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Search Results: 1 - 10 of 325695 matches for " Deanna S Cross "
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Development of a fingerprinting panel using medically relevant polymorphisms
Deanna S Cross, Lynn C Ivacic, Catherine A McCarty
BMC Medical Genomics , 2009, DOI: 10.1186/1755-8794-2-17
Abstract: A panel of polymorphisms associated with at least one disease state in multiple populations was constructed using a cut-off of 0.20 or greater confirmed minor allele frequency in a European Caucasian population. The fingerprinting assay was tested using the MALDI-TOF mass spectrometry method of allele determination on a Sequenom platform with a panel of 28 Caucasian HapMap samples; the results were compared with known genotypes to ensure accuracy. The frequencies of the alleles were compared to the expected frequencies from dbSNP and any genotype that did not achieve Hardy Weinberg equilibrium was excluded from the final assay.The final assay consisted of the AMG sex marker and 36 medically relevant polymorphisms with representation on each chromosome, encompassing polymorphisms on both the Illumina 550K bead array and the Affymetrix 6.0 chip (with over a million polymorphisms) platform. The validated assay has a P(ID) of 6.132 × 10-15 and a Psib(ID) of 3.077 × 10-8. This assay allows unique identification of our biorepository of 20,000 individuals as well and ensures that as we continue to recruit individuals they can be uniquely fingerprinted. In addition, diseases such as cancer, heart disease diabetes, obesity, and respiratory disease are well represented in the fingerprinting assay.The polymorphisms in this panel are currently represented on a number of common genotyping platforms making QA/QC flexible enough to accommodate a large number of studies. In addition, this panel can serve as a resource for investigators who are interested in the effects of disease in a population, particularly for common diseases.With the advent of genome wide association studies large bio-banks will become the stepping stones to tomorrow's medicine. The genome wide association study (GWAS) has recently proved its value with replicable findings for diseases such as coronary artery disease, prostate cancer, and diabetes [1], and many more discoveries are expected in the near future.
Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project
Deanna S Cross, Lynn C Ivacic, Elisha L Stefanski, Catherine A McCarty
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-51
Abstract: Here we used a panel of 51 polymorphisms previously associated with at least one disease and determined the allele frequencies within the entire Personalized Medicine Research Project population based cohort. We compared these allele frequencies to those in dbSNP and other data sources stratified by race. Differences in allele frequencies between self reported race, region of origin, and sex were determined.There were 19544 individuals who self reported a single racial category, 19027 or (97.4%) self reported white Caucasian, and 11205 (57.3%) individuals were female. Of the 11,208 (57%) individuals with an identifiable region of origin 8337 or (74.4%) were German.41 polymorphisms were significantly different between self reported race at the 0.05 level. Stratification of our Caucasian population by self reported region of origin revealed 19 polymorphisms that were significantly different (p = 0.05) between individuals of different origins. Further stratification of the population by gender revealed few significant differences in allele frequencies between the genders.This represents one of the largest population based allele frequency studies to date. Stratification by self reported race and region of origin revealed wide differences in allele frequencies not only by race but also by region of origin within a single racial group. We report allele frequencies for our Asian/Hmong and American Indian populations; these two minority groups are not typically selected for population allele frequency detection. Population wide allele frequencies are important for the design and implementation of studies and for determining the relevance of a disease associated polymorphism for a given population.One of the challenges for translating disease associated polymorphisms into use is the lack of knowledge regarding the frequency of the polymorphism in the targeted population. Without this information, population attributable risk remains unknown. In addition, factors that could
What is a virulence factor?
