bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients
Authors: Staquicini Fernanda I. , Cardó-Vila Marina , Kolonin Mikhail G. , Trepel Martin , Edwards Julianna K. , Nunes Diana N. , Sergeeva Anna , Efstathiou Eleni , Sun Jessica , Almeida Nalvo F. , Tu Shi-Ming , Botz Gregory H. , Wallace Michael J. , O’Connell David J. , Krajewski Stan , Gershenwald Jeffrey E. , Molldrem Jeffrey J. , Flamm Anne L. , Koivunen Erkki , Pentz Rebecca D. , Dias-Neto Emmanuel , Setubal João C. , Cahill Dolores J. , Troncoso Patricia , Do Kim-Ahn , Logothetis Christopher J. , Sidman Richard L. , Pasqualini Renata , Arap Wadih 
Published: November 2011

Molecules differentially expressed in blood vessels among organs or between damaged and normal tissues, are attractive therapy targets; however, their identification within the human vasculature is challenging. Here we screened a peptide library in cancer patients to uncover ligand-receptors common or specific to certain vascular beds. Surveying ∼2.35 × 10
6
motifs recovered from biopsies yielded a nonrandom distribution, indicating that systemic tissue targeting is feasible. High-throughput analysis by similarity search, protein arrays, and affinity chromatography revealed four native ligand-receptors, three of which were previously unrecognized. Two are shared among multiple tissues (integrin α4/annexin A4 and cathepsin B/apolipoprotein E3) and the other two have a restricted and specific distribution in normal tissue (prohibitin/annexin A2 in white adipose tissue) or cancer (RAGE/leukocyte proteinase-3 in bone metastases). These findings provide vascular molecular markers for biotechnology and medical applications.
WORK ORIENTATIONS IN FLUX?
Authors: Turunen Teemu 
Published: November 2011

ABSTRACT
In this article, subjective work goals are studied comparatively among employees in five European countries: Finland, Germany, Great Britain, Spain, and Sweden. Inglehart (2008), West European Politics 31) has claimed that a cultural shift from survival values to self-expression values also brings changing values concerning work in advanced western societies. Inglehart's thesis is tested empirically in this article by using pooled data from World Values Surveys and European Values Studies collected in 1990–1999/2000. The results do not show a clear shift from survival values to self-expression values in work goals, which contradicts Inglehart's thesis. However, there was some support for Inglehart's claims in the data. The results also pointed to differences, as well as some similarities, between these European countries regarding work goals. Advanced western countries should not then be treated as a homogenous category in future research on work goals. The support for intrinsic work goals was also analysed using four independent variables: birth cohort, gender, social class, and job satisfaction. Social class was the main individual determinant of intrinsic work goals in most of the research countries. Higher social classes valued intrinsic work goals more than lower social classes did.
Counsellors’ experiences of working with male victims of female‐perpetrated domestic abuse
Authors: Hogan Kevin F. , Hegarty John R. , Ward Tony , Dodd Lorna J. 
Published: November 2011

AbstractAim:To provide an understanding of counsellors’ experiences of working with male victims of female‐perpetrated domestic abuse. This topic has been virtually unexplored within counselling literature.Method:A qualitative design was adopted to address the objective of this research. Semi‐structured interviews were conducted with six counsellors. Snowball sampling was used to identify suitable participants. Three were males and three females, and all had experience of working with male victims of female‐perpetrated domestic abuse. Results were analysed using Interpretative Phenomenological Analysis (IPA).Findings:Ten over‐arching themes emerged from the transcripts, including a distinct lack of recognition of male victimisation, which was seen as hampering counsellors’ work with clients. Participants, particularly female counsellors, also drew on the significance of their gender. Furthermore, counsellors described changes in their perceptions of women within modern society. A central feature of participants’ accounts was a sense of privilege in sharing clients’ experiences. However, participants described the work as challenging, and employed both personal and professional strategies to help them cope with work‐related difficulties.Discussion:Findings offer an initial understanding as to the experiences of counsellors that have worked with male victims. This may be helpful in leading to the development of more effective strategies employed by counsellors and counselling agencies in successfully working with male victims, whilst increasing awareness of male victimisation.
Prospective study of sport dropout: A motivational analysis as a function of age and gender
Authors: Guzmán Jose Francisco , Kingston Kieran 
Published: November 2011

