bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the genetic diversity of an invasive whitefly (Bemisia tabaci) in China using both mitochondrial and nuclear DNA markers
Authors: Chu D. , Gao C.S. , De Barro P. , Wan F.H. , Zhang Y.J. 
Published: February 2011

AbstractIt is often considered that reduced genetic variation due to bottlenecks and founder effects limits the capacity for species to establish in new environments and subsequently spread. The recent invasion (during the past five years) of an alien whitefly, one member ofBemisia tabacicryptic species complex, referred to as Mediterranean (herein referred to as Q-type) in Shandong Province, China, provides an ideal opportunity to study the changes in genetic variation between its home range in the Mediterranean region and its invasion range. Using both the mitochondrial cytochrome oxidase I (mtCOI) and nuclear (microsatellite) DNA, we show that Q in Shandong likely originated in the western Mediterranean. We also found that the haplotype diversity was low compared with its presumed geographic origin, whereas microsatellite allele diversity showed no such decline. A key factor in invasions is the establishment of females and so bottleneck and founder events can lead to a very rapid and considerable loss of mitochondrial diversity. The lack of haplotype diversity in Shandong supports the interpretation that, at one or more points between the western Mediterranean and China, the invading Q lost haplotype diversity, most probably through the serial process of establishment and redistribution through trade in ornamental plants. However, the loss in haplotype diversity does not necessarily mean that nuclear allelic diversity should also decline. Provided females can mate freely with whichever males are available, allelic diversity can be maintained or even increased relative to the origin of the invader. Our findings may offer some explanation to the apparent paradox between the concept of reduced genetic variation limiting adaptation to new environments and the observed low diversity in successful invaders.
Analysts’ Incentives to Produce Industry-Level versus Firm-Specific Information
Authors: Liu Mark H. 
Published: February 2011

AbstractUsing stock returns around recommendation changes to measure the information produced by analysts, I find that analysts produce more firm-specific than industry-level information. Analysts produce more firm-specific information on stocks with higher idiosyncratic return volatilities. The amount of industry information produced by analysts increases with the absolute value of the stock’s industry beta and decreases with the stock’s idiosyncratic volatility. Other stocks in the industry also respond to the recommendation change, and the magnitude of the response increases with the absolute value of the industry beta of the recommended stock and that of other stocks in the industry. I also offer results on how investors may use analyst research more effectively and potentially improve their investment performance.
Liquidity and Arbitrage in the Market for Credit Risk
Authors: Nashikkar Amrut , Subrahmanyam Marti G. , Mahanti Sriketan 
Published: February 2011

AbstractThe recent credit crisis has highlighted the importance of market liquidity and its interaction with the price of credit risk. We investigate this interaction by relating the liquidity of corporate bonds to the basis between the credit default swap (CDS) spread of the issuer and the par-equivalent bond yield spread. The liquidity of a bond is measured using a recently developed measure called latent liquidity, which is defined as the weighted average turnover of funds holding the bond, where the weights are their fractional holdings of the bond. We find that bonds with higher latent liquidity are more expensive relative to their CDS contracts after controlling for other realized measures of liquidity. Analysis of interaction effects shows that highly illiquid bonds of firms with a greater degree of uncertainty are also expensive, consistent with limits to arbitrage between CDS and bond markets, due to the higher costs of “shorting” illiquid bonds. Additionally, we document the positive effects of liquidity in the CDS market on the CDS-bond basis. We also find that several firm- and bond-level variables related to credit risk affect the basis, indicating that the CDS spread does not fully capture the credit risk of the bond.
Stance, positioning, and alignment in narratives of professional experience
Authors: Baynham Mike 
Published: February 2011

AbstractThis article examines narratives of professional experience in a corpus of forty interviews in which English to Speakers of Other Languages (ESOL) teachers reflect on their professional life histories as well as their current teaching. The notion of “stance” emerged as a major theme: the teachers positioned themselves in relation to the policy environment, to learners, teaching and learning, and their sense of control in their working lives. Narrative was an important discursive resource for doing so and a range of narrative types (personal, generic/iterative, hypothetical, exemplum, and ‘negated’) are identified, each demonstrating performance features. Using Dubois's (2007) definition of stance, I examine the dynamic relationship between stance taking and discursive positioning, discussing the role of performance in these processes. Shifts into performance are shown to depend on participant roles and alignments in the interviews rather than on particular narrative types. Thus, the data contradicts some of Wolfson's (1976) observations on narratives in the research interview. The analysis contributes to our understanding of the research interview as a dynamically co-constructed speech genre rather than as a neutral locus for gathering data. (Professional narrative, performance, stance, alignment, positioning)
Hospital-acquired infections in Belgian acute-care hospitals: an estimation of their global impact on mortality, length of stay and healthcare costs
Authors: VRIJENS F. , HULSTAERT F. , DEVRIESE S. , VAN DE SANDE S. 
Published: February 2011

