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Search Results: 1 - 10 of 246786 matches for " David N. Rider "
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SNPPicker: High quality tag SNP selection across multiple populations
Hugues Sicotte, David N Rider, Gregory A Poland, Neelam Dhiman, Jean-Pierre A Kocher
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-129
Abstract: SNPPicker optimizes the selection of tag SNPs from common bin-tagging programs to design custom genotyping panels. The application uses a multi-step search strategy in combination with a statistical model to maximize the genotyping success of the selected tag SNPs. User preference toward functional SNPs can also be taken into account as secondary criteria. SNPPicker can also optimize tag SNP selection for a panel tagging multiple populations. SNPPicker can optimize custom genotyping panels including all the assay-specific constraints of Illumina's GoldenGate and Infinium assays.A new application has been developed to maximize the success of custom multi-population genotyping panels. SNPPicker also takes into account user constraints including options for controlling runtime. Perl Scripts, Java source code and executables are available under an open source license for download at http://mayoresearch.mayo.edu/mayo/research/biostat/software.cfm webciteDespite the commercial availability of affordable genome wide genotyping panels, custom-designed SNPs panels are frequently used for high resolution genotyping studies focusing on specific genes or chromosomal regions. The design of custom SNP panels for genotyping studies aims to minimize the number of SNPs to genotype while maximizing the information content of the panel.The number of SNPs to genotype can be minimized by taking advantage of linkage disequilibrium (LD) between SNP alleles in the same population. A number of algorithms are available to assess LD between SNPs and select tag SNPs representative of groups of correlated SNPs called bins [1-5]. These bin-tagging algorithms use population specific sets of reference genotypes to compute bins and tag SNPs and report all possible tag SNP candidates for each bin. Note that Tagger, which reports the best tag SNP, also provides an exportable table of r2 values between SNPs that can be used to compute all tag SNPs candidates. Since these tag SNPs candidates are theore
The affine Grassmannian and the Springer resolution in positive characteristic
Pramod N. Achar,Laura Rider
Mathematics , 2014,
Abstract: An important result of Arkhipov-Bezrukavnikov-Ginzburg relates constructible sheaves on the affine Grassmannian to coherent sheaves on the dual Springer resolution. In this paper, we prove a positive-characteristic analogue of this statement, using the framework of "mixed modular sheaves" recently developed by the first author and Riche. As an application, we deduce a relationship between parity sheaves on the affine Grassmannian and Bezrukavnikov's "exotic t-structure" on the Springer resolution.
Parity sheaves on the affine Grassmannian and the Mirkovi?-Vilonen conjecture
Pramod N. Achar,Laura Rider
Mathematics , 2013,
Abstract: We prove the Mirkovi\'c-Vilonen conjecture: the integral local intersection cohomology groups of spherical Schubert varieties on the affine Grassmannian have no p-torsion, as long as p is outside a certain small and explicitly given set of prime numbers. (Juteau has exhibited counterexamples when p is a bad prime.) The main idea is to convert this topological question into an algebraic question about perverse-coherent sheaves on the dual nilpotent cone using the Juteau-Mautner-Williamson theory of parity sheaves.
Phylogeny of the Infraorder Pentatomomorpha Based on Fossil and Extant Morphology, with Description of a New Fossil Family from China
Yunzhi Yao, Dong Ren, David A. Rider, Wanzhi Cai
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0037289
Abstract: Background An extinct new family of Pentatomomorpha, Venicoridae Yao, Ren & Cai fam. nov., with 2 new genera and 2 new species (Venicoris solaris Yao, Ren & Rider gen. & sp. nov. and Clavaticoris zhengi Yao, Ren & Cai gen. & sp. nov.) are described from the Early Cretaceous Yixian Formation in Northeast China. Methodology/Principal Findings A cladistic analysis based on a combination of fossil and extant morphological characters clarified the phylogenetic status of the new family and has allowed the reconstruction of intersuperfamily and interfamily relationships within the Infraorder Pentatomomorpha. The fossil record and diversity of Pentatomomorpha during the Mesozoic is discussed. Conclusions/Significance Pentatomomorpha is a monophyletic group; Aradoidea and the Trichophora are sister groups; these fossils belong to new family, treated as the sister group of remainder of Trichophora; Pentatomoidea is a monophyletic group; Piesmatidae should be separated as a superfamily, Piesmatoidea. Origin time of Pentatomomorpha should be tracked back to the Middle or Early Triassic.
