bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient conformational fluctuation of TePixD during a reaction
Authors: Kuroi Kunisato , Okajima Koji , Ikeuchi Masahiko , Tokutomi Satoru , Terazima Masahide 
Published: September 2014

Significance
The role of conformational fluctuations in protein reactions has been frequently mentioned to discuss the reaction mechanism. Supporting evidence for the importance of the fluctuation has been reported by showing the relationship between the flexibility of the reactant structure and reaction efficiency. However, there has been no direct evidence showing that the fluctuation is indeed enhanced during the reaction, although recent molecular dynamic simulations pointed out the importance. Here, we focused our attention on the experimental proof of enhancement by the time-resolved transient grating method, which is a unique and powerful method. Our results showed that fluctuation is a key to understanding why light-stimulated proteins can transfer the signal without changing the averaged conformation.
Enlight: web-based integration of GWAS results with biological annotations
Authors: Guo Yunfei , Conti David V , Wang Kai 
Published: September 2014

Abstract
Summary: Identifying causal variants remains a key challenge in post-GWAS (genome-wide association study) era, as many GWAS single-nucleotide polymorphisms (SNPs) (including imputed ones) fall into non-coding regions, making it difficult to associate statistical significance with predicted functionality. Therefore, we created a web-based tool, Enlight, which overlays functional annotation information, such as histone modification states, methylation patterns, transcription factor binding sites, eQTL and higher-order chromosomal structure, to GWAS results.
Availability and implementation: Accessible by a Web browser at http://enlight.usc.edu .
Contact: kaiwang@usc.edu
LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis
Authors: He Sha , Zhang Hai , Liu Haihua , Zhu Hao 
Published: September 2014

Abstract
Motivation: In mammalian cells, many genes are silenced by genome methylation. DNA methyltransferases and polycomb repressive complexes, which both lack sequence-specific DNA-binding motifs, are recruited by long non-coding RNA (lncRNA) to specific genomic sites to methylate DNA and chromatin. Increasing evidence indicates that many lncRNAs contain DNA-binding motifs that can bind to DNA by forming RNA:DNA triplexes. The identification of lncRNA DNA-binding motifs and binding sites is essential for deciphering lncRNA functions and correct and erroneous genome methylation; however, such identification is challenging because lncRNAs may contain thousands of nucleotides. No computational analysis of typical lncRNAs has been reported. Here, we report a computational method and program ( LongTarget ) to predict lncRNA DNA-binding motifs and binding sites. We used this program to analyse multiple antisense lncRNAs, including those that control well-known imprinting clusters, and obtained results agreeing with experimental observations and epigenetic marks. These results suggest that it is feasible to predict many lncRNA DNA-binding motifs and binding sites genome-wide.
Availability and implementation: Website of LongTarget : lncrna.smu.edu.cn , or contact: hao.zhu@ymail.com .
Contact: zhuhao@smu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Emmanuel Levinas
Authors: Malenfant Gabriel 
Published: September 2014