SUMMARYAssessing the overall burden of disease which can be attributed to hospital-acquired infections (HAIs) remains a challenge. A matched cohort study was performed to estimate excess mortality, length of stay and costs attributable to HAIs in Belgian acute-care hospitals, using six matching factors (hospital, diagnosis-related group, age, ward, Charlson score, estimated length of stay prior to infection). Information was combined from different sources on the epidemiology and burden of HAIs to estimate the impact at national level. The total number of patients affected by a HAI each year was 125 000 (per 10·9 million inhabitants). The excess mortality was 2·8% and excess length of stay was 7·3 days, corresponding to a public healthcare cost of €290 million. A large burden was observed outside the intensive-care unit setting (87% of patients infected and extra costs, 73% of excess deaths).
Ruminant and industrial sources of trans-fat and cardiovascular and diabetic diseases
Authors: Tardy Anne-Laure , Morio Béatrice , Chardigny Jean-Michel , Malpuech-Brugère Corinne 
Published: February 2011

The various positional isomers of oleic acid (18 : 1Δ9c or 9c-18 : 1) may have distinct biological effects. Detrimental effects of consumption of industrial trans-fatty acids (TFA) (elaidic acid; 18 : 1Δ9t) from partially hydrogenated vegetable oils on CVD risk factors are well documented. In addition, epidemiological data suggest that chronic consumption of industrial sources of TFA could alter insulin sensitivity and predispose for type 2 diabetes. However, intervention studies on this issue have remained inconclusive. Moreover, very little information is available on the effect of natural sources of TFA (vaccenic acid; 18 : 1Δ11t) coming from dairy products and ruminant meat on the development of CVD and type 2 diabetes. The review focuses on the impact of the consumption of ruminant TFA in relation to cardiovascular risk factors, inflammation and type 2 diabetes.
Spatial Bias and Right Hemisphere Function: Sex-Specific Changes with Aging
Authors: Chen Peii , Goedert Kelly M. , Murray Elizabeth , Kelly Karen , Ahmeti Shpresa , Barrett Anna M. 
Published: February 2011

AbstractPatterns of cerebral asymmetry related to visuospatial functions may change with age. The typical leftward bias on a line bisection task may reflect cerebral asymmetry. With age, such leftward bias decreases. This study demonstrated that the age-related decrease of leftward bias may actually be sex-specific. In addition, previous research suggests that young adults’ deviation in line bisection may reflect asymmetric hemispheric activation of perceptual–attentional “where” spatial systems, rather than motor-intentional “aiming” spatial systems; thus, we specifically fractionated “where” and “aiming” bias of men and women ranging in age from 22 to 93 years old. We observed that older men produced greater rightward line bisection errors, of primarily “where” spatial character. However, women's errors remained leftward biased, and did not significantly change with age. “Where” spatial systems may be linked to cortico-cortical processing networks involving the posterior part of the dorsal visuospatial processing stream. Thus, the current results are consistent with the conclusion that reduced right dorsal spatial activity in aging may occur in the male, but not female, adult spatial system development. (JINS, 2011, 17, 455–462)
Profiling alternative food system supporters: The personal and social basis of local and organic food support
Authors: Bean Molly , Sharp Jeff S. 
Published: February 2011

AbstractConsumers appear increasingly interested in how to engage in consumptive practices that lead to a more sustainable food and agricultural system. In this paper, we examine two possible consumptive pathways for achieving sustainability: the purchase of organic foods and/or the purchase of local foods. While there is some debate regarding the integrity and sustainability of organic versus locally produced foods, there is limited information examining the similarities or differences among consumers variably interested in one or the other attribute. Using data from a statewide survey of Ohio, USA, respondents and members of a food cooperative and an environmental and social responsibility organization, a typology is proposed and comparisons are made among different types of local and organic food consumers regarding their attitudes about food, agriculture and the environment. While a large proportion of the survey respondents expressed little or only modest interest in either local or organic foods, distinct groups of respondents interested in primarily the local attribute, primarily the organic attribute, and both attributes are identified. The results reveal similarities and differences across types with the profiles of each type of consumer contributing to a more nuanced view of supporters of these foods that can assist in production decisions, as well as purchasing and marketing decisions among retailers.
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides
Authors: Gleghorn Michael L. , Davydova Elena K. , Basu Ritwika , Rothman-Denes Lucia B. , Murakami Katsuhiko S. 
Published: February 2011

