Hidden Markov Models (HMMs) are a commonly used tool for inference of transcription factor (TF) binding sites from DNA sequence data. We exploit the mathematical equivalence between HMMs for TF binding and the "inverse" statistical mechanics of hard rods in a one-dimensional disordered potential to investigate learning in HMMs. We derive analytic expressions for the Fisher information, a commonly employed measure of confidence in learned parameters, in the biologically relevant limit where the density of binding sites is low. We then use techniques from statistical mechanics to derive a scaling principle relating the specificity (binding energy) of a TF to the minimum amount of training data necessary to learn it.
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http://dx.doi.org/10.1007/s10955-010-0102-x | DOI Listing |
J Infect Dev Ctries
December 2024
Chest Dpt., Ahmed Maher Teaching Hospital, GOTHI, Cairo, Egypt.
Introduction: The present study aimed to explore the epidemiologic threats and factors associated with the coronavirus disease 2019 (COVID-19)-associated mucormycosis (CAM) epidemic that emerged in Egypt during the second COVID-19 wave. The study also aimed to explore the diagnostic features and the role of surgical interventions of CAM on the outcome of the disease in a central referral hospital.
Methodology: The study included 64 CAM patients from a referral hospital for CAM and a similar number of matched controls from COVID-19 patients who did not develop CAM.
J Infect Dev Ctries
December 2024
Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas, Campinas, Brazil.
Introduction: Invasive candidiasis is an important cause of nosocomial infection and recent studies have shown an increase in the number of cases during the coronavirus disease 2019 (COVID-19) pandemic. The present study aimed to evaluate the epidemiology and incidence of invasive candidiasis before and during the COVID-19 pandemic at a reference tertiary hospital in Brazil.
Methodology: A retrospective observational study was performed with 148 patients infected with Candida spp.
Ann Biomed Eng
January 2025
Department of Mechanical and Industrial Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
Purpose: To evaluate the population variation in head-to-helmet contact forces in helmet users.
Methods: Four different size Kevlar composite helmets were instrumented with contact pressure sensors and chinstrap tension meters. A total number of 89 volunteers (25 female and 64 male volunteers) participated in the study.
Sci Rep
January 2025
University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan, 680-749, Republic of Korea.
This study employed large eddy simulation (LES) with the wall-adapting local eddy-viscosity (WALE) model to investigate transitional flow characteristics in an idealized model of a healthy thoracic aorta. The OpenFOAM solver pimpleFoam was used to simulate blood flow as an incompressible Newtonian fluid, with the aortic walls treated as rigid boundaries. Simulations were conducted for 30 cardiac cycles and ensemble averaging was employed to ensure statistically reliable results.
View Article and Find Full Text PDFJ Shoulder Elbow Surg
January 2025
Division of Orthopaedic Surgery, The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada. Electronic address:
Introduction: Primary glenohumeral arthritis is typically associated with glenoid retroversion and posterior bone loss. Glenoid component fixation remains a weak link in the survivorship of anatomical total shoulder arthroplasty, particularly in the B2 glenoid. The aim of this study was to compare biomechanical properties of two glenoid preparation techniques in a B2 glenoid bone loss model.
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