Managing and evaluating the literature review process can be a time-consuming challenge when working one-on-one with students to teach scientific process skills, whether through an independent study, honors contract, or undergraduate research. In this article, I share my solution to address the pedagogical and organizational challenge posed by this type of teaching and mentoring: the citation management software Zotero used in conjunction with a template worksheet. Overall, this approach will save time, introduce students to a new multipurpose software tool, and lead to a set of reusable resources for future teaching.

OBJECTIVE: Metadata for data dIscoverability aNd study rEplicability in obseRVAtional studies (MINERVA), a European Medicines Agency-funded project (EUPAS39322), defined a set of metadata to describe real-world data sources (RWDSs) and piloted metadata collection in a prototype catalogue to assist investigators from data source discoverability through study conduct.
METHODS: A list of metadata was created from a review of existing metadata catalogues and recommendations, structured interviews, a stakeholder survey, and a technical workshop. The prototype was designed to comply with the FAIR principles (findable, accessible, interoperable, reusable), using MOLGENIS software. Metadata collection was piloted by 15 data access partners (DAPs) from across Europe.
RESULTS: A total of 442 metadata variables were defined in six domains: institutions (organizations connected to a data source); data banks (data collections sustained by an organization); data sources (collections of linkable data banks covering a common underlying population); studies; networks (of institutions); and common data models (CDMs). A total of 26 institutions were recorded in the prototype. Each DAP populated the metadata of one data source and its selected data banks. The number of data banks varied by data source; the most common data banks were hospital administrative records and pharmacy dispensation records (10 data sources each). Quantitative metadata were successfully extracted from three data sources conforming to different CDMs and entered into the prototype.
CONCLUSIONS: A metadata list was finalized, a prototype was successfully populated, and a good practice guide was developed. Setting up and maintaining a metadata catalogue on RWDSs will require substantial effort to support discoverability of data sources and reproducibility of studies in Europe.

Molecular HLA typing techniques are currently undergoing a rapid evolution. While real-time PCR is established as the standard method in tissue typing laboratories regarding allocation of solid organs, next generation sequencing (NGS) for high-resolution HLA typing is becoming indispensable but is not yet suitable for deceased donors. By contrast, high-resolution typing is essential for stem cell transplantation and is increasingly required for questions relating to various disease associations. In this multicentre clinical study, the TGS technique using nanopore sequencing is investigated applying NanoTYPE™ kit and NanoTYPER™ software (Omixon Biocomputing Ltd., Budapest, Hungary) regarding the concordance of the results with NGS and its practicability in diagnostic laboratories. The results of 381 samples show a concordance of 99.58% for 11 HLA loci, HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1 and -DPB1. The quality control (QC) data shows a very high quality of the sequencing performed in each laboratory, 34,926 (97.15%) QC values were returned as \'passed\', 862 (2.4%) as \'inspect\' and 162 (0.45%) as \'failed\'. We show that an \'inspect\' or \'failed\' QC warning does not automatically lead to incorrect HLA typing. The advantages of nanopore sequencing are speed, flexibility, reusability of the flow cells and easy implementation in the laboratory. There are challenges, such as exon coverage and the handling of large amounts of data. Finally, nanopore sequencing presents potential for applications in basic research within the field of epigenetics and genomics and holds significance for clinical concerns.

High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software programs for image analysis workflows typically do not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, nucleus registration, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new analysis modules for existing analysis pipelines and to adding new analysis modules. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI software platform for a variety of cell biology applications.

Understanding alignment and gap balancing in Total Knee Arthroplasty (TKA) can be challenging for trainee and experienced orthopedic surgeons. Traditional learning methods may not effectively translate to real-life scenarios. The advent of advanced technologies like robotic surgery and navigation systems has revolutionized intraoperative understanding of gap balancing techniques. This trial aims to investigate the effectiveness of robotic TKA planning software in educating trainees about alignment and ligament balancing. We hypothesize that a single session with the software will significantly enhance trainees\' understanding of these techniques. This UK-based single-center, two-arm, group parallel randomized controlled trial was conducted during a national robotic arthroplasty symposium. It aims to evaluate the effect of robotic knee arthroplasty software training on understanding TKA alignment and gap balancing principles using Multiple Choice Questions (MCQs). The MCQ test was crafted based on established guidelines from a different institution with expert consensus in the field. Our study revealed that baseline knowledge of gap balancing and alignment principles was generally low among all participants. However, the intervention group, which received comprehensive robotic software training, demonstrated a significant improvement in their MCQ scores compared to the control group, which did not undergo the training. In conclusion, our study demonstrates that robotic arthroplasty software training significantly improves the understanding of TKA alignment and balancing principles among orthopedic trainees. Level of Evidence II.

