bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turbulence in supersonic boundary layers at moderate Reynolds number
Authors: Pirozzoli Sergio , Bernardini Matteo 
Published: October 2011

AbstractWe study the organization of turbulence in supersonic boundary layers through large-scale direct numerical simulations (DNS) at${M}_{\infty } = 2$, and momentum-thickness Reynolds number up to${\mathit{Re}}_{{\delta }_{2} } \approx 3900$(corresponding to${\mathit{Re}}_{\tau } \approx 1120$) which significantly extend the current envelope of DNS in the supersonic regime. The numerical strategy relies on high-order, non-dissipative discretization of the convective terms in the Navier–Stokes equations, and it implements a recycling/rescaling strategy to stimulate the inflow turbulence. Comparison of the velocity statistics up to fourth order shows nearly exact agreement with reference incompressible data, provided the momentum-thickness Reynolds number is matched, and provided the mean velocity and the velocity fluctuations are scaled to incorporate the effects of mean density variation, as postulated by Morkovin’s hypothesis. As also found in the incompressible regime, we observe quite a different behaviour of the second-order flow statistics at sufficiently large Reynolds number, most of which show the onset of a range with logarithmic variation, typical of ‘attached’ variables, whereas the wall-normal velocity exhibits a plateau away from the wall, which is typical of ‘detached’ variables. The modifications of the structure of the flow field that underlie this change of behaviour are highlighted through visualizations of the velocity and temperature fields, which substantiate the formation of large jet-like and wake-like motions in the outer part of the boundary layer. It is found that the typical size of the attached eddies roughly scales with the local mean velocity gradient, rather than being proportional to the wall distance, as happens for the wall-detached variables. The interactions of the large eddies in the outer layer with the near-wall region are quantified through a two-point amplitude modulation covariance, which characterizes the modulating action of energetic outer-layer eddies.
Effects of trawling on fish and invertebrates from deep-sea coral facies of Isidella elongata in the western Mediterranean
Authors: Maynou Francesc , Cartes Joan E. 
Published: October 2011

Deep-water corals are known to provide essential habitat for fish and invertebrates along the continental slope in different areas of the world, offering prey to coral predators, protection or attachment substrate to other suspension feeders. In the Mediterranean Sea the coral Isidella elongata (Esper, 1788) characterizes a facies of bathyal compact mud substrates between 500 and 1200 m depth. Based on 4 experimental surveys carried out between 1985 and 2008, we obtained quantitative data on the fauna associated with live coral stands. We show that species richness of invertebrates and crustaceans, as well as abundance and biomass of crustaceans, is higher in areas with large stands of the coral. Some commercial fishery species are also more abundant or reach larger sizes in areas with high density of the coral, particularly the red shrimps Aristeus antennatus (Risso, 1816) and Plesionika martia (A. Milne Edwards, 1883). Trawling over I. elongata facies causes direct impacts on the biological assemblages by removing the habitat-forming corals, decreasing invertebrate species diversity and negatively affecting fisheries production in the long term.
The burden of self-reported acute gastrointestinal illness in Italy: a retrospective survey, 2008–2009
Authors: SCAVIA G. , BALDINELLI F. , BUSANI L. , CAPRIOLI A. 
Published: October 2011

SUMMARYA retrospective telephone survey (n=3490) was conducted in Italy between 2008 and 2009 to estimate the occurrence of self-reported acute gastrointestinal illness (AGI) and to describe subjects' recourse to healthcare, using a symptom-based case definition. Three hundred and ten AGI cases were identified. The annual incidence rate was 1·08 episodes/person-year (95% confidence interval 0·90–1·14). The proportion of subjects consulting physicians was 39·5% while only 0·3% submitted a specimen for laboratory investigation. Risk factors for AGI and medical care-seeking were identified using logistic regression analysis. Females, children and young adults had a significantly higher incidence rate of AGI. Factors associated with medical care-seeking were age <10 years, presence of fever, diarrhoea, and duration of illness >3 days. Our results provide a relevant contribution towards estimating the global burden of AGI using standard methods that ensure a good level of comparability with other studies.
Seroprevalence, correlates and trends of Helicobacter pylori infection in the Israeli population
Authors: MUHSEN K. , COHEN D. , SPUNGIN-BIALIK A. , SHOHAT T. 
Published: October 2011

