Article
Computer Science, Artificial Intelligence
Yi-Ju Tseng, Hsiang-Ju Chiu, Chun Ju Chen
Summary: The dxpr package helps integrate and analyze clinical data, offering mechanisms to address common bottlenecks caused by characteristics such as heterogeneity and sparseness in clinical data. Conducting comorbidity data processes on a cohort of newborns, the package successfully identified significant differences in specific comorbidities between patients with and without certain diagnoses.
PEERJ COMPUTER SCIENCE
(2021)
Article
Environmental Sciences
Dan E. Kelley, Jaimie Harbin, Clark Richards
Summary: The R package argoFloats facilitates identification, downloading, caching, and analysis of oceanographic data collected by Argo profiling floats. The package has close connections with the oce package, making it familiar to R users analyzing oceanographic data of other kinds. Benefits of using argoFloats in everyday tasks specific to Argo data, such as downloading data, quality control, and producing diagnostic plots, are outlined in the paper.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemical Research Methods
Zuguang Gu, Daniel Huebschmann
Summary: Spiral layout has two major advantages in data visualization, improving visualization resolution and revealing periodic patterns. The R package spiralize provides a general solution with numerous graphics functions for users to easily implement self-defined high-level graphics.
Article
Biochemical Research Methods
Antoine Bodein, Marie-Pier Scott-Boyer, Olivier Perin, Kim-Anh Le Cao, Arnaud Droit
Summary: This text introduces the R package timeOmics, a generic analytical framework for integrating longitudinal multi-omics data. The package includes functions for pre-processing, modeling, and clustering to help researchers identify molecular features strongly associated with time. It is demonstrated in a case study to detect seasonal patterns of various molecular and clinical variables in patients with diabetes mellitus.
Article
Computer Science, Interdisciplinary Applications
Andrea Bucci, Giulio Palomba, Eduardo Rossi
Summary: The starvars package is introduced in this paper, which estimates and predicts the Vector Logistic Smooth Transition model in a very general setting, including predetermined variables. It also allows for testing for nonlinearity in a multivariate setting and detecting common breaks.
Article
Biochemical Research Methods
Xiaoyu Liang, Ying Hu, Chunhua Yan, Ke Xu
Summary: The study introduces a novel R package, i2d, for simulating image data through digital convolution, enabling information extraction and analysis in biomedical and biological research. Additionally, the package includes efficient methods for graph clustering based on simulated data to dissect complex gene networks.
Article
Biochemical Research Methods
Zachary B. Abrams, Dwayne G. Tally, Lynne Abruzzo, Kevin R. Coombes
Summary: Cytogenetics data, stored as karyotypes, are now being analyzed on a large scale thanks to tools like CytoGPS. The development of RCytoGPS further facilitates the analysis and visualization of karyotype data, advancing the field of computational cytogenetic pathology.
Article
Computer Science, Interdisciplinary Applications
Niloufar Dousti Mousavi, Hani Aldirawi, Jie Yang
Summary: AZIAD is a newly developed R package for analyzing zero-inflated or zero-altered data, covering a larger class of models with more accurate parameter estimates and greater power for model identification and selection.
JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION
(2021)
Article
Environmental Sciences
Aude Ratier, Virgile Baudrot, Milena Kaag, Aurelie Siberchicot, Christelle Lopes, Sandrine Charles
Summary: This paper introduces the functions and applications of the R-package rbioacc, which can be used to analyze data from bioaccumulation tests. The package provides TK parameter estimates, bioaccumulation metrics, and supports environmental risk assessment, in compliance with regulatory requirements.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Multidisciplinary Sciences
Wikum Dinalankara, Qian Ke, Donald Geman, Luigi Marchionni
Summary: Divergence analysis is a novel framework that transforms high-dimensional omics data into digitized codes, facilitating simple and effective analysis on different omics platforms.
Article
Neurosciences
Damon D. Pham, John Muschelli, Amanda F. Mejia
Summary: There is significant interest in adopting surface-and grayordinate-based analysis of MR data for improved visualization, alignment, and dimensionality reduction. The ciftiTools R package offers a comprehensive environment for working with CIFTI files, providing convenient and user-friendly tools for grayordinate-based analysis of functional MRI data.
