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Search Results: 1 - 10 of 203763 matches for " Jennifer N. Sims "
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Visual Analytics of Surveillance Data on Foodborne Vibriosis, United States, 1973–2010
Jennifer N. Sims,Raphael D. Isokpehi,Gabrielle A. Cooper,Michael P. Bass
Environmental Health Insights , 2011,
Abstract:
Visual Analytics of Surveillance Data on Foodborne Vibriosis, United States, 1973–2010
Jennifer N. Sims, Raphael D. Isokpehi, Gabrielle A. Cooper, Michael P. Bass, Shyretha D. Brown, Alison L. St. John, Paul A. Gulig and Hari H.P. Cohly
Environmental Health Insights , 2012, DOI: 10.4137/EHI.S7806
Abstract: Foodborne illnesses caused by microbial and chemical contaminants in food are a substantial health burden worldwide. In 2007, human vibriosis (non-cholera Vibrio infections) became a notifiable disease in the United States. In addition, Vibrio species are among the 31 major known pathogens transmitted through food in the United States. Diverse surveillance systems for foodborne pathogens also track outbreaks, illnesses, hospitalization and deaths due to non-cholera vibrios. Considering the recognition of vibriosis as a notifiable disease in the United States and the availability of diverse surveillance systems, there is a need for the development of easily deployed visualization and analysis approaches that can combine diverse data sources in an interactive manner. Current efforts to address this need are still limited. Visual analytics is an iterative process conducted via visual interfaces that involves collecting information, data preprocessing, knowledge representation, interaction, and decision making. We have utilized public domain outbreak and surveillance data sources covering 1973 to 2010, as well as visual analytics software to demonstrate integrated and interactive visualizations of data on foodborne outbreaks and surveillance of Vibrio species. Through the data visualization, we were able to identify unique patterns and/or novel relationships within and across datasets regarding (i) causative agent; (ii) foodborne outbreaks and illness per state; (iii) location of infection; (iv) vehicle (food) of infection; (v) anatomical site of isolation of Vibrio species; (vi) patients and complications of vibriosis; (vii) incidence of laboratory-confirmed vibriosis and V. parahaemolyticus outbreaks. The additional use of emerging visual analytics approaches for interaction with data on vibriosis, including non-foodborne related disease, can guide disease control and prevention as well as ongoing outbreak investigations.
Use of conventional and alternative treatment strategies for a case of low back pain in a F/A-18 aviator
Bart N Green, John Sims, Rachel Allen
Chiropractic & Manual Therapies , 2006, DOI: 10.1186/1746-1340-14-11
Abstract: The patient had insidious severe low back pain without radiation or neurological deficit, resulting in 24 hours of hospitalization. Spinal degeneration was discovered upon imaging. Four months later, it still took up to 10 minutes for him to get out of bed and several minutes to exit the jet due to stiffness and pain. He had discontinued his regular Marine Corps fitness training due to pain avoidance. Pain severity ranged from 1.5–7.1 cm on a visual analog scale. His Roland Morris Disability Questionnaire score was 5 out of 24. The pilot's pain was managed with the coordinated efforts of the flight surgeon, physiatrist, physical therapist, and doctor of chiropractic. Following this regimen he had no pain and no functional disability; he was able to fly multiple training missions per week and exercise to Marine Corps standards.A course of care integrating flight medicine, chiropractic, physical therapy, and physiatry appeared to alleviate pain and restore function to this F/A-18 aviator with low back pain.Low back