bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Gene Ontology's Reference Genome Project: *A Unified Framework for Functional Annotation across Species
Authors: Gaudet Pascale ,   Reference Genome Group
Published: April 2009

AbstractComplete functional annotation of genomes is a powerful tool for researchers; however, such annotation is a time-consuming task limited by the availability of experimental data. The function of genes for which there is no experimental data can often be predicted via comparison to related, annotated sequences of known function. We describe here the Reference Genome project, an effort from the Gene Ontology (GO) Consortium to fully annotate twelve genomes to rigorous standards: human, plus eleven organisms that are important models in biomedical research, including mouse, fly, zebrafish, yeast and E. coli. To achieve this, we examine existing experimentally based annotations in a phylogenetic context in order to infer the function(s) of ancestral proteins and propagate these annotations to their descendants. This endeavor faces many difficult challenges, such as: the determination and provision of reference protein sets for each genome; the identification of gene families for curation; the application of consistent best practices for annotation; the development of methodologies for evaluating progress towards our goal; and the development of software tools to support this effort. Annotated genomes are greatly valuable to the research community and will provide the basis for using sequence similarity to annotate further genomes. An overview of the project as well as links to all resources described below can be found at "http://geneontology.org/GO.refgenome.shtml":http://geneontology.org/GO.refgenome.shtmlThis work is supported by NHGRI grant HG002273 (Gene Ontology Consortium) and NIGMS GM081084-01A1 (Phylogenetic tree building and annotation software development). Pascale Gaudet for the Reference Genome Group of the Gene Ontology Consortium. The Reference Genome project is overseen by Pascale Gaudet (dictyBase), Rex Chisholm (dictyBase) and includes these representatives from the curatorial staff: Tanya Berardini (TAIR), Emily Dimmer (GOA), Stacia R. Engel (SGD), Petra Fey (dictyBase), David P. Hill (MGI), Doug Howe (ZFIN), Jim Hu (EcoliWiki), Rachael Huntley (GOA), Varsha K. Khodiyar (UCL), Ranjana Kishore (WormBase), Donghui Li (TAIR), Ruth C. Lovering (UCL), Fiona McCarthy (AgBase), Li Ni (MGI), Victoria Petri (RGD), Deborah A. Siegel (EcoliWiki), Susan Tweedie (FlyBase), Kimberly Van Auken (WormBase), and Valerie Wood (GeneDB)—as well as the following computational staff representatives: Siddhartha Basu (dictyBase), Seth Carbon (BBOP), Mary Dolan (MGI), and Christopher J. Mungall (BBOP)—those establishing the protein families to be annotated: Kara Dolinski (PPOD), Michael S. Livstone (PPOD), and Paul Thomas (PANTHER)—and, the four PIs of the GO Consortium: Michael Ashburner (FlyBase), Judith A. Blake (MGI), J. Michael Cherry (SGD), and Suzanna E. Lewis (BBOP).
Xenopus and Zebrafish Annotation in the UniProt Knowledgebase (UniProtKB)
Authors: Foulger Rebecca , Consortium UniProt 
Published: April 2009

AbstractThe African clawed frog Xenopus laevis and the zebrafish Danio rerio have both proved to be good model organisms for studying early vertebrate cellular and developmental biology. More recently, the related western clawed frog Xenopus tropicalis has become a popular choice in the laboratory, since its shorter life style and diploid genome make it more amenable to genetic analysis. Ongoing sequencing of the X. tropicalis and D. rerio genomes, together with the growing number of EST/cDNA projects, is generating large amounts of sequence data and revealing many human developmental and disease genes that have counterparts in fish and frog.UniProtKB/Swiss-Prot curates Xenopus and zebrafish proteins with functional and sequence annotation from the literature and sequence analysis tools, using both controlled vocabularies (including GO terms) and free text. The tetraploid nature of the X. laevis and D. rerio genomes complicates annotation since the protein copies need to be identified and curated as separate UniProtKB/Swiss-Prot entries. The recent addition of Xenbase cross-references in Xenopus UniProtKB entries has been the result of cross-talk with Xenbase, and we continue to collaborate with ZFIN to ensure consistency between databases. UniProt is mainly supported by the NIH, European Commission FELICS, Swiss Federal Government, PATRIC BRC and NSF grants.
IMGT/GENE-DB: genomic reference sequences for human and mouse IG and TR genes and alleles
Authors: Bellahcene Fatena , Folch Géraldine , Jabado-Michaloud Joumana , Ginestoux Chantal , Duroux Patrice , Giudicelli Véronique , Lefranc Marie-Paule 
Published: April 2009

