bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of nutrition on hormone profiles and patterns of deiodinase activity in the skin and associated patterns of hair follicle activity and moult in cashmere goats
Authors: Rhind S. M. , Kyle C. E. , Riach D. J. , Duff E. I. 
Published: August 2009

AbstractThe effects of nutrition on patterns of live-weight change, hair follicle activity, moult, hormone profiles and associated activities of monodeiodinase enzyme types II and III (MDII and MDIII) in cashmere goats were investigated. From 1 week before the winter solstice (mid December), one group of 15 animals was given a ration designed to provide 2·0 × live weight maintenance requirements (high; H) while a second, similar, group was given 0·8 × live weight maintenance requirements (low; L). After approximately 3 months, L animals had significantly lower mean live weights (P<0·01) than H animals. This was associated with lower (P<0·05) overall mean hair follicle activity in L than H animals during the March to May period and a lower overall mean moult score during March and April in L animals (P<0·01) but a similar mean date of moult onset. Mean concentrations of all of the hormones measured exhibited significant changes (P<0·01) with date of sampling. Overall mean concentrations of insulin, tri-iodothyronine and thyroxine did not differ with treatment but, compared with L animals, H animals exhibited higher mean concentrations of prolactin in April and May (P<0·05) and of insulin-like growth factor-1 in December and January (P<0·001). Rates of activity of MDII and MDIII in skin differed with date (P<0·001) but were not significantly affected by nutritional treatment. The MDIII/MDII ratio differed (P=0·05) with month but was significantly higher (P<0·05) in L than H animals in January, only. It is concluded that the reduction in hair follicle activity and the slower onset of moult associated with reduced nutrition were unlikely to be controlled, directly, by differences in activities of MDII or MDIII in skin tissue.
Effects of monensin and yeast supplementation on blood acid-base balance in finishing feedlot steers fed a high-grain, high-protein diet
Authors: Castillo C. , Hernández J. , Méndez J. , García-Partida P. , Pereira V. , Vázquez P. , Alonso M. López , Benedito J. L. 
Published: August 2009

AbstractThe aim of this study was to evaluate the effects of two dietary supplements (monensin and a live yeast culture) on acid-base balance in steers maintained in a commercial feedlot system, considering effects over the finishing productive cycle. Steers (no. =42) were allotted randomly to one of the three study groups: (1) control group (no supplementation, C), (2) monensin supplementation (MON), and (3) live Saccharomyces cerevisiae strain 47 supplementation (SACC). Venous blood samples were collected for the measurement of acid-base parameters and l-lactate. Production parameters were also used as a complementary tool for understanding the internal changes associated with supplementation. During the finishing period, MON steers tended to gain more efficiently than C and SACC steers. In the C group, the finishing-period diet caused a progressive decline in blood bases, in line with the high-grain diet consumption. In contrast, supplemented animals did not show this trend, although lower HCO3− and base excess values were registered in SACC steers than in MON, indicating that ionophore supplementation is less effective for reducing blood base consumption than yeast supplementation. In our study, the lack of the expected response to yeast supplementation may be attributable to the high crude protein content of the ration, a common feature of commercial feedlot industries.
Holo-analysis of the efficacy of Bio-Mos® in pig nutrition
Authors: Rosen G. D. 
Published: August 2009

AbstractThis exploratory holo-analysis of the efficacy of Bio-Mos®, (BM), an outer cell wall derivative of a strain ofSaccharomyces cerevisiae, is part of an empirical modelling research programme comparing the efficacies of potential replacements for veterinary prescription-free pronutrient antibiotics in pig production. The data resource was mined from 128 saccharide publications of which 31/97 on BM (1997 to 2003) provided 69 negatively controlled start-to-finish tests from 10 countries (USA 71%) using 3778 pigs(30·5 per treatment). Respective food intake, live-weight gain and food conversion responses of 0·0075 kg/day (0·99%), 0·0145 kg/day (3·58%) and −0·0526 (3·07%) have coefficients of variation of 511, 163 and 229% and beneficial gain and conversion frequencies of 73 and 68%, 54% jointly. Holo-analytical multiple regression models of BM food intake, live-weight gain and food conversion effects using conventional and less stringent probabilities contain significant independent variables for negative control performances, dosage, discontinuous dosage, test duration, year of test, non-USA test, male, grower-finisher, slatted floor, processed food, antibacterial foods, animal protein food, main vegetable protein not soya bean, added oil/fat food and factorial data, which account for 11 to 68% of variations in response. The models quantify differences in research and praxis and indicate areas for future modelling research on BM dose-response relations, effects of ration ingredient and nutrient contents, other saccharide efficacy comparisons, including lactose, and BM comparisons and interactions with other proposed antibiotic replacements.
Institutionalizing Water Governance in England and Wales: Potential and Limitations
Authors: Wong Sam 
Published: August 2009

