bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data
Authors: Browning Brian L , Browning Sharon R 
Published: March 2013

AbstractSegments of indentity-by-descent (IBD) detected from high-density genetic data are useful for many applications, including long-range phase determination, phasing family data, imputation, IBD mapping, and heritability analysis in founder populations. We present Refined IBD, a new method for IBD segment detection. Refined IBD achieves both computational efficiency and highly accurate IBD segment reporting by searching for IBD in two steps. The first step (identification) uses the GERMLINE algorithm to find shared haplotypes exceeding a length threshold. The second step (refinement) evaluates candidate segments with a probabilistic approach to assess the evidence for IBD. Like GERMLINE, Refined IBD allows for IBD reporting on a haplotype level, which facilitates determination of multi-individual IBD and allows for haplotype-based downstream analyses. To investigate the properties of Refined IBD, we simulate SNP data from a model with recent superexponential population growth that is designed to match United Kingdom data. The simulation results show that Refined IBD achieves a better power/accuracy profile than fastIBD or GERMLINE. We find that a single run of Refined IBD achieves greater power than 10 runs of fastIBD. We also apply Refined IBD to SNP data for samples from the United Kingdom and from Northern Finland and describe the IBD sharing in these data sets. Refined IBD is powerful, highly accurate, and easy to use and is implemented in Beagle version 4.
Genomic Predictability of Interconnected Biparental Maize Populations
Authors: Riedelsheimer Christian , Endelman Jeffrey B , Stange Michael , Sorrells Mark E , Jannink Jean-Luc , Melchinger Albrecht E 
Published: March 2013

Abstract
Intense structuring of plant breeding populations challenges the design of the training set (TS) in genomic selection (GS). An important open question is how the TS should be constructed from multiple related or unrelated small biparental families to predict progeny from individual crosses. Here, we used a set of five interconnected maize (Zea mays L.) populations of doubled-haploid (DH) lines derived from four parents to systematically investigate how the composition of the TS affects the prediction accuracy for lines from individual crosses. A total of 635 DH lines genotyped with 16,741 polymorphic SNPs were evaluated for five traits including Gibberella ear rot severity and three kernel yield component traits. The populations showed a genomic similarity pattern, which reflects the crossing scheme with a clear separation of full sibs, half sibs, and unrelated groups. Prediction accuracies within full-sib families of DH lines followed closely theoretical expectations, accounting for the influence of sample size and heritability of the trait. Prediction accuracies declined by 42% if full-sib DH lines were replaced by half-sib DH lines, but statistically significantly better results could be achieved if half-sib DH lines were available from both instead of only one parent of the validation population. Once both parents of the validation population were represented in the TS, including more crosses with a constant TS size did not increase accuracies. Unrelated crosses showing opposite linkage phases with the validation population resulted in negative or reduced prediction accuracies, if used alone or in combination with related families, respectively. We suggest identifying and excluding such crosses from the TS. Moreover, the observed variability among populations and traits suggests that these uncertainties must be taken into account in models optimizing the allocation of resources in GS.
Mathematical Modeling Suggests That Periodontitis Behaves as a Non‐Linear Chaotic Dynamical Process
Authors: Papantonopoulos G. , Takahashi K. , Bountis T. , Loos B.G. 
Published: March 2013

Background: This study aims to expand on a previously presented cellular automata model and further explore the non‐linear dynamics of periodontitis. Additionally the authors investigated whether their mathematical model could predict the two known types of periodontitis, aggressive (AgP) and chronic periodontitis (CP).Methods: The time evolution of periodontitis was modeled by an iterative function, based on the hypothesis that the host immune response level determines the rate of periodontitis progression. The chaotic properties of this function were investigated by direct iteration, and the model was validated by immunologic and clinical parameters derived from two clinical study populations.Results: Periodontitis can be described as chaos with the level of the host immune response determining its progression rate; the dynamics of the proposed model suggest that by increasing the host immune response level, periodontitis progression rate decreases. Renormalization transformations show the presence of two overlapping zones of disease activity corresponding to AgP and CP. By k‐means cluster analysis, immunologic parameters corroborated the findings of the renormalization transformations. Periodontitis progression rates are modeled to scale with a power law of 1.3, and the mean exponential speed of the system is found to be 1.85 (metric entropy); clinical datasets confirmed the mathematical estimates.Conclusions: This study introduces a mathematical model that identifies periodontitis as a non‐linear chaotic process. It offers a quantitative assessment of the disease progression rate and identifies two zones of disease activity that correspond to the existing classification of periodontitis in the AgP and CP types.
Type 2 Diabetes and Risk of Rupture of Saccular Intracranial Aneurysm in Eastern Finland
Authors: Lindgren Antti E. , Kurki Mitja I. , Riihinen Annamaija , Koivisto Timo , Ronkainen Antti , Rinne Jaakko , Hernesniemi Juha , Eriksson Johan G. , Jääskeläinen Juha E. , von und zu Fraunberg Mikael 
Published: March 2013