Search for Millicharged Particles Using Optically Levitated Microspheres
David C. Moore,Alexander D. Rider,Giorgio Gratta
Physics , 2014, DOI: 10.1103/PhysRevLett.113.251801
Abstract: We report results from a search for stable particles with charge > $10^{-5}$ e in bulk matter using levitated dielectric microspheres in high vacuum. No evidence for such particles was found in a total sample of 1.4 ng, providing an upper limit on the abundance per nucleon of 2.5 x $10^{-14}$ at the 95% confidence level for the material tested. These results provide the first direct search for single particles with charge < 0.1 e bound in macroscopic quantities of matter and demonstrate the ability to perform sensitive force measurements using optically levitated microspheres in vacuum.
On the Information Rate of MIMO Systems with Finite Rate Channel State Feedback Using Beamforming and Power On/Off Strategy
Wei Dai,Youjian Liu,Vincent K. N. Lau,Brian Rider
Mathematics , 2006,
Abstract: It is well known that Multiple-Input Multiple-Output (MIMO) systems have high spectral efficiency, especially when channel state information at the transmitter (CSIT) is available. When CSIT is obtained by feedback, it is practical to assume that the channel state feedback rate is finite and the CSIT is not perfect. For such a system, we consider beamforming and power on/off strategy for its simplicity and near optimality, where power on/off means that a beamforming vector (beam) is either turned on with a constant power or turned off. The main contribution of this paper is to accurately evaluate the information rate as a function of the channel state feedback rate. Name a beam turned on as an on-beam and the minimum number of the transmit and receive antennas as the dimension of a MIMO system. We prove that the ratio of the optimal number of on-beams and the system dimension converges to a constant for a given signal-to-noise ratio (SNR) when the numbers of transmit and receive antennas approach infinity simultaneously and when beamforming is perfect. Asymptotic formulas are derived to evaluate this ratio and the corresponding information rate per dimension. The asymptotic results can be accurately applied to finite dimensional systems and suggest a power on/off strategy with a constant number of on-beams. For this suboptimal strategy, we take a novel approach to introduce power efficiency factor, which is a function of the feedback rate, to quantify the effect of imperfect beamforming. By combining power efficiency factor and the asymptotic formulas for perfect beamforming case, the information rate of the power on/off strategy with a constant number of on-beams is accurately characterized.
On the Information Rate of MIMO Systems with Finite Rate Channel State Feedback and Power On/Off Strategy
Wei Dai,Youjian Liu,Brian Rider,Vincent K. N. Lau
Mathematics , 2007,
Abstract: This paper quantifies the information rate of multiple-input multiple-output (MIMO) systems with finite rate channel state feedback and power on/off strategy. In power on/off strategy, a beamforming vector (beam) is either turned on (denoted by on-beam) with a constant power or turned off. We prove that the ratio of the optimal number of on-beams and the number of antennas converges to a constant for a given signal-to-noise ratio (SNR) when the number of transmit and receive antennas approaches infinity simultaneously and when beamforming is perfect. Based on this result, a near optimal strategy, i.e., power on/off strategy with a constant number of on-beams, is discussed. For such a strategy, we propose the power efficiency factor to quantify the effect of imperfect beamforming. A formula is proposed to compute the maximum power efficiency factor achievable given a feedback rate. The information rate of the overall MIMO system can be approximated by combining the asymptotic results and the formula for power efficiency factor. Simulations show that this approximation is accurate for all SNR regimes.