Abstract
This paper evaluates the neo-institutional perspective in conceptualizing the public-private partnership in water provision in England and Wales. It questions the simplistic assumptions that effective water governance lies in getting institutions, incentives, and authority right. Drawing upon Mary Douglas's social embeddedness of institutions, this paper demonstrates that use of water is both individually-pursued and socially-shaped. This paper calls for a reorganization of the institutional arrangements to tackle power asymmetries between the regulators, water companies, and the public. It suggests that the design of the regulatory structures needs to cohere with the cultural meaning of water.
Testing the hypothesis of tissue selectivity: the intersection–union test and a Bayesian approach
Authors: Van Deun K. , Hoijtink H. , Thorrez L. , Van Lommel L. , Schuit F. , Van Mechelen I. 
Published: August 2009

Abstract
Motivation: Finding genes that are preferentially expressed in a particular tissue or condition is a problem that cannot be solved by standard statistical testing procedures. A relatively unknown procedure that can be used is the intersection–union test (IUT). However, two disadvantages of the IUT are that it is conservative and it conveys only the information of the least differing target tissue–other tissue pair.
Results: We propose a Bayesian procedure that quantifies how much evidence there is in the overall expression profile for selective over-expression. In a small simulation study, it is shown that the proposed method outperforms the IUT when it comes to finding selectively expressed genes. An application to publicly available data consisting of 22 tissues shows that the Bayesian method indeed selects genes with functions that reflect the specific tissue functions. The proposed method can also be used to find genes that are underexpressed in a particular tissue.
Availability: Both MATLAB and R code that implement the IUT and the Bayesian procedure in an efficient way, can be downloaded at http://ppw.kuleuven.be/okp/software/BayesianIUT/.
Contact: katrijn.vandeun@psy.kuleuven.be
Partition function and base pairing probabilities for RNA–RNA interaction prediction
Authors: Huang Fenix W. D. , Qin Jing , Reidys Christian M. , Stadler Peter F. 
Published: August 2009

Abstract
Motivation: The RNA–RNA interaction problem (RIP) consists in finding the energetically optimal structure of two RNA molecules that bind to each other. The standard model allows secondary structures in both partners as well as additional base pairs between the two RNAs subject to certain restrictions that ensure that RIP is solvabale by a polynomial time dynamic programming algorithm. RNA–RNA binding, like RNA folding, is typically not dominated by the ground state structure. Instead, a large ensemble of alternative structures contributes to the interaction thermodynamics.
Results: We present here an O(N6) time and O(N4) dynamics programming algorithm for computing the full partition function for RIP which is based on the combinatorial notion of ‘tight structures’. Albeit equivalent to recent work by H. Chitsaz and collaborators, our approach in addition provides a full-fledged computation of the base pairing probabilities, which relies on the notion of a decomposition tree for joint structures. In practise, our implementation is efficient enough to investigate, for instance, the interactions of small bacterial RNAs and their target mRNAs.
Availability: The program rip is implemented in C. The source code is available for download from http://www.combinatorics.cn/cbpc/rip.html and http://www.bioinf.uni-leipzig.de/Software/rip.html.
Contact: duck@santafe.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Ethical Guidelines in Pandemic Influenza: Recommendations of the Ethics Subcommittee of the Advisory Committee of the Director, Centers for Disease Control and Prevention
Authors: Kinlaw Kathy , Barrett Drue H. , Levine Robert J. 
Published: August 2009