UNASSIGNED: This study is designed to generalize and depict the research hotspots of endophthalmitis through bibliometric methods and software and analyze the evolutive tendency of the work on this severe disease over the past 30 years.
UNASSIGNED: This study employed a rigorous bibliometric approach. We identified all endophthalmitis-related literature by conducting a comprehensive search of the Science Citation Index Expanded database under the Web of Science Core Collection. The data was then analyzed and visualized using CiteSpace and VOSviewer, two widely recognized software tools in the field of bibliometrics. CiteSpace was used to analyze the country distributions, dual map overlay of journals, keyword bursts, and co-cited references. VOSviewer was employed to describe the authors and co-cited authors, the journals, the co-cited journals, and the keywords co-occurrence network. This robust methodology ensures the reliability and validity of the study\'s findings.
UNASSIGNED: A total of 2960 publications, including 2695 articles and 265 reviews, were included in this bibliometric study. There has been no shortage of endophthalmitis-related publications since 1993, with an apparent upward trend during recent years. Possible correlations with the COVID-19 pandemic are also analyzed. These studies were finished by 11,048 authors from 75 countries worldwide, with the United States in the lead. In the keyword co-occurrence network, except for the endophthalmitis term, cataract surgery becomes the keyword with the highest frequency. Different categories of endophthalmitis, including postoperative, post-injection, post-traumatic, and endogenous endophthalmitis, and antibacterial and anti-inflammatory therapies of infectious endophthalmitis, are discussed by categories. From the perspective of the timeline, postoperative and post-injection endophthalmitis were the dominant forms before and after the year 2000, respectively. Co-citation analyses reveal that the Endophthalmitis Vitrectomy Study (EVS) conducted in 1995 provides pivotal guidance for later research. Diverse pathogenic bacteria (e.g., Coagulase-negative Staphylococci, Propionibacterium acnes, Viridians Streptococci, and Bacillus cereus) or fungi (e.g., Candida, Aspergillus, and Fusarium) contribute to varying treatment principles and clinical prognosis, which should be taken seriously. In addition, intravitreal and intracameral antibiotics are the mainstay for treating and preventing infectious endophthalmitis, respectively.
UNASSIGNED: Our bibliometric analysis provides an overview of dynamic evolution and structural relationships in the research field of endophthalmitis. The displayed hotspots and developmental directions have reference values for future investigation.

Genome-wide association studies (GWAS) have significantly enhanced our understanding of the genetic basis of complex diseases. Despite the technological advancements, gaps in our understanding remain, partly due to small effect sizes and inadequate coverage of genetic variation. Multiancestry GWAS meta-analysis (MAGMA) addresses these challenges by integrating genetic data from diverse populations, thereby increasing power to detect loci and improving fine-mapping resolution to identify causal variants across different ancestry groups. This review provides an overview of the protocols, statistical methods, and software of MAGMA, as well as highlighting some challenges associated with this approach.