OBJECTIVE
Type 2 diabetes is a risk factor for other forms of stroke, but its association with subarachnoid hemorrhage (SAH) from ruptured saccular intracranial aneurysm (sIA) has remained unclear.

RESEARCH DESIGN AND METHODS
Kuopio Intracranial Aneurysm Database (www.uef.fi/ns) includes all ruptured and unruptured sIA cases from a defined catchment population in eastern Finland since 1980. We compared the age-adjusted incidences of type 2 diabetes in 1,058 ruptured and 484 unruptured sIA patients during 1994–2008, using the national registry of prescribed medicine purchases.

RESULTS
Of the 1,058 ruptured sIA patients, 43% were males and 57% females, with a median age at rupture of 51 and 56 years, respectively. From 1994 to 2008 or until death, 9% had been prescribed antidiabetes medication (ADM) with a median starting age of 58 years for males and 66 years for females. Of the 484 unruptured sIA patients, 44% were males and 56% females, with a median age at the diagnosis of 53 and 55 years, respectively, and 9% had used ADM, with a median starting age of 61 years for males and 66 years for females. The incidence of type 2 diabetes was highest in the age-group 60–70 years, with no significant differences between the ruptured and unruptured sIA patients.

CONCLUSIONS
Our study suggests that type 2 diabetes does not increase the risk of rupture of sIA, which is by far the most frequent cause of nontraumatic SAH.
Efficacy and Safety of Lixisenatide Once-Daily Morning or Evening Injections in Type 2 Diabetes Inadequately Controlled on Metformin (GetGoal-M)
Authors: Ahrén Bo , Leguizamo Dimas Aniceto , Miossec Patrick , Saubadu Stéphane , Aronson Ronnie 
Published: March 2013

OBJECTIVE
To examine the efficacy and safety of lixisenatide (20 μg once daily, administered before the morning or evening meal) as add-on therapy in patients with type 2 diabetes insufficiently controlled with metformin alone.

RESEARCH DESIGN AND METHODS
This was a 24-week, randomized, double-blind, placebo-controlled study in 680 patients with inadequately controlled type 2 diabetes (HbA1c 7–10% [53−86 mmol/mol]). Patients were randomized to lixisenatide morning (n = 255), lixisenatide evening (n = 255), placebo morning (n = 85), or placebo evening (n = 85) injections.

RESULTS
Lixisenatide morning injection significantly reduced mean HbA1c versus combined placebo (mean change −0.9% [9.8 mmol/mol] vs. −0.4% [4.4 mmol/mol]; least squares [LS] mean difference vs. placebo −0.5% [5.5 mmol/mol], P &lt; 0.0001). HbA1c was significantly reduced by lixisenatide evening injection (mean change –0.8% [8.7 mmol/mol] vs. –0.4% [4.4 mmol/mol]; LS mean difference –0.4% [4.4 mmol/mol], P &lt; 0.0001). Lixisenatide morning injection significantly reduced 2-h postprandial glucose versus morning placebo (mean change −5.9 vs. −1.4 mmol/L; LS mean difference −4.5 mmol/L, P &lt; 0.0001). LS mean difference in fasting plasma glucose was significant in both morning (–0.9 mmol/L, P &lt; 0.0001) and evening (–0.6 mmol/L, P = 0.0046) groups versus placebo. Mean body weight decreased to a similar extent in all groups. Rates of adverse events were 69.4% in both lixisenatide groups and 60.0% in the placebo group. Rates for nausea and vomiting were 22.7 and 9.4% for lixisenatide morning and 21.2 and 13.3% for lixisenatide evening versus 7.6 and 2.9% for placebo, respectively. Symptomatic hypoglycemia occurred in 6, 13, and 1 patient for lixisenatide morning, evening, and placebo, respectively, with no severe episodes.

