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Search Results: 1 - 10 of 2520 matches for " Stephanie Loomis "
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Feasibility of High-Throughput Genome-Wide Genotyping using DNA from Stored Buccal Cell Samples
Stephanie J. Loomis,Lana M. Olson,Louis R. Pasquale,Janey Wiggs
Biomarker Insights , 2010,
Abstract: It is unclear if buccal cell samples contain sufficient human DNA with adequately sized fragments for high throughput genetic bioassays. Yet buccal cell sample collection is an attractive alternative to gathering blood samples for genetic epidemiologists engaged in large-scale genetic biomarker studies. We assessed the genotyping efficiency (GE) and genotyping concordance (GC) of buccal cell DNA samples compared to corresponding blood DNA samples, from 32 Nurses’ Health Study (NHS) participants using the Illumina Infinium 660W-Quad platform. We also assessed how GE and GC accuracy varied as a function of DNA concentration using serial dilutions of buccal DNA samples. Finally we determined the nature and genomic distribution of discordant genotypes in buccal DNA samples. The mean GE of undiluted buccal cell DNA samples was high (99.32%), as was the GC between the paired buccal and blood samples (99.29%). GC between the dilutions versus the undiluted buccal DNA was also very high (.97%), though both GE and GC notably declined at DNA concentrations less than 5 ng/μl. Most (.95%) genotype determinations in buccal cell samples were of the “missing call” variety (as opposed to the “alternative genotype call” variety) across the spectrum of buccal DNA concentrations studied. Finally, for buccal DNA concentration above 1.7 ng/ul, discordant genotyping calls did not cluster in any particular chromosome. Buccal cell-derived DNA represents a viable alternative to blood DNA for genotyping on a high-density platform.
Exploring genome-wide – dietary heme iron intake interactions and the risk of type 2 diabetes
Louis R. Pasquale,Stephanie J. Loomis,Hugues Aschard,Marilyn C. Cornelis,Lu Qi,Peter Kraft
Frontiers in Genetics , 2013, DOI: 10.3389/fgene.2013.00007
Abstract: Aims/hypothesis: Genome-wide association studies have identified over 50 new genetic loci for type 2 diabetes (T2D). Several studies conclude that higher dietary heme iron intake increases the risk of T2D. Therefore we assessed whether the relation between genetic loci and T2D is modified by dietary heme iron intake.
A New Approach to Value Urban Recreation Using Visitors' Time Allocations
John Loomis
Urban Public Economics Review , 2011,
Abstract: This paper applies a new revealed preference approach to valuing local/urban/suburban recreation sites where travel costs are minimal, by relying upon the cost of time spent on site. The approach relies upon the elasticity of substitution between time spent on visiting the recreation site versus a composite commodity, and the relative time intensity of recreation versus the composite commodity. This new approach is illustrated by valuing near town local recreationareas used by residents of the town of Jackson, Wyoming. The results yield an equivalent variation estimate of welfare of $1004 per year, or $43.65 per day trip. The new method appears to have promise to value heretofore difficult to value urban parks and beach recreation used by locals. En este papel aplicamos un nuevo enfoque de las preferencias acerca de la valoración de los lugares de ocio locales/urbanos/suburbanos, donde los costes de desplazamiento son mínimos, basándonos, fundamentalmente, en el coste del tiempo gastado en el sitio. La perspectiva utilizada se basa en la elasticidad de sustitución entre el tiempo dedicado a visitar el sitio de recreo, frente a un bien compuesto y la intensidad relativa del tiempo de ocio frente a este bien compuesto. El nuevo enfoque, se ilustra en la valoración de las áreas de ocio local, utilizadas por los residentes de la urbe de Jackson, Wyoming. El resultado arroja una estimación de la variación equivalente de bienestar de 1004 $ por a o o 43.65$ por día de viaje. Este nuevo método aproxima valores hasta ahora difíciles de ponderar, tales como la valoración de los parques urbanos o la playa utilizados por los lugare os.
A Cross-Sectional Survey of the Association between Bilateral Topical Prostaglandin Analogue Use and Ocular Adnexal Features
Mamta Shah, Grace Lee, Daniel R. Lefebvre, Benjamin Kronberg, Stephanie Loomis, Stacey C. Brauner, Angela Turalba, Douglas J. Rhee, Suzanne K. Freitag, Louis R. Pasquale
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061638
Abstract: We studied the relation between prostaglandin analogue use and ocular adnexal features. We used a prospective, cross-sectional study involving 157 current, 15 past, and 171 never users of prostaglandin analogues. Patients 50 years of age or older and without conditions affecting ocular adnexal anatomy underwent glaucoma medication use history, external digital photography and systematic external adnexal exam. Two masked readers assessed the digital photos for upper lid dermatochalasis and lower lid steatoblepharon using a validated grading scheme. Another masked clinical examiner also assessed upper lid ptosis, levator muscle function, and inferior scleral show. We performed ordinal logistic regression analysis accounting for multiple covariates to assess the relation between prostaglandin analogue use and adnexal features. Multivariable analyses indicated there was a 230-fold increased risk of incremental involution of dermatochalasis (odds ratio (OR) = 2.30; 95% confidence interval (CI) 1.43–3.69; p = 5.44E-04) and a 249-fold increased risk of incremental loss of lower lid steatoblepharon (OR = 2.49; 95% CI, 1.54–4.03; p = 1.98E-04) associated with current prostaglandin analogue use (bimatoprost 0.03%, travoprost 0.005%, or latanoprost 0.004%) versus prostaglandin analogue never or past users. Upper lid ptosis (OR = 4.04; 95% CI, 2.43–6.72; p = 7.37E-08), levator dysfunction (OR = 7.51; 95% CI, 3.39–16.65; p = 6.74E-07) and lower lid retraction (OR = 2.60; 95% CI, 1.58–4.28; p = 1.72E-04) were highly associated with current prostaglandin analogue use versus prostaglandin analogue never or past users. The associations between prostaglandin analogue use and deepening of the upper lid sulci and between prostaglandin analogue use and loss of inferior periorbital fat are confirmed in this multivariable analysis. The associations between prostaglandin analogue use and levator muscle dysfunction and between prostaglandin analogue use and upper lid ptosis represent significant side effects that could impact visual function in glaucoma patients.
