bluuebunny/crossref_metadata_2025_split huggingface dataset:
Danish strategies to controlCampylobacterin broilers and broiler meat: facts and effects
Authors: ROSENQUIST H. , BOYSEN L. , GALLIANO C. , NORDENTOFT S. , ETHELBERG S. , BORCK B. 
Published: May 2009

SUMMARYThermotolerantCampylobacterspp. have been the most common bacterial cause of human gastrointestinal disease in Denmark since 1999. In 2003, the Danish voluntary strategy to controlCampylobacterwas intensified. The focus was on biosecurity, allocation of meat fromCampylobacter-negative broilers to the production of chilled products, and consumer information campaigns. From 2002 to 2007, the percentage ofCampylobacter-positive broiler flocks at slaughter decreased from 43% to 27%. After processing,Campylobacter-positive samples of chilled broiler meat fell from 18% in 2004 to 8% in 2007. Furthermore, the number of registered humanCampylobactercases decreased by 12%; from 4379 cases in 2002 to 3865 cases in 2007. We believe that the observed decrease in the occurrence ofCampylobacterin broilers and broiler meat and the coincidental fall in the number of registered human cases is, in part, a result of the implemented control strategy.
Estimation of sample sizes for pooled faecal sampling for detection of Salmonella in pigs
Authors: ARNOLD M. E. , COOK A. J. C. 
Published: May 2009

SUMMARYSalmonella infection in breeding pigs was the subject of a European survey in 2008. The prevalence of pig-breeding holdings infected with Salmonella was determined by microbiological culture of pooled pen faecal samples. The objective of this study was to estimate the sensitivity of pooled faecal sampling and to calculate the required sample sizes. To do this, individual and pooled faecal samples were collected from a sample of pens from nine farms. Bayesian methods were used to estimate the sensitivity of individual and pooled faecal sampling, and the degree of clustering of Salmonella at the pen level. Sample sizes were then calculated for various values of design prevalence, taking into account the clustering. Pooling was highly efficient compared to individual sampling, e.g. with 18 pooled samples required to detect a 10% prevalence with 95% certainty, compared to 35 individual rectal samples. We recommend that pooled sampling is used for detection of Salmonella in pigs. Results were influenced by the degree of clustering at pen level, and it is important to take this into account both in the estimation of appropriate sample sizes and the estimation of prevalence from pooled sample data.
Assessment of three generations of mice derived by ICSI using freeze-dried sperm
Authors: Li Ming-Wen , Willis Brandon J. , Griffey Stephen M. , Spearow Jimmy L. , Lloyd K. C. Kent 
Published: May 2009

SummaryAlthough the derivation of mice by intracytoplasmic sperm injection (ICSI) using freeze-dried sperm has been demonstrated previously, a comprehensive analysis of their viability, health, and fertility has not. The purpose of the present study was to determine the extent to which ICSI using freeze-dried sperm stored at 4 °C for 1–2 months from mice on either an inbred (C57BL/6J) or hybrid (B6D2F1/J) genetic background results in genomic instability and/or phenotypic abnormality in mice and two generations of their progeny. Fertilization rates (number of 2-cells per injected oocytes) using ICSI of fresh and freeze-dried sperm were similar within and between mouse strains, although fewer freeze-dried sperm-derived embryos than fresh sperm-derived embryos developed to blastocystsin vitro(C57BL/6J and B6D2F1/J) and liveborn pupsin vivo(B6D2F1/J only). Nevertheless, once born, mice derived by ICSI using freeze-dried sperm in both mouse strains were healthy and reproductively sound. No major differences in litter size, weaning rate, and sex ratio were noted in the two generations of progeny (F2 and F3) of ICSI-derived offspring using freeze-dried sperm compared with that in the natural mating (control) group. Further, there was no evidence that either ICSI or freeze drying induced genomic instability, as determined by microsatellite analysis of the derived mice and subsequent generations when compared with both parental genotypes, nor were there differences in the number or types of pathological changes in any of the three generations of progeny. We conclude that viable, healthy and genomically stable mice can be derived by ICSI using freeze-dried mouse sperm stored in the refrigerator for at least 2 months. Further, because freeze drying is a simpler and more economical technique compared with embryo and sperm cryopreservation, the results of this study justify additional research to continue to develop and enhance the technique for the preservation, storage, and sharing of genetically altered mice.
Development and spindle formation in rat somatic cell nuclear transfer (SCNT) embryos in vitro using porcine recipient oocytes
Authors: Sugawara Atsushi , Sugimura Satoshi , Hoshino Yumi , Sato Eimei 
Published: May 2009

