bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology of bovine Johne's disease (BJD) in beef cattle herds in Australia
Authors: Larsen JWA , Webb Ware JK , Kluver P 
Published: January 2012

Objective  To describe the epidemiology of bovine Johne's disease (BJD) in beef herds in Australia.Design  Retrospective survey of beef herds detected with BJD between 1991 and 2006.Methods  Information about the management and physical characteristics of affected herds, index and clinical cases, testing and control programs, and attitudes to BJD were collated from existing data and personal interviews of herd owners or managers. Herds were excluded if they contained fewer than 30 breeding cows or operated as a dairy farm.Results  Records from 109 herds demonstrated the first detected (‘index’) case was 3.4‐fold more likely to be a beef rather than dairy breed. However, further analysis revealed association with dairy cattle was an important risk factor for introducing BJD. Index cases were most likely detected by veterinarians investigating clinical cases of scouring or ill‐thrifty animals during winter, particularly bulls or aged cows. Most herds with clinical BJD had only a single case, with only one high prevalence herd detected in the survey group. Over the period of observation, test and cull programs did not eradicate BJD unless combined with culling of known high‐risk animals, but removal of high‐risk cattle by partial or total destocking generally restored the trading status of affected herds.Conclusion  Excluding cattle with dairy contact from beef herds, ensuring more effective farm biosecurity, promptly seeking veterinary advice regarding scouring cattle and sourcing replacement cattle from demonstrably low‐risk herds, such as CattleMAP and ‘Beef Only’ herds, are simple strategies that should reduce the risk of introducing BJD infection into beef herds.
Self-Association of Lymphocytic Choriomeningitis Virus Nucleoprotein Is Mediated by Its N-Terminal Region and Is Not Required for Its Anti-Interferon Function
Authors: Ortiz-Riaño Emilio , Cheng Benson Yee Hin , de la Torre Juan C. , Martínez-Sobrido Luis 
Published: January 2012

ABSTRACT
Arenaviruses have a bisegmented, negative-strand RNA genome. Both the large (L) and small (S) genome segments use an ambisense coding strategy to direct the synthesis of two viral proteins. The L segment encodes the virus polymerase (L protein) and the matrix Z protein, whereas the S segment encodes the nucleoprotein (NP) and the glycoprotein precursor (GPC). NPs are the most abundant viral protein in infected cells and virions and encapsidate genomic RNA species to form an NP-RNA complex that, together with the virus L polymerase, forms the virus ribonucleoprotein (RNP) core capable of directing both replication and transcription of the viral genome. RNP formation predicts a self-association property of NPs. Here we document self-association (homotypic interaction) of the NP of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV), as well as those of the hemorrhagic fever (HF) arenaviruses Lassa virus (LASV) and Machupo virus (MACV). We also show heterotypic interaction between NPs from both closely (LCMV and LASV) and distantly (LCMV and MACV) genetically related arenaviruses. LCMV NP self-association was dependent on the presence of single-stranded RNA and mediated by an N-terminal region of the NP that did not overlap with the previously described C-terminal NP domain involved in either counteracting the host type I interferon response or interacting with LCMV Z.
Combination of Biological Screening in a Cellular Model of Viral Latency and Virtual Screening Identifies Novel Compounds That Reactivate HIV-1
Authors: Gallastegui Edurne , Marshall Brett , Vidal David , Sanchez-Duffhues Gonzalo , Collado Juan A. , Alvarez-Fernández Carmen , Luque Neus , Terme Jean-Michel , Gatell Josep M. , Sánchez-Palomino Sonsoles , Muñoz Eduardo , Mestres Jordi , Verdin Eric , Jordan Albert 
Published: January 2012

