explain the association between all three features. Here we analyze grammatical data from a Grambank sample of 1705 languages with phylogenetic causal graph methods. Our results corroborate the claims that verb-final word order generally gives rise to case and, strikingly, establish that case tends to lead to the development of flexible word order. The combination of novel statistical methods and the Grambank database provides a model for the rigorous testing of causal claims about the factors that shape patterns of linguistic diversity.

Harnessing Big Data in Critical Care: Exploring a new European Dataset.

Freely available datasets have become an invaluable tool to propel data-driven research, especially in the field of critical care medicine. However, the number of datasets available is limited. This leads to the repeated reuse of datasets, inherently increasing the risk of selection bias. Additionally, the need arose to validate insights derived from one dataset with another. In 2023, the Salzburg Intensive Care database (SICdb) was introduced. SICdb offers insights in currently 27,386 intensive care admissions from 21,583 patients. It contains cases of general and surgical intensive care from all disciplines. Amongst others SICdb contains information about: diagnosis, therapies (including data on preceding surgeries), scoring, laboratory values, respiratory and vital signals, and configuration data. Data for SICdb (1.0.6) was collected at one single tertiary care institution of the Department of Anesthesiology and Intensive Care Medicine at the Salzburger Landesklinik (SALK) and Paracelsus Medical University (PMU) between 2013 and 2021. This article aims to elucidate on the characteristics of the dataset, the technical implementation, and provides analysis of its strengths and limitations.

Artificial Intelligence in Hand Surgery - How Generative AI is Transforming the Hand Surgery Landscape.

Artificial intelligence (AI) has witnessed significant advancements, reshaping various industries, including healthcare. The introduction of ChatGPT by OpenAI in November 2022 marked a pivotal moment, showcasing the potential of generative AI in revolutionising patient care, diagnosis and treatment. Generative AI, unlike traditional AI systems, possesses the ability to generate new content by understanding patterns within datasets. This article explores the evolution of AI in healthcare, tracing its roots to the term coined by John McCarthy in 1955 and the contributions of pioneers like John Von Neumann and Alan Turing. Currently, generative AI, particularly Large Language Models, holds promise across three broad categories in healthcare: patient care, education and research. In patient care, it offers solutions in clinical document management, diagnostic support and operative planning. Notable advancements include Microsoft's collaboration with Epic for integrating AI into electronic medical records (EMRs), enhancing clinical data management and patient care. Furthermore, generative AI aids in surgical decision-making, as demonstrated in plastic, orthopaedic and hepatobiliary surgeries. However, challenges such as bias, hallucination and integration with EMR systems necessitate caution and ongoing evaluation. The article also presents insights from the implementation of NUHS Russell-GPT, a generative AI chatbot, in a hand surgery department, showcasing its utility in administrative tasks but highlighting challenges in surgical planning and EMR integration. The survey showed unanimous support for incorporating AI into clinical settings, with all respondents being open to its use. In conclusion, generative AI is poised to enhance patient care and ease physician workloads, starting with automating administrative tasks and evolving to inform diagnoses, tailored treatment plans, as well as aid in surgical planning. As healthcare systems navigate the complexities of integrating AI, the potential benefits for both physicians and patients remain significant, offering a glimpse into a future where AI transforms healthcare delivery. Level of Evidence: Level V (Diagnostic).

Landscape of toxin-neutralizing therapeutics for snakebite envenoming (2015-2022): Setting the stage for an R&D agenda.

BACKGROUND: Progress in snakebite envenoming (SBE) therapeutics has suffered from a critical lack of data on the research and development (R&D) landscape. A database characterising this information would be a powerful tool for coordinating and accelerating SBE R&D. To address this need, we aimed to identify and categorise all active investigational candidates in development for SBE and all available or marketed products. METHODOLOGY/PRINCIPAL FINDINGS: In this landscape study, publicly available data and literature were reviewed to canvas the state of the SBE therapeutics market and research pipeline by identifying, characterising, and validating all investigational drug and biologic candidates with direct action on snake venom toxins, and all products available or marketed from 2015 to 2022. We identified 127 marketed products and 196 candidates in the pipeline, describing a very homogenous market of similar but geographically bespoke products and a diverse but immature pipeline, as most investigational candidates are at an early stage of development, with only eight candidates in clinical development. CONCLUSIONS/SIGNIFICANCE: Further investment and research is needed to address the shortfalls in products already on the market and to accelerate R&D for new therapeutics. This should be accompanied by efforts to converge on shared priorities and reshape the current SBE R&D ecosystem to ensure translation of innovation and access.

