bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assigning spectrum-specific P-values to protein identifications by mass spectrometry
Authors: Spirin Victor , Shpunt Alexander , Seebacher Jan , Gentzel Marc , Shevchenko Andrej , Gygi Steven , Sunyaev Shamil 
Published: February 2011

Abstract
Motivation: Although many methods and statistical approaches have been developed for protein identification by mass spectrometry, the problem of accurate assessment of statistical significance of protein identifications remains an open question. The main issues are as follows: (i) statistical significance of inferring peptide from experimental mass spectra must be platform independent and spectrum specific and (ii) individual spectrum matches at the peptide level must be combined into a single statistical measure at the protein level.
Results: We present a method and software to assign statistical significance to protein identifications from search engines for mass spectrometric data. The approach is based on asymptotic theory of order statistics. The parameters of the asymptotic distributions of identification scores are estimated for each spectrum individually. The method relies on new unbiased estimators for parameters of extreme value distribution. The estimated parameters are used to assign a spectrum-specific P-value to each peptide-spectrum match. The protein-level confidence measure combines P-values of peptide-to-spectrum matches.
Conclusion: We extensively tested the method using triplicate mouse and yeast high-throughput proteomic experiments. The proposed statistical approach improves the sensitivity of protein identifications without compromising specificity. While the method was primarily designed to work with Mascot, it is platform-independent and is applicable to any search engine which outputs a single score for a peptide-spectrum match. We demonstrate this by testing the method in conjunction with X!Tandem.
Availability: The software is available for download at ftp://genetics.bwh.harvard.edu/SSPV/.
Contact: ssunyaev@rics.bwh.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Guidelines for large herbivore translocation simplified: black rhinoceros case study
Authors: Linklater Wayne L. , Adcock Keryn , du Preez Pierre , Swaisgood Ron R. , Law Peter R. , Knight Michael H. , Gedir Jay V. , Kerley Graham I.H. 
Published: February 2011

Summary 1. Most hypotheses for translocation success are elaborate, hierarchical, and untested combinations of socio‐ecological predictors. Empirical support for those tested is vulnerable to spurious single‐predictor relationships and does not account for the hierarchy amongst predictors and non‐independence amongst individuals or cohorts. Testing hypotheses as a priori multi‐level models promotes stronger inference. 2. We apply a 25‐year (1981–2005) data base including 89 reintroduction and 102 restocking events that released 682 black rhinoceros Diceros bicornis into 81 reserves to test 24 hypotheses for translocation success, defined as survival to 1 year post‐release. We made information‐theoretic comparisons of hypotheses represented as hierarchical models incorporating random effects for reserve and release cohort predictors of death. 3. Mortality rates after restocking were higher than for reintroductions (13·4 cf. 7·9%, respectively) due largely to intraspecific fighting. No predictors strongly influenced reintroduction success, although cohorts consisting entirely of adult males were 8·2% of individuals but contributed 21·9% of deaths, and reserves with lowest carrying capacities (i.e. <0·1 rhino km−2) had a 16·3% mortality rate. Most models for restocking success were not supported. Only those including age class received substantial support. Age was the only predictor to strongly influence death rates. Predictors previously thought influential, like population density, reserve area and quality, and cohort size, were not supported. 4. Synthesis and applications. Simple rules succeeded where complex ecological and demographic hypotheses failed to predict survival after translocation of critically endangered black rhinoceros. Results support bold attempts by managers at translocations towards species recovery in most ways that they have historically occurred. Groups of rhinoceros of different size and composition can be successfully moved over large distances between different ecological contexts. Also, the release of cohorts into reserves that are relatively small, poorer habitat or already stocked need not be avoided so long as calves and all‐male cohorts are not reintroduced, and only adults used for restocking. Our analysis demonstrates the importance of information‐theoretic comparisons of a priori hierarchical models to test hypotheses for conservation management. We caution against interpreting simple correlations or regression amongst a large number of nested ecological and demographic variables.
An exploration of chronic pain patients’ perceptions of home telerehabilitation services
Authors: Cranen Karlijn , Drossaert Constance H. C. , Brinkman Evelien S. , Braakman‐Jansen Annemarie L. M. , IJzerman Maarten J. , Vollenbroek‐Hutten Miriam M. R. 
Published: February 2011

