A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni

To provide a novel resource for analysis of the genome of Biomphalaria glabrata, members of the international Biomphalaria glabrata Genome Initiative (biology.unm.edu/biomphalaria-genome.html), working with the Arizona Genomics Institute (AGI) and supported by the National Human Genome Research Institute (NHGRI), produced a high quality bacterial artificial chromosome (BAC) library. The BB02 strain B. glabrata, a field isolate (Belo Horizonte, Minas Gerais, Brasil) that is susceptible to several strains of Schistosoma mansoni, was selfed for two generations to reduce haplotype diversity in the offspring. High molecular weight DNA was isolated from ovotestes of 40 snails, partially digested with HindIII, and ligated into pAGIBAC1 vector. The resulting B. glabrata BAC library (BG_BBa) consists of 61824 clones (136.3 kb average insert size) and provides 9.05 × coverage of the 931 Mb genome. Probing with single/low copy number genes from B. glabrata and fingerprinting of selected BAC clones indicated that the BAC library sufficiently represents the gene complement. BAC end sequence data (514 reads, 299860 nt) indicated that the genome of B. glabrata contains ~ 63% AT, and disclosed several novel genes, transposable elements, and groups of high frequency sequence elements. This BG_BBa BAC library, available from AGI at cost to the research community, gains in relevance because BB02 strain B. glabrata is targeted whole genome sequencing by NHGRI.

ParroCha : low-level C# library that wraps libparrot

Parrocha es un envoltorio simple realizado para las plataformas de desarrollo basadas en el estándar CLI de la biblioteca libparrot. Libparrot es una biblioteca de funciones implementada en C, que puede compilarse sobre varias plataformas y en la que se implementa la plataforma de desarrollo Parrot.

Virtual library, a real library?

Les possibilitats ofertes per la virtualitat tenen una gran importància en l'esfera educativa i en tots els aspectes referents a ella. Evidentment, les biblioteques i els centres de documentació no són estranys a aquest nou ambient virtual facilitat pel canvi social, econòmic i, sobretot, tecnològic que ha permès que els bibliotecaris-documentalistes accedeixin a gran quantitat d'informació i de documentació, permetent que actuïn com a agents intermediaris entre aquesta nova situació i l'ús que se'n poden fer pels diversos tipus d'usuaris.

Virtual Library Services for a Virtual University : User-Oriented Virtual Sites in an Open Library

La llegada de las tecnologías de la información, y su uso cada vez mayor y generalizado que se está haciendo de ellas, ha permitido para que una nueva situación aparezca que, a su vez, ha originado - de hecho, que ha precipitado - una serie de cambios de gran importancia en todos los niveles, pero especialmente en los niveles sociales, económicos y culturales. Este nueva escena ha tenido una gran influencia en el entorno pedagógico. De hecho, la aparición de nuevos modelos educativos como resultado de este cambio ha estado sucediendo de una manera continuada e ininterrumpida durante la década pasada. Estos cambios recientes en los sistemas actuales de enseñanza y de aprendizaje han significado un aumento y un cambio en el tipo de demandas hechas desde las bibliotecas y los centros de documentación.

Virtual Library Services for a Virtual University

Es presenta el concepte de biblioteca virtual tal com es desenvolupa a la Universitat Oberta de Catalunya una institució d'educació a distància que proporciona educació universitària. La UOC basa l'organització del seu model educatiu en l'explotació del paradigma del Campus Virtual i en l'ús de les darreres tecnologies disponibles en telemàtica, ordinadors personals i multimèdia. En aquest context, la Biblioteca Virtual de la UOC s'ofereix com un nou model del servei de biblioteca, flexible i dissenyat de manera que els usuaris puguin aprofitar-se de les noves tecnologies de la informació i accedir a les dades registrades i emmagatzemades a qualsevol lloc del món.

A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium

Genome-wide association studies (GWAS) have been successful in identifying common genetic variation involved in susceptibility to etiologically complex disease. We conducted a GWAS to identify common genetic variation involved in susceptibility to upper aero-digestive tract (UADT) cancers. Genome-wide genotyping was carried out using the Illumina HumanHap300 beadchips in 2,091 UADT cancer cases and 3,513 controls from two large European multi-centre UADT cancer studies, as well as 4,821 generic controls. The 19 top-ranked variants were investigated further in an additional 6,514 UADT cancer cases and 7,892 controls of European descent from an additional 13 UADT cancer studies participating in the INHANCE consortium. Five common variants presented evidence for significant association in the combined analysis (p≤5×10−7). Two novel variants were identified, a 4q21 variant (rs1494961, p = 1×10−8) located near DNA repair related genes HEL308 and FAM175A (or Abraxas) and a 12q24 variant (rs4767364, p = 2×10−8) located in an extended linkage disequilibrium region that contains multiple genes including the aldehyde dehydrogenase 2 (ALDH2) gene. Three remaining variants are located in the ADH gene cluster and were identified previously in a candidate gene study involving some of these samples. The association between these three variants and UADT cancers was independently replicated in 5,092 UADT cancer cases and 6,794 controls non-overlapping samples presented here (rs1573496-ADH7, p = 5×10−8; rs1229984-ADH1B, p = 7×10−9; and rs698-ADH1C, p = 0.02). These results implicate two variants at 4q21 and 12q24 and further highlight three ADH variants in UADT cancer susceptibility.

