510 research outputs found
ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS
Genomic changes such as copy number alterations are thought to be one of the major underlying causes of human phenotypic variation among normal and disease subjects [23,11,25,26,5,4,7,18]. These include chromosomal regions with so-called copy number alterations: instead of the expected two copies, a section of the chromosome for a particular individual may have zero copies (homozygous deletion), one copy (hemizygous deletions), or more than two copies (amplifications). The canonical example is Down syndrome which is caused by an extra copy of chromosome 21. Identification of such abnormalities in smaller regions has been of great interest, because it is believed to be an underlying cause of cancer.
More than one decade ago comparative genomic hybridization (CGH)technology was developed to detect copy number changes in a high-throughput fashion. However, this technology only provides a 10 MB resolution which limits the ability to detect copy number alterations spanning small regions. It is widely believed that a copy number alteration as small as one base can have significant downstream effects, thus microarray manufacturers have developed technologies that provide much higher resolution. Unfortunately, strong probe effects and variation introduced by sample preparation procedures have made single-point copy number estimates too imprecise to be useful. CGH arrays use a two-color hybridization, usually comparing a sample of interest to a reference sample, which to some degree removes the probe effect. However, the resolution is not nearly high enough to provide single-point copy number estimates. Various groups have proposed statistical procedures that pool data from neighboring locations to successfully improve precision. However, these procedure need to average across relatively large regions to work effectively thus greatly reducing the resolution. Recently, regression-type models that account for probe-effect have been proposed and appear to improve accuracy as well as precision. In this paper, we propose a mixture model solution specifically designed for single-point estimation, that provides various advantages over the existing methodology. We use a 314 sample database, constructed with public datasets, to motivate and fit models for the conditional distribution of the observed intensities given allele specific copy numbers. With the estimated models in place we can compute posterior probabilities that provide a useful prediction rule as well as a confidence measure for each call. Software to implement this procedure will be available in the Bioconductor oligo packagehttp://www.bioconductor.org)
Kohn Anomalies in Superconductors
I present the detailed behavior of phonon dispersion curves near momenta
which span the electronic Fermi sea in a superconductor. I demonstrate that an
anomaly, similar to the metallic Kohn anomaly, exists in a superconductor's
dispersion curves when the frequency of the phonon spanning the Fermi sea
exceeds twice the superconducting energy gap. This anomaly occurs at
approximately the same momentum but is {\it stronger} than the normal-state
Kohn anomaly. It also survives at finite temperature, unlike the metallic
anomaly. Determination of Fermi surface diameters from the location of these
anomalies, therefore, may be more successful in the superconducting phase than
in the normal state. However, the superconductor's anomaly fades rapidly with
increased phonon frequency and becomes unobservable when the phonon frequency
greatly exceeds the gap. This constraint makes these anomalies useful only in
high-temperature superconductors such as .Comment: 18 pages (revtex) + 11 figures (upon request), NSF-ITP-93-7
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Volcanic constraints on the unzipping of Africa from South America: Insights from new geochronological controls along the Angola margin
The breakup of Africa from South America is associated with the emplacement of the ParanĂĄ-Etendeka flood basalt province from around 134 Ma and the Tristan da Cunha plume. Yet many additional volcanic events occur that are younger than the main pulse of the ParanĂĄ-Etendeka and straddle the rift to drift phases of the main breakup. This contribution reports on new geochronological constraints from the Angolan part of the African Margin. Three coastal and one inland section have been sampled stretching across some 400 Km, with 39Ar/40Ar, U-Pb and Palaeontology used to provide age constraints. Ages from the new data range from ~100 to 81 Ma, with three main events (cr. 100, 91 and 82-81 Ma). Volcanic events are occurring within the Early to Late Cretaceous, along this part of the margin with a general younging towards Namibia. With the constraints of additional age information both onshore and offshore Angola, a clear younging trend at the early stages of rift to drift is recorded in the volcanic events that unzip from North to South. Similar age volcanic events are reported from the Brazilian side of the conjugate margin, and highlight the need to fully incorporate these relatively low volume volcanic pulses into the plate tectonic breakup models of the South Atlantic Margin
Greenhouse production systems for people
Environmentally sound greenhouse production requires that: demand for market products is understood; greenhouse design addresses the climate circum-stances; input resources are available and consumed efficiently, and; there must be a reasonable balance of production products to the environmental impacts from system. Engineering greenhouse production systems to meet these requirements must include: a cost-effective and structurally sound facility; various sub-systems controlled to interact harmoniously together; and educated and experienced system operators. The major components of the environmentally sound greenhouse are: Super-structure and glazing (for a specific location and climate conditions); Climate control sub-systems (ventilation, heating, cooling, CO2 control, pest protection, energy conservation, shading/lighting); Monitoring and control (for system operations data; decision-support systems; and, operations control procedures); Automation systems (for quality control, and effective resource utilization); and Crop nutrient delivery system (for control of plant root zone environment). Effective greenhouse engineering design, operations and management, must incorporate input from academic, private and public sectors of society. Therefore this team of researchers, educators, industry/ business, and experienced crop production operators has cooperated to include a current real-world applications perspective to the presentation. Greenhouse producÂŹtion systems are described that not only include the fundamentals for success, but also the combination of sub-systems, at appropriate technological levels to meet the design requirements and restrictions for success. The collaborators on this presentation have capabilities and experiences of successful greenhouse production systems from around the world that range from simple, low-input systems to highly complex production systems. Our goal is to emphasize the current basics of greenhouse design, and to support the symposium about greenhouse production systems for people
Tomato: a crop species amenable to improvement by cellular and molecular methods
Tomato is a crop plant with a relatively small DNA content per haploid genome and a well developed genetics. Plant regeneration from explants and protoplasts is feasable which led to the development of efficient transformation procedures.
