bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Bayesian Testing of Sets of Variants in Complex Diseases
Authors: Zhang Yu , Ghosh Soumitra , Hakonarson Hakon 
Published: September 2014

Abstract
Rare genetic variants have recently been studied for genome-wide associations with human complex diseases. Existing rare variant methods are based on the hypothesis-testing framework that predefined variant sets need to be tested separately. The power of those methods is contingent upon accurate selection of variants for testing, and frequently, common variants are left out for separate testing. In this article, we present a novel Bayesian method for simultaneous testing of all genome-wide variants across the whole frequency range. The method allows for much more flexible grouping of variants and dynamically combines them for joint testing. The method accounts for correlation among variant sets, such that only direct associations with the disease are reported, whereas indirect associations due to linkage disequilibrium are not. Consequently, the method can obtain much improved power and flexibility and simultaneously pinpoint multiple disease variants with high resolution. Additional covariates of categorical, discrete, and continuous values can also be added. We compared our method with seven existing categories of approaches for rare variant mapping. We demonstrate that our method achieves similar power to the best methods available to date when testing very rare variants in small SNP sets. When moderately rare or common variants are included, or when testing a large collection of variants, however, our method significantly outperforms all existing methods evaluated in this study. We further demonstrate the power and the usage of our method in a whole-genome resequencing study of type 1 diabetes.
Differential Regulation of Germline Apoptosis in Response to Meiotic Checkpoint Activation
Authors: Ye Alice L , Ragle J Matthew , Conradt Barbara , Bhalla Needhi 
Published: September 2014

Abstract
In Caenorhabditis elegans, germline apoptosis is promoted by egl-1 and ced-13 in response to meiotic checkpoint activation. We report that the requirement for these two factors depends on which checkpoints are active. We also identify a regulatory region of egl-1 required to inhibit germline apoptosis in response to DNA damage incurred during meiotic recombination.
Unisexual Reproduction Reverses Muller’s Ratchet
Authors: Roach Kevin C , Heitman Joseph 
Published: September 2014

AbstractCryptococcus neoformans is a pathogenic basidiomycetous fungus that engages in outcrossing, inbreeding, and selfing forms of unisexual reproduction as well as canonical sexual reproduction between opposite mating types. Long thought to be clonal, &gt;99% of sampled environmental and clinical isolates of C. neoformans are MATα, limiting the frequency of opposite mating-type sexual reproduction. Sexual reproduction allows eukaryotic organisms to exchange genetic information and shuffle their genomes to avoid the irreversible accumulation of deleterious changes that occur in asexual populations, known as Muller’s ratchet. We tested whether unisexual reproduction, which dispenses with the requirement for an opposite mating-type partner, is able to purge the genome of deleterious mutations. We report that the unisexual cycle can restore mutant strains of C. neoformans to wild-type genotype and phenotype, including prototrophy and growth rate. Furthermore, the unisexual cycle allows attenuated strains to purge deleterious mutations and produce progeny that are returned to wild-type virulence. Our results show that unisexual populations of C. neoformans are able to avoid Muller’s ratchet and loss of fitness through a unisexual reproduction cycle involving α-α cell fusion, nuclear fusion, and meiosis. Similar types of unisexual reproduction may operate in other pathogenic and saprobic eukaryotic taxa.
A 6DOF super element for nonlinear analysis of composite frames with partial interaction and semi-rigid connections
Authors: Bao Nghi Le Luong , Cong Thanh Bui 
Published: September 2014

This paper presents a displacement-based finite element formulation for nonlinear analysis of steel - concrete composite planar frames subjected to combined action of gravity and lateral loads. A 6DOF super element is proposed for modeling composite beam, allowing for partial interaction between the steel beam and the concrete slab, semi-rigid nature of beam to column composite connection and material nonlinearity. The load control method and the displacement control method are utilized for tracing the structural equilibrium paths, and the direct method is utilized for solving the nonlinear problem. Numerical examples, concerning a two-span continuous composite beam, a portal composite frame and a six-storey composite frame, are performed. The results are compared with experience data or theoretical results from other studies and are discussed for influences of the factors mentioned above on behaviour of composite beams and composite frames.
Finite element simulation of strain localization in inelastic solids by energy relaxation
Authors: Trinh B. T. , Hackl K. 
Published: September 2014

