bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of extinction and recovery of phacopid trilobites during the Frasnian–Famennian (Late Devonian) mass extinction event, Canning Basin, Western Australia
Authors: FEIST RAIMUND , MCNAMARA KENNETH J. , CRÔNIER CATHERINE , LEROSEY-AUBRIL RUDY 
Published: September 2008

AbstractA diverse fauna of phacopid trilobites is described from the Late Devonian (middle Frasnian to early Famennian) of the northern Canning Basin, Western Australia. One new genus and four species in two genera are described from zones 11, 13a and 13b of the middle and late Frasnian:Trimerocephaloides sinevisusgen. nov. and sp. nov.,T.?linguiformissp. nov.,Acuticryphops acuticeps(Kayser, 1889) andA. klapperisp. nov. Late Frasnian phacopines are either blind, as shown for the first time inTrimerocephaloides sinevisus, or show trends to decreasing eye size up to the Frasnian–Famennian ‘Kellwasser’ mass extinction event. This evolutionary trend inAcuticryphopsis demonstrated to have been global at this time. One new genus and six species of early Famennian phacopids are described, from the Uppertriangularis, crepidaandrhomboideazones:Houseopsgen. nov. with the new taxaH. canningensissp. nov.,H. beckerisp. nov. andH.sp. A,Babinops planiventerFeist & Becker, 1997,B. minorsp. nov.,Trimerocephalus tardispinosusFeist & Becker, 1997 andT. mimbisp. nov. In contrast to European sections where exclusively blind phacopids are known in earliest Famennian sites, initial recovery following the mass extinction event in Canning peri-reefal environments is characterized by oculated forms. These trilobites must have evolved from conservative ancestors with normal eyes that had succeeded in surviving the Kellwasser biocrises in reef-related shallow water niches. Thus the origin of post-event phacopids from shallow water environments is demonstrated for the first time. Descendant lineages show increasing eye size, increased cephalic vaulting and effacement during the early Famennian.
Comparing Indonesia's party systems of the 1950s and the post-Suharto era: From centrifugal to centripetal inter-party competition
Authors: Mietzner Marcus 
Published: September 2008

AbstractThis article compares Indonesia's party systems of the 1950s and the post-Suharto period. It explores the question of why the party system of the 1950s collapsed quickly, while that of the contemporary polity appears stable. Challenging established assumptions that party systems fail if their individual parties are weakly institutionalised, I submit that the fundamental difference between the party politics of the 1950s and today's democratic system is related to the character of inter-party competition in both periods. While inter-party contestation in the 1950s took place at the far ends of the politico-ideological spectrum, the competition between parties in the contemporary democracy exhibits centripetal tendencies, stabilising the political system as a whole.
The Ethnography of failure: Middle-class Malays producing capitalism in an ‘Asian miracle’ economy
Authors: Sloane-White Patricia 
Published: September 2008

AbstractSince NEP, the ethno-political measure of Malay progress has emphasised Malay capital ownership, leading social scientists who study the Malay middle class to focus almost exclusively on what this article calls the ‘two poles of consumption and dependency’. This ethnography suggests that certain middle-class Malays use a different calculus to mark out their place in contemporary Malay life. It argues that these Malays portray themselves not only in terms of material and entrepreneurial success, but through their frequent experiences of failure. To them, failure becomes, paradoxically, a virtue that can establish their moral and Islamic distance from the Malays they characterise as the ‘indolent’ poor and the ‘politicking’ rich.
Distribution, extent of inter-annual variability and diet of the bloom-forming jellyfish Rhizostoma in European waters
Authors: Lilley M.K.S. , Houghton J.D.R. , Hays G.C. 
Published: September 2008

