NCBI GEO: archive for high-throughput functional genomic data

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as ‘Minimum Information About a Microarray Experiment’ (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/

Ice core evidence for significant 100-year regional warming on the Antarctic Peninsula

We present a new 150-year, high-resolution, stable isotope record (delta O-18) from the Gomez ice core, drilled on the data sparse south western Antarctic Peninsula, revealing a similar to 2.7 degrees C rise in surface temperatures since the 1950s. The record is highly correlated with satellite-derived temperature reconstructions and instrumental records from Faraday station on the north west coast, thus making it a robust proxy for local and regional temperatures since the 1850s. We conclude that the exceptional 50-year warming, previously only observed in the northern Peninsula, is not just a local phenomena but part of a statistically significant 100-year regional warming trend that began around 1900. A suite of coupled climate models are employed to demonstrate that the 50 and 100 year temperature trends are outside of the expected range of variability from pre-industrial control runs, indicating that the warming is likely the result of external climate forcing. Citation: Thomas, E. R., P. F. Dennis, T. J. Bracegirdle, and C. Franzke (2009), Ice core evidence for significant 100-year regional warming on the Antarctic Peninsula, Geophys. Res. Lett., 36, L20704, doi: 10.1029/2009GL040104

The State of the Region: Hampton Roads 2006

This is Old Dominion University\u27s seventh annual State of the Region report. While it represents the work of many people connected in various ways to the university, the report does not constitute an official viewpoint of Old Dominion, or it\u27s president, Roseann Runte. The report maintains the goal of stimulating thought and discussion that ultimately will make Hampton Roads an even better place to live. We are proud of our region\u27s many successes, but realize that it is possible to improve our performance. In order to do so, we must have accurate information about where we are and a sound understanding of the policy options open to us.https://digitalcommons.odu.edu/economics_books/1012/thumbnail.jp

A multi-gene signature predicts outcome in patients with pancreatic ductal adenocarcinoma.

© 2014 Haider et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Improved usage of the repertoires of pancreatic ductal adenocarcinoma (PDAC) profiles is crucially needed to guide the development of predictive and prognostic tools that could inform the selection of treatment options

Quartic quantum theory: an extension of the standard quantum mechanics

We propose an extended quantum theory, in which the number K of parameters necessary to characterize a quantum state behaves as fourth power of the number N of distinguishable states. As the simplex of classical N-point probability distributions can be embedded inside a higher dimensional convex body of mixed quantum states, one can further increase the dimensionality constructing the set of extended quantum states. The embedding proposed corresponds to an assumption that the physical system described in N dimensional Hilbert space is coupled with an auxiliary subsystem of the same dimensionality. The extended theory works for simple quantum systems and is shown to be a non-trivial generalisation of the standard quantum theory for which K=N^2. Imposing certain restrictions on initial conditions and dynamics allowed in the quartic theory one obtains quadratic theory as a special case. By imposing even stronger constraints one arrives at the classical theory, for which K=N.Comment: 30 pages in latex with 6 figures included; ver.2: several improvements, new references adde

Neutrino and Antineutrino Inclusive Charged-current Cross Section Measurements with the MINOS Near Detector

The energy dependence of the neutrino-iron and antineutrino-iron inclusive charged-current cross sections and their ratio have been measured using a high-statistics sample with the MINOS Near Detector exposed to the NuMI beam from the Main Injector at Fermilab. Neutrino and antineutrino fluxes were determined using a low hadronic energy subsample of charged-current events. We report measurements of neutrino-Fe (antineutrinoFe) cross section in the energy range 3-50 GeV (5-50 GeV) with precision of 2-8% (3-9%) and their ratio which is measured with precision 2-8%. The data set spans the region from low energy, where accurate measurements are sparse, up to the high-energy scaling region where the cross section is well understood.Comment: accepted by PR

Incidence of insulin-requiring diabetes in the US military

The aim of the study was to determine age- and race-related, and overall incidence rates of insulin-requiring diabetes in adults in the US military. Electronic records for admissions to US military and Tricare hospitals during 1990–2005 and visits to military clinics during 2000–2005 were identified using the Career History Archival Medical and Personnel System at the Naval Health Research Center, San Diego, CA, USA. Population data were obtained from the Defense Manpower Data Center and Defense Medical Epidemiology Database. In men there were 2,918 new cases of insulin-requiring diabetes in 20,427,038 person-years at ages 18–44 years (median age 28 years) for a total age-adjusted incidence rate of 17.5 per 100,000 person-years (95% CI 16.4–18.6). Incidence rates were twice as high in black men as in white men (31.5 vs 14.5 per 100,000, p < 0.001). In women there were 414 new cases in 3,285,000 person-years at ages 18–44 years (median age 27 years), for a total age-adjusted incidence rate of 13.6 per 100,000 (95% CI 12.4–14.9). Incidence rates were twice as high in black women as in white women (21.8 vs 9.7 per 100,000, p < 0.001). In a regression model, incidence of insulin-requiring diabetes peaked annually in the winter–spring season (OR 1.46, p < 0.01). Race and seasonal differences persisted in the multivariate analysis. Differences in incidence rates by race and season suggest a need for further research into possible reasons, including the possibility of a contribution from vitamin D deficiency. Cohort studies using prediagnostic serum 25-hydroxyvitamin D should be conducted to further evaluate this relationship

Search for sterile neutrino mixing in the MINOS long-baseline experiment

A search for depletion of the combined flux of active neutrino species over a 735 km baseline is reported using neutral-current interaction data recorded by the MINOS detectors in the NuMI neutrino beam. Such a depletion is not expected according to conventional interpretations of neutrino oscillation data involving the three known neutrino flavors. A depletion would be a signature of oscillations or decay to postulated noninteracting sterile neutrinos, scenarios not ruled out by existing data. From an exposure of 3.18×10^(20) protons on target in which neutrinos of energies between ∼500  MeV and 120 GeV are produced predominantly as ν_μ, the visible energy spectrum of candidate neutral-current reactions in the MINOS far detector is reconstructed. Comparison of this spectrum to that inferred from a similarly selected near-detector sample shows that of the portion of the ν_μ flux observed to disappear in charged-current interaction data, the fraction that could be converting to a sterile state is less than 52% at 90% confidence level (C.L.). The hypothesis that active neutrinos mix with a single sterile neutrino via oscillations is tested by fitting the data to various models. In the particular four-neutrino models considered, the mixing angles θ_(24) and θ_(34) are constrained to be less than 11° and 56° at 90% C.L., respectively. The possibility that active neutrinos may decay to sterile neutrinos is also investigated. Pure neutrino decay without oscillations is ruled out at 5.4 standard deviations. For the scenario in which active neutrinos decay into sterile states concurrently with neutrino oscillations, a lower limit is established for the neutrino decay lifetime τ_3/m_3>2.1×10^(-12) s/eV at 90% C.L