AbstractThe immunoglobulin (IG) and T cell receptor (TR) major loci span about 6 Megabases (Mb) of the human genome on chromosomes 2, 7, 14 and 22, and 9 Mb in mouse on chromosomes 6, 12, 13, 14 and 16. There are seven major loci: three IG loci (IGH, IGK, IGL) and four TR loci (TRA, TRB, TRG, TRD), with a distinct repartition of the variable (V), diversity (D), joining (J) and constant (C) genes. The human genome comprises a total number of 608-665 IG and TR genes (371-422 IG and 237-243 TR), depending on the haplotypes, per haploid genome ^1, 2^ of which 531-588 genes are located in the major loci (distributed in 369-418 V, 32 D, 105-109 J and 25-29 C genes). There are also 77 orphons (68 IG and 9 TR) including two processed IG genes, outside the major loci. The number of functional IG and TR genes is 308-356 (136-171 IG and 172-185 TR) per haploid genome. The mouse genome comprises an approximate number of 876 IG and TR genes (624 IG and 252 TR). All these genomic data are available in the IMGT® gene database, IMGT/GENE-DB ^3^. The major contribution of IMGT/GENE-DB has been to establish, for the first time, a standardized nomenclature of the IG and TR genes and alleles of humans and other vertebrates. In April 2009, IMGT/GENE-DB manages 1999 genes and 3026 alleles. [1] Lefranc M.-P. and Lefranc G., The Immunoglobulin FactsBook, Academic Press, London, 458 pages (2001).[2] Lefranc M.-P. and Lefranc G., The T cell receptor FactsBook, Academic Press, London, 398 pages (2001).[3] Giudicelli V. et al. Nucleic Acids Res., 33, D256-261 (2005).
SGN Database: From QTLs to Genomes
Authors: Tecle Isaak , Menda Naama , Buels Robert , Mueller Lukas 
Published: April 2009

AbstractQuantitative trait loci (QTL) analysis is used to dissect the genetic basis underlying polygenic traits. Several public databases have been storing and making QTL data available to research communities. To our knowledge, current QTL databases rely on manual curation where curators read literature and extract relevant QTL information to store in databases. Evidently, this approach is expensive in terms of expert manpower and time use and limits the type of data that can be curated. At the Solanaceae Genomics Network (SGN) ("http://sgn.cornell.edu":http://sgn.cornell.edu), we have developed a database to store raw phenotype and genotype data from QTL studies, perform, on the fly, QTL analysis using R/QTL statistical software ("http://www.rqtl.org":http://www.rqtl.org) and visualize QTLs on a genetic map. Users can identify peak, and flanking markers for QTLs of traits of interest. The QTL database is integrated with other SGN databases (eg. Marker, BACs, and Unigenes), and analysis tools such as the Comparative Map Viewer. Using the comparative map viewer, users can compare chromosome with QTL regions to genetic maps of interest from the same or different Solanaceae species. As the tomato genome sequencing advances, users can also identify corresponding BAC sequences or locations on the tomato physical map, which can be suggestive of candidate genes for a trait of interest.Furthermore at SGN, images, quantitative phenotype and genotype data, publications, genetic maps generated by QTL studies are displayed and available for download. Currently, data from three F2 and two backcross population QTL studies on fruit morphology traits (18 – 46 traits per population) is available at the SGN website for viewing at population, accession, and trait levels. Traits are described using ontology terms. Phenotype data is presented in tabular and graphical formats such as frequency distributions with basic descriptive statistics. Mapping data showing location of parental alleles on individual accession genetic maps is also available.SGN is a public database hosted at Boyce Thomson Institute, Cornell University, and funded by USDA CSREES and NSF.
The Lexical Restructuring Hypothesis and Graph Theoretic Analyses of Networks Based on Random Lexicons
Authors: Gruenenfelder Thomas M. , Pisoni David B. 
Published: April 2009