SummaryCloning that uses somatic cell nuclear transfer (SCNT) technology with gene targeting could be a potential alternative approach to obtain valuable rat models. In the present study, we determined the developmental competence of rat SCNT embryos constructed using murine and porcine oocytes at metaphase II (MII). Further, we assessed the effects of certain factors, such as: (i) the donor cell type (fetal fibroblasts or cumulus cells); and (ii) premature chromosome condensation (PCC) with normal spindle formation, on the developmental competence of rat interspecies SCNT (iSCNT) embryos. iSCNT embryos that had been constructed using porcine oocytes developed to the blastocyst stage, while those embryos made using murine MII oocytes did not. Rat iSCNT embryos constructed with green fluorescent protein (GFP)-expressing fetal fibroblasts injected into porcine oocytes showed considerable PCC with a normal bipolar spindle formation. The total cell number of iSCNT blastocyst derived from GFP-expressing fetal fibroblasts was higher than the number derived from cumulus cells. In addition, these embryos expressed GFP at the blastocyst stage. This paper is the first report to show that rat SCNT embryos constructed using porcine MII oocytes have the potential to develop to the blastocyst stage in vitro. Thus the iSCNT technique, when performed using porcine MII oocytes, could provide a new bioassay system for the evaluatation of the developmental competence of rat somatic cells.
Church of the In-Between God: Recovering an Ecclesial Sense of Place Down-under
Authors: Pickard Stephen 
Published: May 2009

AbstractThis article examines the significance of ‘place’ as a theme in ecclesiology in the interests of developing an ecclesial sense of place within my own context of Australian Anglicanism. To talk about ecclesiology is to talk about place, about God’s place, about our placement in the world, about how and why our social life operates as it does, about what engenders optimal life enhancing community. From this perspective, place can be a critical concept through which theology, ecclesiology, mission and ministry can be organized and better understood. The primary discipline that has deployed the concept of place is geography. Accordingly, in this article, I consider the theme of place as it is discussed in professional geography and briefly examine some implications for being church and the Anglican Church in particular. This provides the framework for consideration of place within an Australian cultural and ecclesial context. In doing so, I examine the motif of verandah as a depiction of ecclesial place down-under. The key concept of the ‘in-between place’ to depict a post-colonial way of being church is deployed in order to recover an ecclesial sense of place down-under. Underpinning such an approach is the theological concept of the in-between God.
Church Tradition and Psychological Type Preferences among Anglicans in England
Authors: Village Andrew , Francis Leslie J. , Craig Charlotte 
Published: May 2009

AbstractA sample of 290 individuals attending Evangelical Anglican churches and Anglo-Catholic churches in central England completed the Keirsey Temperament Sorter, a measure of psychological type preferences. Overall, there were clear preferences for sensing over intuition, for feeling over thinking, and for judging over perceiving, which is consistent with the findings of two earlier studies profiling the psychological type of Anglican churchgoers. However, there was also a significantly higher proportion of intuitives among Anglo-Catholics than among Evangelical Anglicans, which is consistent with the greater emphasis in Anglo-Catholic churches on mystery, awe, and the centrality of sacraments in worship which may resonate with the intuitive predisposition. The implications of these findings are discussed for the benefits of breadth and diversity within Anglicanism.
DDBJ Activities: Contribution to the Research in Information Biology
Authors: Mashima Jun , Kosuge Takehide , Okido Toshihisa , Kodama Yuichi , Ikeo Kazuho , Sugawara Hideaki , Tateno Yoshio , Gojobori Takashi 
Published: May 2009

AbstractDDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; "http://www.insdc.org/":http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also collecting and releasing gene expression data at CIBEX (Center for Information Biology gene EXpression database; "http://cibex.nig.ac.jp/":http://cibex.nig.ac.jp/). Furthermore, DDBJ contributed to international annotation jamborees such as FANTOM (mouse), H-Inv (human), RAP (rice) and E. coli K12. DDBJ provides many services to the research in information biology or bioinformatics. They include Web-API for Biology (WABI) "http://www.xml.nig.ac.jp/":http://www.xml.nig.ac.jp/ and All-round Retrieval of Sequence and Annotation (ARSA) "http://arsa.ddbj.nig.ac.jp/":http://arsa.ddbj.nig.ac.jp/. These activities are presented with the perspective of DDBJ in the coming years.
Present and future of proteomics data curation at the PRIDE database
Authors: Vizcaino Juan Antonio , Hermjakob Henning , Martens Lennart 
Published: May 2009

AbstractSignificant progress has been made in improving the accessibility and utility of the large amounts of generated high-throughput proteomics data by the introduction of publicly available proteomics repositories. One such repository is PRIDE (the ‘PRoteomics IDEntifications’ database, "http://www.ebi.ac.uk/pride":http://www.ebi.ac.uk/pride). PRIDE stores mass spectrometry related data, including peptide and protein identifications, mass spectra and valuable additional metadata.At present, data curation in PRIDE is limited to data submission support. The format in which all submissions need to take place is PRIDE XML. Mass spectrometry derived data is very heterogeneous in terms of experimental approaches, instrumentation, data formats, etc. This is why conversion of all this different data to PRIDE XML is far from being trivial and can be very time consuming, since tailored submission pipelines must be often constructed. However, the situation has now ameliorated since some new tools like PRIDE converter ("http://code.google.com/p/pride-converter":http://code.google.com/p/pride-converter). are now available for submitters to convert their data to PRIDE XML.In the near future, data curation in PRIDE will be significantly extended. High-quality data will be included in a new repository called PRIDE-plus. First of all, it will be necessary to create a set of minimal requirement rules to decide which datasets can be included in PRIDE-plus. Then, the design and implementation of new curation tools to perform data quality assessment will be essential. It will also be necessary to do research into the automation of these new curation and annotation tasks.
Clostridium difficile Infection in Ohio Hospitals and Nursing Homes During 2006
Authors: Campbell Robert J. , Giljahn Lynn , Machesky Kim , Cibulskas-White Katie , Lane Lisa M. , Porter Kyle , Paulson John O. , Smith Forrest W. , McDonald L. Clifford 
Published: May 2009

Context.Healthcare data suggest that the incidence and severity of Clostridium difficile infection (CDI) in hospitals are increasing. However, the overall burden of disease and the mortality rate associated with CDI, including the contribution from cases of infection that occur in nursing homes, are poorly understood.Objective.To describe the epidemiology, disease burden, and mortality rate of healthcare-onset CDI.Methods.In 2006, active public reporting of healthcare-onset CDI, using standardized case definitions, was mandated for all Ohio hospitals and nursing homes. Incidence rates were determined and stratified according to healthcare facility characteristics. Death certificates that listed CDI were analyzed for trends.Results.There were 14,329 CDI cases reported, including 6,376 cases at 210 hospitals (5,217 initial cases [ie, cases identified more than 48 hours after admission to a healthcare facility in patients who had not had CDI during the previous 6 months] and 1,159 recurrent cases [ie, cases involving patients who had had CDI during the previous 6 months]) and 7,953 cases at 955 nursing homes (4,880 initial and 3,073 recurrent cases). After adjusting for missing data, the estimated total was 18,200 cases of CDI, which included 7,000 hospital cases (5,700 initial and 1,300 recurrent cases) and 11,200 nursing homes cases (6,900 initial and 4,300 recurrent cases). The rate for initial cases was 6.4-7.9 cases/10,000 patient-days for hospitals and 1.7-2.9 cases/10,000 patient-days for nursing homes. The rate for initial cases in nursing homes decreased during the study (P < .001). Nonpediatric hospital status (P = .011), a smaller number of beds (P = .003), and location in the eastern or northeastern region of the state (P = .011) were each independently associated with a higher rate of initial cases in hospitals. Death certificates for 2006 listed CDI among the causes of death for 893 Ohio residents; between 2000 and 2006, this number increased more than 4-fold.Conclusion.Healthcare-onset CDI represents a major public health threat that, when considered in the context of an increasing mortality rate, should justify a major focus on prevention efforts.
Problem gamblers share deficits in impulsive decision‐making with alcohol‐dependent individuals
Authors: Lawrence Andrew J. , Luty Jason , Bogdan Nadine A. , Sahakian Barbara J. , Clark Luke 
Published: May 2009