Alan S Cross
Critical Care , 2008, DOI: 10.1186/cc7127
Abstract: Infections are a leading cause of death in the intensive care unit. With the rising incidence of bacteria resistant to multiple antibiotics and a decreasing antibiotic drug pipeline, clinicians have sought additional therapies to supplement the current standard of care. Originally, such therapies, including anti-endotoxin antibodies and intravenous immunoglobulin, targeted the causative organisms. However, these efforts were supplanted by efforts to modulate the host responses to these organisms that were considered to be responsible for sepsis. Despite extensive clinical trials with biologic response modifiers, there is only one intervention licensed by the US Food and Drug Administration, drotrecogin alpha (Xigris?). Consequently, attention has now returned toward targeting the organisms. This development has been greatly assisted by the advent of genomics and systems biology, which have led to the identification of previously unrecognized targets on bacteria. These disciplines, in conjunction with advances in molecular biologic techniques, have led to striking advances in our understanding of the molecular pathogenesis of infection and the role of an ever-widening array of potential bacterial virulence factors. In their comprehensive review in this issue of Critical Care, Webb and Kahler [1] speculate that targeting virulence may be an attractive therapeutic strategy. Leaving aside the issues of drug formulation and/or delivery, what is required for the identification of a 'drugable' virulence target?Pathogens are perhaps the pre-eminent cell biologists, having over the span of millennia identified special niches or strategies, not only to subvert host defenses, but in some instances (like the polysialic acid K1 capsule of Escherichia coli) to elude detection through bacterial mimicry (by which the bacterial 'wolf' wraps itself in the 'sheep's clothing' of the host's cell). As these authors point out, many of the virulence mechanisms are now defined at precise mo
Dietary intake in the Personalized Medicine Research Project: a resource for studies of gene-diet interaction
Lacie Strobush, Richard Berg, Deanna Cross, Wendy Foth, Terrie Kitchner, Laura Coleman, Catherine A McCarty
Nutrition Journal , 2011, DOI: 10.1186/1475-2891-10-13
Abstract: The PMRP is a population-based DNA, plasma and serum biobank of more than 20,000 adults aged 18 years and older in central Wisconsin. A questionnaire at enrollment captures demographic information as well as self-reported smoking and alcohol intake. The protocol was amended to include the collection of dietary intake and physical activity via self-reported questionnaires: the National Cancer Institute 124-item Diet History Questionnaire and the Baecke Physical Activity Questionnaire. These questionnaires were mailed out to previously enrolled participants. APOE was genotyped in all subjects.The response rate to the mailed questionnaires was 68.2% for subjects who could still be contacted (alive with known address). Participants ranged in age from 18 to 98 years (mean 54.7) and 61% were female. Dietary intake is variable when comparing gender, age, smoking, and APOE4. Over 50% of females are dietary supplement users; females have higher supplement intake than males, but both have increasing supplement use as age increases. Food energy, total fat, cholesterol, protein, and alcohol intake decreases as both males and females age. Female smokers had higher macronutrient intake, whereas male nonsmokers had higher macronutrient intake. Nonsmokers in both genders use more supplements. In females, nonsmokers and smokers with APOE4 had higher supplement use. In males, nonsmokers with APOE4 had higher supplement use between ages 18-39 only, and lower supplement use at ages above 39. Male smokers with APOE4 had lower supplement use.Dietary intake in PMRP subjects is relatively consistent with data from the National Health and Nutrition Examination Survey (NHANES). Findings suggest a possible correlation between the use of supplements and APOE4. The PMRP dietary data can benefit studies of gene-environment interactions and the development of common diseases.With the completion of the Human Genome Project, the laboratory tools to quantify genetic variation in human populations ex
Numerical Bifurcation Diagram for the Two-Dimensional Boundary-fed CDIMA System
S. Setayeshgar,M. C. Cross
Physics , 1998, DOI: 10.1103/PhysRevE.59.4258
Abstract: We present numerical solution of the chlorine dioxide-iodine-malonic acid reaction-diffusion system in two dimensions in a boundary-fed system using a realistic model. The bifurcation diagram for the transition from non-symmetry breaking structures along boundary feed gradients to transverse symmetry breaking patterns in a single layer is numerically determined. We find this transition to be discontinuous. We make connection with earlier results and discuss prospects for future work.
Turing Instability in a Boundary-fed System
S. Setayeshgar,M. C. Cross
Physics , 1998, DOI: 10.1103/PhysRevE.58.4485
Abstract: The formation of localized structures in the chlorine dioxide-idodine-malonic acid (CDIMA) reaction-diffusion system is investigated numerically using a realistic model of this system. We analyze the one-dimensional patterns formed along the gradients imposed by boundary feeds, and study their linear stability to symmetry-breaking perturbations (Turing instability) in the plane transverse to these gradients. We establish that an often-invoked simple local linear analysis which neglects longitudinal diffusion is inappropriate for predicting the linear stability of these patterns. Using a fully nonuniform analysis, we investigate the structure of the patterns formed along the gradients and their stability to transverse Turing pattern formation as a function of the values of two control parameters: the malonic acid feed concentration and the size of the reactor in the dimension along the gradients. The results from this investigation are compared with existing experiments.
Determinates That Influence Food Comsumption among Older Members of a Midwest Community  [PDF]
Deanna Pucciarelli, Adrienne Thomas
Food and Nutrition Sciences (FNS) , 2011, DOI: 10.4236/fns.2011.29136
Abstract: The goal of this study was to record Muncie, Indiana residents’ change in eating habits over time. Objectives: 1) Identify key determinants that influence a change in participants’ eating habits; 2) Analyze the data for convergent themes among participants and draw patterns; and 3) Compare patterns found in this study population with existing literature and/or accepted theories within the field. Hypotheses on changes in food patterns included: 1) Socio-economic status in the middle-class population maintained daily food production to remain inside the home; 2) Women working outside the home reduced labor hours allotted to home cooking; and 3) Social norms valued home cooking resulting in home prepared meals. Methods: The study used a cross-sectional, oral-history, interview format. The study sample consisted of 25 seniors (65y - 100y old) from a convenience sample taken from one, medium-sized, mid-western town, Muncie, Indiana. The study involved use of a semi-structured, questionnaire/interview script, (approved by Ball State University’s IRB committee). Results: Economics greatly influenced, and continues to influence, food consumption patterns for depression-era born adults. Women who grew up on home-only cooked meals, but entered the workforce adjusted traditional meals in favor of convenience. Implications: Health care providers trying to change dietary habits of older residents residing in the Midwest will need to consider foods and food preparatory methods introduced in childhood; these remained key components of the diet later in life and removing them may be met with resistance.
