bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics analysis of candidate genes and mutations in a congenital sensorineural hearing loss pedigree: detection of 52 genes for the DFNA52 locus
Authors: Qiong Pan , Hu Z , Feng Y , Pan Q , Xia J , Xia K 
Published: February 2008

AbstractObjective:Previously, we have mapped the DFNA52 (Online Mendelian Inheritance in Man (OMIM) 607683) locus, using an 8.8-cM interval on the human chromosome 5q31.1-q32, in a large, consanguineous Chinese family with congenital sensorineural hearing loss. In order to identify the responsible pathogenic mutation within the DFNA52 locus, we set out to identify candidate disease genes within that region and to sequentially analyse these candidate genes.Methods:Using bioinformatics analysis, 52 candidate disease genes were identified based on gene expression data, deafness phenotype, and findings from a mouse model and from the literature (including two mouse deafness genes NEUROG1 and SMAD5). Mutation detection was performed for the 52 candidate genes, in patients from the pedigree.Results:In these patients, we found no disease-causing mutations in the coding and splice site regions of these genes, which segregated with the disease. However, 108 single nucleotide polymorphisms were identified, of which 15 were novel. Eleven of these 108 single nucleotide polymorphisms altered the encoded amino acid.Conclusions:Although we identified a number of nucleotide changes in the affected patients, by analysis of coding and splice site regions of the genes, none of these changes are likely to be pathogenic mutations segregating with the disease. The result implies that the genes studied are unlikely to be a cause of DFNA52-linked sensorineural hearing loss.
Ovarian hormones and binge eating: exploring associations in community samples
Authors: Klump K. L. , Keel P. K. , Culbert K. M. , Edler C. 
Published: February 2008

BackgroundSignificant associations between changes in ovarian hormones and binge eating are present across the menstrual cycle in women with bulimia nervosa. However, no study has examined these relationships in a non-clinical sample, despite the need for these data for designing risk-factor studies.MethodIn study 1, we modified several continuous measures of binge eating and identified those that were most sensitive to menstrual-cycle fluctuations in a non-clinical sample of 10 women who completed measures for 35 days. In study 2, we explored associations between ovarian hormones and binge-eating scores in nine women who completed these same measures for 65 days and provided daily saliva samples for assays of estradiol and progesterone concentrations.ResultsIn study 1, the Emotional Eating subscale of the Dutch Eating Behavior Questionnaire exhibited superior reliability and was most sensitive to predicted menstrual-cycle changes in binge eating (i.e. increased scores in the mid-luteal/premenstrual compared with follicular/ovulatory phases). In study 2, this scale showed predicted inverse associations with estradiol and positive associations with progesterone across the menstrual cycle that could not be accounted for by changes in negative affect.ConclusionAssociations between ovarian hormones and binge eating are robust and present in clinical and non-clinical samples. Findings support the ability to examine the role of ovarian hormones as risk factors for binge eating in large-scale prospective studies and twin studies.
Using an Evidence-Based Methodology to Identify the Competences Required to Deliver Effective Cognitive and Behavioural Therapy for Depression and Anxiety Disorders
Authors: Roth Anthony D. , Pilling Stephen 
Published: February 2008

AbstractA number of developments make the formal specification of competences in CBT both timely and relevant, in particular the Improving Access to Psychological Therapies (IAPT) programme, the increasing focus on process and therapist variables in determining outcome, and the increasing diversity of CBT. This paper outlines the development of an evidence-based methodology for determining both a model and a framework for CBT competences, and considers issues related to the implementation of the framework.
Communicative contract analysis: an approach to popular music analysis
Authors: Shave Thomas 
Published: February 2008

AbstractCommunicative contract analysis constructs an analytic methodology, taking musical semiotics as a theoretical basis, to look at the ways in which pieces of popular music define themselves generically, and how they make reference to other genres. By taking the different components of a sound as referential to parent genres or foreign genres, one can tease out these references in hybrid musical forms. The method is then applied to three contemporary works, The Kaiser Chiefs' Ruby, Hadouken!'s That Boy, That Girl and Bjork's Joga, and the pertinent issues raised in these works are discussed.
Contemporary trends in the use of space in electroacoustic music
Authors: Otondo Felipe 
Published: February 2008