ABSTRACTBecause of the importance of including ethical considerations in planning efforts for pandemic influenza, in February 2005 the Centers for Disease Control and Prevention requested that the Ethics Subcommittee of the Advisory Committee to the Director develop guidance that would serve as a foundation for decision making in preparing for and responding to pandemic influenza. Specifically, the ethics subcommittee was asked to make recommendations regarding ethical considerations relevant to decision making about vaccine and antiviral drug distribution prioritization and development of interventions that would limit individual freedom and create social distancing. The ethics subcommittee identified a number of general ethical considerations including identification of clear goals for pandemic planning, responsibility to maximize preparedness, transparency and public engagement, sound science, commitment to the global community, balancing individual liberty and community interests, diversity in ethical decision making, and commitment to justice. These general ethical considerations are applied to the issues of vaccine and antiviral drug distribution and use of community mitigation interventions. (Disaster Med Public Health Preparedness. 2009;3(Suppl 2):S185–S192)
Comorbid personality disorder predicts suicide after major depression: a 10‐year follow‐up
Authors: Hansen P. E. B. , Wang A. G. , Stage K. B. , Kragh‐Sorensen P. ,   The Danish University Antidepressant Group
Published: August 2009

Objective:  To identify psychopathological predictors for suicide in a population of major depressed Diagnostic Statistical Manual‐III (DSM‐III) in‐patients.Method:  A total of 210 previous participants in multicentre antidepressant drug trials, carried out in a randomized double‐blind design, were followed prospectively through a maximum of 10 years. Patients with a drug or alcohol abuse were excluded. The association between suicide and the pretreatment psychopathological profile was analysed using survival statistics.Results:  The suicide rate for non‐melancholic depressed patients was significantly higher than for melancholic depressed patients. Comorbid personality disorder was independently associated with an increased suicide rate [relative hazard 3.41(CI: 1.15–10.10)].Conclusion:  The study indicates that the non‐melancholic aspect of depression, and especially comorbid personality disorder, is associated with an increased suicidal vulnerability.
Archetype JC virus efficiently propagates in kidney‐derived cells stably expressing HIV‐1 Tat
Authors: Nukuzuma Souichi , Kameoka Masanori , Sugiura Shigeki , Nakamichi Kazuo , Nukuzuma Chiyoko , Miyoshi Isao , Takegami Tsutomu 
Published: August 2009

ABSTRACTPathogenic JCV with rearranged regulatory regions (PML‐type) causes PML, a demyelinating disease, in the brains of immunocompromised patients. On the other hand, archetype JCV persistently infecting the kidney is thought to be converted to PML‐type virus during JCV replication in the infected host under immunosuppressed conditions. In addition, Tat protein, encoded by HIV‐1, markedly enhances the expression of a reporter gene under control of the JCV late promoter.In order to examine the influence of Tat on JCV propagation, we used kidney‐derived COS‐7 cells, which only permit archetype JCV, and established COS‐tat cells, which express HIV‐1 Tat stably. We found that the extent of archetype JCV propagation in COS‐tat cells is significantly greater than in COS‐7 cells. On the other hand, COS‐7 cells express SV40 T antigen, which is a strong stimulator of archetype JCV replication. The expression of SV40 T antigen was enhanced by HIV‐1 Tat slightly according to real‐time RT‐PCR, this was not closely related to JCV replication in COS‐tat cells. The efficiency of JCV propagation depended on the extent of expression of functional Tat. To our knowledge, this is the first report of increased production of archetype JCV in a culture system using cell lines stably expressing HIV‐1 Tat. We propose here that COS‐tat cells are a useful tool for studying the role of Tat in archetype JCV replication in the development of PML.
N‐linked glycan‐dependent interaction of CD63 with CXCR4 at the Golgi apparatus induces downregulation of CXCR4
Authors: Yoshida Takeshi , Ebina Hirotaka , Koyanagi Yoshio 
Published: August 2009