AbstractIntroduction: This paper aimed to analyse the predictive ability of a self‐determination theory (SDT) based model describing competitive sport dropout, and variance as a function of age and gender. Variables included in the model were: psychological need satisfaction, self‐determined motivation, perceived conflict between sport and study, intention to practise sport, and dropout.Methods: A prospective study was performed over a period of 19 months. Variables considered as predictors of sport dropout were measured initially, and after 19 months persistence or dropout was assessed. The sample consisted of 857 athletes aged 11–19 (mean value 15.3; standard deviation = 1.77), 680 males and 177 females.Results: Structural equation modelling illustrated support for an “alternative” model that incorporated a direct relationship between psychological need satisfaction and intention to practise sport. Analysis of invariance showed that the model was consistent as a function of age and gender, i.e. no differences were found in regression weights. MANOVA, however, revealed some group differences with respect to the dependent variables. Specifically, in terms of engagement, although assessed at the start of the study, those athletes who persisted at 19 months demonstrated greater need satisfaction, self‐determined motivation and intention to practise sport than those who dropped out. Age related differences were also identified: with increased age self‐determined motivation and intention to practise sport decreased, while there were no differences in need satisfaction or perceived conflict between sport and study. There were no differences related to gender.Discussion: The results support previous studies that had used SDT to predict sport dropout, specifically those that had reported an inverse relationship between self‐determined motivation and perceived conflict between activities. Further, it suggests that other variables (emotional) may play a specific role in predicting intention to continue engagement with sport.Conclusion: The major contribution of the study is in validating a motivational model predicting sport dropout which incorporates perceived conflict and the direct effect of psychological need satisfaction on the intention to practise sport. The invariance of regression weights between age and gender groups suggests that the relationships proposed in the model are universal.
Left ventricular oxidant and antioxidant markers induced by lifestyle modification in rats exposed to lead acetate
Authors: Dabidi Roshan Valiollah , Ranjbar Shima , Hosseinzadeh Mahdi , Myers Jonathan 
Published: November 2011

AbstractResponses of the left ventricle oxidant/antioxidant markers such as glutathione peroxidase (GPx), superoxide dismutase (SOD), malondialdehyde (MDA) and protein carbonyls (PCs) induced by lifestyle modification, including turmeric supplementation and exercise training, were investigated in rats during chronic exposure to lead acetate. Forty male rats were randomly divided into five groups: (1) lead acetate; (2) turmeric; (3) endurance training; (4) training + turmeric; and (5) sham‐operated groups. Enzyme activities were determined in rat hearts after receiving 20 mg·kg−1 of lead acetate (groups 1 to 4) and 30 mg·kg−1 turmeric (groups 2 and 4) for 8 weeks, three times a week. In addition, the rats in groups 3 and 4 performed treadmill running at a speed of 15 to 22 m·min−1 for 25 to 64 min, five times a week for 8 weeks. One way ANOVA analyses indicated that administration of lead evoked a significant increase in MDA and PC and significant decreases in GPx and SOD activity in the left ventricular homogenates. However, endurance training and\or turmeric supplementation resulted in a significant decrease in MDA and PC levels and significantly increased levels of GPx and SOD. These results suggest that lifestyle modification may have a cardioprotective effect by ameliorating lead‐induced cardiotoxicity.
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles
Authors: Cheng Chao , Min Renqiang , Gerstein Mark 
Published: October 2011

Abstract
Motivation: ChIP-seq and ChIP-chip experiments have been widely used to identify transcription factor (TF) binding sites and target genes. Conventionally, a fairly ‘simple’ approach is employed for target gene identification e.g. finding genes with binding sites within 2 kb of a transcription start site (TSS). However, this does not take into account the number of sites upstream of the TSS, their exact positioning or the fact that different TFs appear to act at different characteristic distances from the TSS.
Results: Here we propose a probabilistic model called target identification from profiles (TIP) that quantitatively measures the regulatory relationships between TFs and target genes. For each TF, our model builds a characteristic, averaged profile of binding around the TSS and then uses this to weight the sites associated with a given gene, providing a continuous-valued ‘regulatory’ score relating each TF and potential target. Moreover, the score can readily be turned into a ranked list of target genes and an estimate of significance, which is useful for case-dependent downstream analysis.
Conclusion: We show the advantages of TIP by comparing it to the ‘simple’ approach on several representative datasets, using motif occurrence and relationship to knock-out experiments as metrics of validation. Moreover, we show that the probabilistic model is not as sensitive to various experimental parameters (including sequencing depth and peak-calling method) as the simple approach; in fact, the lesser dependence on sequencing depth potentially utilizes the result of a ChIP-seq experiment in a more ‘cost-effective’ manner.
Contact: mark.gerstein@yale.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
The ‘F‐words’ in childhood disability: I swear this is how we should think!
Authors: Rosenbaum P. , Gorter J. W. 
Published: November 2011

