bluuebunny/crossref_metadata_2025 huggingface dataset:
Fun, Friend, or Foe: Youth Perceptions and Definitions of Online Gambling
Authors: Hume Margee , Mort Gillian Sullivan
Published: February 2011

This article discusses youth consumption of high-speed Internet technology and online youth gambling based on examination of an Australian youth and young adults sample ranging in age from 13 to 30 years of age. This article explores the impact of online gambling on youth well-being and presents organization of the issues confronting youth and gambling behavior online. The article covers current research related to youth and offers a set of narrative definitions of online gambling as offered by 175 youth and young adults. Coupled with this, is a set of industry comments from Australian gambling sector representatives related to this cohort; these offer clarity on how this cohort interacts with current online gambling service providers. There is no doubt that youth underestimate the possible dangers of online gambling and define gambling and online gambling in terms of fun and gaming rather that fully appreciating the risks related to gambling. It is evident there is some legislation and practice protocols ranging in effectiveness that assist in minimizing the access of youth to online gambling.
Organizational Use of a Media Campaign Booklet to Encourage Parent–Child Communication about Waiting to Have Sex
Authors: Gard Jennifer C. , Kan Marni L. , Jones Sarah B. , Williams J. Cassie , Evans W. Douglas , Davis Kevin C.
Published: February 2011

Promoting parent—child communication through the use of print materials may be an important health communication approach for preventing teen sexual activity in the United States. Although prior work has suggested successful methods of disseminating print materials, research has not examined dissemination approaches across organization types. Understanding the use and dissemination of print materials among different organizations is crucial to guiding materials development in a way that maximizes uptake and effectiveness among consumers. Accordingly, this study examined the use of a booklet for parents that encouraged parent–child communication about waiting to have sex as collateral material for a national media campaign. We interviewed staff at 9 community organizations, 9 health care facilities, 5 school-based organizations, and 3 campaign outreach centers. Results suggested variability within and across organization types regarding use of the booklet. Community and outreach center staff tended to walk through the booklet content with parents; health care facilities and education-oriented organizations usually reported both direct and indirect distribution approaches. Staff identified useful elements of the booklet and made suggestions for dissemination in line with prior research. A better understanding of how print materials are utilized to supplement media campaigns can improve their usefulness and potential influence on health behaviors.
Impact of Chlorhexidine Bathing on Hospital-Acquired Infections among General Medical Patients
Authors: Kassakian Steven Z. , Mermel Leonard A. , Jefferson Julie A. , Parenteau Stephen L. , Machan Jason T.
Published: February 2011

Background.

A paucity of data exists regarding the effectiveness of daily Chlorhexidine gluconate (CHG) bathing in non–intensive care unit (ICU) settings.

Objective.

To evaluate the effectiveness of daily CHG bathing in a non-ICU setting to reduce methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enteroccocus (VRE) hospital-acquired infections (HAIs), compared with daily bathing with soap and water.

Design.

Quasi-experimental study design; the primary outcome was the composite incidence of MRSA and VRE HAIs. Clostridium difficile HAI incidence was measured as a nonequivalent dependent variable with which to assess potential confounders.

Setting.

Four general medicine units, with a total of 94 beds, at a 719-bed academic tertiary-care facility in Providence, Rhode Island.

Patients.

A total of 7,102 and 7,699 adult patients were admitted to the medical service in the control and intervention groups, respectively. Patients admitted from January 1 through December 31, 2008, were bathed daily with soap and water (control group), and those admitted from February 1, 2009, through March 31, 2010, were bathed daily with CHG-impregnated cloths (intervention group).

Results.

Daily bathing with CHG was associated with a 64% reduced risk of developing the primary outcome, namely, the composite incidence of MRSA and VRE HAIs (hazard ratio, 0.36 [95% CI, 0.2-0.8]; P = .01). There was no change in the incidence of C. difficile HAIs (P = .6). Colonization with MRSA was associated with an increased risk of developing a MRSA HAI (hazard ratio, 8 [95% CI, 3-19]; P < .001).

Conclusion.

Daily CHG bathing was associated with a reduced HAI risk, using a composite endpoint of MRSA and VRE HAIs, in a general medical inpatient population.
Comparison of the Methicillin-Resistant Staphylococcus aureus Acquisition among Rehabilitation and Nursing Home Residents
Authors: Furuno Jon P. , Shurland Simone M. , Zhan Min , Johnson J. Kristie , Venezia Richard A. , Harris Anthony D. , Roghmann Mary-Claire
Published: February 2011

Objective.

To assess risk factors for methicillin-resistant Staphylococcus aureus (MRSA) acquisition among extended care residents focusing on level of care (residential vs rehabilitation) and room placement with an MRSA-positive resident.

Design.

Prospective cohort study.

Setting.

Extended care units at 2 healthcare systems in Maryland.

Participants.

Four hundred forty-three residents with no history of MRSA and negative MRSA surveillance cultures of the anterior nares and areas of skin breakdown at enrollment.

Methods.