Article
Biochemical Research Methods
Marzia Settino, Mario Cannataro
Summary: MMRFBiolinks is a tool package for integrating and analyzing data from MMRF and NCI-GDC, providing comprehensive analysis through various methods and visualizations. Through two case studies, it demonstrates how the tool overcomes the limitations of other analysis tools, making the retrieval, downloading, and analysis of MMRF data more comprehensive.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Neurosciences
Chenyin Zhao, Tinashe M. Tapera, Joelle Bagautdinovaa, Josiane Bourque, Sydney Covitz, Raquel E. Gur, Ruben C. Gur, Bart Larsen, Kahini Mehta, Steven L. Meisler, Kristin Murtha, John Muschelli, David R. Roalf, Valerie J. Sydnor, Alessandra M. Valcarcel, Russell T. Shinohara, Matthew Cieslak, Theodore D. Satterthwaite
Summary: Diffusion MRI is the dominant non-invasive imaging method for white matter organization. ModelArray is an R package that allows for mass-univariate statistical analysis of fixel-wise data, supporting linear models and generalized additive models. It provides a flexible and efficient platform for analyzing large datasets on personal computers.
Article
Biochemical Research Methods
Jun Yan, Hongning Zhai, Ling Zhu, Sasha Sa, Xiaojun Ding
Summary: obaDIA is a comprehensive automated tool for analyzing quantitative proteomics data, supporting various abundance matrices and providing rich result visualization and analysis functions.
Article
Ecology
Murray G. G. Efford
Summary: Some capture-recapture models for population estimation cannot be easily fitted by conventional methods. A new R package is introduced in this study to refine and extend a simulation and inverse prediction method for estimating population density, including models with varying density, trap interference, and other sources of non-independence among detection histories. The method is applied to a trapping study of brushtail possums in New Zealand, and the impact of time-varying interference on population decline is discussed.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Health Care Sciences & Services
Rosa Parisi, Yiu-Shing Lau, Peter Bower, Katherine Checkland, Jill Rubery, Matt Sutton, Sally J. Giles, Aneez Esmail, Sharon Spooner, Evangelos Kontopantelis
Summary: Primary care in England faces challenges with high turnover of general practitioners (GPs), and it is unclear whether there are specific predictors and associations with poor population health outcomes. This retrospective observational study found that larger practices in deprived areas with higher morbidity burden were more likely to experience persistent high turnover. Persistent high turnover was associated with poorer service indicators and health outcomes.
BMJ QUALITY & SAFETY
(2023)
Article
Medicine, General & Internal
Adrian Wells, David Reeves, Calvin Heal, Peter Fisher, Patrick Doherty, Linda Davies, Anthony Heagerty, Lora Capobianco
Summary: In cardiac rehabilitation, adding self-help metacognitive therapy (Home-MCT) to the usual rehabilitation program effectively reduces anxiety and depression symptoms. This study provides evidence for the potential of home-based psychological interventions in improving mental health outcomes for patients undergoing cardiac rehabilitation.
Review
Oncology
Violante Di Donato, Evangelos Kontopantelis, Ilaria Cuccu, Ludovica Sgamba, Tullio Golia D'Auge, Angelina Pernazza, Carlo Della Rocca, Lucia Manganaro, Carlo Catalano, Giorgia Perniola, Innocenza Palaia, Federica Tomao, Andrea Giannini, Ludovico Muzii, Giorgio Bogani
Summary: This study aimed to assess the role of radiomics analysis in pre-operatively predicting molecular or clinicopathological prognostic factors in patients with endometrial carcinoma. The results showed that MRI has high sensitivity and specificity in predicting high-grade endometrial carcinoma, deep myometrial invasion, lymphovascular space invasion, and nodal metastasis.
INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER
(2023)
Article
Multidisciplinary Sciences
David Reeves, Fiona Holland, Hazel Morbey, Mark Hann, Faraz Ahmed, Linda Davies, John V. Keady, Iracema V. Leroi, Siobhan V. Reilly
Summary: Efforts have been made in England to improve hospital care for people with dementia, but the outcomes for these patients, including length of stay, readmission rates, and mortality rates, remain relatively high. The study found that people with dementia were twice as likely to die within 30 days of discharge compared to those without dementia.
Review
Obstetrics & Gynecology
Ludovico Muzii, Chiara Di Tucci, Giulia Galati, Fabiana Carbone, Innocenza Palaia, Giorgio Bogani, Giorgia Perniola, Federica Tomao, Evangelos Kontopantelis, Violante Di Donato
Summary: The objective of this study is to determine the efficacy of dienogest therapy in reducing the risk of endometriosis recurrence after surgery compared to placebo or alternative treatments. A systematic review and meta-analysis were conducted, using data from PubMed and EMBASE. Dienogest significantly reduced the rate of cyst recurrence compared to placebo, but there was no statistically significant difference compared to GnRH agonist. Dienogest treatment also showed a trend towards reducing pain at 6 months. Comparatively, it had a lower rate of hot flashes and a trend towards lower incidence of vaginal dryness compared to GnRH agonist.