AbstractThe 21st century is witnessing a sea change in our thinking about ‘disability’. Nowhere are these developments more apparent than in the field of childhood disability, where traditional biomedical concepts are being incorporated into – but expanded considerably by – new ways of formulating ideas about children, child development, social‐ecological forces in the lives of children with chronic conditions and their families, and ‘points of entry’ for professionals to be helpful. In this paper, we have tried to package a set of ideas, grounded in the World Health Organization's International Classification of Functioning, Disability and Health (the ICF), into a series of what we have called ‘F‐words’ in child neurodisability – function, family, fitness, fun, friends and future. We hope this will be an appealing way for people to incorporate these concepts into every aspect of clinical service, research and advocacy regarding disabled children and their families.
Effects of incorporating cowpea in a subtropical grass pasture on forage production and quality and the performance of cows and calves
Authors: Vendramini J.M.B , Arthington J. D. , Adesogan A. T. 
Published: November 2011

AbstractThe increasing cost of N fertilizer has stimulated an interest in sourcing protein from warm‐season legumes among beef cattle producers in the tropical/subtropical areas of the world. The objective of this study was to evaluate effects of two strategies of incorporating cowpea [Vigna unguiculata (L.) Walp.] into bahiagrass (Paspalum notatum Flügge) pastures on the herbage characteristics and performance of grazing cow–calf pairs. The study was conducted in Ona, Florida, USA, from May to August in 2007 and 2008. Experimental units were 1·0 ha. Treatments were bahiagrass pasture alone (control), 50:50 bahiagrass–cowpea pasture (cowpea), bahiagrass pasture with a cowpea creep grazing area (0·1 ha, creep grazing) and bahiagrass pasture with a creep‐fed concentrate [(creep feeding; 10 g kg−1 body weight (BW)]. The cowpea pastures had lower herbage mass [HM, 1·8 vs. 3·7 t ha−1] and herbage allowance [HA, 0·8 vs. 1·4 kg DM kg−1 live weight (LW)] compared with the other treatments. Cowpea had greater CP (CP, 160 g kg−1) and in vitro digestible organic matter (IVDOM), (600 g kg−1) than bahiagrass (110 and 490 g kg−1 respectively); however, cowpea HM was only 0·9 t ha−1 in May and 0·7 t ha−1 in June, but it did not persist in July and August. Calves receiving the creep feeding treatments had greater average daily gain (0·8 vs. 0·7 kg d−1) than calves in other treatments. Further research is necessary to exploit the superior nutritive value of cowpea in grazing systems in the south‐eastern USA.
An alternative rotational stocking management designed to favour butterflies in permanent grasslands
Authors: Farruggia A. , Dumont B. , Scohier A. , Leroy T. , Pradel P. , Garel J.‐P. 
Published: November 2011

AbstractGrassland butterflies are on the decline throughout Europe. We tested an ‘alternative rotational stocking’ (ARS) strategy based on theoretical and practical aspects of grassland ecology, designed to increase butterfly diversity while also meeting farmers’ production objectives. This management strategy implies taking animals away from one subplot of the rotation during the main flowering period. Its feasibility and benefits on butterfly diversity were tested by comparing ARS with continuous stocking (CS) in plots grazed by cattle at the same stocking rate: high in 2005 and 2006 then lenient in 2007 and 2008. At the high stocking rate, butterfly abundance (21·9 vs. 8·3, P < 0·01) and butterfly species richness (7·4 vs. 3·7, P < 0·001) were significantly higher in ARS than in CS plots, matching the increase in pasture flowering intensity and sward structural diversity. ARS was led according to the pre‐planned schedule in 2005, but in 2006, the number of heifer grazing days in ARS was reduced by 19% because of unfavourable spring grass growth. At the lenient stocking rate, ARS was less beneficial for butterflies (abundance: 17·4 vs. 13·0, P < 0·10; species richness: 5·9 vs. 5·2, P = 0·35) but would present less risk for farmers in terms of providing livestock with sufficient forage. Alternative rotational stocking thus has potential to be integrated into grassland‐based systems, but would require earlier grazing on the excluded subplot of the rotation in the event of unfavourable grass growth during spring.
The effect of a major road on bat activity and diversity
Authors: Berthinussen Anna , Altringham John 
Published: November 2011

