IView: introgression library visualization and query tool

<p>Abstract</p> <p>Background</p> <p>An introgression library is a family of near-isogenic lines in a common genetic background, each of which carries one or more genomic regions contributed by a donor genome. Near-isogenic lines are powerful genetic resources for the analysis of phenotypic variation and are important for map-base cloning genes underlying mutations and traits. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. </p> <p>Results</p> <p>We have created IView, a tool to graphically display and query near-isogenic line libraries for specific introgressions. This tool incorporates a web interface for displaying the location and extent of introgressions. Each genetic marker is associated with a position on a reference map. Users can search for introgressions using marker names, or chromosome number and map positions. This search results in a display of lines carrying an introgression at the specified position. Upon selecting one of the lines, color-coded introgressions on all chromosomes of the line are displayed graphically.</p> <p>The source code for IView can be downloaded from <url>http://xrl.us/iview</url>. </p> <p>Conclusions</p> <p>IView will be useful for those wanting to make introgression data from their stock of germplasm searchable. </p

Les bulles « robustes »:Pourquoi il faut construire des logements en région parisienne

« Bulle » ou « pas bulle » ? La question taraude les observateurs et les acteurs du marché immobilier français. Nous examinons dans cet article les éléments empiriques et théoriques qui expliquent la hausse des prix récente et sa résistance aux retournements conjoncturels. En combinant la notion de bulle économique, les arguments de l’économie spatiale et une analyse d’économie politique, nous suggérons que la valorisation importante de l’immobilier en France est le résultat d’une logique rationnelle et conforte les intérêts des acteurs locaux. Dès lors, la forte valorisation peut être considérée comme une « bulle robuste », à même de résister à des chocs importants. Cette bulle organise un transfert intergénérationnel et peut avoir des effets positifs. Elle peut également renforcer la ségrégation spatiale, alimenter les inégalités territoriales et empêcher d’exploiter les économies d’agglomération possibles. L’analyse est détaillée sur la région Ile-de-France où ces phénomènes sont particulièrement marqués

The YH database: the first Asian diploid genome database

The YH database is a server that allows the user to easily browse and download data from the first Asian diploid genome. The aim of this platform is to facilitate the study of this Asian genome and to enable improved organization and presentation large-scale personal genome data. Powered by GBrowse, we illustrate here the genome sequences, SNPs, and sequencing reads in the MapView. The relationships between phenotype and genotype can be searched by location, dbSNP ID, HGMD ID, gene symbol and disease name. A BLAST web service is also provided for the purpose of aligning query sequence against YH genome consensus. The YH database is currently one of the three personal genome database, organizing the original data and analysis results in a user-friendly interface, which is an endeavor to achieve fundamental goals for establishing personal medicine. The database is available at http://yh.genomics.org.cn

T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research

T1DBase (http://www.t1dbase.org) is web platform, which supports the type 1 diabetes (T1D) community. It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. This update describes the incorporation of new data sets, tools and curation efforts as well as a new website design to simplify site use. New data sets include curated summary data from four genome-wide association studies relevant to T1D, HaemAtlas—a data set and tool to query gene expression levels in haematopoietic cells and a manually curated table of human T1D susceptibility loci, incorporating genetic overlap with other related diseases. These developments will continue to support T1D research and allow easy access to large and complex T1D relevant data sets

Investigation of transverse collective flow of intermediate mass fragments

The transverse flow of intermediate mass fragments (IMFs) has been investigated for the 35 MeV/u ${}^{70}\mathrm{Zn}+{}^{70}\mathrm{Zn}$, ${}^{64}\mathrm{Zn}+{}^{64}\mathrm{Zn}$, and ${}^{64}\mathrm{Ni}+{}^{64}\mathrm{Ni}$ systems. A transition from the IMF transverse flow strongly depending on the mass of the system, in the most violent collisions, to a dependence on the charge of the system, for the peripheral reactions, is shown. This transition was shown to be sensitive to the density dependence of the symmetry energy using the antisymmetrized molecular-dynamics model. The results present an observable, the IMF transverse flow, that can be used to probe the nuclear equation of state. Comparison with the simulation demonstrated a preference for a stiff density dependence of the symmetry energy