PurposeThe mental lexicon of words used for spoken word recognition has been modeled as a complex network or graph. Do the characteristics of that graph reflect processes involved in its growth (M. S. Vitevitch, 2008) or simply the phonetic overlap between similar-sounding words?MethodThree pseudolexicons were generated by randomly selecting phonological segments from a fixed set. Each lexicon was then modeled as a graph, linking words differing by one segment. The properties of those graphs were compared with those of a graph based on real English words.ResultsThe properties of the graphs built from the pseudolexicons matched the properties of the graph based on English words. Each graph consisted of a single large island and a number of smaller islands and hermits. The degree distribution of each graph was better fit by an exponential than by a power function. Each graph showed short path lengths, large clustering coefficients, and positive assortative mixing.ConclusionThe results suggest that there is no need to appeal to processes of growth or language acquisition to explain the formal properties of the network structure of the mental lexicon. These properties emerged because the network was built based on the phonetic overlap of words.
Prevalence of Hearing Loss in Black and White Elders: Results of the Cardiovascular Health Study
Authors: Pratt Sheila R. , Kuller Lewis , Talbott Evelyn O. , McHugh-Pemu Kathleen , Buhari Alhaji M. , Xu Xiaohui 
Published: April 2009

Purpose
The goal of this study was to determine the impact of age, gender, and race on the prevalence and severity of hearing loss in elder adults, aged 72–96 years, after accounting for income, education, smoking, and clinical and subclinical cardiovascular disease.

Methods
Air-conduction thresholds for standard and extended high-frequency pure-tones were obtained from a cohort of 548 (out of 717) elderly adults (ages 72–96 years) who were recruited during the Year 11 clinical visit (1999–2000) of the Cardiovascular Health Study (CHS) at the Pittsburgh, Pennsylvania site. Participant smoking, income, education, and cardiovascular disease histories were obtained from the CHS database and were included as factors.

Results
Hearing loss was more common and more severe for the participants in their 80s than for those in their 70s—the men more than the women and the White participants more than the Black participants. The inclusion of education, income, smoking, and cardiovascular disease (clinical and subclinical) histories as factors did not substantively impact the overall results.

Conclusion
Although the data reported in this article were cross-sectional and a cohort phenomenon might have been operational, they suggested that hearing loss is more substantive in the 8th than the 7th decade of life and that race and gender influence this decline in audition. Given the high prevalence in the aging population and the differences across groups, there is a clear need to understand the nature and causes of hearing loss across various groups in order to improve prevention and develop appropriate interventions.
Growth hormone resistance in severe heart failure resolves after cardiac transplantation
Authors: Lund Lars H. , Freda Pamela , Williams Jill J. , LaManca John J. , LeJemtel Thierry H. , Mancini Donna M. 
Published: April 2009

AimsSevere heart failure (HF) is associated with cachexia; this is often reversed post cardiac transplantation (HTx) with frequent development of obesity. Growth hormone (GH) resistance is common in HF and may contribute to cachexia. Whether GH resistance resolves post HTx is unknown. We aimed to confirm that HF is associated with GH resistance and to test the hypothesis that GH resistance resolves post HTx.Methods and resultsWe measured GH, insulin‐like growth factor‐1 (IGF‐1), and body composition in 10 HF patients awaiting HTx, in 18 patients 11 ± 8 months post HTx, and seven controls. Body mass index was 23.5 ± 3.2 in HF patients and 29.3 ± 5.7 post HTx. HTx patients had gained 14 ± 8 kg since HTx. GH was elevated in HF (control: 0.21 ± 0.25; HF: 1.13 ± 1.19; HTx: 0.11 ± 0.13 ng/mL; P < 0.007), while IGF‐1 was higher in HTx (control: 114 ± 57; HF: 94 ± 52; HTx: 190 ± 106 ng/mL; P < 0.02). HTx had higher total body and abdominal fat %.ConclusionGH resistance is present in severe HF and resolves post HTx. These findings should be confirmed through larger trials.
The acoustic dead zone: theoretical vs. empirical estimates, and its effect on density measurements of semi-demersal fish
Authors: Mello L. G. S. , Rose G. A. 
Published: April 2009

Abstract
Mello, L. G. S., and Rose, G. A. 2009. The acoustic dead zone: theoretical vs. empirical estimates, and its effect on density measurements of semi-demersal fish. – ICES Journal of Marine Science, 66: 1364–1369. The height of the acoustic dead zone, the region near the seabed where fish cannot be resolved acoustically, was calculated both theoretically (DZt) and empirically (DZe). The DZe was based on measurements of depth and trawl geometry from sensors (SCANMAR) mounted on a bottom trawl deployed during a survey off Newfoundland and Labrador in winter 2007. Acoustic data were acquired while trawling, using a 38-kHz echosounder (Simrad EK500) with a hull-mounted transducer. The DZe was calculated as the difference between the trawl-footrope depth and the corresponding acoustically sensed, seabed depth. EK500 and SCANMAR estimates of seabed depth were significantly different. The fish caught were mostly Atlantic cod (Gadus morhua). The estimates of DZe ranged between 2.0 and 3.5 m and were greater than DZt by 0.1–0.9 m in more than half the cases. Three values of acoustically derived cod densities were estimated for each tow, without dead-zone correction and with corrections for DZt and DZe. When compared with DZt corrections, DZe resulted in negative (6–12%) and positive (9–35%) corrections to cod density. A general linear model revealed that the seabed depth gradient, standard deviation of estimated fish density in the dead zone, and wind direction and force explained 85% of the difference between DZt and DZe estimates. These factors affected the detection of the seabed and biased acoustically derived indices of demersal-fish abundance.
Frontiers in Gastroenterology
Authors: Reilly Joseph , Bini Edmund J. 
Published: April 2009

