bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suicide and Desert Men: The Power and Protection of Kanyirninpa (Holding)
Authors: McCoy Brian 
Published: November 2007

Objective: Fred Myers described kanyirninpa (holding) as a deeply embedded value for desert Aboriginal people. He explained it as authority with nurturance where older people ‘grew up’ and protected younger people. Can a cultural understanding of kanyirninpa provide any insight or response to the high rates of suicide among young Aboriginal men today? Method: This paper draws on qualitative health research that was conducted among desert communities in the southeast Kimberley region of Western Australia between 2001 and 2004. The research was primarily with men and explored cultural understandings of the particular male expressions and praxis of kanyirninpa. The research also occurred at a time when the first suicides of young men, who had grown up within this desert region, were taking place. Results: Research showed that the fracture of kanyirninpa over recent generations has seriously affected key social processes and generational relationships within desert society. This wounding has implications for men's health and can provide an understanding as to why young men attempt self-harm and suicide. However, the social expression of kanyirninpa can also sustain important meanings for young men as they grow up. It can protect them from high-risk behaviour and self-harm. Conclusions: While the experience of suicide continues to deeply wound Aboriginal families and communities, desert people's efforts to sustain and express kanyirninpa offers hope. This is a social process and relationship that can help inform health policy and practice in response to self-harm, suicide ideation and behaviour, particularly for young Aboriginal men.
Intercultural Exchange: An Approach to Training from a Franco-Canadian Perspective
Authors: Parent Roger 
Published: November 2007

Objective: The current challenges of cultural diversity necessitate effective methods for training professionals in health, as well as other sectors, to work with the phenomenon of culture. This paper presents an overview of a semiotic-based approach to training in this regard. Methods: Recent publications by Anti Randviir in semiotics on the textual nature of cultural phenomena and by Annabel Levesque on the healthcare issues of Western, French-speaking Canadians provide the methodological frame and basic cultural reference for the overview. Results: The anthropological definition of culture as a ‘semiotic’, or universe of meaning, offers interdisciplinary common ground for designing practical approaches to cultural analysis, intercultural communication and creativity training. This definition is consistent with convergent findings and research practice in social and cognitive psychology, administrative science, philosophy, ethnography, linguistics and semiotics. Conclusions: Cultural performances such as narrative constitute an effective methodological tool for interdisciplinary data gathering and for analysis of all kinds of cultures: organizational, family, ethnic, regional, transborder, etc. When combined with a functionalist and systemic approach to the study of culture, semiotic approaches to narrative analysis provide useful principles for decoding cultural modes of communication and for designing meaningful change based on cultural specificity.
Hydrogen Peroxide‐Dependent Arteriolar Dilation in Contracting Muscle of Rats Fed Normal and High Salt Diets
Authors: Marvar Paul J. , Hammer Leah W. , Boegehold Matthew A. 
Published: November 2007

ABSTRACTObjective: High dietary salt intake decreases the arteriolar dilation associated with skeletal muscle contraction. Because hydrogen peroxide (H2O2) can be released from contracting muscle fibers, this study was designed to assess the possible contribution of H2O2 to skeletal muscle functional hyperemia and its sensitivity to dietary salt.Methods: The authors investigated the effect of catalase treatment on arteriolar dilation and hyperemia in contracting spinotrapezius muscle of rats fed a normal salt (0.45%, NS) or high salt (4%, HS) diet for 4 weeks. Catalase‐sensitive 2′,7′‐dichlorofluorescein (DCF) fluorescence was measured as an index of H2O2 formation, and the mechanism of arteriolar dilation to H2O2 was probed in each group using pharmacological inhibitors.Results: DCF fluorescence increased with muscle contraction, but not if catalase was present. Catalase also reduced arteriolar dilation and hyperemia during contraction in both dietary groups. Exogenous H2O2 dilated arterioles in both groups, with greater responses in HS rats. Guanylate cyclase inhibition did not affect arteriolar responses to H2O2 in either group, but KCa or KATP channel inhibition equally reduced these responses, and KATP channel inhibition equally reduced functional hyperemia in both groups.Conclusions: These results indicate that locally produced H2O2 contributes to arteriolar dilation and hyperemia in contracting skeletal muscle, and that the effect of H2O2 on arteriolar tone in this vascular bed is mediated largely through K+ channel activation. High dietary salt intake does not reduce the contribution of H2O2 to active hyperemia, or alter the mechanism through which H2O2 relaxes arteriolar smooth muscle.
Genome-wide selection of tag SNPs using multiple-marker correlation
Authors: Hao K. 
Published: November 2007