Flapjack: Data Management and Analysis for Genetic Circuit Characterization.

Flapjack presents a valuable solution for addressing challenges in the Design, Build, Test, Learn (DBTL) cycle of engineering synthetic genetic circuits. This platform provides a comprehensive suite of features for managing, analyzing, and visualizing kinetic gene expression data and associated metadata. By utilizing the Flapjack platform, researchers can effectively integrate the test phase with the build and learn phases, facilitating the characterization and optimization of genetic circuits. With its user-friendly interface and compatibility with external software, the Flapjack platform offers a practical tool for advancing synthetic biology research.This chapter provides an overview of the data model employed in Flapjack and its hierarchical structure, which aligns with the typical steps involved in conducting experiments and facilitating intuitive data management for users. Additionally, this chapter offers a detailed description of the user interface, guiding readers through accessing Flapjack, navigating its sections, performing essential tasks such as uploading data and creating plots, and accessing the platform through the pyFlapjack Python package.

The national distribution of lymphatic filariasis cases in Malawi using patient mapping and geostatistical modelling.

BACKGROUND: In 2020 the World Health Organization (WHO) declared that Malawi had successfully eliminated lymphatic filariasis (LF) as a public health problem. Understanding clinical case distributions at a national and sub-national level is important, so essential care packages can be provided to individuals living with LF symptoms. This study aimed to develop a national database and map of LF clinical cases across Malawi using geostatistical modelling approaches, programme-identified clinical cases, antigenaemia prevalence and climate information. METHODOLOGY: LF clinical cases identified through programme house-to-house surveys across 90 sub-district administrative boundaries (Traditional Authority (TA)) and antigenaemia prevalence from 57 sampled villages in Malawi were used in a two-step geostatistical modelling process to predict LF clinical cases across all TAs of the country. First, we modelled antigenaemia prevalence in relation to climate covariates to predict nationwide antigenaemia prevalence. Second, we modelled clinical cases for unmapped TAs based on our antigenaemia prevalence spatial estimates. PRINCIPLE FINDINGS: The models estimated 20,938 (95% CrI 18,091 to 24,071) clinical cases in unmapped TAs (70.3%) in addition to the 8,856 (29.7%), programme-identified cases in mapped TAs. In total, the overall national number of LF clinical cases was estimated to be 29,794 (95% CrI 26,957 to 32,927). The antigenaemia prevalence and clinical case mapping and modelling found the highest burden of disease in Chikwawa and Nsanje districts in the Southern Region and Karonga district in the Northern Region of the country. CONCLUSIONS: The models presented in this study have facilitated the development of the first national LF clinical case database and map in Malawi, the first endemic country in sub-Saharan Africa. It highlights the value of using existing LF antigenaemia prevalence and clinical case data together with modelling approaches to produce estimates that may be used for the WHO dossier requirements, to help target limited resources and implement long-term health strategies.

REDCapDM: An R package with a set of data management tools for a REDCap project.

BACKGROUND: Research Electronic Data CAPture (REDCap) is a web application for creating and managing online surveys and databases. Clinical data management is an essential process before performing any statistical analysis to ensure the quality and reliability of study information. Processing REDCap data in R can be complex and often benefits from automation. While there are several R packages available for specific tasks, none offer an expansive approach to data management. RESULTS: The REDCapDM is an R package for accessing and managing REDCap data. It imports data from REDCap to R using either an API connection or the files in R format exported directly from REDCap. It has several functions for data processing and transformation, and it helps to generate and manage queries to clarify or resolve discrepancies found in the data. CONCLUSION: The REDCapDM package is a valuable tool for data scientists and clinical data managers who use REDCap and R. It assists in tasks such as importing, processing, and quality-checking data from their research studies.

AagingBase: a comprehensive database of anti-aging peptides.