ABSTRACTEfficient downregulation of CXCR4 cell surface expression by introduction of the CD63 gene has previously been reported by us. In the present study, it was found that CD63 and its mutant efficiently interact with CXCR4 in live cells and that CD63‐induced downregulation and interaction are significantly abrogated by the N‐linked glycosylation inhibitor, TM. Furthermore, the downregulation and interaction were clearly attenuated by alternation of all three N‐linked glycosylation sites in CD63. Either CD63 or CD63ΔN formed a complex with CXCR4 at the Golgi apparatus and the late endosomes, while CD63 GD mutants lost the ability to form a complex with CXCR4 exclusively at the Golgi apparatus. These findings suggest that CD63 interacts with CXCR4 through the N‐linked glycans‐portion of the CD63 protein and that the complex induces direction of CXCR4 trafficking to the endosomes/lysosomes, rather than to the plasma membrane. At the Golgi apparatus, there may be lysosome protein (CD63)‐associated machinery that influences trafficking of other membrane proteins.
A new lineage sheds light on the evolutionary history of Potato virus Y
Authors: MOURY BENOIT 
Published: August 2009

SUMMARY Potato virus Y (PVY) is one of the rare plant viruses for which some biological traits (host range and symptomatology) are highly correlated with phylogeny, allowing the reconstruction of the evolutionary history of these traits. In this article, a new lineage of PVY isolates from Chile is described, showing unique genomic and biological properties. This lineage was found to be the sister group of all other PVY isolates and helped in the reconstruction of the ancestral traits and evolutionary history of PVY, suggesting that veinal necrosis in tobacco is an ancestral state and that adaptation to pepper (Capsicum spp.) and potato (Solanum tuberosum) has been modified several times during PVY history.
A novel population of human CD56+ human leucocyte antigen D-related (HLA-DR+) colonic lamina propria cells is associated with inflammation in ulcerative colitis
Authors: Ng S C , Plamondon S , Al-Hassi H O , English N , Gellatly N , Kamm M A , Knight S C , Stagg A J 
Published: August 2009

SummaryUlcerative colitis (UC) involves inappropriate mucosal immune responses to intestinal microbiota. Gut dendritic cells (DC) are central immunoregulators of the response to commensal bacteria, and the subset of CD11c+ cells within the human leucocyte antigen D-related (HLA-DR+) lineage (lin)–/dim population are activated in inflammatory bowel disease. We hypothesized that CD11c- cells within this population may also be involved in intestinal inflammation. HLA-DR+ lin–/dim cells were identified in freshly isolated lamina propria mononuclear cells by multi-colour flow cytometry in 54 UC patients and 22 controls. Proportion and number of CD11c+ and CD11c- cells, and surface expression of activation markers CD40, CD86, Toll-like receptor (TLR)-2, TLR-4, and CD56+[natural killer (NK) marker], were determined. Cytokine production was assessed by intracellular staining. Lamina propria colonic CD11c- HLA-DR+ lin–/dim cells were increased significantly in inflamed and ‘non-inflamed’ UC tissue, compared with control tissue. CD11c+ HLA-DR+ lin–/dim cells were unchanged. Fewer CD11c- cells expressed activation markers and produced intracellular cytokines than their CD11c+ counterparts, and they were weakly stimulatory in mixed leucocyte reactions. Few CD11c- cells expressed blood plasmacytoid DC markers, but a major subset expressed high levels of CD56. CD11c- cells decreased after inflammation resolved. Intestinal inflammation in UC is associated with the presence of cells that share phenotypic features of both DC and NK cells. This novel population of human colonic CD56+ HLA-DR+ cells may play a role in immune regulation or tissue repair. Their increase in quiescent UC may be a marker of subclinical inflammation.
Interactive effects of mycorrhizal fungi, salt stress, and competition on the herbivores of Baccharis halimifolia
Authors: YOUNGINGER BRETT , BARNOUTI JWAN , MOON DANIEL C. 
Published: August 2009

