bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of a 2-year healthy eating and physical activity intervention for 3–6-year-olds in communities of high and low socio-economic status: the POP (Prevention of Overweight among Pre-school and school children) project
Authors: De Coen Valerie , De Bourdeaudhuij Ilse , Vereecken Carine , Verbestel Vera , Haerens Leen , Huybrechts Inge , Van Lippevelde Wendy , Maes Lea 
Published: March 2012

AbstractObjectiveThe purpose of the present study was to evaluate the effects of a school-based, 2-year, multi-component intervention on BMI, eating and physical activity behaviour in Flanders, Belgium, targeting children aged 3–6 years in communities of high and low socio-economic status (SES).DesignCluster-randomized controlled trial.SettingThirty-one pre-primary and primary schools in three different intervention communities and three paired-matched (on SES profile) control communities in Flanders, Belgium.SubjectsBMI Z-scores at baseline and follow-up were calculated for 1102 children. Questionnaires with sociodemographic data and FFQ were available from 694 of these 1102 children.ResultsNo significant effects were found on BMI Z-scores for the total sample. However, there was a significant decrease in BMI Z-score of 0·11 in the low-SES intervention community compared with the low-SES control community, where the BMI Z-score increased by 0·04 (F = 6·26, P = 0·01). No significant intervention effects could be found for eating behaviour, physical activity or screen-time. There were no significant interaction effects of age and gender of the children on the outcome variables.ConclusionsAlthough no significant effects were found for BMI Z-scores in the total sample, this intervention had a promising effect in the low-SES community of reducing excess weight gain among young children.
Listeria monocytogenes and diet during pregnancy; balancing nutrient intake adequacy v. adverse pregnancy outcomes
Authors: Pezdirc Kristine B , Hure Alexis J , Blumfield Michelle L , Collins Clare E 
Published: March 2012

AbstractObjectiveTo evaluate the impact of adherence to public health recommendations on Listeria monocytogenes food safety to limit exposure to potential food sources on micronutrient intakes of pregnant women and whether more frequent consumption of ‘high-risk’ foods increases risk for adverse pregnancy outcomes.DesignA cohort study in women assessing Listeria exposure from an FFQ based on consumption of potential Listeria-containing food sources, the Listeria Food Exposure Score (LFES). Pregnancy status was defined as pregnant, trying to conceive, had a baby within the previous 12 months, or other. Nutrient intakes were compared with Nutrient Reference Values and self-reported pregnancy outcome history three years later.SettingAustralia.SubjectsWomen aged 25–30 years (n 7486) participating in the Australian Longitudinal Study on Women's Health.ResultsThere were weak positive correlations (r = 0·13–0·37, P < 0·001) between LFES and all nutrients, with fibre, folate, Fe and vitamin E intakes consistently below the Nutrient Reference Values in every quintile of LFES. Women in the highest quintile of LFES reported 19 % more miscarriages (rate ratio = 1·19; 95 % CI 1·02, 1·38) than those in the lowest quintile, after adjusting for important confounding factors.ConclusionsMore frequent consumption of foods potentially containing L. monocytogenes is associated with higher nutrient intakes, but an increased risk of miscarriage. L. monocytogenes pregnancy recommendations require review and should include the list of ‘risky’ food items in addition to low-risk alternatives that would adequately replace nutrient intakes which may be reduced through avoidance strategies.
Outsourcing, Offshoring, Nearshoring, Onshoring – What's Going On?
Authors: Worley Loyita 
Published: March 2012

AbstractLoyita Worley outlines recent developments among law firms where outsourcing has been embraced in relation to their library, information and knowledge functions and services. She defines the terms and themes of the subject – outsourcing, offshoring, nearshoring and onshoring – and offers some thoughts for the future of legal information services in the commercial sector.
Genetic diversity of bean (Phaseolus) landraces and wild relatives from the primary centre of origin of the Southern Andes
Authors: Avila Teresa , Blair Matthew W. , Reyes Ximena , Bertin Pierre 
Published: March 2012