There have been a number of exciting advancements and changes in the gastroenterology field over the last few years. A new mesalamine formulation, balsalazide disodium, is now available for the treatment of ulcerative colitis (UC). Balsalazide may be utilized as first line therapy for patients with UC, or patients who are intolerant to other mesalamine preparations. In the area of irritable bowel syndrome, alosetron was removed from the market after reports that it was associated with severe constipation and death, although a causal relationship could not be established. Published data examines the risk of certain medications and the development of reflux disease and esophageal adenocarcinoma.Also, new proton pump inhibitors (PPIs) are available, esomeprazole, as well as alternate methods of administration for others. The first intravenous PPI, pantoprazole, is available in the United States, although currently there is a paucity of data regarding its efficacy. Peptic ulcer disease is also discussed, including Helicobacter pylori resistance, nonsteroidal anti-inflammatory drugs, and the treatment of bleeding ulcers. With pegylated interferon, progress in the treatment of hepatitis C offers promise for many patients. This review will highlight many recent changes in gastroenterology an offer a perspective on how disease management has changed.
Prevention of Chemotherapy Medication Errors
Authors: Kloth Dwight D. 
Published: April 2009

Prevention of medication errors has long been a concern of pharmacists in all practice settings, including specialty treatment and research centers. Oncology pharmacists have always been particularly aware of this concern because many of the cytotoxic drug therapy regimens we use are already at the maximum tolerated doses, thus leaving no margin for error. During the past 10 years, catastrophic chemotherapy medication errors have occurred in some of the finest hospitals and cancer centers in the United States, bringing unprecedented public and governmental awareness of the risk of such errors. In addition, the March 2000 report by the Institute of Medicine of the National Academy of Sciences, To Err Is Human: Building a Safer Health System, has prompted legislative and executive branch reaction at the federal level aimed toward reducing medical errors of all types, including medication errors. The purpose of this article is to review the types and causes of catastrophic chemotherapy medication errors that have occurred in oncology and to discuss tools and methods aimed at improving the safety of medication use, particularly chemotherapy, in the United States.
Antitumor activity of a dual epidermal growth factor receptor and ErbB2 kinase inhibitor MP‐412 (AV‐412) in mouse xenograft models
Authors: Suzuki Tsuyoshi , Fujii Akihiro , Ohya Junichi , Nakamura Hideo , Fujita Fumiko , Koike Masako , Fujita Masahide 
Published: April 2009

Although epidermal growth factor receptor (EGFR) kinase inhibitors are effective for the treatment of non‐small cell lung cancer (NSCLC), the emergence of mutations resistant to these inhibitors, such as T790M, has become a clinical problem. Recently, ErbB2 mutations have also been identified in a small number of NSCLC patients. Therefore, novel therapies to overcome these mutations are desirable. We describe the antitumor activity of MP‐412 (AV‐412), a dual EGFR/ErbB2 kinase inhibitor, against three lung cancer models with EGFR and ErbB2 mutations and also against various human xenografts with overexpression of these receptors. MP‐412 inhibited phosphorylation of EGFR and its downstream signaling in NCI‐H1650 and NCI‐H1975 cell lines, which harbor the E746‐A750 deletion and L858R + T790M point mutations, respectively, in EGFR. MP‐412 inhibited the growth of these cell lines in vitro and in vivo, whereas the precedent kinase inhibitors lapatinib, erlotinib, and gefitinib were ineffective against NCI‐H1975 cells in vivo. Furthermore, MP‐412 inhibited ErbB2 signaling in the NCI‐H1781 cell line, which harbors the G776V,C insertion in ErbB2, and correlated with its antiproliferation activity. When its antitumor spectrum was further explored in several cancer types overexpressing EGFR or ErbB2, MP‐412 showed potent activity in KPL‐4 and DU145 xenografts, in which lapatinib was ineffective. MP‐412 also inhibited tumor models in which conventional chemotherapies were less effective. These results suggest that MP‐412 is a potent dual inhibitor with the potential for treating solid cancers that overexpress EGFR or ErbB2, including NSCLC cells harboring mutations resistant to the first generation of kinase inhibitors. (Cancer Sci 2009)
Genome‐wide identification of quantitative trait loci for carcass composition and meat quality in a large‐scale White Duroc × Chinese Erhualian resource population
Authors: Ma J. , Ren J. , Guo Y. , Duan Y. , Ding N. , Zhou L. , Li L. , Yan X. , Yang K. , Huang L. , Song Y. , Xie J. , Milan D. , Huang L. 
Published: April 2009