AbstractThis paper describes a survey of contemporary approaches towards the use of spatial design in electroacoustic music, focusing on the type of spatial systems used by a sample of composers and the way they conceive the use of space in their music. Comparing the results with information gathered from seventeen articles by composers written on the topic in 1997, it is shown that composers nowadays are more used to working with different types of spatialisation systems than before. There is also a considerable increase in the use of surround 5.1 as well as four- and eight-channel systems and a decrease in the use of stereo. The compared results also show that, in general, composers nowadays seem to be less concerned with performance and interpretation issues as well as technical aspects of spatialisation. Further studies could consider a more detailed investigation of how the new spatialisation tools have shaped the aesthetical character of the music composed in recent years.
Examining the Tropical Pacific's Response to Global Warming
Authors: Vecchi Gabriel A. , Clement Amy , Soden Brian J. 
Published: February 2008

The response of the tropical Pacific to increasing greenhouse gases represents an exciting intersection of theory, modeling, and observations. In this article, we contrast competing theories for the response of the tropical Pacific to global warming, illustrate the utility of models for understanding and reconciling these theories, and highlight the need for improved instrumental and paleoclimatic reconstructions to better evaluate the fidelity of current model projections.There is a long‐standing debate in the climate community as to how the tropical Pacific will respond to increased greenhouse gases: Will the structure of changes in the ocean surface temperature more closely resemble an El Niño or a La Niña [e.g., Knutson and Manabe, 1995; Clement et al., 1996; Meehl and Washington, 1996; Cane et al., 1997; Cobb et al., 2003; Collins et al., 2005; Vecchi et al., 2006; Zhang and Song, 2006]? This distinction is of profound significance because conditions in the tropical Pacific affect a range of weather phenomena including tropical cyclone activity, global patterns of drought and flood, agricultural productivity, and oceanic biological activity. The debate extends beyond global warming, with El Niño‐ and La Niña‐like responses being invoked as frameworks for interpreting past climate changes on timescales of centuries to millions of years [e.g., Koutavas et al., 2002; Stott et al., 2002; Mann et al., 2005; Wara et al., 2005].
Risk of Infections Associated with Improperly Reprocessed Transrectal Ultrasound–Guided Prostate Biopsy Equipment
Authors: Lessa Fernanda , Tak Sangwoo , DeVader Shannon R. , Goswami Rekha , Anderson Mary , Williams Ian , Gensheimer Kathleen F. , Srinivasan Arjun 
Published: February 2008

Objective.A hospital discovered a lapse in the reprocessing procedures for transrectal ultrasound-guided prostate biopsy equipment. An investigation was initiated to assess the risks of transmission of hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), and bacteria during prostate biopsies.Methods.We offered testing for HBV, HCV, and HIV infection to patients who had undergone prostate biopsies from January 30, 2003, through January 27, 2006. We reviewed their medical records and obtained information on the reprocessing procedures that were in use at the time for the prostate biopsy equipment.Setting.A healthcare facility in Maine.Results.Of the 528 patients exposed to improperly reprocessed prostate biopsy equipment, none tested positive for HIV or HCV. Sixteen patients (3%) tested positive for past HBV infection but had no prebiopsy HBV serologic test results available (ie, transmission from improperly reprocessed biopsy equipment was possible), and 11 (2%) had evidence of postbiopsy bacterial infections. The number of cases of HBV and bacterial infections were within reported ranges for this population and were not clustered in time. Review of the reprocessing procedures in use at the time revealed that the manufacturer-recommended brushes for cleaning the reusable biopsy needle guide were never used. Brushes did not come with the equipment and had to be ordered separately.Conclusions.Despite the lack of evidence of pathogen transmission in this investigation, it is critical to review the manufacturer's reprocessing recommendations and to establish appropriate procedures to avert potential pathogen transmission and subsequent patient concerns. This investigation provides a better understanding of the risks associated with improperly reprocessed transrectal ultrasound prostate biopsy equipment and serves as a methodologic tool for future investigations.
Husimi–Wigner representation of chaotic eigenstates
Authors: Toscano Fabricio , Kenfack Anatole , Carvalho Andre R.R , Rost Jan M , Ozorio de Almeida Alfredo M 
Published: February 2008