ABSTRACT
Although highly active antiretroviral therapy (HAART) has converted HIV into a chronic disease, a reservoir of HIV latently infected resting T cells prevents the eradication of the virus from patients. To achieve eradication, HAART must be combined with drugs that reactivate the dormant viruses. We examined this problem in an established model of HIV postintegration latency by screening a library of small molecules. Initially, we identified eight molecules that reactivated latent HIV. Using them as templates, additional hits were identified by means of similarity-based virtual screening. One of those hits, 8-methoxy-6-methylquinolin-4-ol (MMQO), proved to be useful to reactivate HIV-1 in different cellular models, especially in combination with other known reactivating agents, without causing T-cell activation and with lower toxicity than that of the initial hits. Interestingly, we have established that MMQO produces Jun N-terminal protein kinase (JNK) activation and enhances the T-cell receptor (TCR)/CD3 stimulation of HIV-1 reactivation from latency but inhibits CD3-induced interleukin-2 (IL-2) and tumor necrosis factor alpha (TNF-α) gene transcription. Moreover, MMQO prevents TCR-induced cell cycle progression and proliferation in primary T cells. The present study documents that the combination of biological screening in a cellular model of viral latency with virtual screening is useful for the identification of novel agents able to reactivate HIV-1. Moreover, we set the bases for a hypothetical therapy to reactivate latent HIV by combining MMQO with physiological or pharmacological TCR/CD3 stimulation.
Antiretroviral Therapy Reduces the Magnitude and T Cell Receptor Repertoire Diversity of HIV-Specific T Cell Responses without Changing T Cell Clonotype Dominance
Authors: Conrad Joseph A. , Ramalingam Ramesh K. , Duncan Coley B. , Smith Rita M. , Wei Jie , Barnett Louise , Simons Brenna C. , Lorey Shelly L. , Kalams Spyros A. 
Published: January 2012

ABSTRACTAfter initiation of antiretroviral therapy (ART), HIV loads and frequencies of HIV epitope-specific immune responses decrease. A diverse virus-specific T cell receptor (TCR) repertoire allows the host to respond to viral epitope diversity, but the effect of antigen reduction as a result of ART on the TCR repertoire of epitope-specific CD8+T cell populations has not been well defined. We determined the TCR repertoires of 14 HIV-specific CD8+T cell responses from 8 HIV-positive individuals before and after initiation of ART. We used multiparameter flow cytometry to measure the distribution of memory T cell subsets and the surface expression of PD-1 on T cell populations and T cell clonotypes within epitope-specific responses from these individuals. Post-ART, we noted decreases in the frequency of circulating epitope-specific T cells (P= 0.02), decreases in the number of T-cell clonotypes found within epitope-specific T cell receptor repertoires (P= 0.024), and an overall reduction in the amino acid diversity within these responses (P< 0.0001). Despite this narrowing of the T cell response to HIV, the overall hierarchy of dominant T cell receptor clonotypes remained stable compared to that pre-ART. CD8+T cells underwent redistributions in memory phenotypes and a reduction in CD38 and PD-1 expression post-ART. Despite extensive remodeling at the structural and phenotypic levels, PD-1 was expressed at higher levels on dominant clonotypes within epitope-specific responses before and after initiation of ART. These data suggest that the antigen burden may maintain TCR diversity and that dominant clonotypes are sensitive to antigen even after dramatic reductions after initiation of ART.
Retargeting of Rat Parvovirus H-1PV to Cancer Cells through Genetic Engineering of the Viral Capsid
Authors: Allaume Xavier , El-Andaloussi Nazim , Leuchs Barbara , Bonifati Serena , Kulkarni Amit , Marttila Tiina , Kaufmann Johanna K. , Nettelbeck Dirk M. , Kleinschmidt Jürgen , Rommelaere Jean , Marchini Antonio 
Published: January 2012

ABSTRACTThe rat parvovirus H-1PV is a promising anticancer agent given its oncosuppressive properties and the absence of known side effects in humans. H-1PV replicates preferentially in transformed cells, but the virus can enter both normal and cancer cells. Uptake by normal cells sequesters a significant portion of the administered viral dose away from the tumor target. Hence, targeting H-1PV entry specifically to tumor cells is important to increase the efficacy of parvovirus-based treatments. In this study, we first found that sialic acid plays a key role in H-1PV entry. We then genetically engineered the H-1PV capsid to improve its affinity for human tumor cells. By analogy with the resolved crystal structure of the closely related parvovirus minute virus of mice, we developed anin silicothree-dimensional (3D) model of the H-1PV wild-type capsid. Based on this model, we identified putative amino acids involved in cell membrane recognition and virus entry at the level of the 2-fold axis of symmetry of the capsid, within the so-called dimple region.In situmutagenesis of these residues significantly reduced the binding and entry of H-1PV into permissive cells. We then engineered an entry-deficient viral capsid and inserted a cyclic RGD-4C peptide at the level of its 3-fold axis spike. This peptide binds αvβ3and αvβ5integrins, which are overexpressed in cancer cells and growing blood vessels. The insertion of the peptide rescued viral infectivity toward cells overexpressing αvβ5integrins, resulting in the efficient killing of these cells by the reengineered virus. This work demonstrates that H-1PV can be genetically retargeted through the modification of its capsid, showing great promise for a more efficient use of this virus in cancer therapy.
Comparison of clinical and pathological characteristics of isolated aortitis and Takayasu arteritis with ascending aorta involvement
Authors: Wang Hongyue , Li Li , Wang Linlin , Chang Qian , Pu Jielin 
Published: January 2012