Summary1. It is well known that roads can have a significant impact, usually negative, on species and ecosystems. However, despite their protected status in many countries, little research has been done into the effects of roads on bats. With a view to making more informed management recommendations, we address the simple question: are bat activity and diversity (as measured with ultrasonic detectors) correlated with distance from a major road?2. Broadband acoustic surveys were conducted on 20 walked transects perpendicular to the M6, a major road in Cumbria (UK), with bat activity recorded at eight spot checks per transect at different distances from the road. Climatic and habitat variables were also recorded, and the relationships between bat activity and these variables were investigated using generalised estimated equations (GEE) and ordinal logistic regression.3. Total bat activity, the number of species and the activity of Pipistrellus pipistrellus (the most abundant species) were all positively correlated with distance from the road. Total activity increased more than threefold between 0 and 1600 m from the road. These effects were found to be consistent over 2 years.4. Synthesis and applications. This study is one of the first to show that roads have a major negative impact on bat foraging activity and diversity and is broadly applicable to insectivorous bat communities worldwide. Mitigation requires that roads are made more permeable to bats through the use of effective crossings, such as underpasses and overpasses, and that habitat is improved within 1 km of major roads. Because the effectiveness of current mitigation measures is unknown, well‐designed monitoring of mitigation is essential.
Modelling large‐scale relationships between changes in woodland deer and bird populations
Authors: Newson Stuart E. , Johnston Alison , Renwick Anna R. , Baillie Stephen R. , Fuller Robert J. 
Published: November 2011

Summary1. There is increasing evidence from local studies carried out in several parts of the world to suggest that increases in the abundance of deer may be depressing population levels of breeding woodland bird populations that are associated with dense understorey habitats. We examine whether habitat modification by deer is likely to be a factor contributing to recent large‐scale population declines of woodland birds in lowland England.2. Novel analytical methods are applied to extensive national bird and deer monitoring data, to examine whether populations of 11 woodland bird species that are associated with dense understorey habitats in lowland England may have been depressed following increases in the abundance of three widespread and abundant deer species: Reeves’ muntjac Muntiacus reevesi, roe deer Capreolus capreolus and fallow deer Dama dama. An additional four woodland bird species that are not specifically associated with understorey habitats are included as controls.3. For five of the 11 understorey species considered, there is evidence that increases in deer are associated with large‐scale depression of abundance or population declines in lowland England. Of these species, we suggest that the impacts of deer are likely to have been greatest for two species of conservation concern, common nightingale Luscinia megarhynchos and willow tit Poecile montanus.4. Synthesis and applications. Large‐scale analyses of extensive national monitoring data provide evidence for a negative association between three widespread and abundant deer species and several woodland bird populations that are associated with dense understorey habitats. These findings are consistent with those from small‐scale experimental studies and indicate that deer‐related habitat modification may be affecting some bird species on far larger scales than previously appreciated. Mainly through their effects on understorey vegetation, high deer populations are now likely to be affecting woodland biodiversity over large parts of lowland England and deer management plans, involving integrated exclusion and culling of deer, need to be co‐ordinated on large scales. It is suggested that such management plans could most usefully target areas that still support relatively high populations of species that are sensitive to deer. Knowledge about the form of relationships between deer abundance and habitat quality for birds and other biodiversity is an important knowledge gap that needs to be addressed if sound, collaborative deer management plans are to be developed.
Scaling down distribution maps from atlas data: a test of different approaches with virtual species
Authors: Bombi Pierluigi , D’Amen Manuela 
Published: November 2011

AbstractAim  Conservation managers are increasingly looking for modelled projections of species distributions to inform management strategies; however, the coarse resolution of available data usually compromises their helpfulness. The aim of this paper is to delineate and test different approaches for converting coarse‐grain occurrence data into high‐resolution predictions, and to clarify the conceptual circumstances affecting the accuracy of downscaled models.Location  We used environmental data from a real landscape, southern Africa, and simulated species distributions within this landscape.Methods  We built 10 virtual species at a resolution of 5 arcmin, and for each species we simulated atlas range maps at four decreasing resolutions (15, 30, 60, 120 arcmin). We tested the ability of three downscaling strategies to produce high‐resolution predictions using two modelling techniques: generalized linear models and generalized boosted models. We calibrated reference models with high‐resolution data and we compared the relative reduction of predictive performance in the downscaled models by using a null model approach. We also estimated the applicability of downscaling procedures to different situations by using distribution data for Mediterranean reptiles.Results  All reference models achieved high performance measures. For all strategies, we observed a reduction of predictive performance proportional to the degree of downscaling. The differences in evaluation indices between reference models and downscaled projections obtained from atlases at 15 and 30 arcmin were never statistically significant. The accuracy of projections scaled down from 60 arcmin largely depended on the combination of approach and algorithm adopted. Projections scaled down from 120 arcmin gave misleading results in all cases.Main conclusions  Moderate levels of downscaling allow for reasonably accurate results, regardless of the technique used. The most general effect of scaling down coarse‐grain data is the reduction of model specificity. The models can successfully delineate a species’ environmental association up until a 12‐fold downscaling, although with an increasing approximation that causes the overestimation of true distributions. We suggest appropriate procedures to mitigate the commission error introduced by downscaling at intermediate levels (approximately 12‐fold). Reductions of grain size > 12‐fold are discouraged.