The process of aging is an intrinsic and inevitable aspect of life that impacts every living organism. As biotechnological advancements continue to shape our understanding of medicine, peptide therapeutics have emerged as a promising strategy for anti-aging interventions. This is primarily due to their favorable attributes, such as low immunogenicity and cost-effective production. Peptide-based treatments have garnered widespread acceptance and interest in aging research, particularly in the context of age-related therapies. To effectively develop anti-aging treatments, a comprehensive understanding of the physicochemical characteristics of anti-aging peptides is essential. Factors such as amino acid composition, instability index, hydrophobic areas and other relevant properties significantly determine their efficacy as potential therapeutic agents. Consequently, the creation of 'AagingBase', a comprehensive database for anti-aging peptides, aims to facilitate research on aging by leveraging the potential of peptide therapies. AagingBase houses experimentally validated 282 anti-aging peptides collected from 54 research articles and 236 patents. Employing state-of-the-art computational techniques, the acquired sequences have undergone rigorous physicochemical calculations. Furthermore, AagingBase presents users with various informative analyses highlighting atomic compositions, secondary structure fractions, tertiary structure, amino acid compositions and frequencies. The database also offers advanced search and filtering options and similarity search, thereby aiding researchers in understanding their biological functions. Hence, the database enables efficient identification and prioritization of potential peptide candidates in geriatric medicine and holds immense potential for advancing geriatric medicine research and innovations. AagingBase can be accessed without any restriction. Database URL: https://project.iith.ac.in/cgntlab/aagingbase/.

Simplifying Multimodal Clinical Research Data Management: Introducing an Integrated and User-friendly Database Concept.

BACKGROUND: Clinical research, particularly in scientific data, grapples with the efficient management of multimodal and longitudinal clinical data. Especially in neuroscience, the volume of heterogeneous longitudinal data challenges researchers. While current research data management systems offer rich functionality, they suffer from architectural complexity that makes them difficult to install and maintain and require extensive user training. OBJECTIVES: The focus is the development and presentation of a data management approach specifically tailored for clinical researchers involved in active patient care, especially in the neuroscientific environment of German university hospitals. Our design considers the implementation of FAIR (Findable, Accessible, Interoperable, and Reusable) principles and the secure handling of sensitive data in compliance with the General Data Protection Regulation. METHODS: We introduce a streamlined database concept, featuring an intuitive graphical interface built on Hypertext Markup Language revision 5 (HTML5)/Cascading Style Sheets (CSS) technology. The system can be effortlessly deployed within local networks, that is, in Microsoft Windows 10 environments. Our design incorporates FAIR principles for effective data management. Moreover, we have streamlined data interchange through established standards like HL7 Clinical Document Architecture (CDA). To ensure data integrity, we have integrated real-time validation mechanisms that cover data type, plausibility, and Clinical Quality Language logic during data import and entry. RESULTS: We have developed and evaluated our concept with clinicians using a sample dataset of subjects who visited our memory clinic over a 3-year period and collected several multimodal clinical parameters. A notable advantage is the unified data matrix, which simplifies data aggregation, anonymization, and export. THIS STREAMLINES DATA EXCHANGE AND ENHANCES DATABASE INTEGRATION WITH PLATFORMS LIKE KONSTANZ INFORMATION MINER (KNIME): . CONCLUSION: Our approach offers a significant advancement for capturing and managing clinical research data, specifically tailored for small-scale initiatives operating within limited information technology (IT) infrastructures. It is designed for immediate, hassle-free deployment by clinicians and researchers.The database template and precompiled versions of the user interface are available at: https://github.com/stebro01/research_database_sqlite_i2b2.git.

Quality control data management with unity real-time in molecular virology.

INTRODUCTION: Quality control (QC) is one component of an overarching quality management system (QMS) that aims at assuring laboratory quality and patient safety. QC data must be acceptable prior to reporting patients' results. Traditionally, QC statistics, records, and corrective actions were tracked at the Johns Hopkins Molecular Virology Laboratory using Microsoft Excel. Unity Real-Time (UnityRT), a QMS software (Bio-Rad Laboratories), which captures and analyzes QC data by instrument and control lot per assay, was implemented and its impact on the workflow was evaluated. The clinical utility of real-time QC monitoring using UnityRT is highlighted with a case of subtle QC trending of HIV-1 quantitative control results. METHODS: A comprehensive workflow analysis was performed, with a focus on Epstein Barr Virus (EBV) and BKV quantitative viral load testing (Roche cobas 6800). The number of QC steps and time to complete each step were assessed before and after implementing UnityRT. RESULTS: Our assessment of monthly QC data review revealed a total of 10 steps over 57 min when using Microsoft Excel, versus 6 steps over 11 min when using UnityRT. HIV-1 QC monitoring revealed subtle trending of the low positive control above the mean from November to December 2022, correlating with a change in the reagent kit lot. This associated with a shift in patients' results from positives below the lower limit of quantification to positives between 20 and 100 copies/mL. CONCLUSIONS: UnityRT consolidated QC analyses, monitoring, and tracking corrective actions. UnityRT was associated with significant time savings, which along with the interfaced feature of the QC capture and data analysis, have improved the workflow and reduced the risk of laboratory errors. The HIV-1 case revealed the value of the real-time monitoring of QC.