BACKGROUND: The more accurate we can assess human physical behaviour in free-living conditions the better we can understand its relationship with health and wellbeing. Thigh-worn accelerometry can be used to identify basic activity types as well as different postures with high accuracy. User-friendly software without the need for specialized programming may support the adoption of this method. This study aims to evaluate the classification accuracy of two novel no-code classification methods, namely SENS motion and ActiPASS.
METHODS: A sample of 38 healthy adults (30.8 ± 9.6 years; 53% female) wore the SENS motion accelerometer (12.5 Hz; ±4 g) on their thigh during various physical activities. Participants completed standardized activities with varying intensities in the laboratory. Activities included walking, running, cycling, sitting, standing, and lying down. Subsequently, participants performed unrestricted free-living activities outside of the laboratory while being video-recorded with a chest-mounted camera. Videos were annotated using a predefined labelling scheme and annotations served as a reference for the free-living condition. Classification output from the SENS motion software and ActiPASS software was compared to reference labels.
RESULTS: A total of 63.6 h of activity data were analysed. We observed a high level of agreement between the two classification algorithms and their respective references in both conditions. In the free-living condition, Cohen\'s kappa coefficients were 0.86 for SENS and 0.92 for ActiPASS. The mean balanced accuracy ranged from 0.81 (cycling) to 0.99 (running) for SENS and from 0.92 (walking) to 0.99 (sedentary) for ActiPASS across all activity types.
CONCLUSIONS: The study shows that two available no-code classification methods can be used to accurately identify basic physical activity types and postures. Our results highlight the accuracy of both methods based on relatively low sampling frequency data. The classification methods showed differences in performance, with lower sensitivity observed in free-living cycling (SENS) and slow treadmill walking (ActiPASS). Both methods use different sets of activity classes with varying definitions, which may explain the observed differences. Our results support the use of the SENS motion system and both no-code classification methods.

OBJECTIVE: Longitudinal patient tolerability data collected as part of randomized controlled trials are often summarized in a way that loses information and does not capture the treatment experience. To address this, we developed an interactive web application to empower clinicians and researchers to explore and visualize patient tolerability data.
METHODS: We used adverse event (AE) data (Common Terminology Criteria for Adverse Events) and patient-reported outcomes (PROs) from the NSABP-B35 phase III clinical trial, which compared anastrozole with tamoxifen for breast cancer-free survival, to demonstrate the tools. An interactive web application was developed using R and the Shiny web application framework that generates Sankey diagrams to visualize AEs and PROs using four tools: AE Explorer, PRO Explorer, Cohort Explorer, and Custom Explorer.
RESULTS: To illustrate how users can use the interactive tool, examples for each of the four applications are presented using data from the NSABP-B35 phase III trial and the NSABP-B30 trial for the Custom Explorer. In the AE and PRO explorers, users can select AEs or PROs to visualize within specified time periods and compare across treatments. In the cohort explorer, users can select a subset of patients with a specific symptom, severity, and treatment received to visualize the trajectory over time within a specified time interval. With the custom explorer, users can upload and visualize structured longitudinal toxicity and tolerability data.
CONCLUSIONS: We have created an interactive web application and tool for clinicians and researchers to explore and visualize clinical trial tolerability data. This adaptable tool can be extended for other clinical trial data visualization and incorporated into future patient-clinician interactions regarding treatment decisions.

BACKGROUND: Pakistan has significantly strengthened its capacity for active case finding (ACF) for tuberculosis (TB) that is being implemented at scale in the country. However, yields of ACF have been lower than expected, raising concerns on its effectiveness in the programmatic setting. Distribution of TB in communities is likely to be spatially heterogeneous and targeting of ACF in areas with higher TB prevalence may help improve yields. The primary aim of SPOT-TB is to investigate whether a policy change to use a geographically targeted approach towards ACF supported by an artificial intelligence (AI) software, MATCH-AI, can improve yields in Pakistan.
METHODS: SPOT-TB will use a pragmatic, stepped wedge cluster randomised design. A total of 30 mobile X-ray units and their field teams will be randomised to receive the intervention. Site selection for ACF in the intervention areas will be guided primarily through the use of MATCH-AI software that models subdistrict TB prevalence and identifies potential disease hotspots. Control areas will use existing approaches towards site selection that are based on staff knowledge, experience and analysis of historical data. The primary outcome measure is the difference in bacteriologically confirmed incident TB detected in the intervention relative to control areas. All remaining ACF-related procedures and algorithms will remain unaffected by this trial.
BACKGROUND: Ethical approval has been obtained from the Health Services Academy, Islamabad, Pakistan (7-82/IERC-HSA/2022-52) and from the Common Management Unit for TB, HIV and Malaria, Ministry of Health Services, Regulation and Coordination, Islamabad, Pakistan (26-IRB-CMU-2023). Findings from this study will be disseminated through publications in peer-reviewed journals and stakeholder meetings in Pakistan with the implementing partners and public-sector officials. Findings will also be presented at local and international medical and public health conferences.
BACKGROUND: NCT06017843.