AbstractObjectives  To explore patients’ perceptions regarding prospective telerehabilitation services and the factors that facilitate or impede patients’ intentions to use these services.Design  Using semi‐structured interviews, patients reflected on the pros and cons of various scenarios of prospective telerehabilitation services. Patients’ arguments were first arranged according to the Unified Theory of Acceptance and Use of Technology (UTAUT). Next, using inductive analysis, the data for each UTAUT component were analysed and arranged into subthemes.Setting and participants  Twenty‐five chronic pain patients were selected from a rehabilitation centre in the Netherlands.Results  Overall, participants considered telerehabilitation helpful as a complementary or follow‐up treatment, rather than an autonomous treatment. Arguments mainly related to the UTAUT constructs of ‘performance expectancy’ and ‘facilitating conditions’. Patients valued the benefits such as reduced transportation barriers, flexible exercise hours and the possibility to better integrate skills into daily life. However, many patients feared a loss of treatment motivation and expressed concerns about both reduced fellow sufferer contact and reduced face‐to‐face therapist contact. Few arguments related to ‘social norms’ and ‘effort expectancy’.Conclusions  The effect of telerehabilitation on healthcare strongly depends on patients’ willingness to use. Our study showed that chronic pain patients valued the benefits of telerehabilitation but hesitate to use it as an autonomous treatment. Therefore, future initiatives should maintain traditional care to some degree and focus on patients’ attitudes as well. Either by giving information to increase patients’ confidence in telerehabilitation or by addressing reported drawbacks into the future design of these services. Further quantitative studies are needed to explore patients’ intentions to use telerehabilitation.
High prevalence of founder mutations of the succinate dehydrogenase genes in the Netherlands
Authors: Hensen EF , van Duinen N , Jansen JC , Corssmit EPM , Tops CMJ , Romijn JA , Vriends AHJT , van der Mey AGL , Cornelisse CJ , Devilee P , Bayley JP 
Published: February 2011

Hensen EF, van Duinen N, Jansen JC, Corssmit EPM, Tops CMJ, Romijn JA, Vriends AHJT, van der Mey AGL, Cornelisse CJ, Devilee P, Bayley JP. High prevalence of founder mutations of the succinate dehydrogenase genes in the Netherlands.Mutations in four genes encoding subunits or cofactors of succinate dehydrogenase (SDH) cause hereditary paraganglioma and pheochromocytoma syndromes. Mutations inSDHBandSDHDare generally the most common, whereas mutations inSDHCandSDHAF2are far less frequently observed. A total of 1045 DNA samples from Dutch paraganglioma and pheochromocytoma patients and their relatives were analyzed for mutations ofSDHB,SDHC,SDHDorSDHAF2.Mutations in these genes were identified in 690 cases, 239 of which were index cases. The vast majority of mutation carriers had a mutation inSDHD(87.1%). The second most commonly affected gene wasSDHAF2(6.7%). Mutations inSDHBwere found in only 5.9% of samples, whereasSDHCmutations were found in 0.3% of samples. Remarkably, 69.1% of all carriers of a mutation in an SDH gene in the Netherlands can be attributed to a single founder mutation inSDHD, c.274G>T and p.Asp92Tyr. Moreover, 88.8% of all SDH mutation carriers carry one of just six Dutch founder mutations inSDHB,SDHDandSDHAF2. The dominance ofSDHDmutations is unique to the Netherlands, contrasting with the higher prevalence ofSDHBmutations found elsewhere. In addition, we found that most SDH mutation‐related paragangliomas–pheochromocytomas in the Netherlands can be explained by only six founder mutations inSDHAF2,SDHBandSDHD. The findings underline the regional differences in the SDH mutation spectrum, differences that should be taken into account in the development of effective screening protocols. The results show the crucial role that demographic factors play in the frequency of gene mutations.
Selection on male longevity in a monogamous human population: late‐life survival brings no additional grandchildren
Authors: LAHDENPERÄ M. , LUMMAA V. , RUSSELL A. F. 
Published: February 2011