Jellyfish (Cnidaria: Scyphozoa) are increasingly thought to play a number of important ecosystem roles, but often fundamental knowledge of their distribution, seasonality and inter-annual variability is lacking. Bloom forming species, due to their high densities, can have particularly intense trophic and socio-economic impacts. In northern Europe it is known that one particularly large (up to 30 kg wet weight) bloom forming jellyfish is Rhizostoma spp. Given the potential importance, we set out to review all known records from peer-reviewed and broader public literature of the jellyfish R. octopus (Linnaeus) and R. pulmo (Macri) (Scyphozoa: Rhizostomae) across western Europe. These data revealed distinct hotspots where regular Rhizostoma spp. aggregations appeared to form, with other sites characterized by occasional abundances and a widespread distribution of infrequent observations. Surveys of known R. octopus hotspots around the Irish Sea also revealed marked inter-annual variation with particularly high abundances forming during 2003. The location of such consistent aggregations and inter-annual variances are discussed in relation to physical, climatic and dietary variations.
The prosodic (re)organization of children's early English articles
Authors: DEMUTH KATHERINE , McCULLOUGH ELIZABETH 
Published: September 2008

ABSTRACTResearchers have long been puzzled by children's variable omission of grammatical morphemes, often attributing this to a lack of semantic or syntactic competence. Recent studies suggest that some of this variability may be due to phonological constraints. This paper explored this issue further by conducting a longitudinal study of five English-speaking one- to two-year-olds' acquisition of articles. It found that most children were more likely to produce articles when these could be produced as part of a disyllabic foot. However, acoustic analysis revealed that one child initially produced all articles as independent prosodic words. These findings confirm that some of the variable production of articles is conditioned by constraints on children's early phonologies, providing further support for the Prosodic Licensing Hypothesis. They also hold important implications for our understanding of the emergence of syntactic knowledge.
CBT Supervision: From Reflexivity to Specialization
Authors: Milne Derek 
Published: September 2008

AbstractCognitive-behavioural therapy (CBT) supervision has traditionally been presented as an extension of the therapy, a reflexive strategy that includes a commendable commitment to a principled approach. However, a critical review suggests that this strategy has not been implemented with fidelity. Furthermore, this strategy overlooks potentially valuable ideas from the wider field of clinical supervision, runs counter to CBT's empirical roots, and under-values supervision as a discrete professional specialization. For these reasons, it is argued that new developments should be grafted onto the current approach. In future, this augmented version of CBT supervision should be subjected to the same kinds of research and development (R&D) activity as CBT. Initially, this could include developing a manual to specify and operationalize this innovative approach, evaluation of manual-based training, andN= 1 research to assess its effectiveness. Examples of preliminary work are provided, and future R&D directions identified.
Genetic analysis of self-reported physical activity and adiposity: The Southwest Ohio Family Study
Authors: Choh Audrey C , Demerath Ellen W , Lee Miryoung , Williams Kimberly D , Towne Bradford , Siervogel Roger M , Cole Shelley A , Czerwinski Stefan A 
Published: September 2008

AbstractObjectivePhysical inactivity poses a major risk for obesity and chronic disease, and is influenced by both genetic and environmental factors. However, the genetic association between physical activity (PA) level and obesity is not well characterized. Our aims were to: (i) estimate the extent of additive genetic influences on physical activity while adjusting for household effects; and (ii) determine whether physical activity and adiposity measures share common genetic effects.SubjectsThe sample included 521 (42 % male) adult relatives, 18–86 years of age, from five large families in the Southwest Ohio Family Study.DesignSport, leisure and work PA were self-reported (Baecke Questionnaire of Habitual Physical Activity). Total body and trunk adiposity, including percentage body fat (%BF), were measured using dual-energy X-ray absorptiometry. Abdominal visceral and subcutaneous adipose tissue mass were measured using MRI.ResultsHeritabilities for adiposity and PA traits, and the genetic, household and environmental correlations among them, were estimated using maximum likelihood variance components methods. Significant genetic effects (P< 0·05) were found for sport (h2= 0·26) and leisure PA (h2= 0·17). Significant (P< 0·05) household effects existed for leisure PA (c2= 0·25). Sport PA had a negative genetic correlation with central adiposity measurements adjusted for height (ρG> |−0·40|). Sport and leisure PA had negative genetic correlations with %BF (ρG> |−0·46|).ConclusionsThe results suggest that the association of sport and leisure PA with lower adiposity is due, in part, to a common genetic inheritance of both reduced adiposity and the predisposition to engage in more physical activity.
Association between obesity indices and blood pressure or hypertension: which index is the best?
Authors: Zhou Ziqiang , Hu Dayi , Chen Jie 
Published: September 2008