SummaryCarcass and meat quality traits are economically important in pigs. In this study, 17 carcass composition traits and 23 meat quality traits were recorded in 1028 F2 animals from a White Duroc × Erhualian resource population. All pigs in this experimental population were genotyped for 194 informative markers covering the entire porcine genome. Seventy‐seven genome‐wide significant quantitative trait loci (QTL) for carcass traits and 68 for meat quality were mapped to 34 genomic regions. These results not only confirmed many previously reported QTL but also revealed novel regions associated with the measured traits. For carcass traits, the most prominent QTL was identified for carcass length and head weight at 57 cM on SSC7, which explained up to 50% of the phenotypic variance and had a 95% confidence interval of only 3 cM. Moreover, QTL for kidney and spleen weight and lengths of cervical vertebrae were reported for the first time in pigs. For meat quality traits, two significant QTL on SSC5 and X were identified for both intramuscular fat content and marbling score in the longissimus muscle, while three significant QTL on SSC1 and SSC9 were found exclusively for IMF. Both LM and the semimembranous muscle showed common QTL for colour score on SSC4, 5, 7, 8, 13 and X and discordant QTL on other chromosomes. White Duroc alleles at a majority of QTL detected were favourable for carcass composition, while favourable QTL alleles for meat quality originated from both White Duroc and Erhualian.
CAF in the country: implementing the Common Assessment Framework in a rural area
Authors: Adamson Sue , Deverell Catherine 
Published: April 2009

ABSTRACTThis paper discusses aspects of the implementation of the Common Assessment Framework (CAF) in the UK, introduced under the Change for Children Programme and designed to facilitate early intervention and improve multi‐agency working. The study area was rural in character and findings are compared with evaluation of early CAF implementation which focused primarily on urban areas. The study provided lessons for practice, many of which resonate particularly with rural problems identified in the international literature. There may be advantages in rural areas in ease of involvement of families in processes, in early awareness of practitioners of difficulties in families and in depth of relationships with families. These in turn may support early intervention. Disadvantages centre around resource issues, those of skills and confidence and lack of contact with and therefore distrust of other agencies.
Influence of statin treatment on platelet inhibition by clopidogrel – a randomized comparison of rosuvastatin, atorvastatin and simvastatin co‐treatment
Authors: Malmström R. E. , Östergren J. , Jørgensen L. , Hjemdahl P. ,   for the CASTOR investigators
Published: April 2009

Abstract.Objectives.  Possible interactions between clopidogrel and atorvastatin, simvastatin or rosuvastatin (a ‘non‐CYP3A4’ metabolized statin) were investigated in a randomized prospective study using sensitive and specific ex vivo platelet function tests.Methods.  Patients with coronary artery disease participating in a double‐blind study comparing lipid‐lowering effects of atorvastatin (20–80 mg OD; n = 22) and rosuvastatin (10–40 mg OD; n = 24) were studied before and after 2 weeks treatment with clopidogrel 75 mg OD after completed statin dose titration. In addition, 23 patients were randomized to open‐label simvastatin 40 mg OD.Results.  Clopidogrel inhibited 10 μmol L−1 ADP‐induced platelet aggregation by 40 ± 27%, 57 ± 28% and 51 ± 29%, respectively, in patients on rosuvastatin, atorvastatin and simvastatin treatment. The other platelet tests yielded similar results. No dose‐dependent effects of rosuvastatin or atorvastatin co‐treatment on clopidogrel efficacy were observed.Conclusions.  Treatment with CYP3A4 metabolized statins, atorvastatin or simvastatin, did not attenuate the platelet inhibitory effect of clopidogrel maintenance treatment compared with the non‐CYP3A4 metabolized, rosuvastatin.