Emmanuel Levinas (b. 1906–d. 1995) was a philosopher famous for having developed an original interpretation of Edmund Husserl’s phenomenological method, using the latter to address the foundations of ethics and normativity. Published in more than twenty-five books spanning over eighty years, his oeuvre can be divided into three categories: (1) his philosophical works, which regroup monographs, essays, and interviews, (2) his Talmudic readings and essays on Judaism, and (3) posthumous notes, remarks, and texts, some of which are still being published. Although references will be made to the second and third categories, the first remains the central focus of this article. Apart from the influence of Husserl, Levinas was also inspired by Martin Heidegger as well as by Maurice Blanchot and Jacques Derrida. Of Heidegger, he wrote an uncompromising philosophical critique that addressed the secondary role played by ethics in his phenomenology—a critique he then expanded to the Western philosophical tradition as a whole. Ethics, Levinas argued, had to be reinterpreted and understood as “first philosophy” (i.e., as metaphysics), rather than as a derivative extension based on premises coming from ontological, epistemological, or political narratives. Not unlike Plato centuries before, although in a different manner and with very different implications, Levinas contended that the question of the Good has priority over that of Being, since interhuman relationality precedes any discourse or logos about beings—human or otherwise. His “ethics” is thus not that of the tradition: its aim is not to become prescriptive. Without denying the importance of the following properties or faculties for practical decision making, Levinas’s ethics relies neither on virtues, reason, nor utility. The word “ethics,” for Levinas, refers to the fact that “I” cannot refuse responsibility for the other, since that act of disregarding or refusing responsibility is possible only on the basis of my being always already capable of responding to an other who imposes responsibility on me. It is this ability for responding to the other, this command that I cannot efface (even when I ignore it) that allows for other discourses—such as ontology, epistemology, or political philosophy—to make sense at all. The consequences of this original interpretation of the nature and meaning of ethics are deep and manifold. Therefore, this article does not intend to present an all-encompassing portrait of Emmanuel Levinas’s thought. Rather, its aim is to provide the reader with a selection of texts that represent the wide array of philosophical questions addressed by Levinas and his commentators. Given the immense number of publications by Levinas, this entry proposes a commented list of selected major works and articles by the author (instead of referencing complete collections, for instance). The secondary literature is then organized by themes that correspond to areas of research—both well established and new—within Levinas studies.
Discovery of a W UMa type binary GSC 03553−00845
Authors: Guo Di-Fu , Li Kai , Hu Shao-Ming , Jiang Yun-Guo , Gao Dong-Yang , Chen Xu 
Published: September 2014

Abstract
When observing the transiting extrasolar planets, we discovered a new W UMa type binary GSC 03553−00845. Following observation was carried out using the 1 m telescope at Weihai Observatory of Shandong University. Complete BVR light curves were determined. Using the W-D program, we analyzed the light curves. Photometric solution reveals that GSC 03553−00845 is a W-subtype W UMa type binary with a mass ratio of q = 2.904, it is an overcontact binary system by a contact degree of f = 29.5% with a small temperature difference between the components (ΔT = 206 K) indicating a good thermal contact between the components. More observation of GSC 03553−00845 is needed in order to analyze the light curve variation and orbital period change.
Evaluating the Role of Interdigitated Neoadjuvant Chemotherapy and Radiation in the Management of High-Grade Soft-Tissue Sarcoma
Authors: Raval Raju R. , Frassica Deborah , Thornton Katherine , Meyer Christian , Ettinger David S. , Frassica Frank , Weber Kristin , Terezakis Stephanie A. 
Published: September 2014

Objectives:
High-grade soft-tissue sarcoma (STS) has a poor prognosis. The goal of this study was to review treatment outcomes of patients with high-grade STS treated with interdigitated neoadjuvant chemotherapy (CT) and radiation at our institution.

Materials and Methods:
Patients with high-grade STS (1997 to 2010) were planned for treatment with 3 cycles of neoadjuvant CT, interdigitated preoperative radiation therapy (44 Gy administered in split courses with a potential 16 Gy postoperative boost), and 3 cycles of postoperative CT. Cancer control outcomes at 3 years were analyzed.

Results:
Sixteen patients with high-grade STS were evaluated. Median age was 53 years, the median longest tumor diameter was 14.6 cm, and median follow-up was 33 months. All 16 patients received 2 or 3 cycles of neoadjuvant CT and all patients completed neoadjuvant RT. The estimated 3-year rate for local control was 100%, disease-free survival 62.5%, and overall survival 73.4%.

Conclusions:
Patients with high-grade STS treated with interdigitated neoadjuvant CT and radiation before surgical resection had excellent rates of local control, along with disease-free survival and overall survival similar to previously published reports. This combined-modality approach continues to have a role in the treatment of patients with high-grade STS.
XWAS: a software toolset for genetic data analysis and association studies of the X chromosome
Authors: Gao Feng , Chang Diana , Biddanda Arjun , Ma Li , Guo Yingjie , Zhou Zilu , Keinan Alon 
Published: September 2014