Follow-up cultures were collected every 4 weeks and/or at discharge for a period of 12 weeks. Study data were collected by a research nurse from the medical staff and the electronic medical records. Cox proportional hazards modeling was used to calculate adjusted hazards ratios (aHRs) and 95% confidence intervals (CIs).

Results.

Residents in rehabilitation care had 4-fold higher risk of MRSA acquisition compared with residents in residential care (hazard ratio [HR], 4. [95% CI, 2.2-8.8]). Being bedbound was significantly associated with MRSA acquisition in both populations (residential care, aHR, 4.3 [95% CI, 1.5-12.2]; rehabilitation care, aHR, 4.8 [95% CI, 1.2-18.7]). Having an MRSA-positive roommate was not significantly associated with acquisition in either population (residential care, aHR, 1.4 [95% CI, 0.5-3.9]; rehabilitation care, aHR, 0.5 [95% CI, 0.1-2.2]); based on concordant spa typing, only 2 of 8 residents who acquired MRSA and had room placement with an MRSA-positive resident acquired their MRSA isolate from their roommate.

Conclusion.

Residents in rehabilitation care appear at higher risk and have different risk factors for MRSA acquisition compared to those in residential care.
Evaluation of Hospital Room Assignment and Acquisition of Clostridium difficile Infection
Authors: Shaughnessy Megan K. , Micielli Renee L. , DePestel Daryl D. , Arndt Jennifer , Strachan Cathy L. , Welch Kathy B. , Chenoweth Carol E.
Published: February 2011

Background and Objective.

Clostridium difficile spores persist in hospital environments for an extended period. We evaluated whether admission to a room previously occupied by a patient with C. difficile infection (CDI) increased the risk of acquiring CDI.

Design.

Retrospective cohort study.

Setting.

Medical intensive care unit (ICU) at a tertiary care hospital.

Methods.

Patients admitted from January 1, 2005, through June 30, 2006, were evaluated for a diagnosis of CDI 48 hours after ICU admission and within 30 days after ICU discharge. Medical, ICU, and pharmacy records were reviewed for other CDI risk factors. Admitted patients who did develop CDI were compared with admitted patients who did not.

Results.

Among 1,844 patients admitted to the ICU, 134 CDI cases were identified. After exclusions, 1,770 admitted patients remained for analysis. Of the patients who acquired CDI after admission to the ICU, 4.6% had a prior occupant without CDI, whereas 11.0% had a prior occupant with CDI (P = .002). The effect of room on CDI acquisition remained a significant risk factor (P = .008) when Kaplan-Meier curves were used. The prior occupant's CDI status remained significant (P = .01; hazard ratio, 2.35) when controlling for the current patient's age, Acute Physiology and Chronic Health Evaluation III score, exposure to proton pump inhibitors, and antibiotic use.

Conclusions.

A prior room occupant with CDI is a significant risk factor for CDI acquisition, independent of established CDI risk factors. These findings have implications for room placement and hospital design.
Molecular Characteristics of Outbreaks of Nosocomial Infection with Influenza A/H3N2 Virus Variants
Authors: Oguma Taeko , Saito Reiko , Masaki Hironori , Hoshino Kazuhiko , Zaraket Hassan , Suzuki Yasushi , Caperig-Dapat Isolde , Dapat Clyde , Baranovich Tatiana , Kuroki Reiki , Makimoto Yasushi , Shirahige Yutaka , Asoh Norichika , Degawa Satoshi , Ishikawa Hidefumi , Kageura Hironobu , Hosoi Maki , Suzuki Hiroshi
Published: February 2011

Objective.

To describe outbreaks of nosocomial influenza infection with molecular methods and to elucidate the viral linkages among outbreak case patients including both inpatients and healthcare workers (HCWs).

Setting.

A 180-bed acute and long-term care hospital in Japan.

Methods.

Retrospective observational study of nosocomial outbreaks of infection with influenza A/H3N2. Together with information about onset dates and vaccination history, we obtained nasopharyngeal swab samples from individuals with cases of influenza or influenzalike illness (ILI). The hemagglutinin genes of the recovered viruses were sequenced and compared, along with those of community-circulating strains, for similarity by phylogenetic tree analysis.

Results.

The outbreaks occurred from February 26 through April 3, 2007, during the 2006–2007 epidemic season, and they involved 11 patients and 13 HCWs. The 2 outbreaks involved 2 different genotypes of influenza A/H3N2 viruses. These virus variants were closely related to the influenza strains that were circulating in the community during the same epidemic season.

Conclusion.

