bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution of Long-Range Linkage Disequilibrium and Tajima’s D Values in Scandinavian Populations of Norway Spruce (Picea abies)
Authors: Larsson Hanna , Källman Thomas , Gyllenstrand Niclas , Lascoux Martin 
Published: March 2013

AbstractThe site frequency spectrum of mutations (SFS) and linkage disequilibrium (LD) are the two major sources of information in population genetics studies. In this study we focus on the levels of LD and the SFS and on the effect of sample size on summary statistics in 10 Scandinavian populations of Norway spruce. We found that previous estimates of a low level of LD were highly influenced by both sampling strategy and the fact that data from multiple loci were analyzed jointly. Estimates of LD were in fact heterogeneous across loci and increased within individual populations compared with the estimate from the total data. The variation in levels of LD among populations most likely reflects different demographic histories, although we were unable to detect population structure by using standard approaches. As in previous studies, we also found that the SFS-based test Tajima’s D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in line with recent studies in other conifers that have revealed a more complex and variable pattern of LD than earlier studies suggested and with studies in trees and humans that suggest that Tajima’s D is sensitive to sample size. This has large consequences for the design of future association and population genetic studies in Norway spruce.
Population Structure in a Comprehensive Genomic Data Set on Human Microsatellite Variation
Authors: Pemberton Trevor J , DeGiorgio Michael , Rosenberg Noah A 
Published: March 2013

AbstractOver the past two decades, microsatellite genotypes have provided the data for landmark studies of human population-genetic variation. However, the various microsatellite data sets have been prepared with different procedures and sets of markers, so that it has been difficult to synthesize available data for a comprehensive analysis. Here, we combine eight human population-genetic data sets at the 645 microsatellite loci they share in common, accounting for procedural differences in the production of the different data sets, to assemble a single data set containing 5795 individuals from 267 worldwide populations. We perform a systematic analysis of genetic relatedness, detecting 240 intra-population and 92 inter-population pairs of previously unidentified close relatives and proposing standardized subsets of unrelated individuals for use in future studies. We then augment the human data with a data set of 84 chimpanzees at the 246 loci they share in common with the human samples. Multidimensional scaling and neighbor-joining analyses of these data sets offer new insights into the structure of human populations and enable a comparison of genetic variation patterns in chimpanzees with those in humans. Our combined data sets are the largest of their kind reported to date and provide a resource for use in human population-genetic studies.
The Genomic and Transcriptomic Landscape of a HeLa Cell Line
Authors: Landry Jonathan J M , Pyl Paul Theodor , Rausch Tobias , Zichner Thomas , Tekkedil Manu M , Stütz Adrian M , Jauch Anna , Aiyar Raeka S , Pau Gregoire , Delhomme Nicolas , Gagneur Julien , Korbel Jan O , Huber Wolfgang , Steinmetz Lars M 
Published: March 2013

Abstract
HeLa is the most widely used model cell line for studying human cellular and molecular biology. To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. Effective design and interpretation of molecular genetic studies performed using HeLa cells require accurate genomic information. Here we present a detailed genomic and transcriptomic characterization of a HeLa cell line. We performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile. Segmentation of the genome according to copy number revealed a remarkably high level of aneuploidy and numerous large structural variants at unprecedented resolution. Some of the extensive genomic rearrangements are indicative of catastrophic chromosome shattering, known as chromothripsis. Our analysis of the HeLa gene expression profile revealed that several pathways, including cell cycle and DNA repair, exhibit significantly different expression patterns from those in normal human tissues. Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins. This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology.
Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case
Authors: Reisser Cyrielle , Dick Cynthia , Kruglyak Leonid , Botstein David , Schacherer Joseph , Hess David C 
Published: March 2013

