bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multivariate model for predicting segmental body composition
Authors: Tian Simiao , Mioche Laurence , Denis Jean-Baptiste , Morio Béatrice 
Published: July 2013

The aims of the present study were to propose a multivariate model for predicting simultaneously body, trunk and appendicular fat and lean masses from easily measured variables and to compare its predictive capacity with that of the available univariate models that predict body fat percentage (BF%). The dual-energy X-ray absorptiometry (DXA) dataset (52 % men and 48 % women) with White, Black and Hispanic ethnicities (1999–2004, National Health and Nutrition Examination Survey) was randomly divided into three sub-datasets: a training dataset (TRD), a test dataset (TED); a validation dataset (VAD), comprising 3835, 1917 and 1917 subjects. For each sex, several multivariate prediction models were fitted from the TRD using age, weight, height and possibly waist circumference. The most accurate model was selected from the TED and then applied to the VAD and a French DXA dataset (French DB) (526 men and 529 women) to assess the prediction accuracy in comparison with that of five published univariate models, for which adjusted formulas were re-estimated using the TRD. Waist circumference was found to improve the prediction accuracy, especially in men. For BF%, the standard error of prediction (SEP) values were 3·26 (3·75) % for men and 3·47 (3·95) % for women in the VAD (French DB), as good as those of the adjusted univariate models. Moreover, the SEP values for the prediction of body and appendicular lean masses ranged from 1·39 to 2·75 kg for both the sexes. The prediction accuracy was best for age < 65 years, BMI < 30 kg/m2and the Hispanic ethnicity. The application of our multivariate model to large populations could be useful to address various public health issues.
Phytoplankton community size structure, primary production and copepod production in a subtropical coastal inlet in Hong Kong
Authors: Lie Alle A.Y. , Wong Lik Chi , Wong C. Kim 
Published: July 2013

Phytoplankton primary production and copepod production, and the size composition of the phytoplankton community in Tolo Harbour, a semi-enclosed bay in north-eastern Hong Kong, were studied from February 2008 to March 2009. Chlorophyll-a (Chl a) concentrations decreased from an average of 9.07 µg l−1 in the inner part of the bay to 3.07 µg l−1 at the mouth of the bay. In terms of contribution to total Chl a biomass, the >20 µm size fraction dominated the phytoplankton community. The zooplankton community in Tolo Harbour was dominated by small copepods, with cephalothorax length ranging from ~0.3 to 0.4 mm, and the density of copepods decreased from ~15,000 ind.m−3 in the inner part of the bay to ~9,700 ind.m−3 at the mouth of the bay. Depth-integrated net primary production in Tolo Harbour was high, ranging from 0.34 to 10.40 g C m−2 day−1, with an overall mean of 2.64 g C m−2 day−1. In contrast, copepod production was low, ranging from 0.19 to 16.64 mg C m−3 day−1, with an overall mean of 2.73 mg C m−3 day−1. The low transfer efficiency of 1.4% between phytoplankton primary production and copepod secondary production suggests that the large phytoplankton was inefficiently grazed by the small copepods in Tolo Harbour.
Dimensions of Financial Autonomy in Low-/Moderate-Income Couples from a Gender Perspective and Implications for Welfare Reform
Authors: BENNETT FRAN , SUNG SIRIN 
Published: July 2013

AbstractThe ‘unitary household’ lives on in policymakers’ assumptions about couples sharing their finances. Yet financial autonomy is seen as a key issue in gender relations, particularly for women. This article draws on evidence from semi-structured individual interviews with men and women in thirty low-/moderate-income couples in Britain. The interviews explored whether financial autonomy had any meaning to these individuals; and, if so, to what extent this was gendered in the sense of there being differences in men's and women's understanding of it. We develop a framework for the investigation of financial autonomy, involving several dimensions: achieving economic independence, having privacy in one's financial affairs and exercising agency in relation to household and/or personal spending. We argue that financial autonomy is a relevant issue for low-/moderate-income couples, and that women are more conscious of tensions between financial togetherness and autonomy due to their greater responsibility for managing togetherness and lower likelihood of achieving financial independence. Policymakers should therefore not discount the aspirations of women in particular for financial autonomy, even in low-/moderate-income couples where there remain significant obstacles to achieving this. Yet plans for welfare reform that rely on means testing and ignore intra-household dynamics in relation to family finances threaten to exacerbate these obstacles and reinforce a unitary family model.
A tale of two assemblages: Early Neolithic manufacture and use of beads in the Konya plain
Authors: Baysal Emma 
Published: July 2013