This study showed the dissemination of highly homologous influenza virus variants among inpatients and HCWs within a short period, as a result of nosocomial transmission. These strains were also similar to influenza strains that were circulating in the community.
Factors Associated with Unprotected Exposure to 2009 H1N1 Influenza A among Healthcare Workers during the First Wave of the Pandemic
Authors: Banach David B. , Bielang Rebecca , Calfee David P.
Published: February 2011

Protecting healthcare workers (HCWs) from occupational exposure to 2009 H1N1 influenza was a challenge. During the first wave of the pandemic, many HCWs reported that they had been exposed to 2009 H1N1 when they were not using respiratory personal protective equipment. Unprotected exposures tended to be more frequent among HCWs caring for patients with atypical clinical presentations.
Gene List significance at-a-glance with GeneValorization
Authors: Brancotte Bryan , Biton Anne , Bernard-Pierrot Isabelle , Radvanyi François , Reyal Fabien , Cohen-Boulakia Sarah
Published: February 2011

Motivation: High-throughput technologies provide fundamental informations concerning thousands of genes. Many of the current research laboratories daily use one or more of these technologies and end-up with lists of genes. Assessing the originality of the results obtained includes being aware of the number of publications available concerning individual or multiple genes and accessing information about these publications. Faced with the exponential growth of publications avaliable and number of genes involved in a study, this task is becoming particularly difficult to achieve.

Results: We introduce GeneValorization, a web-based tool that gives a clear and handful overview of the bibliography available corresponding to the user input formed by (i) a gene list (expressed by gene names or ids from EntrezGene) and (ii) a context of study (expressed by keywords). From this input, GeneValorization provides a matrix containing the number of publications with co-occurrences of gene names and keywords. Graphics are automatically generated to assess the relative importance of genes within various contexts. Links to publications and other databases offering information on genes and keywords are also available. To illustrate how helpful GeneValorization is, we will consider the gene list of the OncotypeDX prognostic marker test.

Availability:  http://bioguide-project.net/gv

Contact:  cohen@lri.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Interactive, multiscale navigation of large and complicated biological networks
Authors: Praneenararat Thanet , Takagi Toshihisa , Iwasaki Wataru
Published: February 2011

Motivation: Many types of omics data are compiled as lists of connections between elements and visualized as networks or graphs where the nodes and edges correspond to the elements and the connections, respectively. However, these networks often appear as ‘hair-balls’—with a large number of extremely tangled edges—and cannot be visually interpreted.

Results: We present an interactive, multiscale navigation method for biological networks. Our approach can automatically and rapidly abstract any portion of a large network of interest to an immediately interpretable extent. The method is based on an ultrafast graph clustering technique that abstracts networks of about 100 000 nodes in a second by iteratively grouping densely connected portions and a biological-property-based clustering technique that takes advantage of biological information often provided for biological entities (e.g. Gene Ontology terms). It was confirmed to be effective by applying it to real yeast protein network data, and would greatly help modern biologists faced with large, complicated networks in a similar manner to how Web mapping services enable interactive multiscale navigation of geographical maps (e.g. Google Maps).

Availability: Java implementation of our method, named NaviCluster, is available at http://navicluster.cb.k.u-tokyo.ac.jp/.

Contact:  thanet@cb.k.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
ACT: aggregation and correlation toolbox for analyses of genome tracks
Authors: Jee Justin , Rozowsky Joel , Yip Kevin Y. , Lochovsky Lucas , Bjornson Robert , Zhong Guoneng , Zhang Zhengdong , Fu Yutao , Wang Jie , Weng Zhiping , Gerstein Mark
Published: February 2011

We have implemented aggregation and correlation toolbox (ACT), an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project. It is able to generate aggregate profiles of a given track around a set of specified anchor points, such as transcription start sites. It is also able to correlate related tracks and analyze them for saturation–i.e. how much of a certain feature is covered with each new succeeding experiment. The ACT site contains downloadable code in a variety of formats, interactive web servers (for use on small quantities of data), example datasets, documentation and a gallery of outputs. Here, we explain the components of the toolbox in more detail and apply them in various contexts.

Availability: ACT is available at http://act.gersteinlab.org

Contact:  pi@gersteinlab.org
All-atom knowledge-based potential for RNA structure prediction and assessment
Authors: Capriotti Emidio , Norambuena Tomas , Marti-Renom Marc A. , Melo Francisco
Published: February 2011

Motivation: Over the recent years, the vision that RNA simply serves as information transfer molecule has dramatically changed. The study of the sequence/structure/function relationships in RNA is becoming more important. As a direct consequence, the total number of experimentally solved RNA structures has dramatically increased and new computer tools for predicting RNA structure from sequence are rapidly emerging. Therefore, new and accurate methods for assessing the accuracy of RNA structure models are clearly needed.

Results: Here, we introduce an all-atom knowledge-based potential for the assessment of RNA three-dimensional (3D) structures. We have benchmarked our new potential, called Ribonucleic Acids Statistical Potential (RASP), with two different decoy datasets composed of near-native RNA structures. In one of the benchmark sets, RASP was able to rank the closest model to the X-ray structure as the best and within the top 10 models for ∼93 and ∼95% of decoys, respectively. The average correlation coefficient between model accuracy, calculated as the root mean square deviation and global distance test-total score (GDT-TS) measures of C3′ atoms, and the RASP score was 0.85 and 0.89, respectively. Based on a recently released benchmark dataset that contains hundreds of 3D models for 32 RNA motifs with non-canonical base pairs, RASP scoring function compared favorably to ROSETTA FARFAR force field in the selection of accurate models. Finally, using the self-splicing group I intron and the stem-loop IIIc from hepatitis C virus internal ribosome entry site as test cases, we show that RASP is able to discriminate between known structure-destabilizing mutations and compensatory mutations.