A new approach for the treatment of strain localization in inelastic material is proposed. It is based on energy minimization principles associated with micro-structure developments. Shear bands are treated as micro-shearing of rank-one laminates. It is assumed that the thickness of the shear band represented by its volume fraction tends to zero, and the energy inside the shear band is a function of the norm of the strain field. The existence of shear bands in the structure leads to an ill-posed problem which can be solved by means of energy relaxation. The performance of the proposed concept is demonstrated through numerical simulation of tension test under plane strain conditions. Numerical results show that mesh sensitivity can be completely removed.
About the choice of a plastic-like model for shape memory alloys
Authors: Lexcellent C. , Laydi R. M. 
Published: September 2014

The aim of this paper is to examine the impact of the choice of plasticity theory-inspired model in the prediction of the shape of phase transformation domains. In this field a comparison is made between Huber-Von Mises based model and an another integrating the non-symmetry between tension and compression. The yield surface of phase transformation initiation for a homogeneous body under proportional biaxial loading is discussed. A transport of these surfaces in the space of the "effective transformation strain of martensite tensor" is given.
Standard gradient models and crack simulation
Authors: Son Nguyen Quoc , Giang Nguyen Truong 
Published: September 2014

The standard gradient models have been intensively studied in the literature, cf. Fremond (1985) or Gurtin (1991) for various applications in plasticity, damage mechanics and phase change analysis. The governing equations for a solid have been introduced essentially from an extended version of the virtual equation. It is shown here first that these equations can also be derived from the formalism of energy and dissipation potentials and appear as a generalized Biot equation for the solid. In this spirit, the governing equations for higher gradient models can be straightforwardly given. The interest of gradient models is then discussed in the context of damage mechanics and crack simulation. The phenomenon of strain localization in a time-dependent or time-independent process of damage is explored as a convenient numerical method to simulate the propagation of cracks, in relation with some recent works of theliterature, cf. Bourdin & Marigo [3], Lorentz & al [5], Henry & al [12].
Homogenization of an interface highly oscillating between two concentric ellipses
Authors: Tung Do Xuan , Vinh Pham Chi , Tung Nguyen Kim 
Published: September 2014

The main purpose of this paper is to find the homogenized equation and the associate continuity conditions in the explicit form of a boundary-value problem in a two-dimensional domain with an interface oscillating rapidly between two concentric ellipses. This boundary-value problem originates from various problems in practical applications. By the homogenization method and following the technique presented recently by Vinh and Tung [P. C. Vinh and D. X. Tung, Mech. Res.Comm. 37 (2010), 285-288; P. C. Vinh, D. X. Tung, ASME J. Appl. Mech., 78 (2011), 041014-1; P. C. Vinh and D. X. Tung, Acta Mech. 218 (2011), 333-348], the homogenized equation and the associate continuity conditions in the explicit form are derived.
Solving nonlinear stability problem of imperfect functionally graded circular cylindrical shells under axial compression by Galerkin's method
Authors: Dung Dao Van , Hoa Le Kha 
Published: September 2014

This paper presents an analytical approach to analyze the nonlinear stability of thin closed circular cylindrical shells under axial compression with material properties varying smoothly along the thickness in the power and exponential distribution laws. Equilibrium and compatibility equations are obtained by using Donnel shell theory taking into account the geometrical nonlinearity in von Karman and initial geometrical imperfection. Equations to find the critical load and the load-deflection curve are established by Galerkin's method. Effects of buckling modes, of imperfection, of dimensional parameters and of volume fraction indexes to buckling loads and postbuckling load-deflection curves of cylindrical shells are investigated. In case of perfect cylindrical shell, the present results coincide with the ones of the paper [13] which were solved by Ritz energy method.
Stable control of networked robot subject to communication delay, packet loss, and out-of-order delivery
Authors: Phung Manh Duong , Tran Thuan Hoang , Tran Quang Vinh 
Published: September 2014

