bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and sociodemographic risk factors related to household food security in Aboriginal peoples in Canada
Authors: Willows Noreen D , Veugelers Paul , Raine Kim , Kuhle Stefan 
Published: December 2008

AbstractObjectiveCanada’s Aboriginal population is vulnerable to food insecurity and increasingly lives off-reserve. The Canadian Community Health Survey, Cycle 2.2 Nutrition, was used to compare the prevalence and sociodemographic correlates of food insecurity between non-Aboriginal and off-reserve Aboriginal households.DesignFood insecurity status was based on Health Canada’s revised interpretation of responses to the US Household Food Security Survey Module. Logistic regression was used to assess if Aboriginal households were at higher risk for food insecurity than non-Aboriginal households, adjusting for household sociodemographic factors.SettingCanada.SubjectsHouseholds (n35,107), 1528 Aboriginal and 33 579 non-Aboriginal.ResultsThirty-three per cent of Aboriginal households were food insecure as compared with 9 % of non-Aboriginal households (univariate OR 5·2, 95 % CI 4·2, 6·3). Whereas 14 % of Aboriginal households had severe food insecurity, 3 % of non-Aboriginal households did. The prevalence of sociodemographic risk factors for household food insecurity was higher for Aboriginal households. Aboriginal households were more likely to have three or more children (14 %v. 5 %), be lone-parent households (2 1 %v. 5 %), not have home ownership (52 %v. 31 %), have educational attainment of secondary school or less (43 %v. 26 %), have income from sources other than wages or salaries (38 %v. 29 %), and be in the lowest income adequacy category (33 %v. 12 %). Adjusted for these sociodemographic factors, Aboriginal households retained a higher risk for food insecurity than non-Aboriginal households (OR 2·6, 95 % CI 2·1, 3·2).ConclusionsOff-reserve Aboriginal households in Canada merit special attention for income security and poverty alleviation initiatives.
Vitamin D status of Year 3 children and supplementation through schools with fortified milk
Authors: Graham David , Kira Geoff , Conaglen John , McLennan Stephanie , Rush Elaine 
Published: December 2008

AbstractObjectiveTo evaluate levels of vitamin D3and HDL-cholesterol (HDL-C), and the ratio of HDL-C to LDL-cholesterol (LDL-C), in schoolchildren receiving vitamin-D-fortified, fat-depleted, high-Ca milk in schools.DesignCross-sectional study of previously randomised schools receiving supplemental milk, compared with a matched control group.SettingLow-decile Year 1–6 schools in the Waikato region of New Zealand.SubjectsYear 3 children from either milk schools or control schools, consenting to blood sampling.ResultsFor eighty-nine children receiving supplementary daily milk, vitamin D3levels were significantly higher than in eighty-three control children matched for age, sex, body composition and ethnicity (mean (sd): 49·6 (15·8)v. 43·8 (14·7) nmol/l,P= 0·011), as were HDL-C levels (mean (sd): 1·47 (0·35)v. 1·35 (0·29) mmol/l,P= 0·024) and HDL-C:LDL-C (median: 0·79v. 0·71,P= 0·026). LDL-C levels were similar in both groups (mean (sd): 2·07 (0·55)v. 2·16 (0·60) mmol/l,P= 0·31). Of control children, 32/83 (20·2 %) of the milk group (Pearson’sχ2= 7·00,P= 0·008). Mean 25-hydroxyvitamin D (vitamin D3) levels in the milk group were still below the lower end of the recommended normal range (60 nmol/l).ConclusionsVitamin D3levels are low in low-decile Year 3 children in midwinter. Levels are improved with vitamin-D-fortified milk but still below the recommended range. HDL-C and HDL-C:LDL-C levels are improved in the milk-supplemented group. This supports the supply of vitamin-D-fortified, fat-reduced milk to schools.
Community-specific modifications are essential for objective assessment of maternal dietary intake – Pune Maternal Nutrition Study
Authors: Rao S , Kanade AN , Joshi SR , Yajnik CS 
Published: December 2008