AbstractBackgroundThe association between obesity and blood pressure is well documented and a series of obesity indices are used as risk factors or indicators of blood pressure and/or the presence of hypertension.ObjectiveThe aim of the present study was to explore and determine which obesity index is the best indicator of blood pressure and the presence of hypertension among five frequently used simple anthropometric indices.MethodsSubjects (n 29 079) were selected by cluster sampling from fourteen Chinese general populations. Weight, height, waist circumference (WC), hip circumference and blood pressure were measured for each participant. BMI, waist:hip ratio (WHR), waist:stature ratio (WSR) and conicity index (CI) were calculated. Pearson correlation, multiple logistic regression, multivariate linear regression and receiver-operating characteristic (ROC) curve analyses were used.ResultsA total of 13 558 men and 15 521 women were investigated. All five obesity indices were positively correlated with blood pressures and hypertension. After adjusting for age, WSR in men and BMI in women had the greatest association with the presence of hypertension, irrespective of the statistical method used. BMI had the strongest correlation with continuous blood pressures in both genders.ConclusionThe present results indicate that hypertension is associated with different obesity indices in men and in women. The best indicator for hypertension is WSR in men while it is BMI in women.
A commentary on current practice in mediating variable analyses in behavioural nutrition and physical activity
Authors: Cerin Ester , MacKinnon David P 
Published: September 2008

AbstractObjectiveTo critique current practice in, and provide recommendations for, mediating variable analyses (MVA) of nutrition and physical activity behaviour change.StrategyTheory-based behavioural nutrition and physical activity interventions aim at changing mediating variables that are hypothesized to be responsible for changes in the outcome of interest. MVA are useful because they help to identify the most promising theoretical approaches, mediators and intervention components for behaviour change. However, the current literature suggests that MVA are often inappropriately conducted, poorly understood and inadequately presented. Main problems encountered in the published literature are explained and suggestions for overcoming weaknesses of current practice are proposed.ConclusionThe use of the most appropriate, currently available methods of MVA, and a correct, comprehensive presentation and interpretation of their findings, is of paramount importance for understanding how obesity can be treated and prevented.
Anaerobic glyoxylate cycle activity during simultaneous utilization of glycogen and acetate in uncultured Accumulibacter enriched in enhanced biological phosphorus removal communities
Authors: Burow Luke C , Mabbett Amanda N , Blackall Linda L 
Published: September 2008

Abstract
Enhanced biological phosphorus removal (EBPR) communities protect waterways from nutrient pollution and enrich microorganisms capable of assimilating acetate as polyhydroxyalkanoate (PHA) under anaerobic conditions. Accumulibacter, an important uncultured polyphosphate-accumulating organism (PAO) enriched in EBPR, was investigated to determine the central metabolic pathways responsible for producing PHA. Acetate uptake and assimilation to PHA in Accumulibacter was confirmed using fluorescence in situ hybridization (FISH)-microautoradiography and post-FISH chemical staining. Assays performed with enrichments of Accumulibacter using an inhibitor of glyceraldehyde-3-phosphate dehydrogenase inferred anaerobic glycolysis activity. Significant decrease in anaerobic acetate uptake and PHA production rates were observed using inhibitors targeting enzymes within the glyoxylate cycle. Bioinformatic analysis confirmed the presence of genes unique to the glyoxylate cycle (isocitrate lyase and malate synthase) and gene expression analysis of isocitrate lyase demonstrated that the glyoxylate cycle is likely involved in PHA production. Reduced anaerobic acetate uptake and PHA production was observed after inhibition of succinate dehydrogenase and upregulation of a succinate dehydrogenase gene suggested anaerobic activity. Cytochrome b/b6 activity inferred that succinate dehydrogenase activity in the absence of external electron acceptors may be facilitated by a novel cytochrome b/b6 fusion protein complex that pushes electrons uphill to more electronegative electron carriers. Identification of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase genes in Accumulibacter demonstrated the potential for interconversion of C3 intermediates of glycolysis and C4 intermediates of the glyoxylate cycle. Our findings along with previous hypotheses from analysis of microbiome data and metabolic models for PAOs were used to develop a model for anaerobic carbon metabolism in Accumulibacter.
Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation (PhD Dissertation)
Authors: O’Meara Brian 
Published: September 2008

