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phyddle: software for exploring phylogenetic models with deep learning
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Michael J Landis and Ammon Thompson
Systematic Biology, syaf036, https://doi.org/10.1093/sysbio/syaf036
Published: 14 May 2025
... . phylogenetics statistical models deep learning neural network software O RIGIN A L U N EDITED M AN U SCRIPT Version dated: May 7, 2025 RH: phylogenetic model exploration with phyddle phyddle: software for exploring phylogenetic models with deep learning Michael J. Landis1 Ammon Thompson2 1Department...
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A Note on Ordinal Modeling of Smoking Rate Data
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Donald Hedeker and others
Nicotine & Tobacco Research, ntaf087, https://doi.org/10.1093/ntr/ntaf087
Published: 30 April 2025
...:https://dbpia.nl.go.kr/pages/standard-publication-reuse-rights ) Abstract Introduction This paper discusses statistical models for ordinal data that may be more appropriate for smoking rate outcomes than are models that assume continuous measurement and normality. Smoking rate outcomes often have distributions...
Journal Article
Identification of plasma protein biomarkers for endometriosis and the development of statistical models for disease diagnosis Open Access
E M Schoeman and others
Human Reproduction, Volume 40, Issue 2, February 2025, Pages 270–279, https://doi.org/10.1093/humrep/deae278
Published: 24 December 2024
...., K.P., M.D., M.M., M.R., P.T., R.L., and T.C. are shareholders in Proteomics International. Otherwise, the authors have no conflicts of interest. TRIAL REGISTRATION NUMBER N/A. endometriosis diagnosis proteomics statistical models plasma protein biomarkers The Royal Women’s Hospital...
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A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes Free
Ziyi Wang and others
Briefings in Functional Genomics, Volume 23, Issue 6, November 2024, Pages 702–712, https://doi.org/10.1093/bfgp/elae040
Published: 19 October 2024
... transcriptomics spatial domain recognition statistical models graph neural network contrastive learning Hainan Provincial Natural Science Foundation of China 324MS009 National Natural Science Foundation of China 10.13039/501100001809 62261018 62131004 In the study of spatial resolution...
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Modeling Upper Limb Rehabilitation-Induced Recovery After Stroke: The Role of Attention as a Clinical Confounder Open Access
Silvia Salvalaggio and others
Physical Therapy, Volume 105, Issue 2, February 2025, pzae148, https://doi.org/10.1093/ptj/pzae148
Published: 10 October 2024
..., needing further exploration. Preserved attention and rehabilitation dose are candidate predictors of UL motor recovery. Attention Motor Function Neuroimaging Neurophysiology Prediction Rehabilitation Statistical Models Stroke Italian Ministry of Health 10.13039/501100003196 RF-2018-12366899 GR...
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Increasing temporal sensitivity of omics association studies with epigenome-wide distributed lag models
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Milan N Parikh and others
American Journal of Epidemiology, Volume 194, Issue 5, May 2025, Pages 1418–1425, https://doi.org/10.1093/aje/kwae375
Published: 24 September 2024
... maternal exposure statistical models National Institutes of Health 10.13039/100000002 and T32ES10957 to K.J.B. P30ES006096 R01ES031054 R01LM013222 to C.B. As omics technologies have developed, the need for powerful statistical methods that can overcome the unique challenges of high dimensionality...
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Applying a Bayesian spatiotemporal model to examine excess county-level cardiovascular disease death rates during the COVID-19 pandemic
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Adam S Vaughan and others
American Journal of Epidemiology, kwae330, https://doi.org/10.1093/aje/kwae330
Published: 31 August 2024
... statistics geography spatiotemporal analysis statistical models National Institute of Health’s National Heart, Lung, and Blood Institute R01HL158802 to H.Q. After consistent declines since at least the 1970s, cardiovascular disease (CVD) death rates in the United States began to plateau in 2010...
Journal Article
A goodness of fit framework for relational event models Open Access
Viviana Amati and others
Journal of the Royal Statistical Society Series A: Statistics in Society, Volume 187, Issue 4, October 2024, Pages 967–988, https://doi.org/10.1093/jrsssa/qnae016
Published: 15 March 2024
... reveals distinctive features of relational event models that have been ignored or overlooked in received empirical studies. auxiliary variables goodness of fit healthcare organizations interorganizational networks relational event models statistical models for networks Behavioural units of interest...
Journal Article
PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs Open Access
Pourya Naderi Yeganeh and others
Briefings in Bioinformatics, Volume 24, Issue 6, November 2023, bbad418, https://doi.org/10.1093/bib/bbad418
Published: 20 November 2023
... prioritization pathway analysis bioinformatics computational biology statistical models Harvard Medical School Aging Initiative Pilot US National Institutes on Aging R01 AG082093 National Institutes of Health 10.13039/100000002 R35 CA232105 R01 AG058816-01 National Cancer Institute...
Journal Article
Time-Varying Exposures and Miscarriage: A Comparison of Statistical Models Through Simulation Free
Alexandra C Sundermann and others
American Journal of Epidemiology, Volume 192, Issue 5, May 2023, Pages 790–799, https://doi.org/10.1093/aje/kwad021
Published: 30 January 2023
.... To uncover risk relationships in early pregnancy, it is critical to carefully define the role of exposure timing in the underlying causal hypothesis. alcohol consumption bias data analysis maternal exposure pregnancy spontaneous abortion statistical models National Institutes of Health 10.13039...