CONCLUSIONS
In patients with type 2 diabetes inadequately controlled on metformin, lixisenatide 20 μg once daily administered in the morning or evening significantly improved glycemic control, with a pronounced postprandial effect, and was well tolerated.
Effects of a Single Bout of Interval Hypoxia on Cardiorespiratory Control and Blood Glucose in Patients With Type 2 Diabetes
Authors: Duennwald Tobias , Gatterer Hannes , Groop Per-Henrik , Burtscher Martin , Bernardi Luciano 
Published: March 2013

OBJECTIVE
Hypoxia may cause functional autonomic imbalance in diabetes. Intermittent hypoxia (IH), a technique improving the adaptation to hypoxia, might improve cardiorespiratory reflexes and, ultimately, blood glucose concentrations in patients with type 2 diabetes. We tested whether a single bout of IH could initiate a long-lasting response potentially leading to better adaptation to hypoxia.

RESEARCH DESIGN AND METHODS
In 14 patients with type 2 diabetes without autonomic complications, we measured blood pressure, heart rate, oxygen saturation, chemoreflex (hypoxic and hypercapnic ventilatory responses, ventilatory recruitment threshold), and baroreflex sensitivity before, immediately after, and 3 and 6 h after a 1-h single bout of IH (6-min breathing of 13% oxygen mixture 5 times each separated by 6-min recovery). The measurements were repeated on a placebo day (at least 1 week apart, in random sequence) when subjects were only breathing room air (single-blind protocol).

RESULTS
IH significantly increased hypercapnic ventilatory responses and reduced ventilatory recruitment threshold, and increased oxygen saturation and blood pressures, whereas increases in heart rate variability and baroreflex sensitivity were not significant. Blood glucose significantly decreased after IH. No such changes were observed during the placebo day, except an increase in oxygen saturation. Some of the effects lasted 3 h after IH, and some even persisted until 6 h after IH.

CONCLUSIONS
A single bout of IH induced an initial adaptation to hypoxia, with improvement in cardiorespiratory reflexes and reduction in blood glucose. Patients with type 2 diabetes could potentially benefit from the application of a full (&gt;2 weeks) IH intervention.
Psychometric Properties, Norms, and Factor Structure of the Diabetes Eating Problem Survey–Revised in a Large Sample of Children and Adolescents With Type 1 Diabetes
Authors: Wisting Line , Frøisland Dag Helge , Skrivarhaug Torild , Dahl-Jørgensen Knut , Rø Øyvind 
Published: March 2013

OBJECTIVE
The purpose of this study was to examine the psychometric properties of the Diabetes Eating Problem Survey–Revised (DEPS-R) in a large sample of young patients with type 1 diabetes, to establish norms, and to validate it against the Eating Attitudes Test–12 (EAT-12).

RESEARCH DESIGN AND METHODS
A total of 770 children and adolescents aged 11–19 years with type 1 diabetes completed the DEPS-R and the EAT-12. In addition, age- and sex-standardized BMI and HbA1c data were obtained from the Norwegian Childhood Diabetes Registry. In addition to tests of validity, principal axis factoring was conducted to investigate the factor structure of the 16-item DEPS-R.

RESULTS
The DEPS-R demonstrated satisfactory Cronbach α (0.89) and was significantly correlated with the EAT-12 (0.65; P &lt; 0.01), indicating convergent validity. The mean (SD) DEPS-R scores were 11.0 (10.7) for the total sample and 7.7 (7.4) and 14.2 (2.4) for males and females, respectively.

CONCLUSIONS
This study replicates and extends previous research demonstrating the psychometric properties of the abbreviated 16-item DEPS-R. Findings support the utility of this important screening tool to identify disturbed eating in young patients with type 1 diabetes.
Deux siècles de réfugiés : circulations, qualifications, internationalisation
Authors: Kévonian Dzovinar 
Published: March 2013

Les xix e et xx e siècles ont constitué dans l’histoire pluriséculaire des migrations forcées une période de mutations que nous avons tenté de décrire à grands traits. Aux mutations des conditions de la circulation migratoire à l’échelle mondiale, ont correspondu des infléchissements majeurs de la définition des communautés politiques et des conditions de nationalité et de citoyenneté, dans un contexte de domination européenne du monde puis de dislocation des empires coloniaux. Chacune des deux guerres mondiales du xx e siècle a contribué, par les mouvements massifs qui en sont résultés, à l’émergence de la figure du réfugié « politique », de l’apatride comme d’un statut juridique international des réfugiés. Notre étude vise à mettre en lumière les articulations existantes entre les grands flux de réfugiés et exilés, et les processus de qualification et de catégorisation durant ces deux siècles.
Faire du terrain en pensée politique
Authors: Hauchecorne Mathieu 
Published: March 2013