AbstractXWAS is a new software suite for the analysis of the X chromosome in association studies and similar studies. The X chromosome plays an important role in human disease, especially those with sexually dimorphic characteristics. Special attention needs to be given to its analysis due to the unique inheritance pattern, which leads to analytical complications that have resulted in the majority of genome-wide association studies (GWAS) either not considering X or mishandling it with toolsets that had been designed for non-sex chromosomes. We hence developed XWAS to fill the need for tools that are specially designed for analysis of X. Following extensive, stringent, and X-specific quality control, XWAS offers an array of statistical tests of association, including: (1) the standard test between a SNP (single nucleotide polymorphism) and disease risk, including after first stratifying individuals by sex, (2) a test for a differential effect of a SNP on disease between males and females, (3) motivated by X-inactivation, a test for higher variance of a trait in heterozygous females as compared to homozygous females, and (4) for all tests, a version that allows for combining evidence from all SNPs across a gene. We applied the toolset analysis pipeline to 16 GWAS datasets of immune-related disorders and 7 risk factors of coronary artery disease, and discovered several new X-linked genetic associations. XWAS will provide the tools and incentive for others to incorporate the X chromosome into GWAS, hence enabling discoveries of novel loci implicated in many diseases and in their sexual dimorphism.
Threep-xylene-solvated pseudopolymorphs of bis[1,3-bis(pentafluorophenyl)propane-1,3-dionato]copper(II)
Authors: Hori Akiko , Nakajima Kyosuke , Yuge Hidetaka 
Published: September 2014

The Cu2+ions in the title compounds, namely bis[1,3-bis(pentafluorophenyl)propane-1,3-dionato-κ2O,O′]copper(II)p-xylenen-solvate, [Cu(C15HF10O2)2]·nC8H10, withn= 1, (I),n = 2, (II), andn= 4, (III), are coordinated by two 1,3-bis(pentafluorophenyl)propane-1,3-dionate ligands. The coordination complexes of (I) and (II) have crystallographic inversion symmetry at the Cu atom and thep-xylene molecule in (I) also lies across an inversion centre. Thep-xylene molecules in (I) and (II) interact with the pentafluorophenyl groups of the complexviaarene–perfluoroarene interactions. In the crystal of (III), two of thep-xylene molecules interact with the pentafluorophenyl groupsviaarene–perfluoroarene interactions. The other twop-xylene molecules are located on the CuO4coordination plane, forming a uniform cavity produced by metal...π interactions.
Adaptive discrete-continuous modeling of evolving discontinuities
Authors: Sorg Annika , Bischoff Manfred 
Published: September 2014

Purpose– The purpose of this paper is to develop a method to model entire structures on a large scale, at the same time taking into account localized non-linear phenomena of the discrete microstructure of cohesive-frictional materials.Design/methodology/approach– Finite element (FEM) based continuum methods are generally considered appropriate as long as solutions are smooth. However, when discontinuities like cracks and fragmentation appear and evolve, application of models that take into account (evolving) microstructures may be advantageous. One popular model to simulate behavior of cohesive-frictional materials is the discrete element method (DEM). However, even if the microscale is close to the macroscale, DEMs are computationally expensive and can only be applied to relatively small specimen sizes and time intervals. Hence, a method is desirable that combines efficiency of FEM with accuracy of DEM by adaptively switching from the continuous to the discrete model where necessary.Findings– An existing method which allows smooth transition between discrete and continuous models is the quasicontinuum method, developed in the field of atomistic simulations. It is taken as a starting point and its concepts are extended to applications in structural mechanics in this paper. The kinematics in the method presented herein is obtained from FEM whereas DEM yields the constitutive behavior. With respect to the constitutive law, three levels of resolution – continuous, intermediate and discrete – are introduced.Originality/value– The overall concept combines model adaptation with adaptive mesh refinement with the aim to obtain a most efficient and accurate solution.
An efficient preconditioned Krylov subspace method for large-scale finite element equations with MPC using Lagrange multiplier method
Authors: Hu Zixiang , Zhang Shi , Zhang Yun , Zhou Huamin , Li Dequn 
Published: September 2014