Availability: RASP can be readily applied to assess all-atom or coarse-grained RNA structures and thus should be of interest to both developers and end-users of RNA structure prediction methods. The computer software and knowledge-based potentials are freely available at http://melolab.org/supmat.html.

Contact:  fmelo@bio.puc.cl; mmarti@cipf.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data
Authors: Ahmad Isthiaq , Suits Frank , Hoekman Berend , Swertz Morris A. , Byelas Heorhiy , Dijkstra Martijn , Hooft Rob , Katsubo Dmitry , van Breukelen Bas , Bischoff Rainer , Horvatovich Peter
Published: February 2011

Summary: Warp2D is a novel time alignment approach, which uses the overlapping peak volume of the reference and sample peak lists to correct misleading peak shifts. Here, we present an easy-to-use web interface for high-throughput Warp2D batch processing time alignment service using the Dutch Life Science Grid, reducing processing time from days to hours. This service provides the warping function, the sample chromatogram peak list with adjusted retention times and normalized quality scores based on the sum of overlapping peak volume of all peaks. Heat maps before and after time alignment are created from the arithmetic mean of the sum of overlapping peak area rearranged with hierarchical clustering, allowing the quality control of the time alignment procedure. Taverna workflow and command line tool are provided for remote processing of local user data.

Availability: online data processing service is available at http://www.nbpp.nl/warp2d.html. Taverna workflow is available at myExperiment with title ‘2D Time Alignment—Webservice and Workflow’ at http://www.myexperiment.org/workflows/1283.html. Command line tool is available at http://www.nbpp.nl/Warp2D_commandline.zip.

Contact:  p.l.horvatovich@rug.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
AGRA: analysis of gene ranking algorithms
Authors: Kocbek Simon , Sætre Rune , Stiglic Gregor , Kim Jin-Dong , Pernek Igor , Tsuruoka Yoshimasa , Kokol Peter , Ananiadou Sophia , Tsujii Jun'ichi
Published: February 2011

Summary: Often, the most informative genes have to be selected from different gene sets and several computer gene ranking algorithms have been developed to cope with the problem. To help researchers decide which algorithm to use, we developed the analysis of gene ranking algorithms (AGRA) system that offers a novel technique for comparing ranked lists of genes. The most important feature of AGRA is that no previous knowledge of gene ranking algorithms is needed for their comparison. Using the text mining system finding-associated concepts with text analysis. AGRA defines what we call biomedical concept space (BCS) for each gene list and offers a comparison of the gene lists in six different BCS categories. The uploaded gene lists can be compared using two different methods. In the first method, the overlap between each pair of two gene lists of BCSs is calculated. The second method offers a text field where a specific biomedical concept can be entered. AGRA searches for this concept in each gene lists' BCS, highlights the rank of the concept and offers a visual representation of concepts ranked above and below it.

Availability and Implementation: Available at http://agra.fzv.uni-mb.si/, implemented in Java and running on the Glassfish server.

Contact:  simon.kocbek@uni-mb.si
FNV: light-weight flash-based network and pathway viewer
Authors: Dannenfelser Ruth , Lachmann Alexander , Szenk Mariola , Ma'ayan Avi
Published: February 2011

Motivation: Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways.

Summary: Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials.

Availability: FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV.

Contact:  avi.maayan@mssm.edu
R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data
Authors: Klein Hans-Ulrich , Bartenhagen Christoph , Kohlmann Alexander , Grossmann Vera , Ruckert Christian , Haferlach Torsten , Dugas Martin
Published: February 2011

Summary: The R453Plus1Toolbox is an R/Bioconductor package for the analysis of 454 Sequencing data. Projects generated with Roche's data analysis software can be imported into R allowing advanced and customized analyses within the R/Bioconductor environment for sequencing data. Several methods were implemented extending the current functionality of Roche's software. These extensions include methods for quality assurance and annotation of detected variants. Further, a pipeline for the detection of structural variants, e.g. balanced chromosomal translocations, is provided.

Availability: The R453Plus1Toolbox is implemented in R and available at http://www.bioconductor.org/. A vignette outlining typical workflows is included in the package.

Contact:  h.klein@uni-muenster.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
TetR-family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation
Authors: Agari Yoshihiro , Agari Kazuko , Sakamoto Keiko , Kuramitsu Seiki , Shinkai Akeo
Published: February 2011