Abstract
High concentrations of ammonium at physiological concentrations of potassium are toxic for the standard laboratory strain of Saccharomyces cerevisiae. In the original description of this metabolic phenotype, we focused on the standard laboratory strains of Saccharomyces. In this study, we screened a large collection of S. cerevisiae natural isolates and identified one strain that is resistant to high concentrations of ammonium. This strain, K12, was isolated in sake breweries. When the K12 strain was crossed to the standard laboratory strain (FY4), the resulting tetrads displayed 2:2 segregation of the resistance phenotype, suggesting a single gene trait. Using a bulk segregant analysis strategy, we mapped this trait to a 150-kb region on chromosome X containing the TRK1 gene. This gene encodes a transporter required for high-affinity potassium transport in S. cerevisiae. Data from reciprocal hemizygosity experiments with TRK1 deletion strains in K12 and BY backgrounds, as well as analysis of the deletion of this gene in the K12 strain, demonstrate that the K12 allele of TRK1 is responsible for ammonium toxicity resistance. Furthermore, we determined the minimal amount of potassium required for both the K12 and laboratory strain needed for growth. These results demonstrate that the gene encoded by the K12 allele of TRK1 has a greater affinity for potassium than the standard allele of TRK1 found in Saccharomyces strains. We hypothesize that this greater-affinity allele of the potassium transporter reduces the flux of ammonium into the yeast cells under conditions of ammonium toxicity. These findings further refine our understanding of ammonium toxicity in yeast and provide an example of using natural variation to understand cellular processes.
Involvement of MLPK Pathway in Intraspecies Unilateral Incompatibility Regulated by a Single Locus With Stigma and Pollen Factors
Authors: Takada Yoshinobu , Sato Takahiro , Suzuki Go , Shiba Hiroshi , Takayama Seiji , Watanabe Masao 
Published: March 2013

AbstractPlants have evolved many systems to prevent undesirable fertilization. Among these, incompatibility is a well-organized system in which pollen germination or pollen tube growth is inhibited in pistils. We previously found that a novel one-way pollen–stigma incompatibility response [unilateral incompatibility (UI)] occurred between two self-incompatible Brassica rapa plants, a Turkish line, and a Japanese cultivated hybrid variety, “Osome.” Pollen from the Turkish line is rejected on the stigma of the Osome line, but the reverse cross is compatible; such a UI phenotype closely resembles self-incompatibility (SI). The pollen factor of this UI has been genetically explained by a single locus which is different from the S-locus. In this study, we performed further genetic analyses of this intraspecies UI and showed that the stigma factor was also controlled by a single locus, and we named the loci corresponding to the stigma and pollen factors of the intraspecies UI, stigmatic unilateral incompatibility (SUI), and pollen unilateral incompatibility (PUI) loci, respectively. Interestingly, segregation analyses of SUI and PUI indicated that they are closely linked to each other and behave as a single unit. To investigate the effect of an SI-related gene, MLPK in this UI, we produced segregation lines for SUI and mlpk. A distorted segregation ratio of SUI phenotype in an mlpk background indicated involvement of MLPK in SUI, suggesting the existence of an MLPK-dependent novel pollen–stigma recognition mechanism.
A High-Fidelity Cell Lineage Tracing Method for Obtaining Systematic Spatiotemporal Gene Expression Patterns inCaenorhabditis elegans
Authors: Mace Daniel L , Weisdepp Peter , Gevirtzman Louis , Boyle Thomas , Waterston Robert H 
Published: March 2013

AbstractAdvances in microscopy and fluorescent reporters have allowed us to detect the onset of gene expression on a cell-by-cell basis in a systematic fashion. This information, however, is often encoded in large repositories of images, and developing ways to extract this spatiotemporal expression data is a difficult problem that often uses complex domain-specific methods for each individual data set. We present a more unified approach that incorporates general previous information into a hierarchical probabilistic model to extract spatiotemporal gene expression from 4D confocal microscopy images of developing Caenorhabditis elegans embryos. This approach reduces the overall error rate of our automated lineage tracing pipeline by 3.8-fold, allowing us to routinely follow the C. elegans lineage to later stages of development, where individual neuronal subspecification becomes apparent. Unlike previous methods that often use custom approaches that are organism specific, our method uses generalized linear models and extensions of standard reversible jump Markov chain Monte Carlo methods that can be readily extended to other organisms for a variety of biological inference problems relating to cell fate specification. This modeling approach is flexible and provides tractable avenues for incorporating additional previous information into the model for similar difficult high-fidelity/low error tolerance image analysis problems for systematically applied genomic experiments.
Intrabony Defects, Open‐Flap Debridement, and Decortication: A Randomized Clinical Trial
Authors: Crea Alessandro , Deli Giorgio , Littarru Cristiano , Lajolo Carlo , Orgeas Gianluca Vittorini , Tatakis Dimitris N. 
Published: March 2013