The Southern Andes, especially the inter-Andean valleys of south Bolivia, is thought to be a probable point of domestication within the primary centre of diversity for Andean common beans (Phaseolus vulgarisL.). The nationalPhaseolusgermplasm collection of Bolivia is maintained by the Pairumani Foundation and consists of 449 accessions where most of the accessions are of common bean but some are of related cultivated and wild species. The goal of this study was to determine the genetic diversity of this collection by sampling 174 accessions ofP. vulgarisand an outgroup of eightPhaseolus augusti, twoPhaseolus lunatusand onePhaseolus coccineusgenotype. The genetic diversity and population structure were estimated using 29 microsatellite markers. High levels of polymorphism were found, with a total of 311 alleles identified and an average of 10.7 alleles per marker. Correspondence analysis and an unweighted pair group method with arithmetic mean-based dendrogram distinguishedP. vulgarisfrom the other species ofPhaseolus. Common bean accessions were separated into two groups: the first one including Andean controls and most accessions from high altitudes with morphological characteristics and growth habits typical of this gene pool; the second one including Mesoamerican controls and accessions from low altitudes. Inside the Andean gene pool, the wild accessions were diverse and separated from the weedy and cultivated accessions. Low geographical distances between collection sites (up to 100 km) were shown to be related to low genetic distances. These results are important for the conservation of common beans in the Southern Andes.
Evaluation of momentum and sensible heat fluxes in constant density coordinates: Application to superpressure balloon data during the VORCORE campaign
Authors: Walterscheid R. L. , Gelinas L. J. , Mechoso C. R. , Schubert G. 
Published: March 2012

Expressions for momentum and heat fluxes using density as the vertical coordinate are derived. These are applied in the evaluation of fluxes using data from super‐pressure balloons drifting on constant density surfaces in the Antarctic lower stratosphere during the VORCORE campaign (September 2005 to February 2006). We focus on the core months of October and November. Vertical fluxes of zonal and meridional momentum are calculated using wind, pressure and height data and the vertical flux of sensible heat is calculated using temperature and height data. Calculations were performed in three band passes covering 1–13 h. We find that the largest fluxes are in the vicinity of the Antarctic Peninsula. In October the fluxes in the low period band pass (1–5 h) account for the main part of the total flux of zonal momentum, consistent with topographically forced waves. During November the vertical fluxes of zonal momentum are found mainly in longer period band passes, consistent with weaker winds. The peak campaign‐averaged flux of zonal momentum in the vicinity of the Antarctic Peninsula is ∼−30 mPa. These values are ∼60% larger over the peninsula than those inferred by other authors. The flux of zonal momentum provides a zonal body force of ∼5 m s−1 day−1 assuming a saturated spectrum. We infer downward sensible heat fluxes of ∼3 W m−2. The corresponding cooling rates assuming a saturated spectrum are ∼0.6 K day−1, a significant fraction of the net radiative imbalance in the springtime Antarctic lower stratosphere.
Direct measurement of volume flux in the Faroe‐Shetland Channel and over the Iceland‐Faroe Ridge
Authors: Rossby T. , Flagg C. N. 
Published: March 2012

Determining the exchange of water across the Iceland‐Faroe‐Scotland ridge is of fundamental interest because it measures the rate of transformation of North Atlantic water into dense water and thus the strength of the meridional overturning circulation (MOC). Here we study this exchange by monitoring all water flowing through the area east of Iceland to near the bottom or ∼600 m depth using a 75 kHz acoustic Doppler current profiler (ADCP) mounted on the high‐seas ferry M/F Norröna. Starting in March 2008, currents have been measured in the Faroe‐Shetland Channel (FSC) and along the Iceland‐Faroe Ridge (IFR) on the ferry's weekly round‐trips between Iceland and Denmark. The detided average transports (to the north) across the two sections are 4.1 ± 0.1 Sv (106 m2s−1) through the FSC and 4.4 ± 0.25 Sv across the IFR (this excludes ∼1.6 Sv circulating around the Faroes). The Norröna program is ongoing.
Ecological niche models reveal the importance of climate variability for the biogeography of protosteloid amoebae
Authors: Aguilar María , Lado Carlos 
Published: March 2012

Abstract
Habitat availability and environmental preferences of species are among the most important factors in determining the success of dispersal processes and therefore in shaping the distribution of protists. We explored the differences in fundamental niches and potential distributions of an ecological guild of slime moulds—protosteloid amoebae—in the Iberian Peninsula. A large set of samples collected in a north-east to south-west transect of approximately 1000 km along the peninsula was used to test the hypothesis that, together with the existence of suitable microhabitats, climate conditions may determine the probability of survival of species. Although protosteloid amoebae share similar morphologies and life history strategies, canonical correspondence analyses showed that they have varied ecological optima, and that climate conditions have an important effect in niche differentiation. Maxent environmental niche models provided consistent predictions of the probability of presence of the species based on climate data, and they were used to generate maps of potential distribution in an ‘everything is everywhere’ scenario. The most important climatic factors were, in both analyses, variables that measure changes in conditions throughout the year, confirming that the alternation of fruiting bodies, cysts and amoeboid stages in the life cycles of protosteloid amoebae constitutes an advantage for surviving in a changing environment. Microhabitat affinity seems to be influenced by climatic conditions, which suggests that the micro-environment may vary at a local scale and change together with the external climate at a larger scale.
Molecular evidence of iron limitation and availability in the global diazotroph Trichodesmium
Authors: Chappell Phoebe Dreux , Moffett James W , Hynes Annette M , Webb Eric A 
Published: March 2012