pain (LBP) is a common problem associated with significant losses in work time in the general population [1]. While LBP has been studied extensively in the literature for many populations, few clinical studies discuss LBP in fighter jet aviators. Neck pain in fighter pilots receives much attention, yet spinal disorders leading to back pain are reported to be 2 times more common in fighter aviators than other pilots [2]. One survey reports that fighter pilots have a significantly greater prevalence of chronic LBP, pain requiring bed rest and pain radiating into the leg compared to fixed wing transport and helicopter pilots [3]. Spinal pain can be serious for high performance aviators and severe enough to ground pilots or cause decreased flying time (17% for fighter pilots) [4]. Spinal disorders and LBP are reported to be exacerbated by flight, result in disability [5] and in non-waiver of flight disqualification in approximately 25% of US Navy and US Marine
The Self-Excitation Damping Ratio in Variable Speed Milling
K. Saleh,N.D. Sims
Lecture Notes in Engineering and Computer Science , 2012,
Abstract:
Genetic Analysis of Completely Sequenced Disease-Associated MHC Haplotypes Identifies Shuffling of Segments in Recent Human History
James A Traherne equal contributor,Roger Horton equal contributor,Anne N Roberts equal contributor,Marcos M Miretti equal contributor,Matthew E Hurles,C. Andrew Stewart,Jennifer L Ashurst,Alexey M Atrazhev,Penny Coggill,Sophie Palmer,Jeff Almeida,Sarah Sims,Laurens G Wilming,Jane Rogers,Pieter J. de Jong,Mary Carrington,John F Elliott,Stephen Sawcer,John A Todd,John Trowsdale,Stephan Beck
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020009
Abstract: The major histocompatibility complex (MHC) is recognised as one of the most important genetic regions in relation to common human disease. Advancement in identification of MHC genes that confer susceptibility to disease requires greater knowledge of sequence variation across the complex. Highly duplicated and polymorphic regions of the human genome such as the MHC are, however, somewhat refractory to some whole-genome analysis methods. To address this issue, we are employing a bacterial artificial chromosome (BAC) cloning strategy to sequence entire MHC haplotypes from consanguineous cell lines as part of the MHC Haplotype Project. Here we present 4.25 Mb of the human haplotype QBL (HLA-A26-B18-Cw5-DR3-DQ2) and compare it with the MHC reference haplotype and with a second haplotype, COX (HLA-A1-B8-Cw7-DR3-DQ2), that shares the same HLA-DRB1, -DQA1, and -DQB1 alleles. We have defined the complete gene, splice variant, and sequence variation contents of all three haplotypes, comprising over 259 annotated loci and over 20,000 single nucleotide polymorphisms (SNPs). Certain coding sequences vary significantly between different haplotypes, making them candidates for functional and disease-association studies. Analysis of the two DR3 haplotypes allowed delineation of the shared sequence between two HLA class II–related haplotypes differing in disease associations and the identification of at least one of the sites that mediated the original recombination event. The levels of variation across the MHC were similar to those seen for other HLA-disparate haplotypes, except for a 158-kb segment that contained the HLA-DRB1, -DQA1, and -DQB1 genes and showed very limited polymorphism compatible with identity-by-descent and relatively recent common ancestry (<3,400 generations). These results indicate that the differential disease associations of these two DR3 haplotypes are due to sequence variation outside this central 158-kb segment, and that shuffling of ancestral blocks via recombination is a potential mechanism whereby certain DR–DQ allelic combinations, which presumably have favoured immunological functions, can spread across haplotypes and populations.