SUMMARYWe examined the prevalence, correlates and trends of H. pylori infection in Israel using residual sera obtained in 2007–2008 from 1466 Jewish subjects aged 0–77 years and 897 Arabs aged 0–19 years, and in 2000–2001 from 627 Jewish and 575 Arab subjects aged 0–19 years. H. pylori IgG antibodies were measured by ELISA. The age-adjusted H. pylori seroprevalence was 45·2% in Jewish participants. Seropositivity increased with age, reaching 60% at age ⩾50 years and ranged from 24·3% in subjects originating from North America/Western Europe/Australia, to 63·2% in those from Asia/Africa/South America. Among Arabs, H. pylori seroprevalence was 42·1% and reached 65% in adolescents. There was no significant change in seroprevalence between 2000–2001 and 2007–2008. High prevalence of H. pylori was found in Arabs, and in Jews originating from countries of high H. pylori endemicity. These findings are characteristic of countries of diverse ethnic structure and recent immigration.
Childhood adversity and allostatic overload of the hypothalamic–pituitary–adrenal axis: A vulnerability model for depressive disorders
Authors: Wilkinson Paul O. , Goodyer Ian M. 
Published: October 2011

AbstractChildhood adversity is associated with increased risk for onset of depressive episodes. This review will present evidence that allostatic overload of the hypothalamic–pituitary–adrenal axis (HPAA) partially mediates this association. The HPAA is the physiological system that regulates levels of the stress hormone cortisol. First, data from animals and humans has shown that early environmental adversity is associated with long-term dysregulation of the HPAA. This may occur due to permanent epigenetic modification of the glucocorticoid receptor. Second, data from humans has demonstrated that HPAA dysregulation is associated with increased risk of future depression onset in healthy individuals, and pharmacological correction of HPAA dysregulation reduces depressive symptoms. HPAA dysregulation may result in corticoid-mediated abnormalities in neurogenesis in early life and/or neurotoxicity on neural systems that subserve emotion and cognition.
Allostatic and environmental load in toddlers predicts anxiety in preschool and kindergarten
Authors: Buss Kristin A. , Davis Elizabeth L. , Kiel Elizabeth J. 
Published: October 2011

AbstractPsychobiological models of allostatic load have delineated the effects of multiple processes that contribute to risk for psychopathology. This approach has been fruitful, but the interactive contributions of allostatic and environmental load remain understudied in early childhood. Because this developmental period encompasses the emergence of internalizing problems and biological sensitivity to early experiences, this is an important time to examine this process. In two studies, we examined allostatic and environmental load and links to subsequent internalizing and externalizing problems. Study 1 examined relations between load indices and maladjustment, concurrently and at multiple times between age 2 and kindergarten; Study 2 added more comprehensive risk indices in a sample following a group of highly fearful toddlers from 2 to 3 years of age. Results from both studies showed that increased allostatic load related to internalizing problems as environmental risk also increased. Study 2, in addition, showed that fearfulness interacted with allostatic and environmental load indices to predict greater anxiety among the fearful children who had high levels of allostatic and environmental load. Taken together, the findings support a model of risk for internalizing characterized by the interaction of biological and environmental stressors, and demonstrate the importance of considering individual differences and environmental context in applying models of allostatic load to developmental change in early childhood.
Allostasis and the development of internalizing and externalizing problems: Changing relations with physiological systems across adolescence
Authors: Hastings Paul D. , Shirtcliff Elizabeth A. , Klimes-Dougan Bonnie , Allison Amber L. , Derose Laura , Kendziora Kimberley T. , Usher Barbara A. , Zahn-Waxler Carolyn 
Published: October 2011