Abstract1) Rates of phenotypic evolution have changed throughout the history of life, producing variation in levels of morphological, functional, and ecological diversity among groups. Testing for the presence of these rate shifts is a key component of evaluating hypotheses about what causes them. General predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes. Simulations show that these tests are more powerful than existing tests using standardized contrasts. 2) Species delimitation and species tree inference are difficult problems in the case of recent divergences, especially when different loci have different histories. I quantify the difficulty of the problem and introduce a non-parametric method for simultaneously dividing anonymous samples into different species and inferring a species tree, using individual gene trees as input. This heuristic method seeks to both minimize gene tree – species tree discordance and excess population structure within a species. Analyses suggest that the method may provide useful insights for systematists working at the species level with molecular data.3) The phylogeny of Myrmecocystus ants is estimated using nine loci, finding that none of the three subgenera are monophyletic, implying repeated evolution of foraging times and particular morphologies. A new partitioned likelihood program, MrFisher, is created from MrBayes to aid analysis of multilocus datasets without assuming priors. Simulations show that using a partitioned likelihood approach in the presence of rate heterogeneity and missing data, as is common in supermatrix analyses, can recover correct branch lengths where non-partitioned likelihood gives predictably biased estimates of branch lengths but the correct topology.4) Evolution of foraging time and coevolution of behavior and morphology in Myrmecocystus ants is examined. New models for reconstructing discrete states along branches of a tree and for examining continuous trait evolution and coevolution with discrete traits are developed and implemented. Foraging transitions between diurnal and nocturnal foraging evidently go through crepuscular intermediates. There is some evidence for increased rates of morphological character evolution associated with changes in foraging regime, but little evidence for particular optimum values for morphological traits associated with foraging.
Toward an Understanding of the Interplay Between Culture, Language, and Augmentative and Alternative Communication
Authors: Huer Mary Blake 
Published: September 2008

Abstract
The discovery of appropriate forms and function for linguistic competence in augmentative and alternative communication (AAC) is linked to an understanding of the complexity of culture, cultural choices, the impact of acculturation on practices, societal norms and perceptions, and persons' with complex communication needs (PWCCN) basic human rights to full inclusion in social, educational, economic, and personal experiences on an everyday basis. This article focuses on these topics in order to promote further discussion regarding the influence of culture on the practice of AAC.
Linguistic Competence in Aphasia
Authors: LaPointe Leonard L. 
Published: September 2008

AbstractLoss of implicit linguistic competence assumes a loss of linguistic rules, necessary linguistic computations, or representations. In aphasia, the inherent neurological damage is frequently assumed by some to be a loss of implicit linguistic competence that has damaged or wiped out neural centers or pathways that are necessary for maintenance of the language rules and representations needed to communicate. Not everyone agrees with this view of language use in aphasia. The measurement of implicit language competence, although apparently necessary and satisfying for theoretic linguistics, is complexly interwoven with performance factors. Transience, stimulability, and variability in aphasia language use provide evidence for an access deficit model that supports performance loss. Advances in understanding linguistic competence and performance may be informed by careful study of bilingual language acquisition and loss, the language of savants, the language of feral children, and advances in neuroimaging. Social models of aphasia treatment, coupled with an access deficit view of aphasia, can salve our restless minds and allow pursuit of maximum interactive communication goals even without a comfortable explanation of implicit linguistic competence in aphasia.
OmicsViz: Cytoscape plug-in for visualizing omics data across species
Authors: Xia Tian , Dickerson Julie A. 
Published: September 2008