M-Library in an m-University : changing Models in the Open University of Catalonia

The general perspective of M-technologies and M-Services at the Spanish universities is not still in a very high level when we are ending the first decade of the 21st century. Some Universities and some of their libraries are starting to try out with M-technologies, but are still far from a model of massive exploitation, less than in some other countries. A deep study is needed to know the main reasons, study that we will not do in this paper. This general perspective does not mean that there are no significant initiatives which start to trust in M-technologies from Universities and their libraries. Models based in M-technologies make more sense than ever in open universities and in open libraries. That's the reason why the UOC's Library began in late 90s its first experiences in the M-Technologies and M-Libraries developments. In 1999 the appropriate technology offered the opportunity to carry out the first pilot test with SMS, and then applying the WAP technology. At those moments we managed to link-up mobile phones to the OPAC through a WAP system that allowed searching the catalogue by categories and finding the final location of a document, offering also the address of the library in which the user could loan it. Since then, UOC (and its library) directs its efforts towards adapting the offer of services to all sorts of M-devices used by end users. Left the WAP technology, nowadays the library is experimenting with some new devices like e-books, and some new services to get more feedback through the OPAC and metalibrary search products. We propose the case of Open University of Catalonia, in two levels: M-services applied in the library and M-technologies applied in some other university services and resources.

The deployment of an e-book consultation and loan service : the experience of the Open University of Catalonia Library

La Biblioteca de la UOC (UOC Library) ha ofert durant tres mesos (octubre-desembre 09), en fase de prova pilot, un servei de consulta i préstec de lectors de llibres electrònics (e-readers). Aquest nou desplegament s'ha desenvolupat en consonància amb l'aposta general de la Universitat en innovació en tecnologies aplicades a l'educació, i la voluntat de potenciar les col·leccions de llibres electrònics i l'ús dels dispositius de lectura de llibres electrònics com una extensió més de la tecnologia del Campus 5.0, en el suport a l'aprenentatge dels seus estudiants durant la seva formació a la Universitat. Aquest treball presenta en detall les especificacions de la prova pilot, a més de contenir una anàlisi i avaluació dels resultats obtinguts: punts forts i punts febles, relació dels aspectes a millorar i modificar, de cara a la consolidació final del servei.

What should a virtual University Library environment look like?

Over the past year, the Open University of Catalonia library has been designing its new website with this question in mind. Our main concern has been how to integrate the library in the student day to day study routine to not to be only a satellite tool. We present the design of the website that, in a virtual library like ours, it is not only a website but the whole library itself. The central point of the web is my library, a space that associates the library resources with the student's curriculum and their course subjects. There the students can save the resources as favourites, comment or share them. They have also access to all the services the library offers them. The resources are imported from multiple tools such as Millennium, SFX, Metalib and Dspace to the Drupal CMS. Then the resources' metadata can be enriched with other contextual information from other sources, for example the course subjects. And finally they can be exported in standard, open data formats making them available for linked data applications.

The Chemotherapeutic Drug 5-Fluorouracil Promotes PKR-Mediated Apoptosis in a p53-Independent Manner in Colon and Breast Cancer Cells

The chemotherapeutic drug 5-FU is widely used in the treatment of a range of cancers, but resistance to the drug remains a major clinical problem. Since defects in the mediators of apoptosis may account for chemo-resistance, the identification of new targets involved in 5-FU-induced apoptosis is of main clinical interest. We have identified the ds-RNA-dependent protein kinase (PKR)as a key molecular target of 5-FU involved in apoptosis induction in human colon and breast cancer cell lines. PKR distribution and activation, apoptosis induction and cytotoxic effects were analyzed during 5-FU and 5-FU/IFNalpha treatment in several colon and breast cancer cell lines with different p53 status. PKR protein was activated by 5-FU treatment in a p53-independent manner,inducing phosphorylation of the protein synthesis translation initiation factor eIF-2alpha and cell death by apoptosis. Furthermore, PKR interference promoted a decreased response to 5-FU treatment and those cells were not affected by the synergistic antitumor activity of 5-FU/IFNalpha combination. These results, taken together, provide evidence that PKR is a key molecular target of 5-FU with potential relevance in the clinical use of this drug.