AbstractAllostasis, or the maintenance of stability through physiological change, refers to the process by which individuals adjust to the continually changing demands that are put upon somatic activity by salient events. Bauer and colleagues proposed that allostasis could be detected through patterns of the joint reactivity of the autonomic nervous system (ANS) and hypothalamic–pituitary–adrenal (HPA) axis system under stressful conditions. We examined the associations between ANS and HPA reactivity and the development of externalizing and internalizing problems over 2 years in a sample of 215 adolescents. The interactions of ANS and HPA reactivity were contemporaneously associated with, and longitudinally predictive of, adolescents' emotional and behavioral problems. Adolescents with symmetrical high reactivity across systems had more internalizing and fewer externalizing problems initially. Over time, both symmetrical and asymmetrical reactivity predicted increasing internalizing problems in girls, depending on the measure of ANS activity that was examined, heart rate, or blood pressure reactivity. Implications for the understanding of allostasis and the dynamic nature of the relations between multiple physiological regulatory systems and adolescents' developing psychopathology are discussed.
Developing and applying a socio-ecological model to the promotion of healthy eating in the school
Authors: Townsend Nick , Foster Charlie 
Published: October 2011

AbstractObjectiveTo develop and apply a socio-ecological model (SEM) for healthy eating in school students, to better understand the association between factors at different levels of the SEM and pupils’ dietary choices.DesignStudent-level data, collected through anonymised questionnaires, included reported dietary choices and correlates to these; data on school approaches to food were collected through postal surveys. We used multilevel analysis to study the association of each level of the SEM on student dietary choice while controlling for factors found at other levels.SettingData were collected from secondary schools in Wales that were a part of the 2005/2006 Health Behaviour in School-aged Children (HBSC) study.SubjectsThe final sample for analysis included data from 6693 students aged 11–16 years and 289 teachers from sixty-four secondary schools in Wales.ResultsStudent interpersonal factors, an individual's social environment, had a greater association with the dietary choices students made for lunch than student intrapersonal characteristics, those that reside within the person, which were found to have a greater association with the dietary choices made outside school. School organisational factors, such as rules and policies, had a greater association with whether students ate unhealthy foods, whereas the community nature of the school had a greater association with the choosing of healthy foods.ConclusionsUsing the SEM and multilevel analysis allowed us to study how factors were associated with the choice of different foods at different times of the day by students. Interventions can use an SEM to target specific correlates and change health outcomes in the school.
How much does the Supplemental Nutrition Assistance Program alleviate food insecurity? Evidence from recent programme leavers
Authors: Nord Mark 
Published: October 2011

AbstractObjectiveTo estimate the effect of the US Supplemental Nutrition Assistance Program (SNAP) on the food security (consistent access to adequate food) of recipients, net of the effect of the self-selection of more food-needy households into the programme.DesignThe food security of current SNAP recipients and recent leavers is compared in cross-sectional survey data, adjusting for economic and demographic differences using multivariate logistic regression methods. A similar analysis in 2-year longitudinal panels provides additional control for selection on unobserved variables based on food security status in the previous year.SettingHousehold survey data collected for the US Department of Agriculture by the US Census Bureau.SubjectsHouseholds interviewed in the Current Population Survey Food Security Supplements from 2001 to 2009.ResultsThe odds of very low food security among households that continued on SNAP through the end of a survey year were 28 % lower than among those that left SNAP prior to the 30-d period during which food security was assessed. In 2-year panels with controls for the severity of food insecurity in the previous year, the difference in odds was 45 %.ConclusionsThe results are consistent with, or somewhat higher than, the estimates from the strongest previous research designs and suggest that the ameliorative effect of SNAP on very low food security is in the range of 20–50 %.
Brief exploration of short and mid‐term timeout effects on basketball scoring according to situational variables
Authors: Sampaio Jaime , Lago‐Peñas Carlos , Gómez Miguel A. 
Published: October 2011