Background: Intramarrow penetration (IMP) is often incorporated in regenerative periodontal surgical procedures. However, the actual benefits of adding IMP to such a procedure remain undocumented. The purpose of this randomized controlled trial was to investigate the contribution of IMP to the outcomes of open‐flap debridement (OFD) treatment of intrabony defects.Methods: Forty‐two chronic periodontitis patients, each contributing a 2‐wall, 3‐wall, or combined 2‐ to 3‐wall intrabony defect, were treated. Sites were randomly assigned into one of two groups: control (OFD alone) or test (OFD + IMP). Papilla preservation flaps were raised, and defects were thoroughly debrided. In the control group, complete primary closure of flaps was ensured after debridement. In the test group, IMP was performed before flap closure, using a round bur to penetrate the cortical defect wall. Clinical and radiographic parameters were assessed at baseline and 12 months after treatment.Results: At baseline, there were no statistically significant differences between groups. At 12 months, both groups experienced significant improvements, in terms of probing depth reduction, clinical attachment level (CAL) gain, and bone level (clinical and radiographic). The test group experienced significantly greater clinical bone gain (3.07 ± 1.74 mm) and prevalence of CAL gain ≥2 mm (93% of sites) compared with the control group (1.76 ± 2.71 mm, P <0.03; 62%, P = 0.024). The test treatment benefits were particularly evident in mandibular sites, in which OFD + IMP doubled the radiographic bone gain obtained by OFD alone.Conclusion: Addition of IMP to an OFD procedure used to treat intrabony defects results in statistically and clinically significant enhancement of both clinical and radiographic outcomes.
Periodontal Treatment Reduces Matrix Metalloproteinase Levels in Localized Aggressive Periodontitis
Authors: Gonçalves Patricia Furtado , Huang Hong , McAninley Suzanna , Alfant Barnett , Harrison Peter , Aukhil Ikramuddin , Walker Clay , Shaddox Luciana Macchion 
Published: March 2013

Background: Matrix metalloproteinases (MMPs) are a family of host‐derived proteinases reported to mediate multiple functions associated with periodontal breakdown and inflammation. High MMP levels in African‐American children with localized aggressive periodontitis (LAgP) have been reported previously by the present authors. However, little is known about MMP reductions in gingival crevicular fluid (GCF) after therapy. This study aims to evaluate MMP levels in the GCF after treatment of LAgP and to correlate these levels with clinical response.Methods: GCF samples were collected from 29 African‐American individuals diagnosed with LAgP. GCF was collected from one diseased site (probing depth [PD] >4 mm, bleeding on probing [BOP], and clinical attachment level ≥2 mm) and one healthy site (PD ≤3 mm, no BOP) from each individual at baseline and 3 and 6 months after periodontal treatment, which consisted of full‐mouth scaling and root planing (SRP) and systemic antibiotics. The volume of GCF was controlled using a calibrated gingival fluid meter, and levels of MMP‐1, MMP‐2, MMP‐3, MMP‐8, MMP‐9, MMP‐12, and MMP‐13 were assessed using fluorometric kits.Results: MMP‐1, MMP‐8, MMP‐9, MMP‐12, and MMP‐13 levels were reduced significantly up to 6 months, comparable to healthy sites at the same point. Significant correlations were noted between MMP‐2, MMP‐3, MMP‐8, MMP‐9, MMP‐12, and MMP‐13 levels and percentage of sites with PD >4 mm. MMP‐3, MMP‐12, and MMP‐13 levels also correlated with mean PD of affected sites.Conclusion: Treatment of LAgP with SRP and systemic antibiotics was effective in reducing local levels of specific MMPs in African‐American individuals, which correlated positively with some clinical parameters.
New Analytical and Statistical Approach for Estimating and Analyzing Sand Production Through Plain Square-Mesh Screens During a Sand-Retention Test
Authors: Chanpura Rajesh A. , Mondal Somnath , Andrews Jamie S. , Mathisen Anne-Mette , Ayoub Joseph A. , Parlar Mehmet , Sharma Mukul M. 
Published: March 2013