Journal Article
Dynamic models of obstructive sleep apnea provide robust prediction of respiratory event timing and a statistical framework for phenotype exploration Free
Shuqiang Chen and others
in
Sleep
Sleep, Volume 45, Issue 12, December 2022, zsac189, https://doi.org/10.1093/sleep/zsac189
Published: 06 August 2022
... and distributed under the terms of the Oxford University Press, Standard Journals Publication Model ( https://dbpia.nl.go.kr/pages/standard-publication-reuse-rights ) Graphical Abstract Graphical Abstract point processes sleep apnea statistical models National Institute of Neurological Disorders and Stroke...
Journal Article
COVID-19 Pandemic Impact on Trajectories in Cardiometabolic Health, Physical Activity, and Functioning Among Adults from the 2006–2020 Health and Retirement Study Free
Hind A Beydoun and others
The Journals of Gerontology: Series A, Volume 77, Issue 7, July 2022, Pages 1371–1379, https://doi.org/10.1093/gerona/glac028
Published: 01 February 2022
... syndrome, septic shock, multiorgan failure, and death ( 4 , 5 ). Activities of daily living Coronavirus Lifestyle Obesity Statistical models National Institute on Aging 10.13039/100000049 IRP 10.13039/501100001708 National Institutes of Health 10.13039/100000002 Epidemiologic evidence...
Journal Article
Gender-sensitive word embeddings for healthcare
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Shunit Agmon and others
Journal of the American Medical Informatics Association, Volume 29, Issue 3, March 2022, Pages 415–423, https://doi.org/10.1093/jamia/ocab279
Published: 16 December 2021
... and addressing gender and other representational biases in the clinical trials literature. Conclusion Addressing representational biases in data for training NLP embeddings can lead to better results on downstream tasks for underrepresented populations. word embeddings statistical models bias algorithms...
Journal Article
A comparison among gamma distribution, intravoxel incoherent motion, and mono-exponential models with turbo spin-echo diffusion-weighted MR imaging in the differential diagnosis of orofacial lesions Free
Wannakamon Panyarak and others
Dentomaxillofacial Radiology, Volume 51, Issue 1, 1 January 2022, 20200609, https://doi.org/10.1259/dmfr.20200609
Published: 28 July 2021
... resonance imaging Statistical models Differential diagnosis Orofacial lesions (4) S I b = S I 0 e − b ⋅ A D C The OsiriX MD software programme version 10.0.5 (Pixmeo SARL, Bernex, Switzerland) and ImageJ software programme version 1.5 (National Institutes of Health...
Journal Article
Selection Methods for Models to Predict Feedstuff Associative Effects in Goats
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Yoko Tsukahara and others
Journal of Animal Science, Volume 99, Issue Supplement_2, May 2021, Pages 39–40, https://doi.org/10.1093/jas/skab096.072
Published: 07 May 2021
... goats statistical models Abstract Animal nutrition models can be useful to gain an understanding of factors responsible for and predict biological responses. However, specific models developed can vary among statistical methods employed, especially with relatively small datasets. In this meta-analysis...
Journal Article
Contextualizing temporal arterial magnetic resonance angiography in the diagnosis of giant cell arteritis: a retrospective cohort study Free
Mats Junek and others
in
Rheumatology
Rheumatology, Volume 60, Issue 9, September 2021, Pages 4229–4237, https://doi.org/10.1093/rheumatology/keaa916
Published: 06 January 2021
... temporal artery biopsy). In those with low to medium probability, TA-MRA can help rule out the disease, but this continues to be a challenging diagnostic population. giant cell arteritis magnetic resonance imaging statistical models Rheumatology key messages Negative TA-MRA rules out GCA in those...
Journal Article
Probabilistic forecasting of surgical case duration using machine learning: model development and validation
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York Jiao and others
Journal of the American Medical Informatics Association, Volume 27, Issue 12, December 2020, Pages 1885–1893, https://doi.org/10.1093/jamia/ocaa140
Published: 08 October 2020
.... The more discerning forecast of the ML-based MDN approach affords opportunities for guiding intelligent schedule design and day-of-surgery operational decisions. machine learning perioperative medicine statistical models surgical duration Costs of surgery account for roughly a third of all health-care...
Journal Article
Detecting undiagnosed atrial fibrillation in UK primary care: Validation of a machine learning prediction algorithm in a retrospective cohort study Free
Sara Sekelj and others
European Journal of Preventive Cardiology, Volume 28, Issue 6, June 2021, Pages 598–605, https://doi.org/10.1177/2047487320942338
Published: 13 August 2020
... would benefit from atrial fibrillation screening in the United Kingdom. Atrial fibrillation machine learning statistical models sensitivity and specificity primary health care Atrial fibrillation is the most common arrhythmia (irregular heart rhythm disorder), and is associated with disability...
Journal Article
Choice of statistical model in observational studies of ART Free
Laura E Dodge and others
Human Reproduction, Volume 35, Issue 7, July 2020, Pages 1499–1504, https://doi.org/10.1093/humrep/deaa050
Published: 19 May 2020
...:https://dbpia.nl.go.kr/journals/pages/open_access/funder_policies/chorus/standard_publication_model ) Abstract Analyzing data on ART presents unique and sometimes complicated challenges related to choosing the unit(s) of analysis and the statistical model. In this commentary, we provide examples of how these challenges...
Journal Article
Growth Rate of Plasmodium falciparum: Analysis of Parasite Growth Data From Malaria Volunteer Infection Studies Open Access
Leesa F Wockner and others
The Journal of Infectious Diseases, Volume 221, Issue 6, 15 March 2020, Pages 963–972, https://doi.org/10.1093/infdis/jiz557
Published: 04 November 2019
...) and higher than infections induced by sporozoite (0.47/day), but parasite life-cycles were similar (38.8 hours). CHMI induced blood stage malaria parasite growth rate Plasmodium falciparum 3D7 statistical models The growth rate of Plasmodium parasites in the blood of infected...
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