In view of the current data, the isolation of useful mutants at the cellular level probably will be of limited value in the genetic improvement of tomato. Protoplast fusion may lead to novel combinations of organelle and nuclear DNA (cybrids), whereas this technique also provides a means of introducing genetic information from alien species into tomato. Important developments have come from molecular approaches. Following the construction of an RFLP map, these RFLP markers can be used in tomato to tag quantitative traits bred in from related species. Both RFLP's and transposons are in the process of being used to clone desired genes for which no gene products are known. Cloned genes can be introduced and potentially improve specific properties of tomato especially those controlled by single genes. Recent results suggest that, in principle, phenotypic mutants can be created for cloned and characterized genes and will prove their value in further improving the cultivated tomato.
Predicting substance use behavior among South African adolescents: The role of leisure experiences across time
Using seven waves of data, collected twice a year from the 8th through the 11th grades in a low-resource community in Cape Town, South Africa, we aimed to describe the developmental trends in three specific leisure experiences (leisure boredom, new leisure interests, and healthy leisure) and substance use (cigarettes, alcohol, and marijuana) behaviors and to investigate the ways in which changes in leisure experiences predict changes in substance use behaviors over time. Results indicated that adolescentsâ substance use increased significantly across adolescence, but that leisure experiences remained fairly stable over time. We also found that adolescent leisure experiences predicted baseline substance use and that changes in leisure experiences predicted changes in substance use behaviors over time, with leisure boredom emerging as the most consistent and strongest predictor of alcohol, cigarette, and marijuana use. Implications for interventions that target time use and leisure experiences are discussed.Web of Scienc
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV
Results are presented from a search for a W' boson using a dataset
corresponding to 5.0 inverse femtobarns of integrated luminosity collected
during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV.
The W' boson is modeled as a heavy W boson, but different scenarios for the
couplings to fermions are considered, involving both left-handed and
right-handed chiral projections of the fermions, as well as an arbitrary
mixture of the two. The search is performed in the decay channel W' to t b,
leading to a final state signature with a single lepton (e, mu), missing
transverse energy, and jets, at least one of which is tagged as a b-jet. A W'
boson that couples to fermions with the same coupling constant as the W, but to
the right-handed rather than left-handed chiral projections, is excluded for
masses below 1.85 TeV at the 95% confidence level. For the first time using LHC
data, constraints on the W' gauge coupling for a set of left- and right-handed
coupling combinations have been placed. These results represent a significant
improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe
Measurement of the Lambda(b) cross section and the anti-Lambda(b) to Lambda(b) ratio with Lambda(b) to J/Psi Lambda decays in pp collisions at sqrt(s) = 7 TeV
The Lambda(b) differential production cross section and the cross section
ratio anti-Lambda(b)/Lambda(b) are measured as functions of transverse momentum
pt(Lambda(b)) and rapidity abs(y(Lambda(b))) in pp collisions at sqrt(s) = 7
TeV using data collected by the CMS experiment at the LHC. The measurements are
based on Lambda(b) decays reconstructed in the exclusive final state J/Psi
Lambda, with the subsequent decays J/Psi to an opposite-sign muon pair and
Lambda to proton pion, using a data sample corresponding to an integrated
luminosity of 1.9 inverse femtobarns. The product of the cross section times
the branching ratio for Lambda(b) to J/Psi Lambda versus pt(Lambda(b)) falls
faster than that of b mesons. The measured value of the cross section times the
branching ratio for pt(Lambda(b)) > 10 GeV and abs(y(Lambda(b))) < 2.0 is 1.06
+/- 0.06 +/- 0.12 nb, and the integrated cross section ratio for
anti-Lambda(b)/Lambda(b) is 1.02 +/- 0.07 +/- 0.09, where the uncertainties are
statistical and systematic, respectively.Comment: Submitted to Physics Letters
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