University of South Florida

About: University of South Florida is a education organization based out in Tampa, Florida, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 34231 authors who have published 72644 publications receiving 2538044 citations. The organization is also known as: USF.

Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

Abstract: Molecular dynamics modeling has provided a powerful tool for simulating and understanding diverse systems - ranging from materials processes to biophysical phenomena. Parallel formulations of these methods have been shown to be among the most scalable scientific computing applications. Many instances of this class of methods rely on a static bond structure for molecules, rendering them infeasible for reactive systems. Recent work on reactive force fields has resulted in the development of ReaxFF, a novel bond order potential that bridges quantum-scale and classical MD approaches by explicitly modeling bond activity (reactions) and charge equilibration. These aspects of ReaxFF pose significant challenges from a computational standpoint, both in sequential and parallel contexts. Evolving bond structure requires efficient dynamic data structures. Minimizing electrostatic energy through charge equilibration requires the solution of a large sparse linear system with a shielded electrostatic kernel at each sub-femtosecond long time-step. In this context, reaching spatio-temporal scales of tens of nanometers and nanoseconds, where phenomena of interest can be observed, poses significant challenges. In this paper, we present the design and implementation details of the Purdue Reactive Molecular Dynamics code, PuReMD. PuReMD has been demonstrated to be highly efficient (in terms of processor performance) and scalable. It extends current spatio-temporal simulation capability for reactive atomistic systems by over an order of magnitude. It incorporates efficient dynamic data structures, algorithmic optimizations, and effective solvers to deliver low per-time-step simulation time, with a small memory footprint. PuReMD is comprehensively validated for performance and accuracy on up to 3375 cores on a commodity cluster (Hera at LLNL-OCF). Potential performance bottlenecks to scalability beyond our experiments have also been analyzed. PuReMD is available over the public domain and has been used to model diverse systems, ranging from strain relaxation in Si-Ge nanobars, water-silica surface interaction, and oxidative stress in lipid bilayers (bio-membranes).

Esophagitis associated with the use of alendronate

Abstract: Background Alendronate, an aminobisphosphonate and a selective inhibitor of osteoclast-mediated bone resorption, is used to treat osteoporosis in postmenopausal women and Paget's disease of bone. Aminobisphosphonates can irritate the upper gastrointestinal mucosa. Methods We describe three patients who had severe esophagitis shortly after starting to take alendronate and also analyze adverse esophageal effects reported to Merck, the manufacturer, through postmarketing surveillance. Results As of March 5, 1996, alendronate had been prescribed for an estimated 475,000 patients worldwide, and 1213 reports of adverse effects had been received. A total of 199 patients had adverse effects related to the esophagus; in 51 of these patients (26 percent), including the 3 we describe in case reports, adverse effects were categorized as serious or severe. Thirty-two patients (16 percent) were hospitalized, and two were temporarily disabled. Endoscopic findings generally indicated chemical esophagitis, with erosions o...

Current Status of the Digital Database for Screening Mammography

Abstract: The Digital Database for Screening Mammography1 is a resource for use by researchers investigating mammogram image analysis. In particular, the resource is focused on the context of image analysis to aid in screening for breast cancer. The database now contains substantial numbers of “normal” and “cancer” cases. This paper describes recent improvements and additions to DDSM.

BRCA1 and BRCA2 mutations account for a large proportion of ovarian carcinoma cases

Abstract: BACKGROUND It is believed that BRCA1 and BRCA2 germline mutations account for the majority of hereditary ovarian carcinomas; however, to the authors' knowledge, there are scant data on the prevalence and spectrum of mutations, genotype/phenotype correlations, tumor histology, and family history characteristics. To address this gap, the authors conducted a population-based study of 232 incident epithelial ovarian carcinomas in the Tampa Bay area. METHODS Genetic testing for the BRCA1 and BRCA2 genes was performed through full sequencing and BRCA1 rearrangement testing. RESULTS Of 209 women with invasive ovarian carcinoma, 32 women (15.3%) had mutations in BRCA1 or BRCA2, including 20 BRCA1 mutations and 12 BRCA2 mutations. Of the BRCA2 mutations, 58% were outside the “ovarian cancer cluster region” (OCCR). Variants of uncertain significance were detected in 8.2% of women with invasive ovarian carcinoma. No mutations were identified in women with borderline or invasive mucinous tumors. Among the BRCA mutation-positive women, 63% had serous tumors. A family history of breast and/or ovarian carcinoma was reported in 65%, 75%, and 43.5% of relatives of BRCA1 carriers, BRCA2 carriers, and non-BRCA1/BRCA2 carriers, respectively. CONCLUSIONS The data from this study suggested that 1) previous studies may have underestimated the frequency of BRCA1 and BRCA2 mutations in ovarian carcinomas, especially outside the OCCR; 2) it may be reasonable to offer genetic counseling to any woman with an invasive, nonmucinous epithelial ovarian tumor; and 3) among patients with invasive ovarian carcinoma, family history is not sufficiently accurate to predict mutation status. Cancer 2005. © 2005 American Cancer Society.

Racial/Ethnic Disparities in the Identification of Children With Autism Spectrum Disorders

Abstract: Objectives. We sought to examine racial and ethnic disparities in the recognition of autism spectrum disorders (ASDs).Methods. Within a multisite network, 2568 children aged 8 years were identified as meeting surveillance criteria for ASD through abstraction of evaluation records from multiple sources. Through logistic regression with random effects for site, we estimated the association between race/ethnicity and documented ASD, adjusting for gender, IQ, birthweight, and maternal education.Results. Fifty-eight percent of children had a documented autism spectrum disorder. In adjusted analyses, children who were Black (odds ratio [OR] = 0.79; 95% confidence interval [CI] = 0.64, 0.96), Hispanic (OR = 0.76; CI = 0.56, 0.99), or of other race/ethnicity (OR = 0.65; CI = 0.43, 0.97) were less likely than were White children to have a documented ASD. This disparity persisted for Black children, regardless of IQ, and was concentrated for children of other ethnicities when IQ was lower than 70.Conclusions. Signi...