Just as a coherent state may be considered as a quantum point, its restriction to a factor space of the full Hilbert space can be interpreted as a quantum plane. The overlap of such a factor coherent state with a full pure state is akin to a quantum section. It defines a reduced pure state in the cofactor Hilbert space. Physically, this factorization corresponds to the description of interacting components of a quantum system with many degrees of freedom and the sections could be generated by conceivable partial measurements.
The collection of all the Wigner functions corresponding to a full set of parallel quantum sections defines the Husimi–Wigner representation. It occupies an intermediate ground between the drastic suppression of non-classical features, characteristic of Husimi functions, and the daunting complexity of higher dimensional Wigner functions. After analysing these features for simpler states, we exploit this new representation as a probe of numerically computed eigenstates of a chaotic Hamiltonian. Though less regular, the individual two-dimensional Wigner functions resemble those of semiclassically quantized states.
Predicting species distributions across the Amazonian and Andean regions using remote sensing data
Authors: Buermann Wolfgang , Saatchi Sassan , Smith Thomas B. , Zutta Brian R. , Chaves Jaime A. , Milá Borja , Graham Catherine H. 
Published: February 2008

AbstractAim  We explore the utility of newly available optical and microwave remote sensing data from the Moderate Resolution Imaging Spectroradiometer (MODIS) and QuikSCAT (QSCAT) instruments for species distribution modelling at regional to continental scales. Using eight Neotropical species from three taxonomic groups, we assess the extent to which remote sensing data can improve predictions of their geographic distributions. For two bird species, we investigate the specific contributions of different types of remote sensing variables to the predictions and model accuracy at the regional scale, where the benefits of the MODIS and QSCAT satellite data are expected to be most significant.Location  South America, with a focus on the tropical and subtropical Andes and the Amazon Basin.Methods  Potential geographic distributions of eight species, namely two birds, two mammals and four trees, were modelled with the maxent algorithm at 1‐km resolution over the South American continent using climatic and remote sensing data separately and combined. For each species and model scenario, we assess model performance by testing the agreement between observed and simulated distributions across all thresholds and, in the case of the two focal bird species, at selected thresholds.Results  Quantitative performance tests showed that models built with remote sensing and climatic layers in isolation performed well in predicting species distributions, suggesting that each of these data sets contains useful information. However, predictions created with a combination of remote sensing and climatic layers generally resulted in the best model performance across the three taxonomic groups. In Ecuador, the inclusion of remote sensing data was critical in resolving the known geographically isolated populations of the two focal bird species along the steep Amazonian–Andean elevational gradients. Within remote sensing subsets, microwave‐based data were more important than optical data in the predictions of the two bird species.Main conclusions  Our results suggest that the newly available remote sensing data (MODIS and QSCAT) have considerable utility in modelling the contemporary geographical distributions of species at both regional and continental scales and in predicting range shifts as a result of large‐scale land‐use change.
Panbiogeographical analysis of distribution patterns in hagfishes (Craniata: Myxinidae)
Authors: Cavalcanti Mauro José , Gallo Valéria 
Published: February 2008