Abstract
The activity of the N2-fixing cyanobacterial genus Trichodesmium is critical to the global nitrogen (N) and carbon (C) cycles. Although iron (Fe) has been shown to be an important element limiting the growth and N2 fixation of Trichodesmium, there have been no specific data demonstrating the in situ affect of Fe on Trichodesmium. We surveyed Trichodesmium populations from the Atlantic and Pacific Oceans for Fe limitation using a novel quantitative reverse transcriptase-PCR (qRT-PCR) method monitoring the expression of an Fe limitation-induced gene, isiB. Here we report the first molecular evidence of in situ Fe limitation of Trichodesmium N2 fixation, which was evident in samples from the Pacific Ocean, whereas limitation appeared minimal to nonexistent in Atlantic Ocean samples. As our method is Trichodesmium clade specific, we were also able to determine that representatives from the Trichodesmium tenue clade were the most biologically active group of Trichodesmium in the majority of our samples, which speaks to their dominance in open ocean regimes. Furthermore, comparisons of our field expression and chemical data with laboratory studies suggest that the majority of dissolved Fe in the open ocean is available to Trichodesmium colonies regardless of Fe complexation.
Archaea in metazoan diets: implications for food webs and biogeochemical cycling
Authors: Thurber Andrew R , Levin Lisa A , Orphan Victoria J , Marlow Jeffrey J 
Published: March 2012

Abstract
Although the importance of trophic linkages, including ‘top-down forcing’, on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ13C=−92±4‰; polar lipids −116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as ‘archivory’.
An activity-based probe reveals dynamic protein–protein interactions mediating IGF-1R transactivation by the GABAB receptor
Authors: Lin Xin , Li Xin , Jiang Ming , Chen Linhai , Xu Chanjuan , Zhang Wenhua , Zhao Han , Sun Bing , Xu Xiaoli , Nan Fajun , Liu Jianfeng 
Published: March 2012

Many GPCRs (G-protein-coupled receptors) can activate RTKs (receptor tyrosine kinases) in the absence of RTK ligands, a phenomenon called transactivation. However, the underlying molecular mechanisms remain undefined. In the present study we investigate the molecular basis of GABAB (γ-aminobutyric acid B) receptor-mediated transactivation of IGF-1R (insulin-like growth factor type I receptor) in primary neurons. We take a chemical biology approach by developing an activity-based probe targeting the GABAB receptor. This probe enables us first to lock the GABAB receptor in an inactive state and then activate it with a positive allosteric modulator, thereby permitting monitoring of the dynamic of the protein complex associated with IGF-1R transactivation. We find that activation of the GABAB receptor induces a dynamic assembly and disassembly of a protein complex, including both receptors and their downstream effectors. FAK (focal adhesion kinase), a non-RTK, plays a key role in co-ordinating this dynamic process. Importantly, this dynamic of the GABAB receptor-associated complex is critical for transactivation and transactivation-dependent neuronal survival. The present study has identified an important mechanism underlying GPCR transactivation of RTKs, which was enabled by a new chemical biology tool generally applicable for dissecting GPCR signalling.
Urinary corticosteroid excretion predicts left ventricular mass and proteinuria in chronic kidney disease
Authors: McQuarrie Emily P. , Freel E. Marie , Mark Patrick B. , Fraser Robert , Patel Rajan K. , Dargie Henry G. , Connell John M. C. , Jardine Alan G. 
Published: March 2012

Blockade of the MR (mineralocorticoid receptor) in CKD (chronic kidney disease) reduces LVMI [LV (left ventricular) mass index] and proteinuria. The MR can be activated by aldosterone, cortisol and DOC (deoxycorticosterone). The aim of the present study was to explore the influence of mineralocorticoids on LVMI and proteinuria in patients with CKD. A total of 70 patients with CKD and 30 patients with EH (essential hypertension) were recruited. Patients underwent clinical phenotyping; biochemical assessment and 24 h urinary collection for THAldo (tetrahydroaldosterone), THDOC (tetrahydrodeoxycorticosterone), cortisol metabolites (measured using GC–MS), and urinary electrolytes and protein [QP (proteinuira quantification)]. LVMI was measured using CMRI (cardiac magnetic resonance imaging). Factors that correlated significantly with LVMI and proteinuria were entered into linear regression models. In patients with CKD, significant predictors of LVMI were male gender, SBP (systolic blood pressure), QP, and THAldo and THDOC excretion. Significant independent predictors on multivariate analysis were THDOC excretion, SBP and male gender. In EH, no association was seen between THAldo or THDOC and LVMI; plasma aldosterone concentration was the only significant independent predictor. Significant univariate determinants of proteinuria in patients with CKD were THAldo, THDOC, USod (urinary sodium) and SBP. Only THAldo excretion and SBP were significant multivariate determinants. Using CMRI to determine LVMI we have demonstrated that THDOC is a novel independent predictor of LVMI in patients with CKD, differing from patients with EH. Twenty-four hour THAldo excretion is an independent determinant of proteinuria in patients with CKD. These findings emphasize the importance of MR activation in the pathogenesis of the adverse clinical phenotype in CKD.
Evolutionary inaccuracy of pairwise structural alignments
Authors: Sadowski M. I. , Taylor W. R. 
Published: March 2012