Purpose– The purpose of this paper is to propose an efficient iterative method for large-scale finite element equations of bad numerical stability arising from deformation analysis with multi-point constraint using Lagrange multiplier method.Design/methodology/approach– In this paper, taking warpage analysis of polymer injection molding based on surface model as an example, the performance of several popular Krylov subspace methods, including conjugate gradient, BiCGSTAB and generalized minimal residual (GMRES), with diffident Incomplete LU (ILU)-type preconditions is investigated and compared. For controlling memory usage, GMRES(m) is also considered. And the ordering technique, commonly used in the direct method, is introduced into the presented iterative method to improve the preconditioner.Findings– It is found that the proposed preconditioned GMRES method is robust and effective for solving problems considered in this paper, and approximate minimum degree (AMD) ordering is most beneficial for the reduction of fill-ins in the ILU preconditioner and acceleration of the convergence, especially for relatively accurate ILU-type preconditioning. And because of concerns about memory usage, GMRES(m) is a good choice if necessary.Originality/value– In this paper, for overcoming difficulties of bad numerical stability resulting from Lagrange multiplier method, together with increasing scale of problems in engineering applications and limited hardware conditions of computer, a stable and efficient preconditioned iterative method is proposed for practical purpose. Before the preconditioning, AMD reordering, commonly used in the direct method, is introduced to improve the preconditioner. The numerical experiments show the good performance of the proposed iterative method for practical cases, which is implemented in in-house and commercial codes on PC.
Nonlinear analysis of RC beams using a hybrid shear-flexural fibre beam model
Authors: Ferreira Denise , Bairán Jesús , Marí Antonio , Faria Rui 
Published: September 2014

Purpose
– A nonlinear finite element (FE) beam-column model for the analysis of reinforced concrete (RC) frames with due account of shear is presented in this paper. The model is an expansion of the traditional flexural fibre beam formulations to cases where multiaxial behaviour exists, being an alternative to plane and solid FE models for the nonlinear analysis of entire frame structures. The paper aims to discuss these issues.

Design/methodology/approach
– Shear is taken into account at different levels of the numerical model: at the material level RC is simulated through a smeared cracked approach with rotating cracks; at the fibre level, an iterative procedure guarantees equilibrium between concrete and transversal reinforcement, allowing to compute the biaxial stress-strain state of each fibre; at the section level, a uniform shear stress pattern is assumed in order to estimate the internal shear stress-strain distribution; and at the element level, the Timoshenko beam theory takes into account an average rotation due to shear.

Findings
– The proposed model is validated through experimental tests available in the literature, as well as through an experimental campaign carried out by the authors. The results on the response of RC elements critical to shear include displacements, strains and crack patterns and show the capabilities of the model to efficiently deal with shear effects in beam elements.

Originality/value
– A formulation for the nonlinear shear-bending interaction based on the fixed stress approach is implemented in a fibre beam model. Shear effects are accurately accounted during all the nonlinear path of the structure in a computationally efficient manner.
9 The Alternative Economy: Resilience in the Face of Complexity from the Eastern Lowlands
Authors: Scarborough Vernon L. , Valdez Fred 
Published: September 2014

ABSTRACTThe ancient eastern Maya Lowlands are characterized by both small, highly resilient communities and the growth of large regional centers. The smaller communities, separated by 2–5 kilometers and dispersed across the landscape, established a circle of interdependency between one another and a spatial separation from the largest centers. Degrees of sustainability were achieved through time by way of a negotiated settlement and land use balance within the relatively fragile biophysical environment. Because tropical ecosystems are identified by low specific species richness in any one patch or microenvironment, humans tend to mimic this spatial dispersion—a high‐density “ruralism.” When assessed by way of high humidity and precipitation, decomposition and disease were significant deranging factors affecting surplus and storage. Roads and navigable canal systems shorten the time necessary for distribution of organics—principally food; and when coupled with routinized scheduling (calendars), time and distance were reduced. Salting and “natural” root crop preservation techniques are discussed. A dual or alternative economy is proposed in the context social complexity.
Near‐Net‐Shape Fabrication ofTi3SiC2‐based Ceramics by Three‐Dimensional Printing
Authors: Ma Yuzhao , Yin Xiaowei , Fan Xiaomeng , Wang Lei , Greil Peter , Travitzky Nahum 
Published: September 2014