AbstractBeads and personal ornamentation have often been overlooked in the intense debates that have surrounded archaeological work on the Neolithic settlements of the Konya plain. In this article I assess the bead assemblages from the ninth- to eighth-millennium BC calibrated sites of Pınarbaşı and Boncuklu Höyük to ask what they can tell us about the technology, sense of personal expression and interactions with the wider landscape of Neolithic populations. The two sites in question occupy significantly different positions within the plain: the former right at the edge; the latter next to a low ridge surrounded by wetland. Evidence suggests that these communities adopted some materials, ideas and influences from outside sources, while holding on to their own, very local identities.
Bronze Age höyüks, Iron Age hilltop forts, Roman poleis and Byzantine pilgrimage in Germia and its vicinity. ‘Connectivity’ and a lack of ‘definite places’ on the central Anatolian high plateau
Authors: Niewöhner Philipp , Dikilitaş Gülseren , Erkul Ercan , Giese Stefan , Gorecki Joachim , Prochaska Walter , Sarı Deniz , Stümpel Harald , Vardar Ali , Waldner Alice , Walser Andreas Victor , Woith Heiko 
Published: July 2013

AbstractGermia was a well-connected Byzantine polis in western-central Anatolia, famous for its healing waters and a church of St Michael. After three years of survey the site can now be reconstructed: it included several other churches and monasteries, but little space for ordinary residential buildings. This comes as a surprise, but can be explained by the discovery of two older Roman cities within walking-distance of Germia, where the ordinary people seem to have lived. One of these cities, Mantalos, was home to a local cult of the pagan god Men. This may explain why the Christian healing centre was established at Germia. Later, Mantalos shed its pagan legacy and was apparently renamed Eudoxias after a homonymous member of the Theodosian dynasty. No Roman or Byzantine settlement of the region has a history extending back beyond the Iron Age, when the population retreated to fortified hilltop settlements and many sizable Bronze Age höyüks were deserted. Settlement locations changed often and grew little in central Anatolia, and this may be blamed on the uniform landscape of the high plateau; it lacks the Mediterranean's diverse geography of ‘definite places’ that would favour one site above others and ensure its continuity and growth.
Sample size for detecting transgenic plants using inverse binomial group testing with dilution effect
Authors: Montesinos-López Osval Antonio , Montesinos-López Abelardo , Crossa José , Eskridge Kent 
Published: July 2013

AbstractIn this study we developed a sample size procedure for estimating the proportion of genetically modified plants (adventitious presence of unwanted transgenic plants, AP) under inverse negative binomial group testing sampling, which guarantees that exactlyrpositive pools will be present in the sample. To achieve this aim, pools are drawn one by one until the sample containsrpositive pools. The use of group testing produces significant savings because groups that contain several units (plants) are analysed without having to inspect individual plants. However, when using group testing we need to consider an appropriate pool size (k) because if thekindividuals that form a pool are mixed and homogenized, the AP will be diluted. This effect increases with the size of the pool; it may also decrease the AP concentration in the pool below the laboratory test detection limit (d), thereby increasing the number of false negatives. The method proposed in this study determines the required sample size considering the dilution effect and guarantees narrow confidence intervals. In addition, we derived the maximum likelihood estimator ofpand an exact confidence interval (CI) under negative binomial pool testing considering the detection limit of the laboratory test,d, and the concentration of AP per unit (c). Simulated data were created and tables presented showing different potential scenarios that a researcher may encounter. We also provide an R program that can be used to create other scenarios.
Previously unknown and highly divergent ssDNA viruses populate the oceans
Authors: Labonté Jessica M , Suttle Curtis A 
Published: July 2013

Abstract
Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.
Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts
Authors: Freimann Remo , Bürgmann Helmut , Findlay Stuart E G , Robinson Christopher T 
Published: July 2013

AbstractGlaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.
Detecting Temporal Trends in Freshwater Fisheries Surveys: Statistical Power and the Important Linkages between Management Questions and Monitoring Objectives
Authors: Wagner Tyler , Irwin Brian J , Bence James R , Hayes Daniel B 
Published: July 2013