AbstractObjectiveTo introduce community-specific modifications in the conventional 24 h recall method for objectively estimating maternal dietary intake and validate it with a reference method.DesignA modified 24 h recall method was developed with the visit of trained local girls at the subject’s home to weigh portion sizes at each mealtime over the 24 h recall period. This was validated with the reference method in which weighed records of the foods consumed were obtained and their laboratory analysis was done to obtain nutrient intakes.SettingRural areas located 40–50 km from Pune City, India.SubjectsForty-one pregnant women participated willingly.ResultsThe estimates of intake obtained from the reference method were comparable to those obtained from the modified 24 h recall method for energy (7795 (sd1841) kJ (1863 (sd440) kcal)v. 7615 (sd1824) kJ (1820 (sd436) kcal), respectively), protein (48·6 (sd12·9) gv. 45·3 (sd12·6) g, respectively) and fat (35·3 (sd16·6) gv. 36·0 (sd14·2) g, respectively). Significant correlation was observed between the estimates obtained by the two methods for energy (0·75,P< 0·001), protein (0·71,P< 0·001) and fat (0·56,P< 0·001) and differences in nutrient intake did not reveal any systematic bias. When compared with the reference method, the modified method showed >80 % sensitivity and specificity for identifying inadequate maternal energy intakes.ConclusionsSimple modifications to conventional methods backed by understanding of community specifics and nutritional peculiarities are of immense importance in obtaining objective estimates of daily nutritional intakes of individuals in free-living populations. The approach would be adaptable in similar settings in other developing countries.
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors: Hucka Michael , Hoops Stefan , Keating Sarah , Le Novère Nicolas , Sahle Sven , Wilkinson Darren 
Published: December 2008

AbstractWith the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.This is Release 1 of the specification for SBML Level 2 Version 4, describing the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, "http://sbml.org/":http://sbml.org/.
arrayQualityMetrics—a bioconductor package for quality assessment of microarray data
Authors: Kauffmann Audrey , Gentleman Robert , Huber Wolfgang 
Published: December 2008

Abstract
Summary:: The assessment of data quality is a major concern in microarray analysis. arrayQualityMetrics is a Bioconductor package that provides a report with diagnostic plots for one or two colour microarray data. The quality metrics assess reproducibility, identify apparent outlier arrays and compute measures of signal-to-noise ratio. The tool handles most current microarray technologies and is amenable to use in automated analysis pipelines or for automatic report generation, as well as for use by individuals. The diagnosis of quality remains, in principle, a context-dependent judgement, but our tool provides powerful, automated, objective and comprehensive instruments on which to base a decision.
Availability:: arrayQualityMetrics is a free and open source package, under LGPL license, available from the Bioconductor project at www.bioconductor.org. A users guide and examples are provided with the package. Some examples of HTML reports generated by arrayQualityMetrics can be found at http://www.microarray-quality.org
Contact:: audrey@ebi.ac.uk
Supplementary information:: Supplementary data are available at Bioinformatics online.
Variation in neighbouring genes of the dopaminergic and serotonergic systems affects feather pecking behaviour of laying hens
Authors: Flisikowski K. , Schwarzenbacher H. , Wysocki M. , Weigend S. , Preisinger R. , Kjaer J. B. , Fries R. 
Published: December 2008