Sensitivity of intermediate mass fragment flows to the symmetry energy

The NIMROD-ISiS array was used to study the transverse flow of intermediate mass fragments in 35 MeV/nucleon ${}^{70}\mathrm{Zn}+{}^{70}\mathrm{Zn}$, ${}^{64}\mathrm{Zn}+{}^{64}\mathrm{Zn}$, and ${}^{64}\mathrm{Ni}+{}^{64}\mathrm{Ni}$ reactions. The intermediate mass fragment flow was previously shown to be sensitive to the density dependence of the symmetry energy. To explore the model dependence of the results, the antisymmetrized molecular dynamics, constrained molecular dynamics, and stochastic mean-field models were each compared to the experimental results to extract information on the form of the symmetry energy. The results demonstrate that sensitivity of the models to the nuclear equation of state can vary significantly based on the treatment of the nuclear dynamics. Despite the differences in the sensitivity, improved agreement with the experimental data is observed for each model with a stiff density dependence of the symmetry energy

Transverse collective flow and midrapidity emission of isotopically identified light charged particles

The transverse flow and relative midrapidity yield of isotopically identified light charged particles (LCPs) has been examined for the 35 MeV/nucleon ${}^{70}\mathrm{Zn}+{}^{70}\mathrm{Zn}$, ${}^{64}\mathrm{Zn}+{}^{64}\mathrm{Zn}$, and ${}^{64}\mathrm{Ni}+{}^{64}\mathrm{Ni}$ systems. A large enhancement of the midrapidity yield of the LCPs was observed relative to the yield near the projectile rapidity. In particular, this enhancement was increased for the more neutron-rich LCPs demonstrating a preference for the production of neutron-rich fragments in the midrapidity region. Additionally, the transverse flow of the LCPs was extracted, which provides insight into the average movement of the particles in the midrapidity region. Isotopic and isobaric effects were observed in the transverse flow of the fragments. In both cases, the transverse flow was shown to decrease with an increasing neutron content in the fragments. A clear inverse relationship between the transverse flow and the relative midrapidity yield is shown. The increased relative midrapidity emission produces a decreased transverse flow. The stochastic mean-field model was used for comparison to the experimental data. The results showed that the model was able to reproduce the general isotopic and isobaric trends for the midrapidity emission and transverse flow. The sensitivity of these observables to the density dependence of the symmetry energy was explored. The results indicate that the transverse flow and midrapidity emission of the LCPs are sensitive to the denisty dependence of the symmetry energy

The World Trade Center Disaster and the Health of Workers: Five-Year Assessment of a Unique Medical Screening Program

BACKGROUND: Approximately 40,000 rescue and recovery workers were exposed to caustic dust and toxic pollutants following the 11 September 2001 attacks on the World Trade Center (WTC). These workers included traditional first responders, such as firefighters and police, and a diverse population of construction, utility, and public sector workers. METHODS: To characterize WTC-related health effects, the WTC Worker and Volunteer Medical Screening Program was established. This multicenter clinical program provides free standardized examinations to responders. Examinations include medical, mental health, and exposure assessment questionnaires; physical examinations; spirometry; and chest X rays. RESULTS: Of 9,442 responders examined between July 2002 and April 2004, 69% reported new or worsened respiratory symptoms while performing WTC work. Symptoms persisted to the time of examination in 59% of these workers. Among those who had been asymptomatic before September 11, 61% developed respiratory symptoms while performing WTC work. Twenty-eight percent had abnormal spirometry; forced vital capacity (FVC) was low in 21%; and obstruction was present in 5%. Among nonsmokers, 27% had abnormal spirometry compared with 13% in the general U.S. population. Prevalence of low FVC among nonsmokers was 5-fold greater than in the U.S. population (20% vs. 4%). Respiratory symptoms and spirometry abnormalities were significantly associated with early arrival at the site. CONCLUSION: WTC responders had exposure-related increases in respiratory symptoms and pulmonary function test abnormalities that persisted up to 2.5 years after the attacks. Long-term medical monitoring is required to track persistence of these abnormalities and identify late effects, including possible malignancies. Lessons learned should guide future responses to civil disasters