No evidence for association of inherited variation in genes involved in mitosis and percent mammographic density
Celine M Vachon, Jingmei Li, Christopher G Scott, Per Hall, Kamila Czene, Xianshu Wang, Jianjun Liu, Zachary S Fredericksen, David N Rider, Fang-Fang Wu, Janet E Olson, Julie M Cunningham, Kristen N Stevens, Thomas A Sellers, Shane V Pankratz, Fergus J Couch
Breast Cancer Research , 2012, DOI: 10.1186/bcr3088
Abstract: We investigated 2,058 single nucleotide polymorphisms (SNPs) in 378 genes involved in regulation of mitosis for associations with adjusted PMD among 484 unaffected postmenopausal controls (without breast cancer) from the Mayo Clinic Breast Cancer Study (MCBCS) and replicated the findings in postmenopausal controls (n = 726) from the Singapore and Sweden Breast Cancer Study (SASBAC) study. PMD was assessed in both studies by a computer-thresholding method (Cumulus) and linear regression approaches were used to assess the association of SNPs and PMD, adjusted for age, BMI and postmenopausal hormones. A P-value threshold of 4.2 × 10-5 based on a Bonferroni correction of effective number of independent tests was used for statistical significance. Further, a pathway-level analysis was conducted of all 378 genes using the self-contained gene-set analysis method GLOSSI.A variant in PRPF4, rs10733604, was significantly associated with adjusted PMD in the MCBCS (P = 2.7 × 10-7), otherwise, no single SNP was associated with PMD. Additionally, the pathway analysis provided no evidence of enrichment in the number of associations observed between SNPs in the mitotic genes and PMD (P = 0.60). We evaluated rs10733604 (PRPF4), and 73 other SNPs at P < 0.05 from 51 genes in the SASBAC study. There was no evidence of an association of rs10733604 (PRPF4) with adjusted PMD in SASBAC (P = 0.23). There were, however, consistent associations (P < 0.05) of variants at the putative locus, LOC375190, Aurora B kinase (AURKB), and Mini-chromosome maintenance complex component 3 (MCM3) with adjusted PMD, although these were not statistically significant.Our findings do not support a role of inherited variation in genes involved in regulation of cell division and adjusted percent mammographic density in postmenopausal women.Mammographic density is a trait that represents the proportion of stromal and epithelial tissues in a radiographic image of the breast. Women with > 50% dense tissue are at a
Correlation of Chromosomal Instability, Telomere Length and Telomere Maintenance in Microsatellite Stable Rectal Cancer: A Molecular Subclass of Rectal Cancer
Lisa A. Boardman, Ruth A. Johnson, Kimberly B. Viker, Kari A. Hafner, Robert B. Jenkins, Douglas L. Riegert-Johnson, Thomas C. Smyrk, Kristin Litzelman, Songwon Seo, Ronald E. Gangnon, Corinne D. Engelman, David N. Rider, Russell J. Vanderboom, Stephen N. Thibodeau, Gloria M. Petersen, Halcyon G. Skinner
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080015
Abstract: Introduction Colorectal cancer (CRC) tumor DNA is characterized by chromosomal damage termed chromosomal instability (CIN) and excessively shortened telomeres. Up to 80% of CRC is microsatellite stable (MSS) and is historically considered to be chromosomally unstable (CIN+). However, tumor phenotyping depicts some MSS CRC with little or no genetic changes, thus being chromosomally stable (CIN-). MSS CIN- tumors have not been assessed for telomere attrition. Experimental Design MSS rectal cancers from patients ≤50 years old with Stage II (B2 or higher) or Stage III disease were assessed for CIN, telomere length and telomere maintenance mechanism (telomerase activation [TA]; alternative lengthening of telomeres [ALT]). Relative telomere length was measured by qPCR in somatic epithelial and cancer DNA. TA was measured with the TRAPeze assay, and tumors were evaluated for the presence of C-circles indicative of ALT. p53 mutation status was assessed in all available samples. DNA copy number changes were evaluated with Spectral Genomics aCGH. Results Tumors were classified as chromosomally stable (CIN-) and chromosomally instable (CIN+) by degree of DNA copy number changes. CIN- tumors (35%; n=6) had fewer copy number changes (<17% of their clones with DNA copy number changes) than CIN+ tumors (65%; n=13) which had high levels of copy number changes in 20% to 49% of clones. Telomere lengths were longer in CIN- compared to CIN+ tumors (p=0.0066) and in those in which telomerase was not activated (p=0.004). Tumors exhibiting activation of telomerase had shorter tumor telomeres (p=0.0040); and tended to be CIN+ (p=0.0949). Conclusions MSS rectal cancer appears to represent a heterogeneous group of tumors that may be categorized both on the basis of CIN status and telomere maintenance mechanism. MSS CIN- rectal cancers appear to have longer telomeres than those of MSS CIN+ rectal cancers and to utilize ALT rather than activation of telomerase.