AbstractThe aim of this study was to identify the effects of timeouts on Basketball teams' performance differences, as measured by points scored by the team that calls a timeout and points scored by the opponent team according to game location, the quality of the opponent and the game quarter. Sixty games were analysed using the play‐by‐play game‐related statistics from the Asociación de Clubes de Baloncesto (ACB) League in Spain (2009–2010 season). For each timeout, the points scored in the previous and post 3, 5 and 10 ball possessions were registered for the teams that called the timeout and for the opponents (n=436 and n=427, n=322 and n=319, n=112 and n=110 for 3, 5 and 10 ball possessions, respectively). For the teams that called the timeout, the results reflected positive effects on points scored, with increases of 1.59, 2.10 and 2.29 points during the period within the third, fifth and tenth timeout ball possessions. For the teams that have not called the timeout, the results identified timeout negative effects in points scored, during the period within the third and fifth ball possessions (decreases in points scored of 1.59 and 1.77, respectively). Unexpectedly, the situational variables had little or no effects on points scored, which opens up this important topic for further studies and discussion.
Predicting residue–residue contacts using random forest models
Authors: Li Yunqi , Fang Yaping , Fang Jianwen 
Published: October 2011

Abstract
Motivation: Protein residue–residue contact prediction can be useful in predicting protein 3D structures. Current algorithms for such a purpose leave room for improvement.
Results: We develop ProC_S3, a set of Random Forest algorithm-based models, for predicting residue–residue contact maps. The models are constructed based on a collection of 1490 non–redundant, high-resolution protein structures using &gt;1280 sequence-based features. A new amino acid residue contact propensity matrix and a new set of seven amino acid groups based on contact preference are developed and used in ProC_S3. ProC_S3 delivers a 3-fold cross-validated accuracy of 26.9% with coverage of 4.7% for top L/5 predictions (L is the number of residues in a protein) of long-range contacts (sequence separation ≥24). Further benchmark tests deliver an accuracy of 29.7% and coverage of 5.6% for an independent set of 329 proteins. In the recently completed Ninth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP9), ProC_S3 is ranked as No. 1, No. 3, and No. 2 accuracies in the top L/5, L/10 and best 5 predictions of long-range contacts, respectively, among 18 automatic prediction servers.
Availability: http://www.abl.ku.edu/proc/proc_s3.html.
Contact: jwfang@ku.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
PRINCIPLE: a tool for associating genes with diseases via network propagation
Authors: Gottlieb Assaf , Magger Oded , Berman Igor , Ruppin Eytan , Sharan Roded 
Published: October 2011

Abstract
Summary: PRINCIPLE is a Java application implemented as a Cytoscape plug-in, based on a previously published algorithm, PRINCE. Given a query disease, it prioritizes disease-related genes based on their closeness in a protein–protein interaction network to genes causing phenotypically similar disorders to the query disease.
Availability: Implemented in Java, PRINCIPLE runs over Cytoscape 2.7 or newer versions. Binaries, default input files and documentation are freely available at http://www.cs.tau.ac.il/~bnet/software/PrincePlugin/.
Contact:roded@tau.ac.il; assafgot@tau.ac.il
Arginyl‐Glutamine Dipeptide or Docosahexaenoic Acid Attenuates Hyperoxia‐induced Small Intestinal Injury in Neonatal Mice
Authors: Li Nan , Ma Liya , Liu Xueyan , Shaw Lynn , Calzi Sergio Li , Grant Maria B. , Neu Josef 
Published: October 2011

ABSTRACTBackground and Objective:Supplementation studies of glutamine, arginine, and docosahexaenoic acid (DHA) have established the safety of each of these nutrients in neonates; however, the potential for a more stable and soluble dipeptide, arginyl‐glutamine (Arg‐Gln) or DHA with anti‐inflammatory properties, to exert benefits on hyperoxia‐induced intestinal injury has not been investigated. Arg‐Gln dipeptide has been shown to prevent retinal damage in a rodent model of oxygen‐induced injury. The objective of the present study was to investigate whether Arg‐Gln dipeptide or DHA could also attenuate markers of injury and inflammation to the small intestine in this same model.Methods:Seven‐day‐old mouse pups were placed with their dams in 75% oxygen for 5 days. After 5 days of hyperoxic exposure (P7–P12), pups were removed from hyperoxia and allowed to recover in atmospheric conditions for 5 days (P12–P17). Mouse pups received Arg‐Gln (5 g · kg−1 · day−1) or DHA (5 g · kg−1 · day−1) or vehicle orally started on P12 through P17. Distal small intestine (DSI) histologic changes, myeloperoxidase (MPO), lactate dehydrogenase (LDH), inflammatory cytokines, and tissue apoptosis were evaluated.Results:Hyperoxic mice showed a greater distortion of overall villus structure and with higher injury score (P < 0.05). Arg‐Gln dipeptide and DHA supplementation groups were more similar to the room air control group. Supplementation of Arg‐Gln or DHA reduced hyperoxia‐induced MPO activity (P < 0.05). Supplementation of Arg‐Gln or DHA returned LDH activity to the levels of control. Hyperoxia induced apoptotic cell death in DSIs, and both Arg‐Gln and DHA reversed this effect (P < 0.05).Conclusions:Supplementation with either Arg‐Gln or DHA may limit some inflammatory and apoptotic processes involved in hyperoxic‐induced intestinal injury in neonatal mice.
A Plant Small Polypeptide Is a Novel Component of DNA-Binding Protein Phosphatase 1-Mediated Resistance to Plum pox virus in Arabidopsis
Authors: Castelló María José , Carrasco Jose Luis , Navarrete-Gómez Marisa , Daniel Jacques , Granot David , Vera Pablo 
Published: October 2011