AimsIsolated aortitis (IA) is a newly recognized condition, but its differentiation from Takayasu arteritis (TA) is still a challenge. This study aims to explore the characteristics of IA.MethodsThe clinical and pathological data of 965 cases with excised ascending aortas were obtained by chart and slide review. IA cases were compared with TA cases and examined for CD3, CD4, CD8, CD20, CD68, CD138 and IgG4 of the infiltrates using immunohistochemistry.Results24 cases of IA and eight cases of TA were identified. IA cases tended to be older than TA cases (mean 46.3 vs 33.9 years). Both groups had the same male/female ratio (1.0). IA cases tended to have a bigger aortic diameter (mean 59.7 vs 47.6 mm), statistically less intimal thickening (mean 678 vs 1101 μm), fewer lesions outside the ascending aorta (8% vs 100%), a lower erythrocyte sedimentation rate (mean 14.6 vs 27.0 mm/h) and more active aortitis (75.0% vs 62.5%) than TA cases. The number of CD3+ cells was equal to CD20+ cells in the media but fewer than CD20+ cells in the adventitia of IA cases. Their CD4/CD8+ ratio ranged from 1.0 to 1.8 while the number of CD68+ macrophages varied largely. IgG4+ cells ranged from 0 to 40 (mean 4) cells/HPF and the IgG4+/CD138+ ratio ranged from 0 to 0.36 (mean 0.06) in IA cases.ConclusionsCases of IA tend to have more histologically active inflammation except for a relatively normal erythrocyte sedimentation rate, localised lesions and milder intimal fibrosis than cases of TA. IgG4 abnormality may not be the main cause of IA.
Association of Proton Pump Inhibitor Use on Cardiovascular Outcomes With Clopidogrel and Ticagrelor
Authors: Goodman Shaun G. , Clare Robert , Pieper Karen S. , Nicolau José C. , Storey Robert F. , Cantor Warren J. , Mahaffey Kenneth W. , Angiolillo Dominick J. , Husted Steen , Cannon Christopher P. , James Stefan K. , Kilhamn Jan , Steg P. Gabriel , Harrington Robert A. , Wallentin Lars 
Published: January 2012

Background—
The clinical significance of the interaction between clopidogrel and proton pump inhibitors (PPIs) remains unclear.

Methods and Results—
We examined the relationship between PPI use and 1-year cardiovascular events (cardiovascular death, myocardial infarction, or stroke) in patients with acute coronary syndrome randomized to clopidogrel or ticagrelor in a prespecified, nonrandomized subgroup analysis of the Platelet Inhibition and Patient Outcomes (PLATO) trial. The primary end point rates were higher for individuals on a PPI (n=6539) compared with those not on a PPI (n=12 060) at randomization in both the clopidogrel (13.0% versus 10.9%; adjusted hazard ratio [HR], 1.20; 95% confidence interval [CI], 1.04–1.38) and ticagrelor (11.0% versus 9.2%; HR, 1.24; 95% CI, 1.07–1.45) groups. Patients on non-PPI gastrointestinal drugs had similar primary end point rates compared with those on a PPI (PPI versus non-PPI gastrointestinal treatment: clopidogrel, HR, 0.98; 95% CI, 0.79–1.23; ticagrelor, HR, 0.89; 95% CI, 0.73–1.10). In contrast, patients on no gastric therapy had a significantly lower primary end point rate (PPI versus no gastrointestinal treatment: clopidogrel, HR, 1.29; 95% CI, 1.12–1.49; ticagrelor, HR, 1.30; 95% CI, 1.14–1.49).

Conclusions—
The use of a PPI was independently associated with a higher rate of cardiovascular events in patients with acute coronary syndrome receiving clopidogrel. However, a similar association was observed between cardiovascular events and PPI use during ticagrelor treatment and with other non-PPI gastrointestinal treatment. Therefore, in the PLATO trial, the association between PPI use and adverse events may be due to confounding, with PPI use more of a marker for, than a cause of, higher rates of cardiovascular events.