Abstract
Motivation: OmicsViz is a Cytoscape plug-in for mapping and visualizing large-scale omics datasets across species, including those with many-to-many mappings between homologs. This allows users to map their data onto pathways of related model organisms. Mapping schemas across species or different experimental protocols allow users to comparatively analyze the omics data. The data can also be visualized in parallel-coordinate plots.
Availability: The latest version of OmicsViz with documentation, tutorial and jar files can be downloaded from http://metnet.vrac.iastate.edu/MetNet_fcmodeler.htm
Contact: julied@iastate.edu
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia
Authors: Cosgrove Elissa J. , Zhou Yingchun , Gardner Timothy S. , Kolaczyk Eric D. 
Published: September 2008

AbstractMotivation: DNA microarrays are routinely applied to study diseased or drug-treated cell populations. A critical challenge is distinguishing the genes directly affected by these perturbations from the hundreds of genes that are indirectly affected. Here, we developed a sparse simultaneous equation model (SSEM) of mRNA expression data and applied Lasso regression to estimate the model parameters, thus constructing a network model of gene interaction effects. This inferred network model was then used to filter data from a given experimental condition of interest and predict the genes directly targeted by that perturbation.Results: Our proposed SSEM–Lasso method demonstrated substantial improvement in sensitivity compared with other tested methods for predicting the targets of perturbations in both simulated datasets and microarray compendia. In simulated data, for two different network types, and over a wide range of signal-to-noise ratios, our algorithm demonstrated a 167% increase in sensitivity on average for the top 100 ranked genes, compared with the next best method. Our method also performed well in identifying targets of genetic perturbations in microarray compendia, with up to a 24% improvement in sensitivity on average for the top 100 ranked genes. The overall performance of our network-filtering method shows promise for identifying the direct targets of genetic dysregulation in cancer and disease from expression profiles.Availability: Microarray data are available at the Many Microbe Microarrays Database (M3D, http://m3d.bu.edu). Algorithm scripts are available at the Gardner Lab website (http://gardnerlab.bu.edu/SSEMLasso).Contact: kolaczyk@math.bu.eduSupplementary information: Supplementary Data are available at Bioinformatics on line.
The role of closed areas in rebuilding monkfish populations in the Gulf of Maine
Authors: Smith Melissa D. , Grabowski Jonathan H. , Yund Philip O. 
Published: September 2008

Abstract
Smith, M. D., Grabowski, J. H., and Yund, P. O. 2008. The role of closed areas in rebuilding monkfish populations in the Gulf of Maine. – ICES Journal of Marine Science, 65: 1326–1333. The use of fish closures as a management tool to protect juvenile fish habitat and adult spawning grounds has become increasingly popular, although knowledge of the direct effects of marine closures on juvenile fish populations is limited. Given that monkfish landings account for a considerable percentage of the monetary value derived from the groundfish fishery in new England, investigating the factors that influence monkfish population dynamics will assist managers in sustaining this important natural resource. We conducted bottom-trawl surveys to determine the effects of closure status [inside vs. outside the Western Gulf of Maine Closure Area (WGMCA)] and habitat type (mud bottom in isolation from gravel or cobble bottom vs. mud that is next to these more complex habitats) on the distribution, abundance, and diet composition of monkfish (Lophius americanus) in the Gulf of Maine. Surprisingly, the abundance of adult monkfish did not differ in vs. out of the closure, and juvenile monkfish were more abundant outside of the WGMCA, where they also exhibited higher feeding intensity and consumed more prey biomass. Monkfish diet and condition results implied that the boulder and ledge bottom is essential monkfish habitat and that these effects were independent of the WGMCA.