Stabilization control of networked robot system faces uncertain factors caused by the network. Our approach for this problem consists of two steps. First, the Lyapunov stability theory is employed to derive control laws that stabilize the non-networked robot system. Those control laws are then extended to the networked robot system by implementing a predictive filter between the sensor and controller. The filter compensates influences of the network to acquire accurate estimate of the system state and consequently ensures the convergence of the control laws. The optimality of the filter in term of minimizing the mean square error is theoretically proven. Many simulations and experiments have been conducted. The result confirmed the validity of the proposed approach.
Improving Traffic Noise Simulations Using Space Syntax: Preliminary Results from Two Roadway Systems
Authors: M. Dzhambov Angel , D. Dimitrova Donka , H. Turnovska Tanya 
Published: September 2014

AbstractNoise pollution is one of the four major pollutions in the world. In order to implement adequate strategies for noise control, assessment of traffic-generated noise is essential in city planning and management. The aim of this study was to determine whether space syntax could improve the predictive power of noise simulation. This paper reports a record linkage study which combined a documentary method with space syntax analysis. It analyses data about traffic flow as well as field-measured and computer-simulated traffic noise in two Bulgarian agglomerations. Our findings suggest that space syntax might have a potential in predicting traffic noise exposure by improving models for noise simulations using specialised software or actual traffic counts. The scientific attention might need to be directed towards space syntax in order to study its further application in current models and algorithms for noise prediction.
Self-cross-linked Hyaluronic Acid Hydrogel in Ethmoidectomy: A Randomized, Controlled Trial
Authors: Matheny Keith E. , Tseng Ewen Y. , Carter Kenny B. , Cobb William B. , Fong Karen J. 
Published: September 2014

Background This study was designed to evaluate the safety and efficacy of a novel, self–cross-linked hyaluronic acid (HA) hydrogel compared with carboxymethylcellulose (CMC) viscous foam in promoting healing when applied after ethmoidectomy. A prospective, randomized, controlled, blinded clinical trial was performed. The study was performed by four surgeons operating in two community hospitals. Methods Thirty patients with bilateral chronic rhinosinusitis underwent bilateral total ethmoidectomy. Intraoperatively, each patient received 5 mL of HA hydrogel in one ethmoid cavity and 5 mL of CMC contralaterally. The material applied within each ethmoid cavity was randomly assigned before surgery. An independent surgeon, blinded to the material used to treat each ethmoid cavity, evaluated postoperative endoscopic video at 1 and 2 weeks for edema, crusting, and mucopurulence and at 6 and 12 weeks for remucosalization and scarring/synechiae. Twenty-item Sino-Nasal Outcome Test SNOT-20 data were collected at each visit. A small sample underwent endoscopic mucosal biopsy. Results Twenty-nine of 30 patients completed the protocol. The difference in edema, crusting, and mucopurulence at 1 and 2 weeks was not statistically significant; however, at 6 and 12 weeks, the HA hydrogel showed statistically significant reduction in both overall endoscopic grade (p < 0.05), as well as synechiae formation (p < 0.05), with a trend toward superiority in remucosalization (p = 08). Histological analysis of six subjects at 12 weeks showed a nonsignificant trend toward a greater amount of regenerated cilia present with the HA hydrogel (p = 0.23). SNOT-20 scores declined 78.8% from preoperative scores. Conclusion Self–cross-linked HA hydrogel provides superior wound healing to CMC after ethmoidectomy.
The Re-emergence of the Minimal Running Shoe
Authors: Davis Irene S. 
Published: September 2014

Synopsis The running shoe has gone through significant changes since its inception. The purpose of this paper is to review these changes, the majority of which have occurred over the past 50 years. Running footwear began as very minimal, then evolved to become highly cushioned and supportive. However, over the past 5 years, there has been a reversal of this trend, with runners seeking more minimal shoes that allow their feet more natural motion. This abrupt shift toward footwear without cushioning and support has led to reports of injuries associated with minimal footwear. In response to this, the running footwear industry shifted again toward the development of lightweight, partial minimal shoes that offer some support and cushioning. In this paper, studies comparing the mechanics between running in minimal, partial minimal, and traditional shoes are reviewed. The implications for injuries in all 3 conditions are examined. The use of minimal footwear in other populations besides runners is discussed. Finally, areas for future research into minimal footwear are suggested. J Orthop Sports Phys Ther 2014;44(10):775–784. Epub 11 September 2014. doi:10.2519/jospt.2014.5521
Measuring Peritoneal Absorption with the Prolonged Peritoneal Equilibration Test from 4 to 8 Hours Using Various Glucose Concentrations
Authors: Teixidó–Planas Josep , Troya–Saborido Maria Isabel , Pedreira–Robles Guillermo , Del-Rio–Lafuente Milagros , Romero–Gonzalez Ramon , Bonet–Sol Josep 
Published: September 2014