In the extremely thermophilic bacteriumThermus thermophilusHB8, one of the four TetR-family transcriptional regulators, which we namedT.thermophilusFadR, negatively regulated the expression of several genes, including those involved in fatty acid degradation, bothin vivoandin vitro.T.thermophilusFadR repressed the expression of the target genes by binding pseudopalindromic sequences covering the predicted −10 hexamers of their promoters, and medium-to-long straight-chain (C10–18) fatty acyl-CoA molecules were effective for transcriptional derepression. An X-ray crystal structure analysis revealed thatT.thermophilusFadR bound one lauroyl (C12)-CoA molecule per FadR monomer, with its acyl chain moiety in the centre of the FadR molecule, enclosed within a tunnel-like substrate-binding pocket surrounded by hydrophobic residues, and the CoA moiety interacting with basic residues on the protein surface. The growth ofT.thermophilusHB8, with palmitic acid as the sole carbon source, increased the expression of FadR-regulated genes. These results indicate that inT.thermophilusHB8, medium-to-long straight-chain fatty acids can be used for metabolic energy under the control of FadR, although the major fatty acids found in this strain areiso- andanteiso-branched-chain (C15 and 17) fatty acids.
Secreted glutamic protease rescues aspartic protease Pep deficiency in Aspergillus fumigatus during growth in acidic protein medium
Authors: Sriranganadane Dev , Reichard Utz , Salamin Karine , Fratti Marina , Jousson Olivier , Waridel Patrice , Quadroni Manfredo , Neuhaus Jean-Marc , Monod Michel
Published: February 2011

In an acidic protein medium Aspergillus fumigatus secretes an aspartic endoprotease (Pep) as well as tripeptidyl-peptidases, a prolyl-peptidase and carboxypeptidases. In addition, LC-MS/MS revealed a novel glutamic protease, AfuGprA, homologous to Aspergillus niger aspergillopepsin II. The importance of AfuGprA in protein digestion was evaluated by deletion of its encoding gene in A. fumigatus wild-type D141 and in a pepΔ mutant. Either A. fumigatus Pep or AfuGprA was shown to be necessary for fungal growth in protein medium at low pH. Exoproteolytic activity is therefore not sufficient for complete protein hydrolysis and fungal growth in a medium containing proteins as the sole nitrogen source. Pep and AfuGprA constitute a pair of endoproteases active at low pH, in analogy to A. fumigatus alkaline protease (Alp) and metalloprotease I (Mep), where at least one of these enzymes is necessary for fungal growth in protein medium at neutral pH. Heterologous expression of AfuGprA in Pichia pastoris showed that the enzyme is synthesized as a preproprotein and that the propeptide is removed through an autoproteolytic reaction at low pH to generate the mature protease. In contrast to A. niger aspergillopepsin II, AfuGprA is a single-chain protein and is structurally more similar to G1 proteases characterized in other non-Aspergillus fungi.
Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes
Authors: Warren René L. , Freeman J. Douglas , Zeng Thomas , Choe Gina , Munro Sarah , Moore Richard , Webb John R. , Holt Robert A.
Published: February 2011

Massively parallel sequencing is a useful approach for characterizing T-cell receptor diversity. However, immune receptors are extraordinarily difficult sequencing targets because any given receptor variant may be present in very low abundance and may differ legitimately by only a single nucleotide. We show that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy. At two timepoints, 1 wk apart, we isolated bulk PBMC plus naïve (CD45RA+/CD45RO−) and memory (CD45RA−/CD45RO+) T-cell subsets from a healthy donor. From T-cell receptor beta chain (TCRB) mRNA we constructed and sequenced multiple libraries to obtain a total of 1.7 billion paired sequence reads. The sequencing error rate was determined empirically and used to inform a high stringency data filtering procedure. The error filtered data yielded 1,061,522 distinct TCRB nucleotide sequences from this subject which establishes a new, directly measured, lower limit on individual T-cell repertoire size and provides a useful reference set of sequences for repertoire analysis. TCRB nucleotide sequences obtained from two additional donors were compared to those from the first donor and revealed limited sharing (up to 1.1%) of nucleotide sequences among donors, but substantially higher sharing (up to 14.2%) of inferred amino acid sequences. For each donor, shared amino acid sequences were encoded by a much larger diversity of nucleotide sequences than were unshared amino acid sequences. We also observed a highly statistically significant association between numbers of shared sequences and shared HLA class I alleles.
Immunoglobulin G4‐positive plasma cell infiltration in explanted livers for primary sclerosing cholangitis
Authors: Zen Yoh , Quaglia Alberto , Portmann Bernard
Published: February 2011

Zen Y, Quaglia A & Portmann B (2011) Histopathology58, 414–422 Immunoglobulin G4‐positive plasma cell infiltration in explanted livers for primary sclerosing cholangitis

Aims:  To explore whether immunoglobulin (Ig)G4‐related sclerosing cholangitis (IgG4‐SC) contributes to end‐stage primary sclerosing cholangitis (PSC) in the United Kingdom.

Methods and results:  This study consisted of 41 patients who underwent liver transplantation for advanced PSC. Explanted livers were examined histologically with an emphasis on IgG4‐positive plasma cell infiltration. Thirty‐nine cases (95%) had minimal or mild infiltration of IgG4‐positive plasma cells (≤30 cells/high‐power field). In contrast, two cases (5%) showed plasma cell IgG4‐positivity in more than 100 cells/high‐power field. IgG4‐positive plasma cells were accumulated preferentially in a (xantho)granulomatous tissue within large bile ducts. Except for the presence of IgG4‐positive plasma cells, there was no significant histological difference between IgG4‐positive and negative cases. Both showed sclerosing cholangitis with bile duct erosion and xanthogranulomatous reaction more in keeping with PSC than typical IgG4‐SC. Clinically, the two patients differed from typical IgG4‐related disease, in that both had associated ulcerative colitis, and one of them was younger than expected for IgG4‐SC (28 years old).