ABSTRACT
Monitoring to detect temporal trends in biological and habitat indices is a critical component of fisheries management. Thus, it is important that management objectives are linked to monitoring objectives. This linkage requires a definition of what constitutes a management-relevant “temporal trend.” It is also important to develop expectations for the amount of time required to detect a trend (i.e., statistical power) and for choosing an appropriate statistical model for analysis. We provide an overview of temporal trends commonly encountered in fisheries management, review published studies that evaluated statistical power of long-term trend detection, and illustrate dynamic linear models in a Bayesian context, as an additional analytical approach focused on shorter term change. We show that monitoring programs generally have low statistical power for detecting linear temporal trends and argue that often management should be focused on different definitions of trends, some of which can be better addressed by alternative analytical approaches.
RESUMEN
el monitoreo que se realiza para detectar tendencias en el tiempo de indices biológicos y de hábitat es un componente critico para el manejo de pesquerias. Por tanto, es crucial que los objetivos de manejo estén concertados con los objetivos de monitoreo. Estas relaciones requieren de la definición de los constituyentes de una “tendencia temporal” que sea relevante para el manejo. También es importante desarrollar expectativas acerca de la cantidad de tiempo necesaria para detectar una tendencia (i.e. poder estadistico) y elegir un modelo estadistico apropiado para el análisis. En este trabajo (1) se presenta un panorama de las tendencias temporales que comúnmente se encuentran en el manejo de pesquerias, (2) se revisa la literatura publicada sobre evaluación del poder estadistico en la detección de tendencias temporales y (3) se aplicaron modelos lineales dinámicos de contexto Bayesiano, como un enfoque analitico adicional enfocado en cambios de corto plazo. Se muestra que los programas de monitoreo generalmente tienen bajo poder estadistico para detectar tendencias lineales en el tiempo y se argumenta que el manejo debiera enfocarse en diferentes definiciones de tendencias, algunas de las cuales pudieran ser mejor estudiadas mediante enfoques analiticos alternativos.
Studies on the Salinity Tolerance of the Juvenile Dark Sleeper
Authors: Lu Genhai , Zhang Haiming , Shi Yonghai , Zhang Genyu , Liu Jianzhong 
Published: July 2013

Abstract
Acute and chronic experiments were conducted to evaluate the effect of salinity on survival and growth of the juvenile Dark Sleeper Odontobutis potamophila. For the acute experiment, half-lethal concentrations (LC50) of salinity for the juvenile Dark Sleeper after exposures for 12, 24, 48, 72 and 96 h were determined. Mean survival time (MST) and half-survival time (ST50) at salinity of 32‰ were also recorded. For the chronic experiment, a 22-day trial focused on comparing the effects of different salinity levels (0, 2, 4, 6, 8, and 10‰) on survival rate and growth of the juvenile Dark Sleeper. Results revealed that the 96-h LC50 was 13.79‰ salinity. MST and ST50 at 32‰ were 35.4 min and 37.0 min, respectively. In the 22-d trial, survival rate and specific growth rate (SGR) decreased with salinity. Survival rate of groups in 8‰ and 10‰ salinity were significantly lower than that of other groups. The SGR for body length and body weight of the 10‰ group was significantly lower than that of the other groups. This study indicates that the optimal salinity level for satisfactory survival and growth of juvenile Dark Sleeper in cultures should be below 6‰.
A genomic random interval model for statistical analysis of genomic lesion data
Authors: Pounds Stan , Cheng Cheng , Li Shaoyu , Liu Zhifa , Zhang Jinghui , Mullighan Charles 
Published: July 2013