AbstractAim   To analyse the worldwide distribution patterns of hagfishes using panbiogeographical track analysis, and to attempt to correlate these patterns with the tectonic history of the ocean basins.Location   Atlantic and Pacific oceans.Method   The distributions of 47 out of 70 species of hagfish (in the genera Eptatretus, Myxine, Nemamyxine, Neomyxine, and Paramyxine) were studied by the panbiogeographical method of track analysis. The analysis was performed using distributional data obtained from the collections included in the Ocean Biogeographic Information System (OBIS, http://www.iobis.org) and FishBase (http://www.fishbase.org), with additional records from the literature. Individual tracks were obtained for each species by plotting localities and connecting them by minimum‐spanning trees. Generalized tracks were determined from the spatial overlap between individual tracks.Results   Six generalized tracks were found: in the Gulf of Mexico, Caribbean Sea, South‐eastern Atlantic, Western Pacific, North‐eastern Pacific and South‐eastern Pacific.Main conclusions   The distribution patterns of myxinids are marked by a high degree of endemism and vicariance, and are correlated with the tectonic features involved in many of the events that led to the development of oceanic basins. The main massing of the group is around the Pacific Basin. In the Atlantic Ocean, the distribution of Myxine glutinosa seems to correspond to a classic trans‐oceanic track and vicariance resulting from the opening of the Atlantic Ocean during the Cretaceous. In the Pacific Ocean, the distribution of the Eptatretus and Paramyxine species is clearly associated with the margins of the Pacific tectonic plate. The generalized tracks of hagfishes are shared by several other groups of marine organisms, including many from shallow tropical waters, implying a common history for this marine biota. Overall, vicariance is a major feature of hagfish distribution, suggesting vicariant differentiation of widespread ancestors as a result of sea‐floor spreading between continents in connection with ocean formation.
Survival of tree seedlings on different species of decaying wood maintains tree distribution in Michigan hemlock–hardwood forests
Authors: Marx Laura , Walters Michael B. 
Published: February 2008

Summary

Seedlings of some tree species are strongly associated with decaying wood in the germination or establishment period. Despite recognition of this pattern in forests around the world, few studies have compared the ability of different species of decaying wood to support seedlings.
We measured the abundance, survival, and age distribution of seedlings of Tsuga canadensis (eastern hemlock), Betula alleghaniensis (yellow birch), and Acer saccharum (sugar maple) among forest floor substrates at field sites in Upper Michigan, USA. Seedlings were censused on decaying wood of the same three species and on soil to determine whether species of decaying wood and soil differ in their ability to support seedlings. We hypothesized that Tsuga and Betula seedling abundance and survival are higher on Tsuga wood than on Acer wood or soil.
Independent of seed fall, light and size of wood piece, Tsuga wood generally supported the highest densities of first‐year and established (> 1 year‐old) seedlings of Betula and Tsuga. Averaged over three sites, established seedlings per metre square on Tsuga wood, Betula wood, Acer wood and soil were 0.42, 0.21, 0.08 and 0.01, respectively, for Tsuga, 0.60, 0.15, 0.10 and 0.01, respectively, for Betula and 0.09, 0.03, 0.04 and 0.98, respectively for Acer. Long‐term seedling survival was also greatest on Tsuga wood which supported seedlings as old as 13 years, while on Acer wood seedlings > 3 years‐old were rare. Despite a strong general pattern in seedling densities, there were large site differences perhaps related to water availability.
Synthesis. We conclude that the strong association of Tsuga and Betula seedlings with Tsuga decaying wood and not with Acer wood or soil, combined with the distribution of Tsuga wood, helps explain (i) the close Tsuga–Betula association, (ii) the maintenance of distinct, temporally stable Tsuga‐ and Acer‐dominated patches; and (iii) the decline of Tsuga in selectively logged forests as mature trees are harvested and decaying Tsuga wood is scarce. Differences between Tsuga and Acer wood may reflect general differences in the suitability of conifer vs. angiosperm wood for seedling establishment.
Patterns of nucleotide variation and reproductive isolation between aMimulusallotetraploid and its progenitor species
Authors: SWEIGART A. L. , MARTIN N. H. , WILLIS J. H. 
Published: February 2008

AbstractHere we report our characterization of a widespread, highly selfingMimulusallotetraploid formed by interspecific hybridization betweenM. nasutusandM. guttatus. Nucleotide variation at two nuclear loci (mCYCAandmAP3) within and among tetraploid populations resolves two haplotype clusters for each locus: one shares near identity with sequences fromM. nasutusand the other group shares substantial variation withM. guttatus. With respect to the two loci studied, each allotetraploid individual is a ‘fixed heterozygote’ carrying sequences from both clusters. Moreover,mCYCAvariation is consistent with at least two evolutionary origins for theMimulusallotetraploid. We show that the allotetraploid is strongly reproductively isolated fromM. nasutusandM. guttatus; interploidy crosses produce almost no viable seeds. By extension, we infer strong triploid block and argue thatMimulusallotetraploid formation might proceed in one step via the union of unreduced gametes in anM. nasutus–M. guttatusF1hybrid. We also discuss the potential roles of mating system and flowering asynchrony in allotetraploid establishment.
Identifying footprints of directional and balancing selection in marine and freshwater three‐spined stickleback (Gasterosteus aculeatus) populations
Authors: MÄKINEN H. S. , CANO J. M. , MERILÄ J. 
Published: February 2008