SummaryFeather pecking is a behavioural disorder of laying hens and has serious animal welfare and economic implications. One of the several aetiological hypotheses proposes that the disorder results from redirected exploratory behaviour. Variation in the gene encoding the dopamine D4 receptor (DRD4) has been shown to be associated with exploratory behaviour in several species, including in a passerine bird species. We therefore considered DRD4 as a candidate gene for feather pecking. We have annotated DRD4 in the chicken genome and have re‐sequenced it in 140 animals belonging to: experimental layer lines divergently selected for high and low propensity to feather pecking; the unselected founder population; and two commercial lines with low and high propensity to feather pecking. We have identified two sub‐haplotypes of DRD4 that are highly significantly associated with feather pecking behaviour in the experimental (P = 7.30 × 10−7) as well as in the commercial lines (P = 2.78 × 10−6). Linkage disequilibrium (LD) extends into a neighbouring gene encoding deformed epidermal autoregulatory factor 1 (DEAF1). The product of DEAF1 regulates the transcription of the gene encoding the serotonin (5‐hydroxytryptamine) 1A receptor. Thus, DEAF1 represents another candidate gene for feather pecking. Re‐sequencing of five animals homozygous for the ‘low‐pecking’ sub‐haplotype and of six animals homozygous for the ‘high‐pecking’ sub‐haplotype delineated an LD block of 14 833 bases spanning the two genes. None of the variants in the LD block is obviously functional. However, the haplotype information will be useful to select against the propensity to feather pecking in chicken and to elucidate the functional implications of the variants.
Depletion of γδ+ T cells increases CD4+ FoxP3 (T regulatory) cell response in coxsackievirus B3‐induced myocarditis
Authors: Huber Sally A. 
Published: December 2008

SummaryCoxsackievirus B3 (CVB3) causes severe myocarditis in BALB/c mice which depends upon CD4+ T helper type 1 [Th1; i.e. interferon‐γ+ (IFN‐γ+)] and γδ+ cells. Depleting γδ+ cells using anti‐γδ antibody suppresses myocarditis and CD4+ IFN‐γ+ cell numbers in the spleen and heart of infected mice while increasing CD4+ FoxP3+ cells. Mice deficient in γδ+ cells have increased numbers of naïve (CD44lo CD62Lhi) and fewer effector (CD44hi CD62lo) memory CD4+ cells than infected γδ+‐cell‐sufficient mice. Virus neutralizing antibody titres are not significantly different between γδ+ T‐cell‐sufficient and ‐deficient animals. To confirm that the memory cell response differs in acutely infected mice lacking γδ+ cells, CD4+ cells were purified and adoptively transferred into naïve recipients, which were rested for 4 weeks then infected with CVB3. Recipients given either 0·5 × 106 or 1·0 × 106 CD4+ from infected donors developed over twice the severity myocarditis and 10‐fold less cardiac virus titre compared with recipients given equivalent numbers of CD4+ cells from infected and γδ+‐cell‐depleted donor animals. Additionally, to show that more functionally active T regulatory cells are present in γδ+ T‐cell‐depleted mice, CD4+ CD25+ and CD4+ CD25− cells were isolated and adoptively transferred into infected recipients. Mice receiving CD4+ CD25+ cells from γδ+ T‐cell‐depleted donors developed significantly less myocarditis and CD4+ Th1 cell responses compared with mice receiving equal numbers of CD4+ CD25+ cells from infected γδ+ T‐cell‐sufficient animals. This study shows that γδ+ cells promote CD4+ IFN‐γ+ acute and memory responses by limiting FoxP3+ T regulatory cell activation.
Restricting activation‐induced cytidine deaminase tumorigenic activity in B lymphocytes
Authors: Casellas Rafael , Yamane Arito , Kovalchuk Alexander L. , Potter Michael 
Published: December 2008

SummaryDNA breaks play an essential role in germinal centre B cells as intermediates to immunoglobulin class switching, a recombination process initiated by activation‐induced cytidine deaminase (AID). Immunoglobulin gene hypermutation is likewise catalysed by AID but is believed to occur via single‐strand DNA breaks. When improperly repaired, AID‐mediated lesions can promote chromosomal translocations (CTs) that juxtapose the immunoglobulin loci to heterologous genomic sites, including oncogenes. Two of the most studied translocations are the t(8;14) and T(12;15), which deregulate cMyc in human Burkitt’s lymphomas and mouse plasmacytomas, respectively. While a complete understanding of the aetiology of such translocations is lacking, recent studies using diverse mouse models have shed light on two important issues: (1) the extent to which non‐specific or AID‐mediated DNA lesions promote CTs, and (2) the safeguard mechanisms that B cells employ to prevent AID tumorigenic activity. Here we review these advances and discuss the usage of pristane‐induced mouse plasmacytomas as a tool to investigate the origin of Igh–cMyc translocations and B‐cell tumorigenesis.
Leptosphaeria maculans avirulence gene AvrLm4‐7 confers a dual recognition specificity by the Rlm4 and Rlm7 resistance genes of oilseed rape, and circumvents Rlm4‐mediated recognition through a single amino acid change
Authors: Parlange Francis , Daverdin Guillaume , Fudal Isabelle , Kuhn Marie‐Line , Balesdent Marie‐Hélène , Blaise Françoise , Grezes‐Besset Bruno , Rouxel Thierry 
Published: December 2008