Conclusions:  No classical IgG4‐SC could be identified in patients explanted for PSC. The two cases identified with numerous IgG4‐positive plasma cells suggest a superimposed immune mechanism of uncertain nature. A prospective study is needed to assess whether such cases will be steroid‐sensitive.
Handling and reporting of transurethral resection specimens of the bladder in Europe: a web‐based survey by the European Network of Uropathology (ENUP)
Authors: Lopez‐Beltran Antonio , Algaba Ferran , Berney Daniel M , Boccon‐Gibod Liliane , Camparo Philippe , Griffiths David , Mikuz Gregor , Montironi Rodolfo , Varma Murali , Egevad Lars
Published: February 2011

Lopez‐Beltran A, Algaba F, Berney D M, Boccon‐Gibod L, Camparo P, Griffiths D, Mikuz G, Montironi R, Varma M & Egevad L (2011) Histopathology 58, 579–585 Handling and reporting of transurethral resection specimens of the bladder in Europe: a web‐based survey by the European Network of Uropathology (ENUP)

Aims:  To collect of information about European practices on handling and reporting of transurethral resection specimens of the bladder.

Methods and results:  The European Network of Uropathology is a communication network that includes 335 pathology laboratories in 15 western European countries. A web‐based questionnaire was answered by 52.2% of members. Some routines were adopted by a majority: formalin fixation (92.5%), separate containers for tumour and resection base (72%) and embedding of the entire specimen (60%). Cancer along/in adipose tissue would be reported as pT3a by 19.5% and non‐invasive urothelial carcinoma in prostatic ducts/glands as pT4a by 16.1%. Papillary urothelial neoplasia of low malignant potential is recognized by 72.6% but rarely reported. Immunohistochemistry is rarely or sometimes used for diagnosing bladder cancer by 91.7%, and the most frequently used markers are CK20 (76.9%), CK7 (66.7%) and Ki67 (38.8%). Only 24.8% report prognostic markers, with Ki67 (84.4%) and p53 (64.4%) being most common. Only 50.9% use the International Society of Urological Pathology 1998/World Health Organization (WHO) 2004 grading system, followed by WHO 1973 (43.4%) and WHO 1999 (31.4%).

Conclusions:  There is still variability in routine practice and a need for standardization of methodologies. These results may be helpful when judging what recommendations are reasonable to issue.
A truncating mutation in GPSM2 is associated with recessive non‐syndromic hearing loss
Authors: Yariz KO , Walsh T , Akay H , Duman D , Akkaynak AC , King M‐C , Tekin M
Published: February 2011

Yariz KO, Walsh T, Akay H, Duman D, Akkaynak AC, King M‐C, Tekin M. A truncating mutation in GPSM2 is associated with recessive non‐syndromic hearing loss.

Hereditary deafness is a genetically heterogeneous phenotype for which more than 100 genomic loci have been identified thus far. By analysis of a consanguineous Palestinian family, GPSM2 was recently discovered to be the cause of autosomal recessive non‐syndromic hearing loss DFNB82. Here, we report a second truncating mutation, GPSM2 p.Q562X, identified via autozygosity mapping in a consanguineous Turkish family. This report provides evidence for allelic heterogeneity of GPSM2 and confirms its causative role for non‐syndromic deafness.
Pathophysiology of renal tissue damage by iodinated contrast media
Authors: Sendeski Mauricio M
Published: February 2011

1. The present review focuses on the cytotoxic effects of iodinated contrast media (CM) that are shared by all types of CM.

2. Although the clinical nephrotoxicity of CM has been progressively improved, all currently available CM still possess a level of cytotoxicity, which is probably caused by iodine.

3. The toxicity caused by specific CM properties, such as osmolarity, viscosity and ionic strength, can be differentiated from the cytotoxicity common to all CM in studies using cell culture, isolated blood vessels and isolated tubules.

4. The cytotoxicity induced by CM leads to apoptosis and cell death of endothelial and tubular cells and may be initiated by cell membrane damage, together with oxidative stress.

5. Cell damage may be aggravated by factors such as tissue hypoperfusion and hypoxia, properties of individual CM, such as ionic strength, high osmolarity and/or viscosity, and clinically unfavourable conditions.