AbstractHumans are exceptionally long‐lived for mammals of their size. In men, lifespan is hypothesized to evolve from benefits of reproduction throughout adult life. We use multi‐generational data from pre‐industrial Finland, where remarriage was possible only after spousal death, to test selection pressures on male longevity in four monogamous populations. Men showed several behaviours consistent with attempting to accrue direct fitness throughout adult life and sired more children in their lifetimes if they lost their first wife and remarried. However, remarriage did not increase grandchild production because it compromised the success of motherless first‐marriage offspring. Overall, grandchild production was not improved by living beyond 51 years and was reduced by living beyond 65. Our results highlight the importance of using grandchild production to understand selection on human life‐history traits. We conclude that selection for (or enforcement of) lifetime monogamy will select for earlier reproductive investment and against increased lifespan in men.
2,3,4′,5‐Tetrahydroxystilbene‐2‐O‐β‐d‐glucoside inhibits platelet‐derived growth factor‐induced proliferation of vascular smooth muscle cells by regulating the cell cycle
Authors: Xu Xiao‐Le , Huang Yan‐Juan , Wang Yu‐Qin , Chen Xiang‐Fan , Zhang Wei 
Published: February 2011

Summary1. 2,3,4′,5‐Tetrahydroxystilbene‐2‐O‐β‐d‐glucoside (TSG) has been shown to have an anti‐atherosclerotic effect. Vascular smooth muscle cell (VSMC) proliferation contributes to the pathobiology of atherosclerosis. The aim of the present study was to investigate the effects of TSG on platelet‐derived growth factor (PDGF)‐BB‐induced VSMC proliferation and to explore the molecular mechanisms underlying the effects.2. Cultured rat VSMC were pretreated with TSG (l–50 μmol/L) for 1 h, followed by exposure to PDGF‐BB (10 ng/mL) for 24 h, after which cell proliferation and cell cycle stages were examined. The expression of protein cell cycle regulators, including retinoblastoma (Rb), cyclin D1/E, cyclin‐dependent kinase (CDK) 2/4, CDK inhibitors p21 and p27 and proliferative cell nuclear antigen (PCNA), was examined. Activation of extracellular signal‐regulated kinase (ERK) 1/2 was evaluated to elucidate the possible upstream mechanism by which TSG affects cell cycle regulators.3. The results showed that TSG dose‐dependently inhibited PDGF‐BB‐induced VSMC proliferation, possibly by blocking the progression of the cell cycle from the G1 to S phase. In addition, TSG significantly inhibited PDGF‐BB‐induced phosphorylation of Rb and the expression of cyclin D1, CDK4, cyclin E, CDK2 and PCNA. In addition, TSG suppressed PDGF‐BB‐induced downregulation of p27 and upregulation of p21, as well as PDGF‐BB‐induced activation of ERK1/2.4. Together, the findings of the present study provide the first evidence that TSG can inhibit PDGF‐BB‐stimulated VSMC proliferation via cell cycle arrest in association with modulation of the expression of cell cycle regulators, which may be mediated, at least in part, by suppression of ERK1/2 activation.
Behavioural weight management for the primary careprovider
Authors: Rutledge T. , Groesz L. M. , Linke S. E. , Woods G. , Herbst K. L. 
Published: February 2011

SummaryPrimary care providers (PCPs) provide the majority of weight management care in clinical settings; however, they often lack the time or resources to apply strategies recommended in treatment guidelines. This review surveyed randomized clinical trials and prospective weight management studies from 1990 to present to identify evidence‐based behavioural strategies for weight management applicable to the PCP treatment environment. Data supported, time‐limited weight management strategies included self‐monitoring, portion control, sleep hygiene, restaurant eating and television viewing. The current review suggests that a number of behavioural strategies are available to enhance the effectiveness of PCPs weight management interventions. Increasing PCP awareness of these evidence‐based strategies may increase their attention to overweight and obesity concerns in clinical encounters and encourage more collaborative efforts with patients towards weight management goals.
Will Capitalists Live Happily Ever After? – Political Myth: On the Use and Abuse of Biblical Themes – By Roland Boer
Authors: Kim Uriah Y. 
Published: February 2011