Summary Leptosphaeria maculans is the ascomycete responsible for one of the most damaging diseases of oilseed rape (Brassica napus), stem canker of crucifers. Both avirulence (AvrLm) genes in the fungus and resistance (Rlm) genes in the plant are genetically clustered. Using a map‐based cloning strategy, we delineated a 238 kb region containing the AvrLm7 locus. Structural features of the region were reminiscent of those previously found on another chromosome for genomic regions encompassing AvrLm1 and AvrLm6, i.e. GC‐equilibrated, gene‐rich isochores alternating with AT‐rich, recombination‐deficient, gene‐poor isochores. These latter corresponded to mosaics of degenerated and truncated transposable elements. AvrLm7 is the only gene located within a 60 kb AT‐rich isochore. It induced resistance responses in plants harbouring either Rlm7 or Rlm4, and was thus renamed AvrLm4‐7. It encodes a 143‐amino‐acid cysteine‐rich protein, predicted to be secreted, and strongly induced during early stages of plant infection. Sequencing and restriction analyses of AvrLm4–AvrLm7 or avrLm4–AvrLm7 alleles in L. maculans field isolates, and targeted point mutagenesis strongly suggested that one single base mutation, leading to the change of a glycine to an arginine residue, was responsible for the loss of AvrLm4 specificity whereas AvrLm7 recognition was unaltered.
Immune and Nervous Systems Share Molecular and Functional Similarities: Memory Storage Mechanism
Authors: Habibi L. , Ebtekar M. , Jameie S. B. 
Published: December 2008

AbstractOne of the most complex and important features of both the nervous and immune systems is their data storage and retrieval capability. Both systems encounter a common and complex challenge on how to overcome the cumbersome task of data management. Because each neuron makes many synapses with other neurons, they are capable of receiving data from thousands of synaptic connections. The immune system B and T cells have to deal with a similar level of complexity because of their unlimited task of recognizing foreign antigens. As for the complexity of memory storage, it has been proposed that both systems may share a common set of molecular mechanisms. Here, we review the molecular bases of memory storage in neurons and immune cells based on recent studies and findings. The expression of certain molecules and mechanisms shared between the two systems, including cytokine networks, and cell surface receptors, are reviewed. Intracellular signaling similarities and certain mechanisms such as diversity, memory storage, and their related molecular properties are briefly discussed. Moreover, two similar genetic mechanisms used by both systems is discussed, putting forward the idea that DNA recombination may be an underlying mechanism involved in CNS memory storage.
Effects of Haemofiltration and Mannitol Treatment on Cardiopulmonary‐Bypass Induced Immunosuppression
Authors: Ziegeler S. , Raddatz A. , Schneider S. O. , Sandmann I. , Sasse H. , Bauer I. , Kubulus D. , Mathes A. , Lausberg H. F. , Rensing H. 
Published: December 2008