Background Peritoneal fluid flows such as small-pore ultrafiltration and free water transport can now be calculated by means of the modified peritoneal equilibration test (PET). To calculate peritoneal fluid absorption, volume markers have been used, but that method is not easily applicable in clinical practice. Alternatively, absorption can be estimated using the personal dialysis capacity test. However, a method of measuring overall peritoneal absorption together with the PET is lacking. The aim of the present study was to assess whether overall peritoneal absorption was different when measured from the 4th to 8th hour in a prolonged PET using three different glucose solutions. Methods The study enrolled 32 stable peritoneal dialysis (PD) patients from a tertiary university hospital, who underwent three 8-hour prolonged PETs with 1.36%, 2.27%, and 3.86% glucose solution. The PETs were performed in random order over a period of less than 1 month. During the prolonged PET, the peritoneal volume was emptied and reinfused at 60 and 240 minutes and drained at 480 minutes. Peritoneal absorption was calculated as the volume difference between the 4th and the 8th hour. Results The dialysate-to-plasma ratio (D/P) of urea, the D/P creatinine, and the mass transfer area coefficient (MTC) of creatinine at 240 minutes were not significantly different with the three glucose solutions. The end-to-initial (D/D0) glucose, MTC urea, and MTC glucose were significantly different. All water transport parameters were significantly different, except for the 4- to 8-hour absorption volumes and rates. The peritoneal absorption rates were, for 1.36% solution, 1.03 ± 0.58 mL/min [95% confidence interval (CI): 0.83 to 1.24 mL/min]; for 2.27% solution, 0.86 ± 0.71 mL/min (95% CI: 0.61 to 1.11 mL/min); and for 3.86% solution, 1.05 ± 0.78 mL/min (95% CI: 0.77 to 1.33 mL/min). Peritoneal absorption volumes and rates from the 4th to the 8th hour showed good correlations for the various solutions. Conclusions Using any glucose solution, the prolonged PET with voiding and reinfusion at the 4th hour could be a practical method for calculating overall peritoneal absorption from the 4th to the 8th hour in PD patients.
La question de l’égalité des parcours en faculté de médecine : les conditions d’entrée à l’université des nouvelles carabines
Authors: Avenel Céline 
Published: September 2014

Au cours de ces vingt dernières années, les études de médecine ont connu une féminisation massive de ces effectifs d’étudiant-e-s du premier au dernier cycle. Les filles sont devenues largement majoritaires (64 %) parmi les étudiants de première année en 2002 (Hérault et Labarthe, 2003). Cette féminisation massive actuelle représente donc une véritable « bascule» historique. Nous proposons une lecture socio-sexuée de cette féminisation, évolution majeure du système universitaire français, au regard de la combinaison de deux principes : celui de l’égalité des parcours en médecine et celui de l’égalité des sexes. Quelles peuvent être les incidences d’un mouvement d’une telle ampleur en termes de trajectoires des futur-e-s étudiant-e-s de médecine ? Cette féminisation participe-t-elle à une égalité d’accès aux études de médecine, en termes d’origines sociales ?
Une méthode pour approcher les présentations de soi dans les communications : l’analyse des adresses
Authors: Dutoit Martine 
Published: September 2014