AbstractNatural selection is expected to leave an imprint on the neutral polymorphisms at the adjacent genomic regions of a selected gene. While directional selection tends to reduce within‐population genetic diversity and increase among‐population differentiation, the reverse is expected under balancing selection. To identify targets of natural selection in the three‐spined stickleback (Gasterosteus aculeatus) genome, 103 microsatellite and two indel markers including expressed sequence tags (EST) and quantitative trait loci (QTL)‐associated loci, were genotyped in four freshwater and three marine populations. The results indicated that a high proportion of loci (14.7%) might be affected by balancing selection and a lower proportion (2.8%) by directional selection. The strongest signatures of directional selection were detected in a microsatellite locus and two indel markers located in the intronic regions of the Eda‐gene coding for the number of lateral plates. Yet, other microsatellite loci previously found to be informative in QTL‐mapping studies revealed no signatures of selection. Two novel microsatellite loci (Stn12andStn90) located in chromosomes I and VIII, respectively, showed signals of directional selection and might be linked to genomic regions containing gene(s) important for adaptive divergence. Although the coverage of the total genomic content was relatively low, the predominance of balancing selection signals is in agreement with the contention that balancing, rather than directional selection is the predominant mode of selection in the wild.
PTPRC (CD45) variation and disease association studied using single nucleotide polymorphism tagging
Authors: Hennig B. J. , Fry A. E. , Hirai K. , Tahara H. , Tamori A. , Moller M. , Hopkin J. , Hill A. V. , Bodmer W. , Beverley P. , Tchilian E. 
Published: February 2008

AbstractCD45 is a haemopoietic tyrosine phosphatase, crucial for lymphocyte signalling. Two polymorphisms (C77G and A138G), which alter CD45 isoform expression, are associated with autoimmune and infectious diseases. Using HapMap data, we show that there is substantial linkage disequilibrium across the CD45 gene (PTPRC), with similar patterns in different populations. Employing a set of single nucleotide polymorphisms, correlated with a substantial proportion of variation across this gene, we tested for association with type 1 diabetes, Graves’ disease in a Japanese population, hepatitis C in UK population and tuberculin response in a Chinese population. A limited number of common haplotypes was found. Most 138G alleles are present on only one haplotype, which is associated with Graves’ disease, supporting previous data that A138G is a functionally important CD45 polymorphism.
Genetic variation in Polish strains of Gremmeniella abietina
Authors: Kraj W. , Kowalski T. 
Published: February 2008

SummaryThirty‐nine strains of Gremmeniella abietina were isolated between 1980 and 2005 from diseased or symptomless Pinus sylvestris and Pinus nigra, or sporadically Pinus jeffreyi and Pinus armandii from four regions of Poland with varying climatic conditions. Thirty‐five of the strains were genetically similar to the G. abietina A type found in Scandinavia, whereas four were similar to the B type. On the basis of random amplified microsatellite markers, very high intrapopulation and interpopulation genetic variation was detected among the strains. The average value of the Jaccard genetic similarity coefficients among strains was 0.56 for A type and 0.47 for B type, and the monomorphic loci partition was small, at 14% of all analysed loci for the A type. The degree of genetic variation of the fungal strains within each of the four regions was similar, showing no significant differences. The Jaccard coefficient for the strains isolated from P. sylvestris and P. nigra differed significantly, at 0.57 and 0.54 respectively. The genetic distance among A type strains from the investigated regions, expressed using Nei’s coefficient, was not correlated with geographic distance; however, it was highly dependent on elevation (correlation coefficient r = 0.92).