Summary
There are two types of sand-retention tests (SRTs) generally used in the industry to evaluate the performance of sand-control screens for standalone-screen (SAS) applications—prepack tests and slurry tests. They represent complete hole collapse and gradual rock failure around the wellbore, respectively.
In this paper, we present analytical models and Monte Carlo (MC) simulations to estimate sand production in slurry-type SRTs with square-mesh screens while taking into account the full particle-size distribution (PSD) of the formation sand. We also compare the model results with four sets of experimental data and demonstrate that this approach can be used to predict sand production for different sand-size-distribution/screen-size combinations without the need for physical tests (provided that both an accurate representation of the formation-sand PSD and an accurate representation of screen pore sizes are available). This work augments previously published slurry-test models that were limited to wire-wrapped screens (WWSs), and enables the comparison of the performance of square-mesh screens with WWSs.
The analytical model and the MC simulations provide a direct and reliable way to estimate the amount of sand that will be produced for a given sand-size distribution and a given screen size. Because the proposed methods are much more quantitative, they represent a significant improvement that surpasses current methods that rely on single design points or rules of thumb for screen selection.
The Effect of Intensive Glucose Lowering on Lipoprotein Particle Profiles and Inflammatory Markers in the Veterans Affairs Diabetes Trial (VADT)
Authors: Koska Juraj , Saremi Aramesh , Bahn Gideon , Yamashita Shizuya , Reaven Peter D. ,   for the Veterans Affairs Diabetes Trial Investigators
Published: March 2013

OBJECTIVE
Intensive glucose-lowering therapy (INT) did not reduce macrovascular events in the recent randomized trials, possibly because it did not improve or worsen other traditional or novel cardiovascular risk factors.

RESEARCH DESIGN AND METHODS
Standard plasma lipids, cholesterol content of lipoprotein subfractions, and plasma inflammatory and prothrombotic markers were determined in a subgroup of the Veterans Affairs Diabetes Trial (VADT) participants (n = 266) at baseline and after 9 months of INT or standard therapy.

RESULTS
INT lowered glycated hemoglobin (by a median of 2% vs. a median of 0.7% by standard treatment; P &lt; 0.0001); increased BMI (4 vs. 1%; P &lt; 0.001), total HDL (9 vs. 4%; P &lt; 0.05), HDL2 (14 vs. 0%; P = 0.009), LDL2 (36 vs. 1%; P &lt; 0.0001), and plasma adiponectin (130 vs. 80%; P &lt; 0.01); and reduced triglycerides (−13 vs. −4%; P = 0.02) and small, dense LDL4 (−39 vs. −13%; P &lt; 0.001), but had no effect on levels of plasma apolipoproteins B-100 and B-48, C-reactive protein, interleukin-6, lipoprotein-associated phospholipase A2, myeloperoxidase, fibrinogen, and plasminogen activator inhibitor 1. Incident macrovascular events were associated with baseline interleukin-6 (hazard ratio per each quartile increase 1.33 [95% CI 1.06–1.66]), total LDL (1.25 [1.01–1.55]), apolipoprotein B-100 (1.29 [1.01–1.65]), and fibrinogen (1.26 [1.01–1.57]) but not changes in any cardiovascular risk factors at 9 months.

CONCLUSIONS
INT was associated with improved adiponectin, lipid levels, and a favorable shift in LDL and HDL subfractions after 9 months. These data suggest that the failure of INT to lower cardiovascular outcomes occurred despite generally favorable changes in standard and novel risk factors early in the study.
Characterization of microsatellite loci in Tilia platyphyllos (Malvaceae) and cross‐amplification in related species
Authors: Phuekvilai Prattana , Wolff Kirsten 
Published: March 2013

• Premise of the study: Microsatellite markers in the genus Tilia were developed to investigate the genetic variation in T. platyphyllos and its relationship with T. cordata.• Methods and Results: Fifteen microsatellite markers were developed using a microsatellite enrichment protocol. Most loci show a high level of polymorphism in two T. platyphyllos populations from France. The number of alleles ranged from one to 15, with a mean of 8.96. The mean observed and expected heterozygosities were 0.71 and 0.70, respectively. Cross‐amplification results indicated that 12 out of 15 loci amplified polymorphic loci in 23 species in the genus.• Conclusions: These markers will be useful tools for investigating the phylogeography and hybridization of Tilia species.
Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon‐primed, intron‐spanning nuclear loci
Authors: McDaniel Stuart F. , van Baren Marijke J. , Jones Kelly S. , Payton Adam C. , Quatrano Ralph S. 
Published: March 2013