REPRODUCTIVE SCIENCES
(2023)
Article
Medicine, General & Internal
Magdalena Nowakowska, Salwa S. Zghebi, Li-Chia Chen, Darren M. Ashcroft, Evangelos Kontopantelis
Summary: This study used data from the Health Survey for England waves 1997-2014 to analyze the relationship between age and prescription opioid use in different socioeconomic groups. The findings showed that the association between age and opioid use varies across income and education levels. Higher income and education were associated with a lower probability of reported opioid use. The highest probability of opioid use was observed in the 40-60 age group among those with lower income and education. Employment status did not significantly affect opioid use. Further research is needed to understand opioid use patterns in older people, especially those from disadvantaged socioeconomic backgrounds.
Article
Medicine, General & Internal
Christos Grigoroglou, Kieran Walshe, Evangelos Kontopantelis, Jane Ferguson, Gemma Stringer, Darren Ashcroft, Thomas Allen
Summary: This study aimed to quantify and describe the use of locum doctors in NHS trusts in England from 2019 to 2021. The results showed significant variations in locum use among different trusts, with lower-rated and smaller trusts using locums more intensively. The study also highlighted a growing demand for locum doctors, as evidenced by the increasing number of unfilled shifts.
Article
Medicine, General & Internal
Daniel R. Morales, Mark Minchin, Evangelos Kontopantelis, Martin Roland, Matt Sutton, Bruce Guthrie
Summary: This study aimed to compare the impact of the withdrawal of the Quality and Outcomes Framework (QOF) scheme in primary care in Scotland in 2016 on the recorded quality of care, compared with England where the scheme continued. The results showed a significant decrease in performance for most quality of care indicators in Scotland after the abolition of QOF.
BMJ-BRITISH MEDICAL JOURNAL
(2023)
Article
Medicine, General & Internal
Rathi Ravindrarajah, Matt Sutton, David Reeves, Sarah Cotterill, Emma Mcmanus, Rachel Meacock, William Whittaker, Claudia Soiland-Reyes, Simon Heller, Peter Bower, Evangelos Kontopantelis
Summary: This study examines whether adults referred to the NHS Healthier You Diabetes Prevention Programme in England are less likely to develop type 2 diabetes mellitus. The findings show that people referred to the programme have a 20% lower risk of developing type 2 diabetes compared to those who were not referred. These results support the rapid implementation of the programme in England and suggest its continuation and expansion to other parts of the United Kingdom.
Article
Computer Science, Artificial Intelligence
Bradley Walters, Sandra Ortega-Martorell, Ivan Olier, Paulo J. G. Lisboa
Summary: A lack of transparency in machine learning models can limit their application. ANOVA methods can extract interpretable predictive models from them by decomposing them into functions of fewer variables. Retaining the terms involving only one or two variables in the ANOVA summation provides an efficient method to open black box classifiers.
Article
Multidisciplinary Sciences
Salwa S. Zghebi, Martin K. Rutter, Louise Y. Sun, Waqas Ullah, Muhammad Rashid, Darren M. Ashcroft, Douglas T. Steinke, Stephen Weng, Evangelos Kontopantelis, Mamas A. Mamas
Summary: This study analyzed the data of AMI patients admitted to hospitals in the United States in 2018. The study identified distinct phenogroups based on comorbidities and found that these phenogroups were associated with in-hospital outcomes.
Article
Cardiac & Cardiovascular Systems
Alyaa M. Ajabnoor, Rosa Parisi, Salwa S. Zghebi, Darren M. Ashcroft, Corinne Faivre-Finn, Charlotte Morris, Mamas A. Mamas, Evangelos Kontopantelis
Summary: The study examines the association between certain types of cancer and the balance between stroke and bleeding risk in patients with atrial fibrillation.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2023)
Article
Primary Health Care
Alexander Hodkinson, Salwa S. Zghebi, Evangelos Kontopantelis, Christos Grigoroglou, Darren M. Ashcroft, Mark Hann, Carolyn A. Chew-Graham, Rupert A. Payne, Paul Little, Simon de Lusignan, Anli Zhou, Aneez Esmail, Maria Panagioti
Summary: The study found that the well-being of GPs is associated with the overprescribing of strong opioids and antibiotics in primary care. GPs with higher levels of burnout symptoms, job dissatisfaction, and turnover intentions are more likely to overprescribe these medications. Additionally, longer working hours and practices located in the north of England are also associated with increased prescribing of strong opioids and antibiotics.
BRITISH JOURNAL OF GENERAL PRACTICE
(2023)
Article
Primary Health Care
Joseph Hutchinson, Kath Checkland, Jon Gibson, Evangelos Kontopantelis, Matt Sutton
Summary: This study examines the impact of surrounding general practice closures on the funding, list size, workforce composition, and quality of surviving practices. The findings indicate that higher exposure to closures leads to larger practice sizes, reduced funding per patient, and decreased patient satisfaction with services.
BRITISH JOURNAL OF GENERAL PRACTICE
(2023)