bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
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 cholangitisAims:  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

Summary1. 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

SummaryThe 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

SummarySmart 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.