6. Clinically detectable renal failure may result from the summation of all these factors.
Body mass index in midlife and late‐life as a risk factor for dementia: a meta‐analysis of prospective studies
Authors: Anstey K. J. , Cherbuin N. , Budge M. , Young J.
Published: February 2011

The relationship between body mass index (BMI) (in midlife and late‐life) and dementia was investigated in meta‐analyses of 16 articles reporting on 15 prospective studies. Follow‐ups ranged from 3.2 to 36.0 years. Meta‐analyses were conducted on samples including 25 624 participants evaluated for Alzheimer's disease (AD), 15 435 participants evaluated for vascular dementia (VaD) and 30 470 followed for any type of dementia (Any Dementia). Low BMI in midlife was associated with 1.96 [95% confidence interval (CI): 1.32, 2.92] times the risk of developing AD. The pooled relative risks for AD, VaD and Any Dementia for overweight BMI in midlife compared with normal BMI were 1.35 (95% CI:1.19, 1.54), 1.33 (95% CI: 1.02, 1.75) and 1.26 (95% CI: 1.10, 1.44), respectively. The pooled relative risks of AD and Any Dementia for obese BMI in midlife compared to normal BMI were 2.04 (95% CI: 1.59, 2.62) and 1.64 (95% CI: 1.34, 2.00), respectively. Continuous BMI in late‐life was not associated with dementia. Small numbers of studies included in pooled analyses reduce generalizability of findings, and emphasize the need for publication of additional findings. We conclude that underweight, overweight and obesity in midlife increase dementia risk. Further research evaluating late‐life BMI and dementia is required.
A systematic review of built environment factors related to physical activity and obesity risk: implications for smart growth urban planning
Authors: Durand C. P. , Andalib M. , Dunton G. F. , Wolch J. , Pentz M. A.
Published: February 2011

Smart growth is an approach to urban planning that provides a framework for making community development decisions. Despite its growing use, it is not known whether smart growth can impact physical activity. This review utilizes existing built environment research on factors that have been used in smart growth planning to determine whether they are associated with physical activity or body mass. Searching the MEDLINE, Psycinfo and Web‐of‐Knowledge databases, 204 articles were identified for descriptive review, and 44 for a more in‐depth review of studies that evaluated four or more smart growth planning principles. Five smart growth factors (diverse housing types, mixed land use, housing density, compact development patterns and levels of open space) were associated with increased levels of physical activity, primarily walking. Associations with other forms of physical activity were less common. Results varied by gender and method of environmental assessment. Body mass was largely unaffected. This review suggests that several features of the built environment associated with smart growth planning may promote important forms of physical activity. Future smart growth community planning could focus more directly on health, and future research should explore whether combinations or a critical mass of smart growth features is associated with better population health outcomes.
A review of electronic interventions for prevention and treatment of overweight and obesity in young people
Authors: Nguyen B. , Kornman K. P. , Baur L. A.
Published: February 2011

The objective of this systematic review is to provide a qualitative comparison of interactive electronic media interventions for the prevention or treatment of obesity and/or obesity‐related behaviours in children and adolescents. Literature searches of 12 databases from the earliest publication date until March 2010 were conducted. Twenty‐four studies in which children and/or adolescents interacted with electronic interventions delivered as adjunct or sole interventions for the prevention or treatment of obesity and/or obesity‐related behaviours met the inclusion criteria. Fifteen focussed on obesity prevention and nine on treatment interventions. The average study quality design score was 45%. Most studies demonstrated some form of significant outcome (e.g. reported changes in dietary and/or physical activity behaviours) in participants receiving interactive electronic interventions, with 11 out of 15 studies leading to positive changes in measured or reported adiposity outcomes. In 87% of studies, the effects of interactive electronic interventions were not separately evaluated from other intervention components. These results should be viewed with caution because of the overall poor quality of the studies. Studies were mostly conducted in the USA, largely in minority populations, and the direct transferability of interventions to other populations is unclear. Further high quality research is needed in this area to accurately inform the evidence base.
Cardiovascular benefits of bariatric surgery in morbidly obese patients
Authors: Athyros V. G. , Tziomalos K. , Karagiannis A. , Mikhailidis D. P.
Published: February 2011

Morbid obesity is associated with increased morbidity and represents a major healthcare problem with increasing incidence worldwide. Bariatric surgery is considered an effective option for the management of morbid obesity. We searched MEDLINE, Current Contents and the Cochrane Library for papers published on bariatric surgery in English from 1 January 1990 to 20 July 2010. We also manually checked the references of retrieved articles for any pertinent material. Bariatric surgery results in resolution of major comorbidities including type 2 diabetes mellitus, hypertension, dyslipidemia, metabolic syndrome, non‐alcoholic fatty liver disease, nephropathy, left ventricular hypertrophy and obstructive sleep apnea in the majority of morbidly obese patients. Through these effects and possibly other independent mechanisms bariatric surgery appears to reduce cardiovascular morbidity and mortality. Laparoscopic Roux‐en‐Y gastric bypass (LRYGB) appears to be more effective than laparoscopic adjustable gastric banding (LAGB) in terms of weight loss and resolution of comorbidities. Operation‐associated mortality rates after bariatric surgery are low and LAGB is safer than LRYGB. In morbidly obese patients bariatric surgery is safe and appears to reduce cardiovascular morbidity and mortality.
Dairy consumption and metabolic syndrome: a systematic review of findings and methodological issues
Authors: Crichton G. E. , Bryan J. , Buckley J. , Murphy K. J.
Published: February 2011