AbstractWhat would our world be like if all oppositions to capitalism were to be removed? The author describes a doomsday scenario instead of everlasting plenitude if capitalists have their ways. This conclusion comes from the author's masterful discussion of political myth and analysis of the narrative of Genesis to Joshua as a political myth. The narrative of the Hexateuch constructs and at the same time punishes all sorts of rebels who oppose the theocratic state it wishes to establish. But myth is uncanny in that the rebellion hides what it fears the most, the impossibility of such a state to come true, and needs what it desires to annihilate in order to persist as an unfulfilled fantasy that powers a political movement. The author argues that some politicians in Australia and the USA are abusing the logic of the political myth of the Hexateuch in order to support their capitalistic agendas and, therefore, the Left must tell the ending of the capitalist fantasy of endless production and expansion in order to reveal its contradictions.
Prevalence and socio‐demographic associations of overweight and obesity among children attending child‐care services in rural and regional Australia
Authors: WOLFENDEN Luke , HARDY Louise L. , WIGGERS John , MILAT Andrew J. , BELL Colin , SUTHERLAND Rachel 
Published: February 2011

AbstractAim:  To describe the prevalence and socio‐demographic characteristics associated with body mass index among children attending child‐care services in New South Wales, Australia.Methods:  Cross‐sectional study of parent‐reported socio‐demographic characteristics and objectively measured height and weight among children aged two to five years attending 40 randomly selected long day care centres and preschools.Results:  Seven hundred and sixty‐four children, 11% of whom were Indigenous, participated in the study (response rate = 66%). Overall, 16.7% of children and 24.6% of Indigenous children were overweight or obese. Overweight and obesity was higher among children whose mothers did not have a university education (OR 1.91: 95% CI 1.15, 3.12) and who were Indigenous (OR 1.74: 95% CI 1.05, 2.90). No differences in prevalence were found between geographic areas. Multivariate analysis indicated that after adjusting for age, child‐care service hours and other demographic covariates, only maternal education remained a significant predictor of weight status (OR 2.06: 95% CI 1.16, 3.66).Conclusion:  The high prevalence of overweight and obesity among children attending child‐care services underscores the importance of obesity prevention interventions in early child‐care settings, and particularly those catering for Indigenous children.
‘It's very hard to find what to put in the kid's lunch’: What Perth parents think about food for school lunch boxes
Authors: BATHGATE Katherine , BEGLEY Andrea 
Published: February 2011

AbstractAim:  To describe the factors affecting school food selection by parents of young children attending low socioeconomic schools in Perth and recommend the features of resources parents need to make healthier choices.Methods:  Nine focus groups of parents of young children attending low socioeconomic status schools in Perth were conducted where parents were asked about the food their children ate at school and their opinions of school food resources.Results:  Focus group discussion centred on the themes of the challenge of being a good parent by providing healthy lunch box food; making compromises in what their children eat at school and the barriers to healthy eating in the school environment. Parents were concerned about what their children were eating at school but the barriers of convenience, child preference, cost and food safety prevented them from including healthier food in the lunch box. The amount of time allowed for eating and lack of refrigeration were school‐based barriers that impacted on the type and amount of food selected. Parents liked colourful, practical school food resources with recipes and nutrition information aimed at children.Conclusions:  Parents want help with selecting lunch box food/drinks that are nutritious, convenient, inexpensive and appealing for children to eat. Schools need to be supported to introduce healthy eating programs and should review the time given for young children to eat at school. Dietitians need to consider the home food environment and what motivates parents to make food choices for their children.
A valid depression case finding instrument to assist dietitians in identifying patients at risk of depression in an enhanced HIV care setting
Authors: DI GUILMI Aaron , JEGANATHAN Sarangapany , HOUTZAGER Louise , PURNOMO Julianita , BEGLEY Kim 
Published: February 2011