Cette contribution vise à réfléchir aux modalités possibles du recours à l’ethnographie dans l’étude de la pensée politique à travers la présentation d’une enquête de terrain réalisée auprès des médiateurs français du philosophe étasunien John Rawls et des théories anglo-étasuniennes de la justice sociale. L’article revient tout d’abord sur le cadre analytique adopté, celui d’une histoire sociale des idées politiques, et sur la manière dont l’enquête s’inscrit à l’intérieur des renouvellements récents de l’histoire intellectuelle en France et à l’étranger. Il revient ensuite sur les raisons qui ont motivé le recours, relativement inhabituel en pensée politique, à l’ethnographie, et sur les différents sites autour desquels a été construit le terrain. L’enquête mise en œuvre est qualifiée d’ethnographique en un double sens : au titre des techniques d’enquête utilisées (observations et entretiens dans le cadre d’une immersion au sein du milieu d’interconnaissance formé par les importateurs), et au regard du type de point de vue adopté (démarche réflexive, attention aux catégories « indigènes », analyse des dispositifs corporels et matériels).
Faire face aux imprévus sans être pris au dépourvu : le cas des chefs de culture dans de petites entreprises horticoles
Authors: Zara-Meylan Valérie 
Published: March 2013

Comment faire face aux imprévus sans être pris au dépourvu ? Cette question est au cœur du métier de chef de culture que nous avons observé au cours d’interventions ergonomiques dans de petites entreprises de l’horticulture ornementale. En mettant en évidence des configurations redoutées par des chefs de culture dans leur activité, nous analysons les modalités par lesquelles ils gèrent et anticipent les risques pour leur santé et celle des ouvriers qu’ils encadrent. Cette analyse permet de comprendre que certaines contraintes qui sembleraient inévitables peuvent pourtant faire partie du champ des transformations de l’organisation du travail.
Le catch et la lutte entre certitude et incertitude : quelle pratique de combat pour le IIIe millénaire ?
Authors: Loyer Frédéric 
Published: March 2013

Bien que sport à part entière, la lutte reste une pratique discrète et peu développée. Inversement, le catch, activité truquée par excellence connaît l’intérêt d’un nombre de pratiquants toujours plus important. Comment expliquer ce fait surprenant ? Ne dit-on pas que le sport est l’aboutissement de la motricité ludique ? Les caractéristiques du sport coubertinien organisées autour de l’incertitude ne sont peut-être plus celles recherchées exclusivement par les pratiquants d’aujourd’hui, attirés par des pratiques moins institutionnalisées et moins réglementées. Nous cherchons à vérifier cette hypothèse à travers l’étude ethnographique d’une troupe de catcheurs en gala complétée par une série d’entretiens. Contrairement à la lutte où domine la compétition sportive (agôn), le catch permet une pratique où alea, mimicry, ilinx et agôn s’organisent selon les attentes liées aux profils socioculturels des catcheurs.
Maxwell curl equation datuming for GPR based on the Kirchhoff integral solution and application in a tunnel grouting test
Authors: Zhao Yonghui , Xie Xiongyao , Wu Jiansheng , Chen Jun , Ge Shuangchen 
Published: March 2013

ABSTRACTIn two‐dimensional (2D) ground‐penetrating radar (GPR) data, the reflections from detection targets in depth can be severely obscured by strong scattering generated from near‐surface non‐target structures. By using GPR as a geotechnical non‐destructive testing device, it is still a challenge to eliminate the strong scattering caused by near‐surface rebars in a tunnel lining and to image and asses the grouting condition behind the tunnel lining. This study proposes a method for the reconstruction of GPR images, termed Maxwell curl equation datuming. To eliminate the deleterious effect caused by near‐surface diffractive scattering, we have redefined the reference surface to an actual geologic/engineered interface by using Maxwell curl equation datuming methodology based on the Kirchhoff integral solution. The datuming procedure can redefine the reference surface to a deeper horizon on which GPR transmitters and receivers appear to be located. We conducted a comparison between the datuming and migration to synthetic examples and case studies are presented for a physical model and real GPR data for assessments of shield tunnel grouting in the Shanghai Metro line No.9. The results show that the datuming technique is able to eliminate the strong scattering related to near‐surface rebars in a tunnel lining and improves the quality of deeper images beneath the tunnel lining. The datuming images make it easy to identify the distribution of tunnel grouting.
Spectral velocity analysis for the determination of ground‐wave velocities and their uncertainties in multi‐offset GPR data
Authors: Hamann Göran , Tronicke Jens , Steelman Colby M. , Endres Anthony L. 
Published: March 2013