Abstract.1. Plant stress and association with mycorrhizal fungi have been shown to significantly influence plant quality, yet their roles in influencing plant–insect interactions remain unclear. Even less is known about how these factors might interact with or be modified by within‐trophic level interactions.2. In the present study, the results of a factorial field experiment are reported in which the effects of within‐trophic‐level interactions, plant stress, and mycorrhizae on three herbivores of Baccharis halimifolia were examined.3. Plant stress was increased by adding salt to the soil, and availability of mycorrhizal fungi was increased by inoculating plant roots. These treatments were applied to plants with either low or high densities of a competitor (Trirhabda baccharidis).4. For the two leaf miners, Amauromyza maculosa and Liriomyza trifolii, increased soil salinity and high densities of the competitor Trirhabdabaccharidis resulted in significant decreases in density. Neither of these treatments affected the gall maker Neolasioptera lathami.5. Mycorrhizal fungi increased the densities of all three herbivores, possibly by increasing foliar nitrogen levels. For the two leaf miners, there was also evidence that mycorrhizae ameliorated the negative effects of salt stress. There was also evidence that high levels of competition dampened the positive effects of mycorrhizae on the two leaf miners.
Unravelling complexities in benthic food webs using a dual stable isotope (hydrogen and carbon) approach
Authors: DEINES PETER , WOOLLER MATTHEW J. , GREY JONATHAN 
Published: August 2009

Summary1. Stable carbon isotope studies have been an essential component of research regarding the contribution of methane (CH4)‐derived carbon to freshwater food webs and results have suggested that benthic macroinvertebrates in billabongs, streams and lakes may be partially, and in some instances, significantly ‘fuelled’ by methanotrophic biomass. However, the singular use of carbon isotopes can lead to ambiguous interpretations concerning the origin of carbon, especially in systems where phototrophs are likely to be using carbon respired sources and hence show more 13C‐depleted values.2. These uncertainties can be further resolved by the inclusion of additional isotopic data. Stable hydrogen isotopes are being increasingly used in food web studies with a marked advantage that sources may be isotopically distinct by one or two orders of magnitude greater than stable carbon or nitrogen, the isotopes most commonly used to delineate trophic interactions. By using hydrogen as a second biogeochemical tracer we provide further supportive evidence for the assimilation of methanotrophic microbial biomass by chironomid larvae.3. Moreover, the hydrogen and carbon isotope values we found in chironomid tissues appear to reflect the original substrate used during methanogenesis; either acetate fermentation or carbonate reduction. Use of the former tends to result in relatively heavy carbon and light hydrogen isotope values due to kinetic isotope effects, whereas use of the latter results in relatively lighter carbon and heavier hydrogen isotope values.4. We provide preliminary evidence to suggest that hydrogen and carbon isotope values in macroinvertebrates may be used to distinguish between CH4 formation pathways and help to explain inter‐depth and inter‐specific differences between co‐existing chironomid species found in the same lake.
Direct and indirect effects of viral pathogens and the environment on invasive grass fecundity in Pacific Coast grasslands
Authors: Seabloom Eric W. , Borer Elizabeth T. , Jolles Anna , Mitchell Charles E. 
Published: August 2009

Summary 1.  Pathogens can have strong effects on their hosts and can be important determinants of biological invasions. In natural systems, host–pathogen interactions may be mediated by direct environmental effects on pathogen communities and host fitness. 2.  While environmental mediation of host–pathogen interactions has been investigated experimentally and at single sites, there have been few studies tracking pathogen effects on lifetime host fecundity across large naturally occurring environmental gradients. 3.  If environmental factors directly mediate both pathogen transmission and host fecundity, laboratory and local‐scale studies may not predict pathogen effects across large spatial scales. 4.  Here we investigate the relationship between host fecundity and infection by a suite of RNA viral pathogens, by surveying two invasive annual grasses at 18 locations along a 1200‐km latitudinal gradient on the west coast of North America. 5.  Infected hosts of both species had 28–30% lower fecundity than uninfected hosts in our field surveys. However, the correlation of reduced fecundity to infection arose from indirect effects of the environment on both host fecundity and pathogen prevalence, rather than direct effects of the pathogen on the host. Pathogen prevalence was highest at sites where uninfected hosts had lowest fecundity. 6.
Synthesis. In past experimental inoculations, virus infection reduced fecundity of these host species. Against this background, the results of our geographic‐scale survey demonstrate the challenges not only of inferring cause from correlation, but also of extrapolating from local studies and experimental inoculations to larger spatial scales. Our results highlight a need for experimentally manipulating infection across environmental gradients. Such an integrated approach would allow quantification of the fitness impacts of infection, even when the environment directly affects both prevalence and host fecundity.