AbstractCardiac surgery using cardiopulmonary bypass (CPB) causes a systemic inflammatory response. Additionally, an impairment of the responsiveness of peripheral blood mononuclear cells (PBMC) to further immunological stimuli has been observed. The aim of our present study was to evaluate the ability of antioxidant therapy with mannitol or haemofiltration during CPB to modulate this immunosuppression after CPB. Forty‐five patients undergoing elective heart‐surgery were prospectively enrolled and randomized into three groups (control, mannitol, haemofiltration). Blood samples were taken after induction of anaesthesia (T1), 20 min after CPB (T2) and 24 h post‐operatively (T3). Expression density of the monocytic surface receptor CD14, HLA‐DR expression and cytokine release (TNF‐α and IL10) after lipopolysaccharide‐stimulation were evaluated. At T2, the CD14dim cell population was maintained in both intervention groups while in the control group there was a decrease of this proinflammatory monocytic phenotype. No significant differences regarding HLA‐DR expression or cytokine release could be demonstrated. This study shows that the suppression of the stimulated immune response after CPB can potentially be alleviated by mannitol or haemofiltration in an experimental in‐vitro setting. In the light of data showing that this depression of the immune response might affect the post‐operative course of patients, these results could have a potential clinical relevance.
An Alkaloid Extract of Evanta, Traditionally Used as Anti‐leishmania Agent in Bolivia, Inhibits Cellular Proliferation and Interferon‐γ Production in Polyclonally Activated Cells
Authors: Calla‐Magarinos J. , Giménez A. , Troye‐Blomberg M. , Fernández C. 
Published: December 2008

AbstractTraditional medicine and scientific studies have shown that the raw extract of Evanta [Galipea longiflora, Angostura longiflora (Krause) Kallunki] exhibits anti‐leishmanial activity. We hypothesized that the healing observed when using this plant might not only be due to the direct action on the parasite, but possibly to a parallel effect on the host immune response to the parasite involved in the healing process. We show here that an alkaloid extract of Evanta (AEE) directly killed the parasite already at a dose of 10 μg/ml, but at this low concentration, AEE did not have a major effect on viability and proliferation of eukaryotic cells. The whole extract was also found to be stronger than 2‐phenylquinoline, the most prominent alkaloid in AEE. AEE was not directly stimulating B or T cells or J774 macrophages. However, it interfered with the activation of both mouse and human T cells, as revealed by a reduction of in vitro cellular proliferation and interferon‐gamma (IFN‐γ) production. The effect was more evident when the cells were pretreated with AEE and subsequently stimulated with the polyclonal T‐cell activators Concanavalin A and anti‐CD3. Taken together, our results suggest that Evanta have a direct leishmanicidal effect and due to the effect on IFN‐γ production it might contribute to control the chronic inflammatory reaction that characterize Leishmania infection pathology, but in vivo studies are necessary to corroborate this finding.
The genesis of late Quaternary caliche nodules in Mission Bay, Texas: stable isotopic compositions and palaeoenvironmental interpretation
Authors: ZHOU JIE , CHAFETZ HENRY S. 
Published: December 2008

AbstractCaliche is a fairly widespread pedogenic carbonate that commonly has been used to reconstruct palaeoclimatological conditions. Stable isotopic analyses of three types of caliche nodules from Mission Bay, Texas, provide insights into the values and limitations in palaeoenvironmental interpretations. Soft incipient nodules (type I) and partially lithified chalky nodules (type II), composed of low Mg‐calcite, are in situ pedogenic products in the late Quaternary soils; they represent young to intermediate caliche nodules with no obvious diagenesis and, with constraints, can be used to investigate palaeoenvironmental conditions. The well‐lithified hard nodules (type III) dispersed on the beach and shallow bay exhibit complex shapes, fabrics, mineralogy and geochemical compositions. They are mature nodules that have undergone substantial diagenesis and, therefore, are believed to have lost their initial environmental signatures. The incipient nodules in the presently active grey soil and the older subjacent brown soil display significantly different δ13C values, −8·4 and −4·4‰, respectively, which indicates a change in palaeovegetation from C3/C4 mixed to C3‐dominated flora. The δ13C values probably reflect a marked climate shift from warm and dry to cool and wet conditions in the middle Holocene. However, in the same grey soil, there is a sub‐set of incipient caliche nodules with δ13C values around 0·1‰, which is probably due to the input of localized carbon sources in the soil (e.g. shell fragments). The occurrence of essentially identical nodules appearing from the same modern soil horizon with significantly different δ13C values questions the universal reliability of this type of data for palaeoenvironmental interpretation. This study demonstrates that, whereas the stable isotopic compositions of caliche nodules can be used for palaeoenvironmental reconstruction, diagenesis and the influence of localized carbonate sources in the soils could lead to erroneous interpretations.