ABSTRACTAims  Problem gambling has been proposed to represent a ‘behavioural addiction’ that may provide key insights into vulnerability mechanisms underlying addiction in brains that are not affected by the damaging effects of drugs. Our aim was to investigate the neurocognitive profile of problem gambling in comparison with alcohol dependence. We reasoned that shared deficits across the two conditions may reflect underlying vulnerability mechanisms, whereas impairments specific to alcohol dependence may reflect cumulative effects of alcohol consumption.Design  Cross‐sectional study.Setting  Out‐patient addiction treatment centres and university behavioural testing facilities.Participants  A naturalistic sample of 21 male problem and pathological gamblers, 21 male alcohol‐dependent out‐patients and 21 healthy male control participants.Measurements  Neurocognitive battery assessing decision‐making, impulsivity and working memory.Findings  The problem gamblers and alcohol‐dependent groups displayed impairments in risky decision‐making and cognitive impulsivity relative to controls. Working memory deficits and slowed deliberation times were specific to the alcohol‐dependent group.Conclusions  Gambling and alcohol‐dependent groups shared deficits in tasks linked to ventral prefrontal cortical dysfunction. Tasks loading on dorsolateral prefrontal cortex were selectively impaired in the alcohol‐dependent group, presumably as a consequence of long‐term alcohol use.
Comparison of costs and utilization among buprenorphine and methadone patients
Authors: Barnett Paul G. 
Published: May 2009

ABSTRACTAims  Buprenorphine is an effective alternative to methadone for treatment of opioid dependence, but economic concerns represent a barrier to implementation. The economic impacts of buprenorphine adoption by the US Veterans Health Administration (VHA) were examined.Design  Prescriptions of buprenorphine, methadone treatment visits, health‐care utilization and cost, and diagnostic data were obtained for 2005.Findings  VHA dispensed buprenorphine to 606 patients and methadone to 8191 other patients during the study year. An analysis that controlled for age and diagnosis found that the mean cost of care for the 6 months after treatment initiation was $11 597 for buprenorphine and $14 921 for methadone (P < 0.001). Cost was not significantly different in subsequent months. The first 6 months of buprenorphine treatment included an average of 66 ambulatory care visits, significantly fewer than the 137 visits in methadone treatment (P < 0.001). In subsequent months, buprenorphine patients had 8.4 visits, significantly fewer than the 21.0 visits of methadone patients (P < 0.001). Compared to new methadone episodes, new buprenorphine episodes had 0.634 times the risk of ending [95% confidence interval 0.547–0.736]. Implementation of buprenorphine treatment was not associated with an influx of new opioid‐dependent patients.Conclusion  Despite the higher cost of medication, buprenorphine treatment was no more expensive than methadone treatment. VHA methadone treatment costs were higher than reported by other providers. Although new buprenorphine treatment episodes lasted longer than new methadone episodes, buprenorphine is recommended for more adherent patients.
Gene–environment interactions and alcohol use and dependence: current status and future challenges
Authors: Van Der Zwaluw Carmen S. , Engels Rutger C. M. E. 
Published: May 2009

ABSTRACTAim  To discuss the current status of gene–environment interaction research with regard to alcohol use and dependence. Further, we highlight the difficulties concerning gene–environment studies.Methods  Overview of the current evidence for gene–environment interactions in alcohol outcomes, and of the associated challenges in gene–environment studies.Results  Attention to the causative roles of gene–environment interactions in alcohol use and dependence is increasing. Studies with twin designs are beginning to examine gene‐shared environment effects, and animal studies have investigated gene–environment interaction effects on alcohol intake in primates. Thirteen studies incorporated gene–environment interactions in examining alcohol use or dependence in humans. These studies held a variety of candidate genes and environmental risk factors and their heterogeneity made it impossible to draw firm general conclusions.Conclusions  Challenges for future gene–environment studies are abundant, and consist of, for example, the development of clear theoretical assumptions about neurobiological mechanisms and the recruitment of large longitudinal samples that already start in childhood. Replication is essential to prevent an overload of false‐positive results. Despite the difficulties, it is crucial to include gene–environment interactions in future studies in order to unravel the aetiological factors of human alcohol outcomes.
Drugs and violent death: comparative toxicology of homicide and non‐substance toxicity suicide victims
Authors: Darke Shane , Duflou Johan , Torok Michelle 
Published: May 2009