• Premise of the study: We developed and tested primers for 218 nuclear loci for studying population genetics, phylogeography, and genome evolution in bryophytes.• Methods and Results: We aligned expressed sequence tags (ESTs) from Ceratodon purpureus to the Physcomitrella patens genome sequence, and designed primers that are homologous to conserved exons but span introns in the P. patens genome. We tested these primers on four isolates from New York, USA; Otavalo, Ecuador; and two laboratory isolates from Austria (WT4 and GG1). The median genome‐wide nucleotide diversity was 0.008 substitutions/site, but the range was large (0–0.14), illustrating the among‐locus heterogeneity in the species.• Conclusions: These loci provide a valuable resource for finely resolved, genome‐wide population genetic and species‐level phylogenetic analyses of C. purpureus and its relatives.
L'Europe et les réfugiés : une politique peu solidaire
Authors: Guiraudon Virginie 
Published: March 2013

La coopération intergouvernementale afin de limiter les demandes d’asile date des années 1980 même si ce n’est qu’en 1999 que les chefs d’État et de gouvernement des États membres de l’Union européenne s’engagent à créer une politique d’asile commune. L’entrée en vigueur du traité d’Amsterdam donne en effet aux institutions de l’Union un rôle plus important dans l’élaboration des politiques d’immigration, d’asile et de gestion des frontières extérieures. Cela dit, les textes législatifs visent à harmoniser a minima les pratiques des États membres. Plutôt qu’une politique d’asile européenne, se dessine très vite en fait une politique de non-accès au droit d’asile en rendant les visas obligatoires pour l’accès au territoire européen, en imposant des sanctions contre les transporteurs et en codifiant les notions de pays « sûrs » et de demandes « manifestement infondées ». Plus qu’une politique commune, les accords de Dublin et la base de données eurodac permettent de renvoyer les demandeurs d’un pays à un autre. La politique d’asile est donc peu solidaire et ne profite qu’aux ministères des pays qui ont élaboré entre eux de façon informelle dès 1985 un système pour ne plus accueillir de réfugiés.
Peut-on ne pas être constructiviste ?
Authors: Lemieux Cyril 
Published: March 2013

Les chercheurs qui se réclament du constructivisme ont souvent du mal à tenir jusqu’au bout l’idée selon laquelle la réalité est une construction sociale. Aussi est-il fréquent de les voir céder à la tentation de renaturaliser clandestinement une partie du monde social, renaturalisation qui leur semble nécessaire pour éviter de sombrer dans le relativisme. Cette stratégie, qui est devenue la norme, est régressive du point de vue des ambitions de la sociologie : non seulement elle conduit à de graves incohérences, que cet article identifie sous les noms de charcutage ontologique, de déréalisation et de critique de l’artificialité, mais encore elle limite considérablement le potentiel critique de la posture constructiviste en en faisant une théorie régionale et non plus universelle. Une position beaucoup plus conséquente peut être trouvée dans les thèses durkheimiennes sur l’origine sociale des catégories, à condition de les lire avec suffisamment d’attention pour y réévaluer un aspect en général négligé : l’importance que Durkheim attribuait à la question du contrôle par l’expérience pour rendre compte des processus de transformation des catégories.
L'habitus du dehors
Authors: Mariot Nicolas 
Published: March 2013

Ce court article propose de revenir sur ce que les chercheurs font lorsqu’ils se lancent, via des questionnaires, entretiens, ou archives, dans la collecte des croyances des acteurs à propos d’épreuves fortement encadrées et instituées (examens, cérémonies, entretiens officiels, etc.). Il s’interroge sur trois cas de non-réponse dans des enquêtes par questionnaires en tentant d’interpréter ces silences : de quoi sont-ils l’indice ? Au terme de cet examen, deux points de vue sont avancés. D’une part, la collecte des raisons s’avère souvent vaine parce qu’elle conduit à attester l’infinie diversité des réactions. De l’autre, elle pose problème parce que la quête des croyances conduit le chercheur à oublier que, très souvent, les acteurs s’en passent fort bien tout en agissant « comme il faut » : il s’agit précisément d’activités où les actions individuelles peuvent être portées par les institutions.