Developmental Regulation of Genes Encoding Universal Stress Proteins in Schistosoma mansoni
Raphael D. Isokpehi, Ousman Mahmud, Andreas N. Mbah, Shaneka S. Simmons, Lívia Avelar, Rajendram V. Rajnarayanan, Udensi K. Udensi, Wellington K. Ayensu, Hari H. Cohly, Shyretha D. Brown, Centdrika R. Dates, Sonya D. Hentz, Shawntae J. Hughes, Dominique R. Smith-McInnis, Carvey O. Patterson, Jennifer N. Sims, Kelisha T. Turner, Baraka S. Williams, Matilda O. Johnson, Taiwo Adubi, Judith V. Mbuh, Chiaka I. Anumudu, Grace O. Adeoye, Bolaji N. Thomas, Oyekanmi Nashiru and Guilherme Oliveira
Gene Regulation and Systems Biology , 2012, DOI: 10.4137/GRSB.S7491
Abstract: The draft nuclear genome sequence of the snail-transmitted, dimorphic, parasitic, platyhelminth Schistosoma mansoni revealed eight genes encoding proteins that contain the Universal Stress Protein (USP) domain. Schistosoma mansoni is a causative agent of human schistosomiasis, a severe and debilitating Neglected Tropical Disease (NTD) of poverty, which is endemic in at least 76 countries. The availability of the genome sequences of Schistosoma species presents opportunities for bioinformatics and genomics analyses of associated gene families that could be targets for understanding schistosomiasis ecology, intervention, prevention and control. Proteins with the USP domain are known to provide bacteria, archaea, fungi, protists and plants with the ability to respond to diverse environmental stresses. In this research investigation, the functional annotations of the USP genes and predicted nucleotide and protein sequences were initially verified. Subsequently, sequence clusters and distinctive features of the sequences were determined. A total of twelve ligand binding sites were predicted based on alignment to the ATP-binding universal stress protein from Methanocaldococcus jannaschii. In addition, six USP sequences showed the presence of ATP-binding motif residues indicating that they may be regulated by ATP. Public domain gene expression data and RT-PCR assays confirmed that all the S. mansoni USP genes were transcribed in at least one of the developmental life cycle stages of the helminth. Six of these genes were up-regulated in the miracidium, a free-swimming stage that is critical for transmission to the snail intermediate host. It is possible that during the intra-snail stages, S. mansoni gene transcripts for universal stress proteins are low abundant and are induced to perform specialized functions triggered by environmental stressors such as oxidative stress due to hydrogen peroxide that is present in the snail hemocytes. This report serves to catalyze the formation of a network of researchers to understand the function and regulation of the universal stress proteins encoded in genomes of schistosomes and their snail intermediate hosts.
Uniqueness theorems for topological higher-rank graph C*-algebras
Jean N. Renault,Aidan Sims,Dana P. Williams,Trent Yeend
Mathematics , 2009,
Abstract: We consider the boundary-path groupoids of topological higher-rank graphs. We show that the all such groupoids are topologically amenable. We deduce that the C*-algebras of topological higher-rank graphs are nuclear and prove versions of the gauge-invariant uniqueness theorem and the Cuntz-Krieger uniqueness theorem. We then provide a necessary and sufficient condition for simplicity of a topological higher-rank graph C*-algebra, and a condition under which it is also purely infinite.
Detection of Canonical Hedgehog Signaling in Breast Cancer by 131-Iodine-Labeled Derivatives of the Sonic Hedgehog Protein
Jennifer Sims-Mourtada,David Yang,Izabela Tworowska,Richard Larson,Daniel Smith,Ning Tsao,Lynn Opdenaker,Firas Mourtada,Wendy Woodward
Journal of Biomedicine and Biotechnology , 2012, DOI: 10.1155/2012/639562
Abstract: Activation of hedgehog (HH) pathway signaling is observed in many tumors. Due to a feedback loop, the HH receptor Patched (PTCH-1) is overexpressed in tumors with activated HH signaling. Therefore, we sought to radiolabel the PTCH-1 ligand sonic (SHH) for detection of cancer cells with canonical HH activity. Receptor binding of 131I-SHH was increased in cell lines with high HH pathway activation. Our findings also show that PTCH-1 receptor expression is decreased upon treatment with HH signaling inhibitors, and receptor binding of 131I-SHH is significantly decreased following treatment with cyclopamine. In vivo imaging and biodistribution studies revealed significant accumulation of 131I-SHH within tumor tissue as compared to normal organs. Tumor-to-muscle ratios were approximately 8 : 1 at 5 hours, while tumor to blood and tumor to bone were 2 : 1 and 5 : 1, respectively. Significant uptake was also observed in liver and gastrointestinal tissue. These studies show that 131I-SHH is capable of in vivo detection of breast tumors with high HH signaling. We further demonstrate that the hedgehog receptor PTCH-1 is downregulated upon treatment with hedgehog inhibitors. Our data suggests that radiolabeled SHH derivatives may provide a method to determine response to SHH-targeted therapies.