Consumer Ideology Determines Shopping Preferences at Farmers Markets in Two US Geographical Regions  [PDF]
Deanna Pucciarelli, Stacey Faith
Food and Nutrition Sciences (FNS) , 2014, DOI: 10.4236/fns.2014.519205
Abstract: The purpose of this study was to identify if there were differences that existed in the behaviors, attitudes, awareness, and motivating factors that influenced people to shop at farmers’ markets and purchase USDA certified organic food in two geographic regions: Corvallis, Oregon and Muncie, Indiana. A survey was administered to consumers who shopped at the Minnetrista Farmers’ Market (MFM) and the Corvallis-Albany Farmers’ Market (CAFM) in the summer of 2012 to measure the shoppers’ purchasing perceptions. Specific areas of interest in this study included consumer values towards supporting local farmers and consuming USDA certified organic food. A comparison of responses between regions was analyzed. Results of the study provide insights on consumers’ purchasing attitudes and behaviors regarding USDA certified organic products, and why they chose to shop at Farmers’ Markets. Ideology was the strongest predictor for consumer purchasing behaviors. Understanding how regional differences affect food choice has implications for wellness programs and industry marketing materials.
Modeling a falling slinky
R. C. Cross,M. S. Wheatland
Physics , 2012, DOI: 10.1119/1.4750489
Abstract: A slinky is an example of a tension spring: in an unstretched state a slinky is collapsed, with turns touching, and a finite tension is required to separate the turns from this state. If a slinky is suspended from its top and stretched under gravity and then released, the bottom of the slinky does not begin to fall until the top section of the slinky, which collapses turn by turn from the top, collides with the bottom. The total collapse time t_c (typically ~0.3 s for real slinkies) corresponds to the time required for a wave front to propagate down the slinky to communicate the release of the top end. We present a modification to an existing model for a falling tension spring (Calkin 1993) and apply it to data from filmed drops of two real slinkies. The modification of the model is the inclusion of a finite time for collapse of the turns of the slinky behind the collapse front propagating down the slinky during the fall. The new finite-collapse time model achieves a good qualitative fit to the observed positions of the top of the real slinkies during the measured drops. The spring constant k for each slinky is taken to be a free parameter in the model. The best-fit model values for k for each slinky are approximately consistent with values obtained from measured periods of oscillation of the slinkies.
Vegetarian diets are associated with healthy mood states: a cross-sectional study in Seventh Day Adventist adults
Bonnie L Beezhold, Carol S Johnston, Deanna R Daigle
Nutrition Journal , 2010, DOI: 10.1186/1475-2891-9-26
Abstract: We examined associations between mood state and polyunsaturated fatty acid intake as a result of adherence to a vegetarian or omnivorous diet in a cross-sectional study of 138 healthy Seventh Day Adventist men and women residing in the Southwest. Participants completed a quantitative food frequency questionnaire, Depression Anxiety Stress Scale (DASS), and Profile of Mood States (POMS) questionnaires.Vegetarians (VEG:n = 60) reported significantly less negative emotion than omnivores (OMN:n = 78) as measured by both mean total DASS and POMS scores (8.32 ± 0.88 vs 17.51 ± 1.88, p = .000 and 0.10 ± 1.99 vs 15.33 ± 3.10, p = .007, respectively). VEG reported significantly lower mean intakes of EPA (p < .001), DHA (p < .001), as well as the omega-6 fatty acid, arachidonic acid (AA; p < .001), and reported higher mean intakes of shorter-chain α-linolenic acid (p < .001) and linoleic acid (p < .001) than OMN. Mean total DASS and POMS scores were positively related to mean intakes of EPA (p < 0.05), DHA (p < 0.05), and AA (p < 0.05), and inversely related to intakes of ALA (p < 0.05), and LA (p < 0.05), indicating that participants with low intakes of EPA, DHA, and AA and high intakes of ALA and LA had better mood.The vegetarian diet profile does not appear to adversely affect mood despite low intake of long-chain omega-3 fatty acids.Although adherence to vegetarian diets has been associated with physical health benefits, most notably a low risk of mortality from ischemic heart disease [1], vegetarian mental health is not well documented. Emerging evidence suggests that fish consumption has a protective effect on mental health due to the long-chain omega-3 fatty acid content [2]. Traditional vegetarian diets omit all flesh foods, and low intakes of the long-chain omega-3 fats, eicosapentaenoic acid [EPA] and docosahexaenoic acid [DHA], have been widely reported in vegetarians [3-6]. EPA and DHA favorably impact neural function by displacing the long-chain omega-6 fatty aci
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