Diagnostic accuracy, effectiveness and cost for cognitive impairment and dementia screening of three short cognitive tests applicable to illiterates

BACKGROUND Illiteracy, a universal problem, limits the utilization of the most widely used short cognitive tests. Our objective was to assess and compare the effectiveness and cost for cognitive impairment (CI) and dementia (DEM) screening of three short cognitive tests applicable to illiterates. METHODS Phase III diagnostic test evaluation study was performed during one year in four Primary Care centers, prospectively including individuals with suspicion of CI or DEM. All underwent the Eurotest, Memory Alteration Test (M@T), and Phototest, applied in a balanced manner. Clinical, functional, and cognitive studies were independently performed in a blinded fashion in a Cognitive Behavioral Neurology Unit, and the gold standard diagnosis was established by consensus of expert neurologists on the basis of these results. Effectiveness of tests was assessed as the proportion of correct diagnoses (diagnostic accuracy [DA]) and the kappa index of concordance (k) with respect to gold standard diagnoses. Costs were based on public prices at the time and hospital accounts. RESULTS The study included 139 individuals: 47 with DEM, 36 with CI, and 56 without CI. No significant differences in effectiveness were found among the tests. For DEM screening: Eurotest (k = 0.71 [0.59-0.83], DA = 0.87 [0.80-0.92]), M@T (k = 0.72 [0.60-0.84], DA = 0.87 [0.80-0.92]), Phototest (k = 0.70 [0.57-0.82], DA = 0.86 [0.79-0.91]). For CI screening: Eurotest (k = 0.67 [0.55-0.79]; DA = 0.83 [0.76-0.89]), M@T (k = 0.52 [0.37-0.67]; DA = 0.80 [0.72-0.86]), Phototest (k = 0.59 [0.46-0.72]; DA = 0.79 [0.71-0.86]). There were no differences in the cost of DEM screening, but the cost of CI screening was significantly higher with M@T (330.7 ± 177.1 €, mean ± sd) than with Eurotest (294.1 ± 195.0 €) or Phototest (296.0 ± 196. 5 €). Application time was shorter with Phototest (2.8 ± 0.8 min) than with Eurotest (7.1 ± 1.8 min) or M@T (6.8 ± 2.2 min). CONCLUSIONS Eurotest, M@T, and Phototest are equally effective. Eurotest and Phototest are both less expensive options but Phototest is the most efficient, requiring the shortest application time.

An R Library for Compositional Data Analysis in Archaeometry

Compositional data naturally arises from the scientific analysis of the chemicalcomposition of archaeological material such as ceramic and glass artefacts. Data of thistype can be explored using a variety of techniques, from standard multivariate methodssuch as principal components analysis and cluster analysis, to methods based upon theuse of log-ratios. The general aim is to identify groups of chemically similar artefactsthat could potentially be used to answer questions of provenance.This paper will demonstrate work in progress on the development of a documentedlibrary of methods, implemented using the statistical package R, for the analysis ofcompositional data. R is an open source package that makes available very powerfulstatistical facilities at no cost. We aim to show how, with the aid of statistical softwaresuch as R, traditional exploratory multivariate analysis can easily be used alongside, orin combination with, specialist techniques of compositional data analysis.The library has been developed from a core of basic R functionality, together withpurpose-written routines arising from our own research (for example that reported atCoDaWork'03). In addition, we have included other appropriate publicly availabletechniques and libraries that have been implemented in R by other authors. Availablefunctions range from standard multivariate techniques through to various approaches tolog-ratio analysis and zero replacement. We also discuss and demonstrate a smallselection of relatively new techniques that have hitherto been little-used inarchaeometric applications involving compositional data. The application of the libraryto the analysis of data arising in archaeometry will be demonstrated; results fromdifferent analyses will be compared; and the utility of the various methods discussed

Genome-wide association study of multiple sclerosis confirms a novel locus at 5p13.1.

Multiple Sclerosis (MS) is the most common progressive and disabling neurological condition affecting young adults in the world today. From a genetic point of view, MS is a complex disorder resulting from the combination of genetic and non-genetic factors. We aimed to identify previously unidentified loci conducting a new GWAS of Multiple Sclerosis (MS) in a sample of 296 MS cases and 801 controls from the Spanish population. Meta-analysis of our data in combination with previous GWAS was done. A total of 17 GWAS-significant SNPs, corresponding to three different loci were identified:HLA, IL2RA, and 5p13.1. All three have been previously reported as GWAS-significant. We confirmed our observation in 5p13.1 for rs9292777 using two additional independent Spanish samples to make a total of 4912 MS cases and 7498 controls (ORpooled = 0.84; 95%CI: 0.80-0.89; p = 1.36 × 10-9). This SNP differs from the one reported within this locus in a recent GWAS. Although it is unclear whether both signals are tapping the same genetic association, it seems clear that this locus plays an important role in the pathogenesis of MS.

Is a Virtual Library cost effective?

The Andalusian Public Health System Virtual Library (Biblioteca Virtual del Sistema Sanitario Público de Andalucía, BV-SSPA), was created in June 2006. In this paper an evaluation is made to see whether the investment made by the Andalusian Government has been worthwhile. The cost-effectiveness and efficiency of the project together with the management criteria are explored.