Clinical Trial Registration—

http://www.clinicaltrials.gov
. Unique identifier: NCT00391872.
Downscaling Extremes—An Intercomparison of Multiple Statistical Methods for Present Climate
Authors: Bürger G. , Murdock T. Q. , Werner A. T. , Sobie S. R. , Cannon A. J. 
Published: January 2012

Abstract
Five statistical downscaling methods [automated regression-based statistical downscaling (ASD), bias correction spatial disaggregation (BCSD), quantile regression neural networks (QRNN), TreeGen (TG), and expanded downscaling (XDS)] are compared with respect to representing climatic extremes. The tests are conducted at six stations from the coastal, mountainous, and taiga region of British Columbia, Canada, whose climatic extremes are measured using the 27 Climate Indices of Extremes (ClimDEX; http://www.climdex.org/climdex/index.action) indices. All methods are calibrated from data prior to 1991, and tested against the two decades from 1991 to 2010. A three-step testing procedure is used to establish a given method as reliable for any given index. The first step analyzes the sensitivity of a method to actual index anomalies by correlating observed and NCEP-downscaled annual index values; then, whether the distribution of an index corresponds to observations is tested. Finally, this latter test is applied to a downscaled climate simulation. This gives a total of 486 single and 162 combined tests. The temperature-related indices pass about twice as many tests as the precipitation indices, and temporally more complex indices that involve consecutive days pass none of the combined tests. With respect to regions, there is some tendency of better performance at the coastal and mountaintop stations. With respect to methods, XDS performed best, on average, with 19% (48%) of passed combined (single) tests, followed by BCSD and QRNN with 10% (45%) and 10% (31%), respectively, ASD with 6% (23%), and TG with 4% (21%) of passed tests. Limitations of the testing approach and possible consequences for the downscaling of extremes in these regions are discussed.
Interpretation of Accurate UV Polarization Lidar Measurements: Application to Volcanic Ash Number Concentration Retrieval
Authors: Miffre A. , David G. , Thomas B. , Chacra M. Abou , Rairoux P. 
Published: January 2012

Abstract
In this paper, accurate UV polarization measurements are performed on a volcanic ash cloud after long-range transport at Lyon, France (45.76°N, 4.83°E). The volcanic particles are released from the mid-April 2010 eruption of the Eyjafjallajökull Icelandic volcano (63.63°N, 19.62°W). The aerosol UV depolarization, which arises from nonspherical volcanic ash particles, serves as an independent means to discriminate ash from nonash particles in the volcanic cloud. This discrimination is only feasible if the intrinsic ash particle depolarization ration δash is accurately determined. In this paper, the δash value [δash = (40.5 ± 2.0)%] is derived from literature laboratory measurements on a scattering matrix to ensure ash particle specificity. It is shown that traditional approaches, based on direct lidar depolarization ratio δa measurements, are only valid very close to the source region, because δa may be very different from δash, when nonash particles are present. For the first time, observed lidar depolarization ratios, in the range from a few percent to 40%, are hence interpreted in comparison with δash taken as a reference. It is then shown how to use the sensitive and accurate UV polarization measurements to access to the size-averaged number concentration vertical profile of volcanic ash particles in the troposphere. Vertical profiles of the backscattering coefficient specific to volcanic ash particles, providing altitude-resolved ash particle number concentrations, are presented in the troposphere after optical scattering computation. This new methodology can be applied to other aerosols events and for other optical remote sensing experiments.
Reversal of the British trends in place of death: Time series analysis 2004–2010
Authors: Gomes Barbara , Calanzani Natalia , Higginson Irene J 
Published: January 2012