We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groups of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.
Cross-platform comparison of microarray data using order restricted inference
Authors: Klinglmueller Florian , Tuechler Thomas , Posch Martin 
Published: February 2011

Abstract
Motivation: Titration experiments measuring the gene expression from two different tissues, along with total RNA mixtures of the pure samples, are frequently used for quality evaluation of microarray technologies. Such a design implies that the true mRNA expression of each gene, is either constant or follows a monotonic trend between the mixtures, applying itself to the use of order restricted inference procedures. Exploiting only the postulated monotonicity of titration designs, we propose three statistical analysis methods for the validation of high-throughput genetic data and corresponding preprocessing techniques.
Results: Our methods allow for inference of accuracy, repeatability and cross-platform agreement, with minimal required assumptions regarding the underlying data generating process. Therefore, they are readily applicable to all sorts of genetic high-throughput data independent of the degree of preprocessing. An application to the EMERALD dataset was used to demonstrate how our methods provide a rich spectrum of easily interpretable quality metrics and allow the comparison of different microarray technologies and normalization methods. The results are on par with previous work, but provide additional new insights that cast doubt on the utility of popular preprocessing techniques, specifically concerning the EMERALD projects dataset.
Availability: All datasets are available on EBI's ArrayExpress web site http://www.ebi.ac.uk/microarray-as/ae/) under accession numbers E-TABM-536, E-TABM-554 and E-TABM-555. Source code implemented in C and R is available at: http://statistics.msi.meduniwien.ac.at/float/cross_platform/.
Methods for testing and variance decomposition have been made available in the R-package orQA, which can be downloaded and installed from CRAN http://cran.r-project.org.
Contact: martin.posch.mail@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome
Authors: Siddle K. J. , Goodship J. A. , Keavney B. , Santibanez-Koref M. F. 
Published: February 2011

Abstract
Mononucleotide repeats (MNRs) are abundant in eukaryotic genomes and exhibit a high degree of length variability due to insertion and deletion events. However, the relationship between these repeats and mutation rates in surrounding sequences has not been systematically investigated. We have analyzed the frequency of single nucleotide polymorphisms (SNPs) at positions close to and within MNRs in the human genome. Overall, we find a 2- to 4-fold increase in the SNP frequency at positions immediately adjacent to the boundaries of MNRs, relative to that at more distant bases. This relationship exhibits a strong asymmetry between 3′ and 5′ ends of repeat tracts and is dependent upon the repeat motif, length and orientation of surrounding repeats. Our analysis suggests that the incorporation or exclusion of bases adjacent to the boundary of the repeat through substitutions, in which these nucleotides mutate towards or away from the base present within the repeat, respectively, may be another mechanism by which MNRs expand and contract in the human genome.
Contact: kjsiddle@pasteur.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated analysis of biological oscillator models using mode decomposition
Authors: Konopka Tomasz 
Published: February 2011

Abstract
Motivation: Oscillating signals produced by biological systems have shapes, described by their Fourier spectra, that can potentially reveal the mechanisms that generate them. Extracting this information from measured signals is interesting for the validation of theoretical models, discovery and classification of interaction types, and for optimal experiment design.
Results: An automated workflow is described for the analysis of oscillating signals. A software package is developed to match signal shapes to hundreds of a priori viable model structures defined by a class of first-order differential equations. The package computes parameter values for each model by exploiting the mode decomposition of oscillating signals and formulating the matching problem in terms of systems of simultaneous polynomial equations. On the basis of the computed parameter values, the software returns a list of models consistent with the data. In validation tests with synthetic datasets, it not only shortlists those model structures used to generate the data but also shows that excellent fits can sometimes be achieved with alternative equations. The listing of all consistent equations is indicative of how further invalidation might be achieved with additional information. When applied to data from a microarray experiment on mice, the procedure finds several candidate model structures to describe interactions related to the circadian rhythm. This shows that experimental data on oscillators is indeed rich in information about gene regulation mechanisms.
Availability: The software package is available at http://babylone.ulb.ac.be/autoosc/.
Contact: tkonopka@ulb.ac.be
Supplementary information: Supplementary data are available at Bioinformatics online.
Network clustering: probing biological heterogeneity by sparse graphical models
Authors: Mukherjee Sach , Hill Steven M. 
Published: February 2011