AbstractMotivations: The tag SNP approach is a valuable tool in whole genome association studies, and a variety of algorithms have been proposed to identify the optimal tag SNP set. Currently, most tag SNP selection is based on two-marker (pairwise) linkage disequilibrium (LD). Recent literature has shown that multiple-marker LD also contains useful information that can further increase the genetic coverage of the tag SNP set. Thus, tag SNP selection methods that incorporate multiple-marker LD are expected to have advantages in terms of genetic coverage and statistical power.Results: We propose a novel algorithm to select tag SNPs in an iterative procedure. In each iteration loop, the SNP that captures the most neighboring SNPs (through pair-wise and multiple-marker LD) is selected as a tag SNP. We optimize the algorithm and computer program to make our approach feasible on today's typical workstations. Benchmarked using HapMap release 21, our algorithm outperforms standard pair-wise LD approach in several aspects. (i) It improves genetic coverage (e.g. by 7.2% for 200 K tag SNPs in HapMap CEU) compared to its conventional pair-wise counterpart, when conditioning on a fixed tag SNP number. (ii) It saves genotyping costs substantially when conditioning on fixed genetic coverage (e.g. 34.1% saving in HapMap CEU at 90% coverage). (iii) Tag SNPs identified using multiple-marker LD have good portability across closely related ethnic groups and (iv) show higher statistical power in association tests than those selected using conventional methods.Availability: A computer software suite, multiTag, has been developed based on this novel algorithm. The program is freely available by written request to the author at ke_hao@merck.comContact: ke_hao@163.comSupplementary information: Supplementary data are available at Bioinformatics online.
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
Authors: Lindgreen Stinus , Gardner Paul P. , Krogh Anders 
Published: November 2007

AbstractMotivation: As more non–coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction.Result: We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency.Availability: Source code available from http://mastr.binf.ku.dk/Contact: stinus@binf.ku.dk
Determination and validation of principal gene products
Authors: Tress Michael L. , Wesselink Jan-Jaap , Frankish Adam , López Gonzalo , Goldman Nick , Löytynoja Ari , Massingham Tim , Pardi Fabio , Whelan Simon , Harrow Jennifer , Valencia Alfonso 
Published: November 2007

Abstract
Motivation: Alternative splicing has the potential to generate a wide range of protein isoforms. For many computational applications and for experimental research, it is important to be able to concentrate on the isoform that retains the core biological function. For many genes this is far from clear.
Results: We have combined five methods into a pipeline that allows us to detect the principal variant for a gene. Most of the methods were based on conservation between species, at the level of both gene and protein. The five methods used were the conservation of exonic structure, the detection of non-neutral evolution, the conservation of functional residues, the existence of a known protein structure and the abundance of vertebrate orthologues. The pipeline was able to determine a principal isoform for 83% of a set of well-annotated genes with multiple variants.
Contact: mtress@cnio.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Fast protein fold estimation from NMR-derived distance restraints
Authors: Ángyán Annamária F. , Perczel András , Pongor Sándor , Gáspári Zoltán 
Published: November 2007

Abstract
Summary: PRIDE-NMR is a fast novel method to relate known protein folds to NMR distance restraints. It can be used to obtain a first guess about a structure being determined, as well as to estimate the completeness or verify the correctness of NOE data.
Availability: The PRIDE-NMR server is available at http://www.icgeb.org/pride
Contact: szpari@chem.elte.hu
Supplementary information: Description of the server and details of the tests presented can be found at http://www.icgeb.org/pride
Modulation of mucosal immunity in a murine model of food‐induced intestinal inflammation
Authors: Cardoso C. R. , Teixeira G. , Provinciatto P. R. , Godoi D. F. , Ferreira B. R. , Milanezi C. M. , Ferraz D. B. , Rossi M. A. , Cunha F. Q. , Silva J. S. 
Published: November 2007