This paper focuses on the preparation of near‐net‐shaped denseTi3SiC2‐based materials via an indirect three‐dimensional printing (3Dprinting) and postreactive melt infiltration (RMI) processes.TiCpreforms with bimodal pore size distribution were fabricated through 3Dprinting, followed by the infiltration of Si melt and Al–Si alloy (Al40Si60andAl70Si30). Dense composites with density of ~4.1 g/cm3were obtained after the infiltration. No volume shrinkage was obtained after the reactive infiltration withAl–Si alloy. The participation of Al during the infiltration process promoted the formation ofTi3SiC2. The as‐fabricatedTi3SiC2‐based materials showed enhanced mechanical and electromagnetic interference shielding properties.
Identifying Training Needs for Mainstream Healthcare Professionals, to Prepare Them for Working with Individuals with Intellectual Disabilities: A Systematic Review
Authors: Hemm Cahley , Dagnan Dave , Meyer Thomas D. 
Published: September 2014

BackgroundResearch suggests there is a high prevalence of physical and mental ill health among individuals with intellectual disabilities and that staff working in mainstream healthcare services lack knowledge, skills and positive attitudes in supporting this client group. This review aimed to locate, extract themes from and evaluate the current literature that had assessed the training needs of mainstream health professionals within this area.MethodsThis review utilized a mixed‐methods approach, with systematic elements used to locate and evaluate the literature (n = 13) and a narrative approach used to explore patterns and themes identified. The search was completed across four databases, using the search terms felt most likely to capture the relevant literature.ResultsThree main themes of perceived training need were identified across a range of professional groups: general communication, knowledge/information and profession‐specific needs.ConclusionsThis review highlights the existing themes of training needs as identified by mainstream healthcare staff. It would appear that it may be possible to produce a core training package, suitable across professions with elements that are profession specific and therefore tailored accordingly. Limitations of the literature are explored within this review, as are recommendations for the directions of future research.
Effects of Thoracic Epidural Anesthesia on Cardiac Function and Myocardial Cell Apoptosis in Isoproterenol‐Induced Chronic Heart Failure Rats
Authors: GE TONG , QIN HAO , WANG XU , YANG SHU‐SEN , GUO LI , HAN WEI , CHANG HUI‐YING 
Published: September 2014

ObjectiveThis study aimed to investigate the effects of thoracic epidural anesthesia (TEA) on cardiac function and myocardial cell apoptosis in isoproterenol (ISO) induced chronic heart failure (CHF) rats.MethodRats were classified into 4 groups: the healthy control, ISO‐induced CHF, ISO + TEA, and sham‐treated groups. After 4 weeks, the animals in each group were examined by echocardiography. Invasive hemodynamic measurements were also preformed.ResultsEchocardiographic findings suggested that rats in the ISO + TEA group exhibited decreased left ventricular end‐systolic (LVES) and left ventricular end‐diastolic (LVED), and increased left ventricular ejection fraction (LVEF) and left ventricular shortening fraction (LVFS) compared with rats in the ISO‐induced CHF group. Rats in the ISO + TEA group showed improved left ventricular systolic pressure (LVSP) and left ventricular end‐diastolic pressure (LVEDP) compared with rats in the ISO‐induced CHF group. Additionally, rats in the ISO + TEA group had significant decrease in LV and RV mass indexes (LVMI and RVMI) compared with rats in the ISO‐induced CHF rats. Myocardial ultrastructure in the ISO + TEA group significantly improved compared with the ISO‐induced CHF group. TEA significantly reduced the percent of TUNEL‐positive cells in the ISO + TEA group compared with the ISO‐induced CHF group. Compared with the ISO‐induced CHF group, Bcl‐2 expression of rats in the ISO + TEA group was significantly increased, while Bax expression was significantly attenuated.ConclusionOur findings suggest that TEA may reduce myocardial apoptosis and decrease extent of structural damage and abnormalities in the myocardium. (J Interven Cardiol 2014;27:446–455)