Un grand nombre de recherches, ayant d’autres objets que la présentation de soi, notamment des recherches en éducation et formation, utilisent de fait comme matériau des informations obtenues en situation de présentation de soi, ce qui pose d’emblée la question de l’influence de cette situation de communication sur les énoncés recueillis par le chercheur. Bien souvent, ce dernier croit avoir accès à une parole personnelle et privée, alors qu’il s’agit d’une parole adressée. Difficile dans ces conditions de ne pas mettre en rapport les contenus du discours et les adressages du discours avant d’en faire une utilisation pour la recherche. L’objet de cet article est d’exposer et d’explorer une approche méthodologique et ses résultats pour l’analyse des présentations de soi en groupe dans une situation de communication. La situation de référence est une situation de communication publique de personnes étiquetées (patients de la psychiatrie) visant à changer les représentations de leurs destinataires sur leur groupe d’appartenance. Il a été choisi, notamment, de privilégier l’analyse des « adresses» du discours.
Alpha-1 Antitrypsin Augmentation Therapy Corrects Accelerated Neutrophil Apoptosis in Deficient Individuals
Authors: Hurley Killian , Lacey Noreen , O’Dwyer Ciara A. , Bergin David A. , McElvaney Oliver J. , O’Brien M. Emmet , McElvaney Oisín F. , Reeves Emer P. , McElvaney Noel G. 
Published: September 2014

Abstract
Alpha-1 antitrypsin (AAT) deficiency (AATD) is characterized by neutrophil-driven lung destruction and early emphysema in a low AAT, and high neutrophil elastase environment in the lungs of affected individuals. In this study, we examined peripheral blood neutrophil apoptosis and showed it to be accelerated in individuals with AATD by a mechanism involving endoplasmic reticulum stress and aberrant TNF-α signaling. We reveal that neutrophil apoptosis in individuals homozygous for the Z allele (PiZZ) is increased nearly 2-fold compared with healthy controls and is associated with activation of the external death pathway. We demonstrate that in AATD, misfolded AAT protein accumulates in the endoplasmic reticulum of neutrophils, leading to endoplasmic reticulum stress and the expression of proapoptotic signals, including TNF-α, resulting in increased apoptosis and defective bacterial killing. In addition, treatment of AATD individuals with AAT augmentation therapy decreased neutrophil ADAM-17 activity and apoptosis in vivo and increased bacterial killing by treated cells. In summary, this study demonstrates that AAT can regulate neutrophil apoptosis by a previously unidentified and novel mechanism and highlights the role of AAT augmentation therapy in ameliorating inflammation in AATD.
Autoimmune Predisposition in Down Syndrome May Result from a Partial Central Tolerance Failure due to Insufficient Intrathymic Expression of AIRE and Peripheral Antigens
Authors: Giménez-Barcons Mireia , Casteràs Anna , Armengol Maria del Pilar , Porta Eduard , Correa Paula A. , Marín Ana , Pujol-Borrell Ricardo , Colobran Roger 
Published: September 2014

Abstract
Down syndrome (DS), or trisomy of chromosome 21, is the most common genetic disorder associated with autoimmune diseases. Autoimmune regulator protein (AIRE), a transcription factor located on chromosome 21, plays a crucial role in autoimmunity by regulating promiscuous gene expression (pGE). To investigate if autoimmunity in DS is promoted by the reduction of pGE owing to dysregulation of AIRE, we assessed the expression of AIRE and of several peripheral tissue-restricted Ag genes by quantitative PCR in thymus samples from 19 DS subjects and 21 euploid controls. Strikingly, despite the 21 trisomy, AIRE expression was significantly reduced by 2-fold in DS thymuses compared with controls, which was also confirmed by fluorescent microscopy. Allele-specific quantification of intrathymic AIRE showed that despite its lower expression, the three copies are expressed. More importantly, decreased expression of AIRE was accompanied by a reduction of pGE because expression of tissue-restricted Ags, CHRNA1, GAD1, PLP1, KLK3, SAG, TG, and TSHR, was reduced. Of interest, thyroid dysfunction (10 cases of hypothyroidism and 1 of Graves disease) developed in 11 of 19 (57.9%) of the DS individuals and in none of the 21 controls. The thymuses of these DS individuals contained significantly lower levels of AIRE and thyroglobulin, to which tolerance is typically lost in autoimmune thyroiditis leading to hypothyroidism. Our findings provide strong evidence for the fundamental role of AIRE and pGE, namely, central tolerance, in the predisposition to autoimmunity of DS individuals.