Abstract
Motivation: Tumors exhibit numerous genomic lesions such as copy number variations, structural variations and sequence variations. It is difficult to determine whether a specific constellation of lesions observed across a cohort of multiple tumors provides statistically significant evidence that the lesions target a set of genes that may be located across different chromosomes but yet are all involved in a single specific biological process or function.
Results: We introduce the genomic random interval (GRIN) statistical model and analysis method that evaluates the statistical significance of the abundance of genomic lesions that overlap a specific locus or a pre-defined set of biologically related loci. The GRIN model retains certain biologically important properties of genomic lesions that are ignored by other methods. In a simulation study and two example analyses of leukemia genomic lesion data, GRIN more effectively identified important loci as significant than did three methods based on a permutation-of-markers model. GRIN also identified biologically relevant pathways with a significant abundance of lesions in both examples.
Availability: An R package will be freely available at CRAN and www.stjuderesearch.org/site/depts/biostats/software.
Contact: stanley.pounds@stjude.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Topologically inferring risk-active pathways toward precise cancer classification by directed random walk
Authors: Liu Wei , Li Chunquan , Xu Yanjun , Yang Haixiu , Yao Qianlan , Han Junwei , Shang Desi , Zhang Chunlong , Su Fei , Li Xiaoxi , Xiao Yun , Zhang Fan , Dai Meng , Li Xia 
Published: July 2013

Abstract
Motivation: The accurate prediction of disease status is a central challenge in clinical cancer research. Microarray-based gene biomarkers have been identified to predict outcome and outperform traditional clinical parameters. However, the robustness of the individual gene biomarkers is questioned because of their little reproducibility between different cohorts of patients. Substantial progress in treatment requires advances in methods to identify robust biomarkers. Several methods incorporating pathway information have been proposed to identify robust pathway markers and build classifiers at the level of functional categories rather than of individual genes. However, current methods consider the pathways as simple gene sets but ignore the pathway topological information, which is essential to infer a more robust pathway activity.
Results: Here, we propose a directed random walk (DRW)-based method to infer the pathway activity. DRW evaluates the topological importance of each gene by capturing the structure information embedded in the directed pathway network. The strategy of weighting genes by their topological importance greatly improved the reproducibility of pathway activities. Experiments on 18 cancer datasets showed that the proposed method yielded a more accurate and robust overall performance compared with several existing gene-based and pathway-based classification methods. The resulting risk-active pathways are more reliable in guiding therapeutic selection and the development of pathway-specific therapeutic strategies.
Availability: DRW is freely available at http://210.46.85.180:8080/DRWPClass/
Contact: lixia@hrbmu.edu.cn or dm42298@126.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Allosite: a method for predicting allosteric sites
Authors: Huang Wenkang , Lu Shaoyong , Huang Zhimin , Liu Xinyi , Mou Linkai , Luo Yu , Zhao Yanlong , Liu Yaqin , Chen Zhongjie , Hou Tingjun , Zhang Jian 
Published: July 2013

Abstract
Motivation: The use of allosteric modulators as preferred therapeutic agents against classic orthosteric ligands has colossal advantages, including higher specificity, fewer side effects and lower toxicity. Therefore, the computational prediction of allosteric sites in proteins is receiving increased attention in the field of drug discovery. Allosite is a newly developed automatic tool for the prediction of allosteric sites in proteins of interest and is now available through a web server.
Availability: The Allosite server and tutorials are freely available at http://mdl.shsmu.edu.cn/AST
Contact: jian.zhang@sjtu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
A computational method to preclude multistationarity in networks of interacting species
Authors: Feliu Elisenda , Wiuf Carsten 
Published: July 2013

AbstractMotivation: Modeling and analysis of complex systems are important aspects of understanding systemic behavior. In the lack of detailed knowledge about a system, we often choose modeling equations out of convenience and search the (high-dimensional) parameter space randomly to learn about model properties. Qualitative modeling sidesteps the issue of choosing specific modeling equations and frees the inference from specific properties of the equations. We consider classes of ordinary differential equation (ODE) models arising from interactions of species/entities, such as (bio)chemical reaction networks or ecosystems. A class is defined by imposing mild assumptions on the interaction rates. In this framework, we investigate whether there can be multiple positive steady states in some ODE models in a given class.Results: We have developed and implemented a method to decide whether any ODE model in a given class cannot have multiple steady states. The method runs efficiently on models of moderate size. We tested the method on a large set of models for gene silencing by sRNA interference and on two publicly available databases of biological models, KEGG and Biomodels. We recommend that this method is used as (i) a pre-screening step for selecting an appropriate model and (ii) for investigating the robustness of non-existence of multiple steady state for a given ODE model with respect to variation in interaction rates.Availability and Implementation: Scripts and examples in Maple are available in the Supplementary Information.Contact: wiuf@math.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.