SummaryBackground
Hypersensitivity or uncontrolled responses against dietary antigens can lead to inflammatory disorders like food allergy and current models reflect a variety of causes but do not reveal the detailed modulation of gut immunity in response to food antigens after breakdown in mucosal tolerance.Objective
To develop and characterize a murine model for food‐induced intestinal inflammation and to demonstrate the modulation of gut immune response by dietary allergenic antigens.Methods
C57BL/6 mice were sensitized with peanut proteins, challenged with peanut seeds and their sera and gut segments were collected for subsequent analyses.Results
Sensitization and challenged with peanut seeds led to alterations in gut architecture with inflammatory response characterized by oedema in lamina propria and cell infiltrate composed mainly by eosinophils, mast cells, phagocytes, natural killer and plasma cells, together with low percentage of γδ+ and CD4+CD25+Foxp3+ cells in Peyer's patches. These animals also presented high levels of specific IgE and IgG1 in sera and modulation of mucosal immunity was mediated by increased expression of GATA‐3, IL‐4, IL‐13 and TNF‐α in contrast to low IFN‐γ in the gut.Conclusion
A murine model for food‐induced intestinal inflammation was characterized in which modulation of gut immunity occurs by peanut antigens in consequence of T‐helper type 2 (Th2) allergic response and failure of regulatory mechanisms necessary for mucosa homeostasis, resembling food allergy. This work shed some light on the understanding of the pathogenesis of gastrointestinal disorders and intolerance in the gut and supports the development of therapies for food‐related enteropathies like food allergy, focusing on gut‐specific immune response.
Seed yielding ability of landraces of lucerne in Italy
Authors: Annicchiarico P. , Pecetti L. , Romani M. 
Published: November 2007

AbstractSeed yield is of crucial importance for the marketing of lucerne varieties. Statistical records for farmers’ production of certified seed suggested a slightly higher seed‐yielding ability of Italian landraces over improved varieties (proportionately 0·052). The aims were to: (i) assess the variation among landraces, and compare the germplasm of landrace and improved varieties, for seed‐yielding ability; and (ii) investigate the relationships between seed yield, environment of origin and forage yield of the landraces. Thirteen farm landraces belonging to the seven commercial ecotypes of northern Italy and four improved varieties were evaluated for seed yield in the third cropping year and for herbage yield over twelve harvests. Landraces differed in seed yield and herbage yield (P < 0·05). Landrace material, compared with variety germplasm, showed a non‐significant trend towards higher seed yield (proportionately 0·047) and had similar herbage yield and plant density at the onset of the third cropping year. Seed yield of landraces was unrelated to forage yield and was associated with frequent mowing and earlier year of seed production on its farm of origin.
Seasonal productivity and nutritive value of temperate grasses found in semi‐natural pastures in Europe: responses to cutting frequency and N supply
Authors: Pontes L. S. , Carrère P. , Andueza D. , Louault F. , Soussana J. F. 
Published: November 2007

AbstractMonocultures of thirteen perennial C3 grass species that co‐occur in temperate semi‐natural grassland communities in Europe were compared in a factorial field design of two levels of N supply and two levels of cutting frequency. Above‐ground yield of dry matter (DM), crude protein (CP) concentration and pepsin‐cellulase DM digestibility of herbage were measured in two successive years. Species was the largest source of variability in yield of DM and DM digestibility of herbage, while CP concentration of herbage responded more to management factors. The highest mean DM yields and values of DM digestibility of herbage were achieved in spring for Festuca arundinacea and in autumn for Phleum pratense. Poa trivialis and Festuca rubra had the lowest DM yield and DM digestibility values, respectively, regardless of seasons and treatments. For all species CP concentration in herbage increased in response to an increase in cutting frequency and N supply by an average of 46 and 34 g kg−1 DM respectively. Differences between years and seasons indicated the importance of plant phenology on nutritional variables and the influence of environmental factors on species performance. Species ranking was compared according to their annual digestible DM and CP yields. The results show that some grasses have a nutritive value which is comparable to that of forages selected for high yields.
Inhibition of HIV‐1 transmission in trans from dendritic cells to CD4+ T lymphocytes by natural antibodies to the CRD domain of DC‐SIGN purified from breast milk and intravenous immunoglobulins
Authors: Requena Mary , Bouhlal Hicham , Nasreddine Nadine , Saidi Hela , Gody Jean‐Chrysostome , Aubry Sylvie , Grésenguet Gérard , Kazatchkine Michel D. , Sekaly Rafick‐Pierre , Bélec Laurent , Hocini Hakim 
Published: November 2007