Background: Increased attention is being paid to the place where people die with a view to providing choice and adequately planning care for terminally ill patients. Secular trends towards an institutionalised dying have been reported in Britain and other developed world regions. Aim: This study aimed to examine British national trends in place of death from 2004 to 2010. Design and setting: Descriptive analysis of death registration data from the Office for National Statistics, representing all 3,525,564 decedents in England and Wales from 2004 to 2010. Results: There was a slow but steady increase in the proportion of deaths at home, from 18.3% in 2004 to 20.8% in 2010. Absolute numbers of home deaths increased by 9.1%, whilst overall numbers of deaths decreased by 3.8%. The rise in home deaths was more pronounced in cancer, happened for both genders and across all age groups, except for those younger than 14 years and for those aged 65–84, but only up to 2006. The rise was more evident when ageing was accounted for (age–gender standardised proportions of home deaths increased from 20.6% to 23.5%). Conclusions: Following trends in the USA and Canada, dying is also shifting to people’s homes in Britain. Home deaths increased for the first time since 1974 amongst people aged 85 years and over. There is an urgent need across nations for comparative evidence on the outcomes and the costs of dying at home.
Effects of progesterone application on antioxidant enzyme activities and K+/Na+ ratio in bean seeds exposed to salt stress
Authors: Erdal Serkan , Genisel Mucip , Turk Hulya , Gorcek Zeynep 
Published: January 2012

This study aimed to investigate the influence of progesterone, a mammalian sex hormone, on germination of bean ( Phaseolus vulgaris L.) seeds exposed to salt stress. The exogenous addition of 10−6, 10−8 and 10−10 M progesterone to the stressing media in which bean seeds were germinated in combination with the salt (100 mM NaCl) stressor induced significant protective changes in the germination and early growth parameters. The mitigating effect of progesterone was evaluated by the measurement of radicle and plumule lengths, activities of antioxidant enzymes superoxide dismutase (SOD), peroxidase (POX) and catalase (CAT). In addition, it is the first study that exhibited changes in K/Na ratio. The obtained results showed that progesterone application stimulated germination and growth of salt-stressed seeds. Similarly, it stimulated significantly SOD, POX and CAT activities compared to both control and salt control. Salt stress significantly increased the lipid peroxidation compared to the control seeds. However, parallel to the increase in antioxidant activity, lipid peroxidation was significantly reduced by progesterone application. The best stimulatory effects on investigated parameters were recorded at 10−8 M progesterone-applied seeds. On the other hand, salt stress reduced remarkably K/Na ratio by 50% in radicle and by 80% in plumule. However, progesterone application significantly mitigated the reduction in K/Na ratio. These findings clearly demonstrate that progesterone has a positive role in moderate detrimental effects induced by salt.
Cadmium and lead content in several brands of rice grains (Oryza sativa) in central Iran
Authors: Shakerian A , Rahimi E , Ahmadi M 
Published: January 2012

The aim of this study was to investigate the cadmium (Cd) and lead (Pb) content of several commercially available brands of rice grains ( Oryza sativa) in central Iran. A total of 67 samples of the most widely consumed brands of rice grains were purchased from local bazaar markets in Shahrekord, Iran. The first step, grains of raw rice were digested by acid digestion method and then were analyzed by atomic absorption spectrometer. The results showed that Cd concentration in rice grains ranged from 0.0378 to 0.1225 ppm dry weight and its average concentration was 0.062 ± 0.019 ppm and Pb content ranged from 0.0405 to 0.1281 ppm dry weight and its average concentration was 0.068 ± 0.0185 ppm. Cd and Pb concentrations in the sampled rice grains were lower in comparison with their upper limits (0.2 and 0.2 ppm for Cd and Pb, respectively) approved by food sanitary standard. Therefore, it can be concluded that there is no health problems due to the consumption of brands of rice grains, for these two elements. The results indicated that weekly intake of Cd and Pb from rice grains was below the provisional tolerable weekly intakes recommended by WHO/FAO.
VTS Operator Performance and Acceptance of a Short-Term Path Prediction Display in a Low Density Traffic Area
Authors: Wiersma Erik , Jarvis Dominic , Granholm Goran 
Published: January 2012

Vessel traffic management and control systems are employed to ensure the safety and efficiency of maritime traffic. In search for optimal support of Vessel Traffic Service (VTS) operators in performing their task, tools are developed continuously. This paper describes how the real users of the systems (VTS operators and managers) were involved in the design and testing of new tools. This was achieved by creating a user forum for discussing the results of the research. At the same time a performance based method for measuring situation awareness of VTS operators (SA Test) was developed tested and implemented. As an example of the procedure used, one such tool is presented. The tool tested in this experiment is a path prediction tool for VTS use in a non-dense traffic area - (the Finnish archipelago). The tool predicts the future path position of vessels one-minute ahead. To see whether this tool could have implications for grounding avoidance monitoring by VTS, it was presented to the user forum and tested using SA Test. This paper presents the results of the tests.