Genetic variation in stromal proteins decorin and lumican with breast cancer: investigations in two case-control studies
Linda E Kelemen, Fergus J Couch, Shahana Ahmed, Alison M Dunning, Paul DP Pharoah, Douglas F Easton, Zachary S Fredericksen, Robert A Vierkant, V Shane Pankratz, Ellen L Goode, Christopher G Scott, David N Rider, Xianshu Wang, James R Cerhan, Celine M Vachon
Breast Cancer Research , 2008, DOI: 10.1186/bcr2201
Abstract: We investigated associations of 14 common polymorphisms in the DCN and LUM genes with 798 breast cancer cases and 843 controls from Mayo Clinic, MN, USA. One polymorphism per gene with the strongest risk association in the Mayo Clinic sample was genotyped in 4,470 breast cancer cases and 4,560 controls from East Anglia, England (Studies of Epidemiology and Risk Factors in Cancer Heredity (SEARCH)).In the Mayo Clinic sample, six polymorphisms were associated with breast cancer risk (Ptrend ≤ 0.05). The association with LUM rs2268578, evaluated further in SEARCH, was positive, although the odds ratios (OR) were weaker and not statistically significant. ORs were 1.4 (95% confidence interval [CI], 1.1 to 1.8) for heterozygotes and 2.2 (95% CI, 1.1 to 4.3; P2 df = 0.002) for homozygotes in the Mayo Clinic sample, and were 1.1 (95% CI, 0.9 to 1.2) for heterozygotes and 1.4 (95% CI, 1.0 to 2.1; P2 df = 0.13) for homozygotes in the SEARCH sample. In combined analyses, the ORs were 1.1 (95% CI, 1.0 to 1.2) for heterozygotes and 1.6 (95% CI, 1.2 to 2.3; P2 df = 0.005) for homozygotes. Positive associations for this polymorphism were observed for estrogen receptor-positive tumors in both the Mayo Clinic sample (OR for heterozygotes = 1.5, 1.1 to 1.9 and OR for homozygotes = 2.5, 1.2 to 5.3;P2 df = 0.001) and the SEARCH sample (OR for heterozygotes = 1.0, 0.9 to 1.1 and OR for homozygotes = 1.6, 1.0 to 2.5; P2 df = 0.10). In combined analyses, the ORs were 1.1 (95% CI, 0.9 to 1.2) for heterozygotes and 1.9 (95% CI, 1.3 to 2.8; P2 df = 0.001) for homozygotes.Although LUM rs2268578 was associated with breast cancer in the Mayo Clinic study, particularly estrogen receptor-positive breast cancer, weaker and modest associations were observed in the SEARCH sample. These modest associations will require larger samples to adequately assess the importance of this polymorphism in breast cancer.Stromal changes are well documented in breast tumors [1,2] and in preinvasive breast lesions [2
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