AbstractAim:  The present study aimed to test the validity, reliability and sensitivity of a two‐question depression screening instrument with the Center for Epidemiologic Studies Depression Scale in human immunodeficiency virus‐infected subjects.Methods:  The present study is a self‐administered questionnaire of the two‐question depression screening instrument and the Center for Epidemiologic Studies Depression Scale‐D10 completed contemporaneously by participants to assess the validity, reliability and sensitivity of the instrument.Results:  Eighty participants (76 men and 4 women) with a mean age of 43.4 years were enrolled to the study. In this cohort the prevalence of depression was found to be 36%. A significant correlation (rho= 0.68, P < 0.0001) was found between the depression screening instrument and Center for Epidemiologic Studies Depression Scale indicating adequate validity. The internal reliability of the depression screening instrument was found to be 0.77. The two‐question instrument yielded a sensitivity of 89.7% and a specificity of 58.8%. The false positive rate was 41.2%. However, the false negative rate in this population was found to be only 10.3%. The negative predictive value was 90.9%.Conclusions:  The results of the present study indicated that the two‐question depression screening instrument was valid, reliable and sensitive for detecting individuals at risk of depression in a cohort of people living with human immunodeficiency virus attending a nutrition clinic in an enhanced care setting.
Availability, affordability and quality of a healthy food basket in Adelaide, South Australia
Authors: WONG Kwan Chiu , COVENEY John , WARD Paul , MULLER Robert , CARTER Patricia , VERITY Fiona , TSOURTOS George 
Published: February 2011

AbstractAim:  To investigate the cost, affordability, availability and quality of a healthy food basket in high and low household income areas of Adelaide, and to investigate food promotion in supermarkets.Methods:  A cross‐sectional survey was undertaken in May 2009 with a sample of 61 supermarkets, 27 greengrocers and 34 butchers in metropolitan Adelaide. Samples were selected based on household income for extreme tertiles across Adelaide.Results:  Low‐income families were significantly worse off in comparison with high‐income families (P < 0.05) regarding affordability of the healthy food basket. The data analysis demonstrated that families on welfare payments and low incomes would need to spend 28–34% of their income in order to be able to afford a healthy food basket. However, there was no significant difference in the cost, availability, and quality of the healthy food basket and food promotions between high and low household income areas.Conclusion:  The present study examined the cost, affordability, availability and quality of the healthy food basket, as well as an assessment of food promotions in supermarkets, finding no difference between high and low household income areas. The study provides valuable information to assist in a deeper understanding of food security in Adelaide. It is recommended that a longitudinal study would assist in establishing a reliable healthy food basket monitoring system that could lead to more robust policy outcomes.
WA health practitioners and cooking: How well do they mix?
Authors: COOPER Sheri , BEGLEY Andrea 
Published: February 2011

AbstractAim:  The aim of the present study was to assess the views and experiences of WA practitioners on the use of cooking as a public health nutrition intervention.Methods:  A 39‐point online questionnaire was constructed using Survey Monkey. The questionnaire was distributed via email distribution lists targeting practitioners working in public health nutrition. Questions were focused around four objectives relating to: the value of cooking skills in public health, practitioner cooking skills and training, practitioner views on cooking as a health intervention and practitioner experiences in conducting cooking demonstrations.Results:  A total of 84 practitioners completed the questionnaire, of which over half (58%) were employed in dietetic specific positions at the time of the survey. There was overwhelming agreement that cooking skills are an important factor in the prevention of nutrition‐related disease, and that cooking skill interventions have the potential to change dietary intakes. However, only one quarter of practitioners indicated that cooking skill interventions were a significant part of their current role. Over half (58%) of the practitioners surveyed had either conducted or assisted in a cooking demonstration or cooking class in the last 12 months.Conclusions:  WA practitioners place a high value on the use of cooking as a public health nutrition intervention. Practitioners felt they have good knowledge and skills in cooking but indicated the need to know more about conducting cooking skill interventions. The findings suggest the need to improve outcome evaluation as a component of cooking skill interventions to assess long‐term behaviour change.