AbstractMotivation: Structural alignment methods are widely used to generate gold standard alignments for improving multiple sequence alignments and transferring functional annotations, as well as for assigning structural distances between proteins. However, the correctness of the alignments generated by these methods is difficult to assess objectively since little is known about the exact evolutionary history of most proteins. Since homology is an equivalence relation, an upper bound on alignment quality can be found by assessing the consistency of alignments. Measuring the consistency of current methods of structure alignment and determining the causes of inconsistencies can, therefore, provide information on the quality of current methods and suggest possibilities for further improvement.Results: We analyze the self-consistency of seven widely-used structural alignment methods (SAP, TM-align, Fr-TM-align, MAMMOTH, DALI, CE and FATCAT) on a diverse, non-redundant set of 1863 domains from the SCOP database and demonstrate that even for relatively similar proteins the degree of inconsistency of the alignments on a residue level is high (30%). We further show that levels of consistency vary substantially between methods, with two methods (SAP and Fr-TM-align) producing more consistent alignments than the rest. Inconsistency is found to be higher near gaps and for proteins of low structural complexity, as well as for helices. The ability of the methods to identify good structural alignments is also assessed using geometric measures, for which FATCAT (flexible mode) is found to be the best performer despite being highly inconsistent. We conclude that there is substantial scope for improving the consistency of structural alignment methods.Contact: msadows@nimr.mrc.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
AntigenMap 3D: an online antigenic cartography resource
Authors: Barnett J. Lamar , Yang Jialiang , Cai Zhipeng , Zhang Tong , Wan Xiu-Feng 
Published: March 2012

Abstract
Summary: Antigenic cartography is a useful technique to visualize and minimize errors in immunological data by projecting antigens to 2D or 3D cartography. However, a 2D cartography may not be sufficient to capture the antigenic relationship from high-dimensional immunological data. AntigenMap 3D presents an online, interactive, and robust 3D antigenic cartography construction and visualization resource. AntigenMap 3D can be applied to identify antigenic variants and vaccine strain candidates for pathogens with rapid antigenic variations, such as influenza A virus.
Availability and implementation: http://sysbio.cvm.msstate.edu/AntigenMap3D
Contact: wan@cvm.msstate.edu; wanhenry@yahoo.com
The Autoregulation Gene SUNN Mediates Changes in Root Organ Formation in Response to Nitrogen through Alteration of Shoot-to-Root Auxin Transport
Authors: Jin Jian , Watt Michelle , Mathesius Ulrike 
Published: March 2012

Abstract
We tested whether a gene regulating nodule number in Medicago truncatula, Super Numeric Nodules (SUNN ), is involved in root architecture responses to carbon (C) and nitrogen (N) and whether this is mediated by changes in shoot-to-root auxin transport. Nodules and lateral roots are root organs that are under the control of nutrient supply, but how their architecture is regulated in response to nutrients is unclear. We treated wild-type and sunn-1 seedlings with four combinations of low or increased N (as nitrate) and C (as CO2) and determined responses in C/N partitioning, plant growth, root and nodule density, and changes in auxin transport. In both genotypes, nodule density was negatively correlated with tissue N concentration, while only the wild type showed significant correlations between N concentration and lateral root density. Shoot-to-root auxin transport was negatively correlated with shoot N concentration in the wild type but not in the sunn-1 mutant. In addition, the ability of rhizobia to alter auxin transport depended on N and C treatment as well as the SUNN gene. Nodule and lateral root densities were negatively correlated with auxin transport in the wild type but not in the sunn-1 mutant. Our results suggest that SUNN is required for the modulation of shoot-to-root auxin transport in response to altered N tissue concentrations in the absence of rhizobia and that this controls lateral root density in response to N. The control of nodule density in response to N is more likely to occur locally in the root.