Feasibility of High-Throughput Genome-Wide Genotyping using DNA from Stored Buccal Cell Samples
Stephanie J. Loomis, Lana M. Olson, Louis R. Pasquale, Janey Wiggs, Daniel Mirel, Andrew Crenshaw, Melissa Parkin, Brandon Rahhal, Stephanie Tetreault, Peter Kraft, Shelley S. Tworoger, Jonathan L. Haines and Jae H. Kang
Biomarker Insights , 2012, DOI: 10.4137/BMI.S5062
Abstract: It is unclear if buccal cell samples contain sufficient human DNA with adequately sized fragments for high throughput genetic bioassays. Yet buccal cell sample collection is an attractive alternative to gathering blood samples for genetic epidemiologists engaged in large-scale genetic biomarker studies. We assessed the genotyping efficiency (GE) and genotyping concordance (GC) of buccal cell DNA samples compared to corresponding blood DNA samples, from 32 Nurses’ Health Study (NHS) participants using the Illumina Infinium 660W-Quad platform. We also assessed how GE and GC accuracy varied as a function of DNA concentration using serial dilutions of buccal DNA samples. Finally we determined the nature and genomic distribution of discordant genotypes in buccal DNA samples. The mean GE of undiluted buccal cell DNA samples was high (99.32%), as was the GC between the paired buccal and blood samples (99.29%). GC between the dilutions versus the undiluted buccal DNA was also very high (.97%), though both GE and GC notably declined at DNA concentrations less than 5 ng/μl. Most (.95%) genotype determinations in buccal cell samples were of the “missing call” variety (as opposed to the “alternative genotype call” variety) across the spectrum of buccal DNA concentrations studied. Finally, for buccal DNA concentration above 1.7 ng/ul, discordant genotyping calls did not cluster in any particular chromosome. Buccal cell-derived DNA represents a viable alternative to blood DNA for genotyping on a high-density platform.
Visual space perception: phenomenology and function
Loomis, Jack M.;
Arquivos Brasileiros de Oftalmologia , 2003, DOI: 10.1590/S0004-27492003000600004
Abstract: this article presents a brief overview of visual space perception. it begins by noting the significance of visual space perception to broader issues in philosophy and science and observes that the appreciation of visual space perception as a scientific topic is impeded by na?ve realism. the second section notes the longstanding interest in the phenomenology of visual space and focuses on one issue, the dissocation between perceived location and perceived shape in visual space. the last section discusses three conceptions of how vision controls action, with special attention to the role of visual space.
Spatial updating of targets in front and behind
Horn, David;Loomis, Jack;
Paidéia (Ribeir?o Preto) , 2004, DOI: 10.1590/S0103-863X2004000100010
Abstract: this research compared the accuracy of spatial updating of targets in front with that of targets behind. the participant viewed a target on the ground several meters away and then, without vision, sidestepped along a guide rope while trying to mentally update the location of the target. on some trials, the target location was in front as the person sidestepped and, on other trials, the target location was behind. participants responded by facing the updated target location with eyes closed. the results indicate that people are able to update target locations behind them very nearly as well as target locations in front.
Visual space perception: phenomenology and function
Loomis Jack M.
Arquivos Brasileiros de Oftalmologia , 2003,
Abstract: This article presents a brief overview of visual space perception. It begins by noting the significance of visual space perception to broader issues in philosophy and science and observes that the appreciation of visual space perception as a scientific topic is impeded by na ve realism. The second section notes the longstanding interest in the phenomenology of visual space and focuses on one issue, the dissocation between perceived location and perceived shape in visual space. The last section discusses three conceptions of how vision controls action, with special attention to the role of visual space.
Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage.
Song,Xu,Olsen,Loomis
PLOS Computational Biology , 2005,
Abstract: The Amoebozoa are a sister clade to the fungi and the animals, but are poorly sampled for completely sequenced genomes. The social amoeba Dictyostelium discoideum and amitochondriate pathogen Entamoeba histolytica are the first Amoebozoa with genomes completely sequenced. Both organisms are classified under the Conosa subphylum. To identify Amoebozoa-specific genomic elements, we compared these two genomes to each other and to other eukaryotic genomes. An expanded phylogenetic tree built from the complete predicted proteomes of 23 eukaryotes places the two amoebae in the same lineage, although the divergence is estimated to be greater than that between animals and fungi, and probably happened shortly after the Amoebozoa split from the opisthokont lineage. Most of the 1,500 orthologous gene families shared between the two amoebae are also shared with plant, animal, and fungal genomes. We found that only 42 gene families are distinct to the amoeba lineage; among these are a large number of proteins that contain repeats of the FNIP domain, and a putative transcription factor essential for proper cell type differentiation in D. discoideum. These Amoebozoa-specific genes may be useful in the design of novel diagnostics and therapies for amoebal pathologies.
Millipeds Principally Collected by Professor V. E. Shelford in the Eastern and Southeastern States
H. F. Loomis
Psyche , 1944, DOI: 10.1155/1944/69580
Abstract:
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