AbstractMotivation: Networks and pathways are important in describing the collective biological function of molecular players such as genes or proteins. In many areas of biology, for example in cancer studies, available data may harbour undiscovered subtypes which differ in terms of network phenotype. That is, samples may be heterogeneous with respect to underlying molecular networks. This motivates a need for unsupervised methods capable of discovering such subtypes and elucidating the corresponding network structures.Results: We exploit recent results in sparse graphical model learning to put forward a ‘network clustering’ approach in which data are partitioned into subsets that show evidence of underlying, subset-level network structure. This allows us to simultaneously learn subset-specific networks and corresponding subset membership under challenging small-sample conditions. We illustrate this approach on synthetic and proteomic data.Availability: go.warwick.ac.uk/sachmukherjee/networkclusteringContact: s.n.mukherjee@warwick.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
eGOB: eukaryotic Gene Order Browser
Authors: López Marcela Dávila , Samuelsson Tore 
Published: February 2011

Abstract
Summary: A large number of genomes have been sequenced, allowing a range of comparative studies. Here, we present the eukaryotic Gene Order Browser with information on the order of protein and non-coding RNA (ncRNA) genes of 74 different eukaryotic species. The browser is able to display a gene of interest together with its genomic context in all species where that gene is present. Thereby, questions related to the evolution of gene organization and non-random gene order may be examined. The browser also provides access to data collected on pairs of adjacent genes that are evolutionarily conserved.
Availability: eGOB as well as underlying data are freely available at http://egob.biomedicine.gu.se
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: tore.samuelsson@medkem.gu.se
Topological entropy of DNA sequences
Authors: Koslicki David 
Published: February 2011

Abstract
Motivation: Topological entropy has been one of the most difficult to implement of all the entropy-theoretic notions. This is primarily due to finite sample effects and high-dimensionality problems. In particular, topological entropy has been implemented in previous literature to conclude that entropy of exons is higher than of introns, thus implying that exons are more ‘random’ than introns.
Results: We define a new approximation to topological entropy free from the aforementioned difficulties. We compute its expected value and apply this definition to the intron and exon regions of the human genome to observe that as expected, the entropy of introns are significantly higher than that of exons. We also find that introns are less random than expected: their entropy is lower than the computed expected value. We also observe the perplexing phenomena that introns on chromosome Y have atypically low and bimodal entropy, possibly corresponding to random sequences (high entropy) and sequences that posses hidden structure or function (low entropy).
Availability: A Mathematica implementation is available at http://www.math.psu.edu/koslicki/entropy.nb
Contact: koslicki@math.psu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Spatial and temporal variability in the structure of aggregations of Antarctic krill (Euphausia superba) around South Georgia, 1997–1999
Authors: Cox Martin J. , Watkins Jonathan L. , Reid Keith , Brierley Andrew S. 
Published: February 2011

Abstract
Cox, M. J., Watkins, J. L., Reid, K., and Brierley, A. S. 2011. Spatial and temporal variability in the structure of aggregations of Antarctic krill (Euphausia superba) around South Georgia, 1997–1999. – ICES Journal of Marine Science, 68: . Antarctic krill are important in the South Georgia (54°S 35°W) marine ecosystem. They form aggregations that vary widely in packing density (<1 to 1000 s of individuals m−3), length (tens to thousands of metres), and height (tens of metres). Acoustic surveys are often used to estimate krill biomass and provide data that give insight into aggregation structure. Using dual-frequency (38 and 120 kHz) acoustic data collected during six surveys conducted around South Georgia during the 1997, 1998, and 1999 austral summers, we isolated 2990 aggregations by applying the Shoal Analysis and Patch Estimation System algorithm in Echoview and a krill-length-dependent acoustic identifier (ΔSv120–38). Multivariate cluster (partition) analysis was applied to metrics from each of the aggregations, resulting in three aggregation types with an overall proportional split of 0.28:0.28:0.44. Types 1 and 3 had low mean densities (<2 g m−3), whereas Type 2 had a mean density of 94 g m−3. Intersurvey differences were found between the effort-corrected numbers of aggregation types (p = 2.5e−6), and between on- and off-continental shelf areas (p = 1.5e−7), with a greater number of Type 2 aggregations being found on-shelf. The findings suggest intersurvey variation in krill catchability, with krill being more likely to be caught on-shelf.