ABSTRACTIn many hydrological applications, ground‐wave velocity measurements are increasingly used to map and monitor shallow soil water content. In this study, we propose an automated spectral velocity analysis method to determine the direct ground‐wave (DGW) velocity from common midpoint (CMP) or multi‐offset ground‐penetrating radar (GPR) data. The method introduced in this paper is a variation of the well‐known spectral velocity analysis for seismic and GPR reflection events where velocity spectra are computed using different coherency measures along hyperbolas following the normal moveout model. Here, the unnormalized cross‐correlation is computed between waveforms across data gathers that are corrected with a linear moveout equation using a predefined range of velocities. Peaks in the resulting velocity spectra identify linear events in the GPR data gathers like DGW events and allow for estimating the corresponding velocities. In addition to obtaining a DGW velocity measurement, we propose a robust method to estimate the associated velocity uncertainties based on the width of the peak in the calculated velocity spectrum. Our proposed method is tested on synthetic data examples to evaluate the influence of subsurface velocity, surveying geometry and signal frequency on the accuracy of estimated ground‐wave velocities. In addition, we investigate the influence of such velocity uncertainties on subsequent soil water content estimates using an established petrophysical relationship. Furthermore, we apply our approach to analyse field data, which were collected across a test site in Canada to monitor a wide range of seasonal soil moisture variations. A comparison between our spectral velocity estimates and results derived from manually picked ground‐wave arrivals shows good agreement, which illustrates that our spectral velocity analysis is a feasible tool to analyse DGW arrivals in multi‐offset GPR data gathers in an objective and more automated manner.
Role of Fatty-Acid Synthesis in Dendritic Cell Generation and Function
Authors: Rehman Adeel , Hemmert Keith C. , Ochi Atsuo , Jamal Mohsin , Henning Justin R. , Barilla Rocky , Quesada Juan P. , Zambirinis Constantinos P. , Tang Kerry , Ego-Osuala Melvin , Rao Raghavendra S. , Greco Stephanie , Deutsch Michael , Narayan Suchithra , Pachter H. Leon , Graffeo Christopher S. , Acehan Devrim , Miller George 
Published: March 2013

Abstract
Dendritic cells (DC) are professional APCs that regulate innate and adaptive immunity. The role of fatty-acid synthesis in DC development and function is uncertain. We found that blockade of fatty-acid synthesis markedly decreases dendropoiesis in the liver and in primary and secondary lymphoid organs in mice. Human DC development from PBMC precursors was also diminished by blockade of fatty-acid synthesis. This was associated with higher rates of apoptosis in precursor cells and increased expression of cleaved caspase-3 and BCL-xL and downregulation of cyclin B1. Further, blockade of fatty-acid synthesis decreased DC expression of MHC class II, ICAM-1, B7-1, and B7-2 but increased their production of selected proinflammatory cytokines including IL-12 and MCP-1. Accordingly, inhibition of fatty-acid synthesis enhanced DC capacity to activate allogeneic as well as Ag-restricted CD4+ and CD8+ T cells and induce CTL responses. Further, blockade of fatty-acid synthesis increased DC expression of Notch ligands and enhanced their ability to activate NK cell immune phenotype and IFN-γ production. Because endoplasmic reticulum (ER) stress can augment the immunogenic function of APC, we postulated that this may account for the higher DC immunogenicity. We found that inhibition of fatty-acid synthesis resulted in elevated expression of numerous markers of ER stress in humans and mice and was associated with increased MAPK and Akt signaling. Further, lowering ER stress by 4-phenylbutyrate mitigated the enhanced immune stimulation associated with fatty-acid synthesis blockade. Our findings elucidate the role of fatty-acid synthesis in DC development and function and have implications to the design of DC vaccines for immunotherapy.