SummaryThe present study demonstrates that human breast milk and normal human polyclonal immunoglobulins purified from plasma [intravenous immunoglobulins (IVIg)] contain functional natural immunoglobulin A (IgA) and IgG antibodies directed against the carbohydrate recognition domain (CRD) domain of the dendritic cell‐specific intercellular adhesion molecule‐3‐grabbing non‐integrin (DC‐SIGN) molecule, which is involved in the binding of human immunodeficiency virus (HIV)‐1 to dendritic cells (DCs). Antibodies to DC‐SIGN CRD were affinity‐purified on a matrix to which a synthetic peptide corresponding to the N‐terminal CRD domain (amino‐acid 342–amino‐acid 371) had been coupled. The affinity‐purified antibodies bound to the DC‐SIGN peptide and to the native DC‐SIGN molecule expressed by HeLa DC‐SIGN+ cells and immature monocyte‐derived dendritic cells (iMDDCs), in a specific and dose‐dependent manner. At an optimal dose of 200 µg/ml, natural antibodies to DC‐SIGN CRD peptide purified from breast milk and IVIg stained 25 and 20% of HeLa DC‐SIGN+ cells and 32 and 12% of iMDDCs, respectively. Anti‐DC‐SIGN CRD peptide antibodies inhibited the attachment of virus to HeLa DC‐SIGN by up to 78% and the attachment to iMDDCs by only 20%. Both breast milk‐ and IVIg‐derived natural antibodies to the CRD peptide inhibited 60% of the transmission in trans of HIV‐1JRCSF, an R5‐tropic strain, from iMDDCs to CD4+ T lymphocytes. Taken together, these observations suggest that the attachment of HIV to DCs and transmission in trans to autologous CD4+ T lymphocytes occur through two independent mechanisms. Our data support a role of natural antibodies to DC‐SIGN in the modulation of postnatal HIV transmission through breast‐feeding and in the natural host defence against HIV‐1 in infected individuals.
Appetite stimulants in cystic fibrosis: a systematic review
Authors: Chinuck R. S. , Fortnum H. , Baldwin D. R. 
Published: November 2007

AbstractBackground  The use of appetite stimulants in cystic fibrosis (CF) is controversial because of doubts concerning efficacy and side‐effects. The aim of the review was to establish whether appetite stimulants should be recommended in CF.Materials and methods  Medline, AMED, British Nursing Index, Cinahl, Embase, The Cochrane Library, National Research Register and Google were searched. Unpublished studies, case reports and conference abstracts were sought from experts, including authors of identified published articles, and suppliers of appetite stimulants.Results  Fifty‐four articles were located. Fifteen studies were suitable for inclusion in the review: 10 studied, megesterol acetate (MA); 1, dronabinol; 2, mirtazapine; and 2, cyproheptadine. MA showed a beneficial effect on lung function, weight, appetite, fat free and fat mass. Adverse effects for MA included adrenal suppression, abnormalities of glycaemic control, mood changes and testicular failure. There was no consistency in the dose, frequency and duration of therapy for MA.Conclusions  The review shows MA may have a role in the management of anorexia associated with CF. It is not possible to be conclusive for the other agents given the low numbers in the studies. Larger randomized, controlled trials of MA are necessary to confirm its safety and validate efficacy in CF.
PilO of Pseudomonas aeruginosa 1244: subcellular location and domain assignment
Authors: Qutyan Mohammed , Paliotti Michael , Castric Peter 
Published: November 2007