A growing body of observational research suggests that dairy consumption may have a beneficial effect on the metabolic syndrome (MetS). MetS is a clustering of cardiometabolic risk factors within an individual that carries with it an increased risk of developing cardiovascular disease. A systematic search of electronic databases identified cross‐sectional studies (n = 10) and prospective cohort studies (n = 3) that assessed dairy intake in relation to MetS. The quality of the included studies was assessed based on study methodology, measurement and reporting of dietary intake, use of standardized MetS diagnostic criteria and statistical analysis. Dairy intake was inversely associated with incidence or prevalence of MetS in seven out of 13 studies. Three studies found no association between dairy and MetS. Three studies reported mixed relationships between specific dairy foods and MetS. The majority of studies suggested a potential benefit of dairy consumption on the risk of having MetS, but methodological differences, potential biases and other limitations in the studies conducted prevent conclusions to be drawn. Future randomized controlled trials are needed to confirm the effect of dairy consumption on MetS.
Overweight and obesity in a representative sample of schoolchildren – exploring the urban–rural gradient in Sweden
Authors: Sjöberg A. , Moraeus L. , Yngve A. , Poortvliet E. , Al‐Ansari U. , Lissner L.
Published: February 2011

To present the prevalence and urban‐rural differences of overweight and obesity in 7–9‐year‐old Swedish schoolchildren, we used anthropometric data from a nationally representative survey performed in 2008. Trained staff weighed and measured 4538 children in grades 1 and 2 in 94 primary schools. Weight classification was performed using the IOTF reference and school areas were classified based on level of urbanization and area‐level education. Overweight was found in 17% of the children including 3% obese. For overweight, odds‐ratios were 1.33 and 1.61 (significant) in semi‐urban and rural areas, relative to urban areas. After adjusting for area‐level education, differences by degree of urbanisation were greatly attenuated and non‐significant. For obesity urban‐rural differences were observed in boys only and remained after adjustment for area‐level education. For area‐level education, risk estimates were significantly elevated and unaffected by urbanization and gender, odds‐ratios 1.75 and 2.21 for overweight and 2.62 and 3.69 for obesity, in medium‐ and low‐education areas compared to high‐education areas. This supports earlier reports identifying areas with low socioeconomic status as high‐risk areas for overweight and obesity. However, this study also suggests that gender should be considered when targeting children in urban as well as rural communities for health promoting interventions.
Right alignment
Authors: Boles Nick , Pack Mark , Snowdon Peter
Published: February 2011

Does the Coalition government represent a real and lasting realignment of the centre‐right in British politics, or is it just the product of political expedience? Could a pact bind the two parties together for electoral success? In his book, Which Way is Up?, Nick Boles MP argues that the Conservatives and Liberal Democrats share a common ground of values on which the Coalition government is built, a foundation that is about much more than parliamentary arithmetic. He sets out a liberal conservative policy agenda which goes beyond the Coalition Agreement, addressing the major policy challenges facing the UK.

We asked two political commentators with an in‐depth knowledge of the Coalition parties to respond to Boles' vision for the future of British centre‐right politics. Below, Mark Pack and Peter Snowdon offer contrasting perspectives on the prospects for a lasting union.
Where next for Scottish devolution?
Authors: Gallagher Jim
Published: February 2011

After four years of SNP government, Jim Gallagher reviews the fight for Scottish independence and, in the party's current ideas on fiscal independence, finds a thinly disguised plan to end the Union. As the parties jostle for position ahead of the upcoming Scottish elections, what will the SNP do next?
‘Our leaders are all Aristotelians now’
Authors: Evans Jules
Published: February 2011

Or so one British newspaper recently announced, heralding the rise of a new politics of the Good Life and the Good Society, which finds its inspiration in the ethics and politics of Aristotle. Jules Evans asks how Greek philosophy and wellbeing science is changing modern politics and whether the change is all for the good.
Review of current guidelines on adolescent bariatric surgery
Authors: Aikenhead A. , Lobstein T. , Knai C.
Published: February 2011

A variety of European, North American and, recently, Middle East and Australasian guidelines are now available for clinicians treating obese children and adolescents. This review aims to synthesize recommendations from recent guidance to provide direction to clinicians on the appropriate use of bariatric surgery in adolescents. A literature search for English‐language guidelines endorsed by national governments or professional health associations or societies was conducted, and subject experts were consulted to identify the most recently released guidance. Fifteen sets of guidelines were found, released in the past 6 years, of which nearly all suggested that bariatric surgery is indicated for obese paediatric patients after previous failed attempts at weight loss. Guidance was broadly similar in terms of the categories addressed (patient selection criteria, requirements of the surgical team and institution, and suggested preoperative and postoperative protocols), although relatively little consensus was evident among the criteria specified within these categories. Recommendations differed regarding the appropriate age and degree of obesity at which to intervene. Fewer guidelines addressed preoperative and postoperative care requirements, and of those that did the emphasis varied between familial care and involvement, psychological state and patient motivation, and the importance of long term care. There is a lack of uniformity in the guidance in this area, indicative of the complex nature of obesity management for younger patients. While guidance is necessary to inform and update clinicians, obese paediatric patients require individualized assessment and care.