ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.

UNLABELLED: It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API. AVAILABILITY: The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.

Efficacy and Safety of Direct Oral Anticoagulants for Acute Treatment of Venous Thromboembolism in Older Adults: A Network Meta-Analysis of Randomised Controlled Trials.

OBJECTIVE: This systematic review and network meta-analysis aimed to evaluate the efficacy and safety of direct oral anticoagulants (DOACs) in adults aged 75 and over undergoing acute venous thromboembolism (VTE) treatment. METHODS: PubMed, Embase and the CENTRAL were searched up to 25 December 2023. The incidence of VTE recurrence and bleeding events was assessed. Employing a frequentist network meta-analysis approach, interventions not directly compared could be indirectly assessed through the 95% confidence interval (CI), enhancing the interpretability of the search results. The surface under the cumulative ranking curves (SUCRA) was utilized to generate the relative ranking probabilities for each group. RESULTS: Our study, analysing 6 randomised controlled trials with 3665 patients, compares direct oral anticoagulants (DOACs) and vitamin K antagonists (VKAs) in adults aged 75 and over with acute venous thromboembolism. Edoxaban reduces VTE recurrence risk compared with VKAs (risk ratio [RR] .50, 95% CI 0.27 - .95), while apixaban significantly decreases bleeding risk compared with VKAs (RR .23, 95% CI 0.08 - .69), edoxaban (RR .28, 95% CI 0.09 - .86) and rivaroxaban (RR .28, 95% CI 0.09 - .86). Despite low overall evidence quality, apixaban consistently ranks highest for both efficacy and safety. Findings underscore the nuanced efficacy-safety balance in this population, emphasizing cautious interpretation due to evidence limitations. CONCLUSION: Apixaban emerges as a favourable choice for acute VTE treatment in the elderly, displaying reduced bleeding risk compared to other treatments while maintaining comparable efficacy. Future studies should explore diverse anticoagulants efficacy and safety in older populations. Additionally, clinical prediction models tailored to geriatric cohorts are crucial for guiding treatment duration decisions.

Incidence and Risk Factors of Delayed Intracranial Hemorrhage in Anticoagulated Head Trauma Patients: A Systematic Review and Meta-Analysis.

OBJECTIVES: This study aims to provide a current and comprehensive analysis of the incidence of delayed intracerebral hemorrhage (dICH) in head trauma patients on oral anticoagulants (ACs) and to evaluate various potential risk factors. METHODS: We conducted a systematic review and meta-analysis following Preferred Reporting Items for Systematic Reviews and Meta-Analyses and Meta-Analysis of Observational Studies in Epidemiology guidelines. PubMed and Cochrane Central Register of Controlled Trials were searched for studies on dICH in anticoagulated head trauma patients undergoing repeat computed tomography scans. Studies reporting dICH incidence on repeat computed tomography within 24 hours of an initial negative scan were included. Data on demographics, AC type, risk factors, and clinical outcomes were extracted and analyzed. RESULTS: From 634 identified articles, 26 studies with 7218 patients were included. The overall incidence of dICH was 2.0%, with 43.8% of these cases requiring hospital admission or changes in clinical management. Only 0.1% required neurosurgical intervention, and 0.1% resulted in death. Meta-analysis of 20 studies revealed pooled dICH incidence per 1000 persons at risk was 27.1 for vitamin K antagonists and 20.5 for direct oral ACs. Significant risk factors for dICH included Glasgow Coma Scale <15, loss of consciousness, post-traumatic amnesia, and Abbreviated Injury Scale head ≥3. CONCLUSIONS: A low incidence of dICH requires neurosurgical intervention; however, further studies are required to assess the need for other medical management in these patients. Furthermore, selective imaging for high-risk patients could improve care and resource allocation.

Characterization of dietary protein among older adults in the United States: amount, animal sources, and meal patterns.

Although protein intakes in the United States are widely regarded as adequate, attention has been given to potential inadequacy of recommendations or patterns of intake in older adults. The objectives of this research were to update and expand estimates of protein intake and adequacy in older US adults, with additional focus on contributions of animal source protein. Data were obtained from 1,768 adults aged 51 years and older in the National Health and Nutrition Examination Survey 2005-2006, the Food and Nutrient Database for Dietary Studies, and US Department of Agriculture Standard Reference datasets. Estimates of inadequate intakes ranged from <1% to 5% of men aged 51 to 70 years to 9% to 24% of women aged ≥71 years, depending on whether adjusted or actual body weights were used to calculate grams of protein per kilogram of body weight. Mean usual protein intakes were 94±22 g/day and 56±13 g/day in those same groups, with 15.3%±2.3% and 15.4%±2.4% of energy from protein. Animal sources provided >60% of protein intake, on average. In regression models with energy intake, age, sex, ethnicity, and education as covariables, percent protein from animal sources predicted protein intake and odds of meeting the Recommended Dietary Allowances (P<0.001). Consumption of total and animal-source protein was skewed to the evening meal. Findings highlight the influence of body weight choice (actual vs adjusted) on estimates of protein inadequacy, and suggest the need for careful consideration of protein source in adults at risk for inadequacy. Research is needed to establish optimal protein intakes, sources, and patterns.