SummaryPilO of Pseudomonas aeruginosa 1244 catalyses the attachment of an O‐antigen repeating unit to the β‐carbon of the pilin C‐terminal residue, a serine. The present study was conducted to locate the regions of this enzyme important in catalysis and to establish the cellular location of the pilin glycosylation reaction. While PilO was not detectable in extracts of P. aeruginosa or Escherichia coli, even under conditions of overexpression, it was found that an intact MalE–PilO fusion protein was produced in significant amounts. This fusion complemented a P. aeruginosa 1244 mutant containing a pilO deletion and targeted to the cytoplasmic membrane of E. coli. Wzy and WaaL, enzymes that also utilize the O‐antigen repeating unit as substrate, were found to share a sequence pattern with PilO even though these proteins have little overall sequence similarity. PilO constructs in which portions of this common sequence were deleted or altered by site‐directed mutagenesis lacked pilin glycosylating activity. Deletions of segments downstream from the common region also prevented enzyme activity. Topology studies showed that the two PilO regions associated with enzyme activity were located in the periplasm. These results establish regions of this enzyme important for catalysis and present evidence that pilin glycosylation occurs in the periplasmic space of this organism.
SipC multimerization promotes actin nucleation and contributes to Salmonella‐induced inflammation
Authors: Chang JiHoon , Myeni Sebenzile K. , Lin Tsang Long , Wu Ching Ching , Staiger Chris J. , Zhou Daoguo 
Published: November 2007

SummaryActin nucleation is the rate‐limiting step in actin assembly and is regulated by actin‐binding proteins and signal transduction molecules. Salmonella enterica serovar Typhimurium exploits actin dynamics by reorganizing the host actin cytoskeleton to facilitate its own uptake. SipC is a Salmonella actin‐binding protein that nucleates actin filament formation in vitro. The molecular mechanism by which SipC nucleates actin is not known. We show here that SipC199–409 forms multimers to promote actin nucleation. We found that wild‐type SipC199–409 forms dimers and multimers while SipC199–409#1, a nucleation mutant, is less efficient in dimer and multimer formation. Biochemical analysis suggested that SipC199–409 might form parallel dimers in an extended conformation. Furthermore, a mutant Salmonella strain that was defective in forming the SipC multimer and deficient in actin nucleation failed to cause severe colitis in a mouse model. These results allow us to present a model in which SipC forms multimers to promote actin nucleation.
CD69 upregulation on T cells as an in vitro marker for delayed‐type drug hypersensitivity
Authors: Beeler A. , Zaccaria L. , Kawabata T. , Gerber B. O. , Pichler W. J. 
Published: November 2007

Background:  T cells play a key role in delayed‐type drug hypersensitivity reactions. Their reactivity can be assessed by their proliferation in response to the drug in the lymphocyte transformation test (LTT). However, the LTT imposes limitations in terms of practicability, and an alternative method that is easier to implement than the LTT would be desirable.Methods:  Four months to 12 years after acute drug hypersensitivity reactions, CD69 upregulation on T cells of 15 patients and five healthy controls was analyzed by flow cytometry.Results:  All 15 LTT‐positive patients showed a significant increase of CD69 expression on T cells after 48 h of drug‐stimulation exclusively with the drugs incriminated in drug‐hypersensitivities. A stimulation index of 2 as cut‐off value allowed discrimination between nonreactive and reactive T cells in LTT and CD69 upregulation. T cells (0.5–3%) showed CD69 up‐regulation. The reactive cell population consisted of a minority of truly drug reactive T cells secreting cytokines and a higher number of bystander T cells activated by IL‐2 and possibly other cytokines.Conclusions:  CD69 upregulation was observed after 2 days in all patients with a positive LTT after 6 days, thus appearing to be a promising tool to identify drug‐reactive T cells in the peripheral blood of patients with drug‐hypersensitivity reactions.