ABSTRACTAims  To determine the comparative toxicology of death by homicide and suicide by means other than substance toxicity.Design  Cross‐sectional (autopsy reports).Setting  Sydney, Australia.Cases  A total of 1723 cases of violent death were identified, comprising 478 homicide (HOM) cases and 1245 non‐substance toxicity suicide (SUI) cases.Findings  Substances were detected in 65.5% of cases, and multiple substances in 25.8%, with no group differences. Illicit drugs were detected in 23.9% of cases, and multiple illicit in 5.3%. HOM cases were significantly more likely to have an illicit drug [odds ratio (OR) 2.09] and multiple illicits (OR 2.94), detected, HOM cases being more likely to have cannabis (OR 2.39), opioids (OR 1.53) and psychostimulants (OR 1.59) present. HOM cases were, however, significantly less likely to have benzodiazepines (OR 0.53), antidepressants (OR 0.22) and antipsychotics (OR 0.23) present. Alcohol was present in 39.6% of cases (median blood alcohol concentration = 0.12), with no group difference in prevalence.Conclusions  The role drugs play in premature death extends far beyond overdose and disease, with illicit drugs associated strongly with homicide.
Urinary ethyl glucuronide (EtG) and ethyl sulphate (EtS) assessment: valuable tools to improve verification of abstention in alcohol‐dependent patients during in‐patient treatment and at follow‐ups
Authors: Junghanns Klaus , Graf Iris , Pflüger Juliane , Wetterling Gunnar , Ziems Christian , Ehrenthal Dieter , Zöllner Maike , Dibbelt Leif , Backhaus Jutta , Weinmann Wolfgang , Wurst Friedrich M. 
Published: May 2009

ABSTRACTAims  The aims of this study were (i) to assess the effect of additional urinary ethyl glucuronide (EtG) and ethyl sulphate (EtS) assessment on diagnosed relapse rates in detoxified alcohol‐dependent patients; and (ii) to compare dropout rates between EtG‐ and EtS‐negative and ‐positive patients.Design  Two studies on detoxified alcohol‐dependent patients. If patients had no indication of relapse they were asked for a urinary sample at discharge from in‐patient treatment 3, 6 and 12 weeks after discharge (study 1) and 1, 3 and 6 weeks after discharge (study 2), respectively.Setting  Department of Psychiatry, University of Luebeck, Germany.Participants  A total of 107 and 32 detoxified alcohol‐dependent patients having participated in a 3‐week in‐patient motivation enhancement programme.Measurement  Personal interviews, breathalyzer tests, assessment of urinary EtG and EtS with liquid chromatography‐tandem mass spectrometry (LC‐MS/MS analysis).Finding  Urinary EtG and EtS were always positive at the same time. In the first study 13.5% of the patients were already positive before being discharged from hospital. At the follow‐ups 3, 6 and 12 weeks after discharge 12.2, 19.4 and 28.0%, respectively, of the patients coming to the follow‐up and denying relapse were positive on urinary EtG and EtS. In the second study, of those patients showing up for follow‐up after 1 week and denying relapse, EtG and EtS were positive in four cases (17.4%). Only one EtG‐ and EtS‐positive relapser (3.1%) came to the next follow‐ups. In both studies the rates of detected relapses were significantly higher for early follow‐ups if urinary EtG and EtS results were considered additionally. Dropout rates until the next follow‐up were significantly higher among positive than EtG‐ and EtS‐negative patients.Conclusion  Urinary EtG and EtS improve verification of abstinence in studies of alcohol‐dependent patients.