The Bell Laboratories (13)CO Survey: Longitude-Velocity Maps

A survey is presented of the Galactic plane in the J=1-0 transition of (13)CO. About 73,000 spectra were obtained with the 7 m telescope at Bell Laboratories over a ten-year period. The coverage of survey is (l, b) = (-5 to 117, -1 to +1), or 244 square degrees, with a grid spacing of 3' for |b| < 0.5, and a grid spacing of 6' for |b| > 0.5. The data presented here have been resampled onto a 3' grid. For 0.68 km/s channels, the rms noise level of the survey is 0.1 K on the $T_R^*$ scale. The raw data have been transformed into FITS format, and all the reduction processes, such as correcting for emission in the reference positions, baseline removal and interpolation were conducted within IRAF using the FCRAO task package and additional programs. The reduced data are presented here in the form of longitude-velocity color maps at each latitude. These data allow identification and classification of molecular clouds with masses in excess of ~ 1,000 solar masses throughout the first quadrant of the Galaxy. Spiral structure is manifested by the locations of the largest and brightest molecular clouds.Comment: 23 pages, 7 figures, ApJS submitted (out of 41 frames of Figure4, only one is included becaue of size limit

STRATEGIC MULTIPLE SENSOR DATA FUSION FOR TIME-CRITICAL NATURAL DISASTER RESPONSE

Recently, large-scale natural disasters have been occurred in the various areas of the world. The super-sized multi-hazards over the world have required more and more scientific and systematic measurement technologies in the fields of management and response of natural disaster. The purpose of this study is to suggest a multi-sources data fusion approach like LiDAR, aerial images, and satellite imagery and evaluate its applicability for timely natural disaster response. In order to achieve a high-accurate mapping in time in disaster situation, we proposed strategic approach using multi-sensors data fusion in this paper. The data fusion approach using the satellite imagery, low altitude aerial imagery from the mini-UAV and the small manned helicopter, and LiDAR point data simultaneously is expected to enhance the capability for more accurate damage analysis and the faster hazard mapping

VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations.

BACKGROUND: The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics, through the application of genotyping and population genetics analyses. This paper describes VivaxGEN (http://vivaxgen.menzies.edu.au), a web-based platform that has been developed to support P. vivax short tandem repeat data sharing and comparative analyses. RESULTS: The VivaxGEN platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools. The query system of the platform enables users to filter, select and differentiate samples and alleles based on their specified criteria. Key population genetic analyses are supported including measures of population differentiation (FST), expected heterozygosity (HE), linkage disequilibrium (IAS), neighbor-joining analysis and Principal Coordinate Analysis. Datasets can also be formatted and exported for application in commonly used population genetic software including GENEPOP, Arlequin and STRUCTURE. To date, data from 10 countries, including 5 publicly available data sets have been shared with VivaxGEN. CONCLUSIONS: VivaxGEN is well placed to facilitate regional overviews of P. vivax transmission dynamics in different endemic settings and capable to be adapted for similar genetic studies of P. falciparum and other organisms

Lattice instabilities of cubic NiTi from first principles

The phonon dispersion relation of NiTi in the simple cubic B2 structure is computed using first-principles density-functional perturbation theory with pseudopotentials and a plane-wave basis set. Lattice instabilities are observed to occur across nearly the entire Brillouin zone, excluding three interpenetrating tubes of stability along the (001) directions and small spheres of stability centered at R. The strongest instability is that of the doubly degenerate M5' mode. The atomic displacements of one of the eigenvectors of this mode generate a good approximation to the observed B19' ground-state structure.Comment: 11 pages, 3 figure

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants.

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date

Epicardial adipose tissue volume and left ventricular myocardial function using 3-dimensional speckle tracking echocardiography

Background: Although epicardial adipose tissue (EAT) volume is associated with increased incidence of coronary artery disease (CAD), its role in myocardial systolic dysfunction is unclear. The present study aimed to identify independent determinants of EAT volume in patients without obstructive CAD, and to evaluate the association between EAT volume (vs other measures of obesity) and myocardial systolic strain analysis

Serum Adipocyte Fatty Acid–Binding Protein Levels Are Associated With Nonalcoholic Fatty Liver Disease in Type 2 Diabetic Patients

OBJECTIVE—Adipocyte fatty acid–binding protein (A-FABP) is a major cytoplasmic protein in adipocytes and macrophages and is closely associated with metabolic syndrome, type 2 diabetes, and atherosclerosis. Here, we investigated whether A-FABP was associated with nonalcoholic fatty liver disease (NAFLD) in type 2 diabetes

The urologic epithelial stem cell database (UESC) – a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder

Background: Public databases are crucial for analysis of high-dimensional gene and protein expression data. The Urologic Epithelial Stem Cells (UESC) database http://scgap.systemsbiology.net/ is a public database that contains gene and protein information for the major cell types of the prostate, prostate cancer cell lines, and a cancer cell type isolated from a primary tumor. Similarly, such information is available for urinary bladder cell types. Description: Two major data types were archived in the database, protein abundance localization data from immunohistochemistry images, and transcript abundance data principally from DNA microarray analysis. Data results were organized in modules that were made to operate independently but built upon a core functionality. Gene array data and immunostaining images for human and mouse prostate and bladder were made available for interrogation. Data analysis capabilities include: (1) CD (cluster designation) cell surface protein data. For each cluster designation molecule, a data summary allows easy retrieval of images (at multiple magnifications). (2) Microarray data. Single gene or batch search can be initiated with Affymetrix Probeset ID, Gene Name, or Accession Number together with options of coalescing probesets and/or replicates. Conclusion: Databases are invaluable for biomedical research, and their utility depends on data quality and user friendliness. UESC provides for database queries and tools to examine cell typespecific gene expression (normal vs. cancer), whereas most other databases contain only whole tissue expression datasets. The UESC database provides a valuable tool in the analysis of differential gene expression in prostate cancer genes in cancer progression.This work was supported by grant 1U01 DK63630 from NIDDK. Additional funding came from grants CA85859, CA98699 and CA111244 from NCI

Seminal plasma as a source of prostate cancer peptide biomarker candidates for detection of indolent and advanced disease

Background:Extensive prostate specific antigen screening for prostate cancer generates a high number of unnecessary biopsies and over-treatment due to insufficient differentiation between indolent and aggressive tumours. We hypothesized that seminal plasma is a robust source of novel prostate cancer (PCa) biomarkers with the potential to improve primary diagnosis of and to distinguish advanced from indolent disease. &lt;br&gt;Methodology/Principal Findings: In an open-label case/control study 125 patients (70 PCa, 21 benign prostate hyperplasia, 25 chronic prostatitis, 9 healthy controls) were enrolled in 3 centres. Biomarker panels a) for PCa diagnosis (comparison of PCa patients versus benign controls) and b) for advanced disease (comparison of patients with post surgery Gleason score &#60;7 versus Gleason score &#62;&gt;7) were sought. Independent cohorts were used for proteomic biomarker discovery and testing the performance of the identified biomarker profiles. Seminal plasma was profiled using capillary electrophoresis mass spectrometry. Pre-analytical stability and analytical precision of the proteome analysis were determined. Support vector machine learning was used for classification. Stepwise application of two biomarker signatures with 21 and 5 biomarkers provided 83% sensitivity and 67% specificity for PCa detection in a test set of samples. A panel of 11 biomarkers for advanced disease discriminated between patients with Gleason score 7 and organ-confined (&#60;pT3a) or advanced (&#8805;pT3a) disease with 80% sensitivity and 82% specificity in a preliminary validation setting. Seminal profiles showed excellent pre-analytical stability. Eight biomarkers were identified as fragments of N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase​,prostatic acid phosphatase, stabilin-2, GTPase IMAP family member 6, semenogelin-1 and -2. Restricted sample size was the major limitation of the study.&lt;/br&gt; &lt;br&gt;Conclusions/Significance: Seminal plasma represents a robust source of potential peptide makers for primary PCa diagnosis. Our findings warrant further prospective validation to confirm the diagnostic potential of identified seminal biomarker candidates.&lt;/br&gt

Perilipin 2 (PLIN2)-Deficiency Does Not Increase Cholesterol-Induced Toxicity in Macrophages

Interventions on macrophages/foam cells to redirect intracellular cholesterol towards efflux pathways could become a very valuable addition to our therapeutic arsenal against atherosclerosis. However, certain manipulations of the cholesteryl ester cycle, such as the inhibition of ACAT1, an ER-resident enzyme that re-esterifies cholesterol, are not well tolerated. Previously we showed that targeting perilipin-2 (PLIN2), a major lipid droplet (LD)-associated protein in macrophages, prevents foam cell formation and protects against atherosclerosis. Here we have assessed the tolerance of PLIN2-deficient bone marrow derived macrophages (BMM) to several lipid loading conditions similar to the found during atherosclerosis development, including exposure to modified low-density lipoprotein (mLDL) and 7-ketocholesterol (7-KC), a free cholesterol (FC) metabolite, in media with or without cholesterol acceptors. BMM isolated from mice that do or do not express PLIN2 were tested for apoptosis (TUNEL and cleaved caspase-3), ER stress (CHOP induction and XBP-1 splicing), and inflammation (TNF-α and IL-6 mRNA levels). Like in other cell types, PLIN2 deficiency impairs LD buildup in BMM. However, while most stress parameters were elevated in macrophages under ACAT inhibition and 7-KC loading, PLIN2 inactivation was well tolerated. The data support the safety of targeting PLIN2 to prevent foam cell formation and atherosclerosis