Abstract
DNA-binding protein phosphatases (DBPs) have been identified as a novel class of plant-specific regulatory factors playing a role in plant-virus interactions. NtDBP1 from tobacco (Nicotiana tabacum) was shown to participate in transcriptional regulation of gene expression in response to virus infection in compatible interactions, and AtDBP1, its closest relative in the model plant Arabidopsis (Arabidopsis thaliana), has recently been found to mediate susceptibility to potyvirus, one of the most speciose taxa of plant viruses. Here, we report on the identification of a novel family of highly conserved small polypeptides that interact with DBP1 proteins both in tobacco and Arabidopsis, which we have designated DBP-interacting protein 2 (DIP2). The interaction of AtDIP2 with AtDBP1 was demonstrated in vivo by bimolecular fluorescence complementation, and AtDIP2 was shown to functionally interfere with AtDBP1 in yeast. Furthermore, reducing AtDIP2 gene expression leads to increased susceptibility to the potyvirus Plum pox virus and to a lesser extent also to Turnip mosaic virus, whereas overexpression results in enhanced resistance. Therefore, we describe a novel family of conserved small polypeptides in plants and identify AtDIP2 as a novel host factor contributing to resistance to potyvirus in Arabidopsis.
Review article: the effectiveness of standard triple therapy for Helicobacter pylori has not changed over the last decade, but it is not good enough
Authors: Gisbert J. P. , Calvet X. 
Published: October 2011

Aliment Pharmacol Ther 2011; 34: 1255–1268SummaryBackground  A decrease in the Helicobacter pylori eradication rate after standard triple therapy has been suggested in recent years.Aim  To assess the efficacy of standard triple therapy in the eradication of H. pylori through an epidemiological analysis of all published Spanish trials. A secondary aim was to review the prevalence of clarithromycin resistance in Spain.Methods  Articles on H. pylori eradication in Spain published in peer‐reviewed journals were identified through MEDLINE searches. Studies that included a triple therapy consisting of any proton pump inhibitor with clarithromycin (500 mg b.d.) and amoxicillin (1 g b.d.) for up to 14 days were selected. Spanish studies evaluating the prevalence of clarithromycin resistance were also reviewed. Meta‐analysis was performed using the generic inverse variance method.Results  The pooled eradication rates by year from Spanish studies evaluating the efficacy of the standard triple regimen revealed a relatively constant rate over the years. Overall, the analysis of the 32 studies (4727 patients) showed a mean H. pylori cure rate of 80% (95% CI = 77–82%) by intention‐to‐treat and 83% (81–86%) by per‐protocol. When only peptic ulcer disease or 7‐day regimens were considered, results were similar. Based on 13 studies (3293 patients), mean clarithromycin resistance rate was 8% (5–10%).Conclusion  Although a decrease in the H. pylori eradication rate after triple therapy has been suggested in recent years, cure rates with this regimen did not change in Spain between 1997 and 2008. However, this by no means indicates that the efficacy of standard triple therapy in Spain is acceptable, as it has been calculated to be around only 80%. Therefore, it is evident that new strategies to improve first‐line treatment are urgently needed.