Developing a patient-centered outcome measure for complementary and alternative medicine therapies II: Refining content validity through cognitive interviews
Jennifer J Thompson, Kimberly L Kelly, Cheryl Ritenbaugh, Allison L Hopkins, Colette M Sims, Stephen J Coons
BMC Complementary and Alternative Medicine , 2011, DOI: 10.1186/1472-6882-11-136
Abstract: We conducted cognitive interviews across five iterations of questionnaire refinement with a culturally diverse sample of 28 CAM users. In each iteration, participant critiques were used to revise the questionnaire, which was then re-tested in subsequent rounds of cognitive interviews. Following all five iterations, transcripts of cognitive interviews were systematically coded and analyzed to examine participants' understanding of the format and content of the final questionnaire. Based on this data, we established summary descriptions and selected exemplar quotations for each word pair on the final questionnaire.The final version of the Self-Assessment of Change questionnaire (SAC) includes 16 word pairs, nine of which remained unchanged from the original draft. Participants consistently said that these stable word pairs represented opposite ends of the same domain of experience and the meanings of these terms were stable across the participant pool. Five pairs underwent revision and two word pairs were added. Four word pairs were eliminated for redundancy or because participants did not agree on the meaning of the terms. Cognitive interviews indicate that participants understood the format of the questionnaire and considered each word pair to represent opposite poles of a shared domain of experience.We have placed lay language and direct experience at the center of questionnaire revision and refinement. In so doing, we provide an innovative model for the development of truly patient-centered outcome measures. Although this instrument was designed and tested in a CAM-specific population, it may be useful in assessing multi-dimensional shifts in well-being across a broader patient population.Patients receiving complementary and alternative medicine (CAM) therapies often report experiencing effects beyond those associated with their specific treatment goals, including unanticipated outcomes and multi-dimensional shifts in overall well-being, energy, clarity of thought
Sea urchin vault structure, composition, and differential localization during development
Phoebe L Stewart, Miriam Makabi, Jennifer Lang, Carrie Dickey-Sims, Anthony J Robertson, James A Coffman, Kathy A Suprenant
BMC Developmental Biology , 2005, DOI: 10.1186/1471-213x-5-3
Abstract: The sequence of the sea urchin major vault protein (MVP) was assembled from expressed sequence tags and genome traces, and the predicted protein was found to have 64% identity and 81% similarity to rat MVP. Sea urchin MVP includes seven ~50 residue repeats in the N-terminal half of the protein and a predicted coiled coil domain in the C-terminus, as does rat MVP. A cryoelectron microscopy (cryoEM) reconstruction of isolated sea urchin vaults reveals the assembly to have a barrel-shaped external structure that is nearly identical to the rat vault structure. Analysis of the molecular composition of the sea urchin vault indicates that it contains components that may be homologs of the mammalian vault RNA component (vRNA) and protein components (VPARP and TEP1). The sea urchin vault appears to have additional protein components in the molecular weight range of 14–55 kDa that might correspond to molecular contents. Confocal experiments indicate a dramatic relocalization of MVP from the cytoplasm to the nucleus during sea urchin embryogenesis.These results are suggestive of a role for the vault in delivering macromolecules to the nucleus during development.The sea urchin Strongylocentrotus purpuratus is an important model system in developmental biology and its genome is currently being sequenced by the Human Genome Sequencing Center at the Baylor College of Medicine under the auspices of the National Human Genome Research Institute (NHGRI). Sea urchin embryos are well suited for biochemical approaches to studying the cell biology of development, as large quantities of eggs can easily be obtained, and their fertilization initiates the synchronous development of optically transparent embryos [1]. Sea urchins occupy an important phylogenetic position as basal deuterostomes, and are thus more closely related to humans than are other invertebrate model organisms such as Drosophila and C. elegans. In addition, the echinoderm lineage leading to sea urchins diverged from chordat
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