bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting toric SU(3) structures
Authors: Larfors M. 
Published: October 2013

AbstractThree‐dimensional smooth compact toric varieties (SCTV) admit SU(3) structures, and may thus be relevant for string compactifications, if they have even first Chern class (c1). This condition can be fulfilled by infinitely many SCTVs, including ℂℙ3 and ℂℙ1 bundles over all two‐dimensional SCTVs. We show that as long as c1 is even, toric SU(3) structures can be constructed using a method proposed in [1]. We perform a systematic study of the parametric freedom of the resulting SU(3) structures, with a particular focus on the metric and the torsion classes. Although metric positivity constrains the SU(3) parameters, we find that every SCTV admits several toric SU( 3) structures and that parametric choices can sometimes be made to match requirements of string vacua. We also provide a short review on the constraints that an SU(3) structure must meet to be relevant for four‐dimensional, maximally symmetric &#55349;&#56489; = 1 or &#55349;&#56489; = 0 string vacua.
Function‐based assessment of structural similarity measurements using metal co‐factor orientation
Authors: Senn Stefan , Nanda Vikas , Falkowski Paul , Bromberg Yana 
Published: October 2013

ABSTRACTStructure comparison is widely used to quantify protein relationships. Although there are several approaches to calculate structural similarity, specifying significance thresholds for similarity metrics is difficult due to the inherent likeness of common secondary structure elements. In this study, metal co‐factor location is used to assess the biological relevance of structural alignments. The distance between the centroids of bound co‐factors adds a chemical and function‐relevant constraint to the structural superimposition of two proteins. This additional dimension can be used to define cut‐off values for discriminating valid and spurious alignments in large alignment sets. The hypothesis underlying our approach is that metal coordination sites constrain structural evolution, thus revealing functional relationships between distantly related proteins. A comparison of three related nitrogenases shows the sequence and fold constraints imposed on the protein structures up to 18 Å away from the centers of their bound metal clusters. Proteins 2014; 82:648–656. © 2013 Wiley Periodicals, Inc.
Optimal controller location in wireless networked control systems
Authors: Xin Kefei , Cao Xianghui , Chen Jiming , Cheng Peng , Xie Lihua 
Published: October 2013

SUMMARYThe control performance of wireless networked control systems (WNCS) has been shown to heavily depend on the packet delivery quality of both the sensor‐to‐controller and controller‐to‐actuator communications. Such quality relies on the relative distance between the wireless transmitter and receiver, which naturally raises the challenging problem of controller placement in WNCS for optimal control performance. In this paper, we investigate the optimal controller location (OCL) problem in WNCS based on linear‐quadratic‐Gaussian control strategy. For the one‐hop network case where the controller can only be placed at either the sensor side or the actuator side, we derive a simple yet effective criterion to determine the OCL. For the more general multi‐hop case where the controller can be located at either one of the sensors, relays, or actuators, we obtain the necessary and sufficient condition under which the closed‐loop system is guaranteed to be stable. On the basis of these results, we further transform the OCL problem into an optimization problem that can be solved efficiently. Numerical results are provided to verify our analysis. Copyright © 2013 John Wiley & Sons, Ltd.
Robust H ∞  filtering for singular time‐delayed systems with uncertain Markovian switching probabilities
Authors: Wang Guoliang , Xu Shengyuan 
Published: October 2013

SUMMARYThis paper is concerned with the robust H ∞  filter design for a class of uncertain singular time‐delayed Markovian jump systems, whose transition rate matrix has elementwise bounded uncertainties. By the LMI approach, a novel bounded real lemma is proposed such that the singular Markovian jump system is robustly exponentially mean‐square admissible with a prescribed H ∞  performance index. Based on this, a sufficient condition for the existence of a robust H ∞  filter is developed in terms of LMIs. Finally, a numerical example is provided to show the effectiveness of the theoretical results. Copyright © 2013 John Wiley & Sons, Ltd.
Studying the laws of software evolution in a long‐lived FLOSS project
Authors: Gonzalez‐Barahona Jesus M. , Robles Gregorio , Herraiz Israel , Ortega Felipe 
Published: October 2013

SUMMARYSome free, open‐source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long‐lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case. © 2013 The Authors. Journal of Software: Evolution and Process published by John Wiley & Sons Ltd.
Detecting asynchrony and dephase change patterns by mining software repositories
Authors: Jaafar Fehmi , Guéhéneuc Yann‐Gaël , Hamel Sylvie , Antoniol Giuliano 
Published: October 2013

SUMMARYSoftware maintenance accounts for the largest part of the costs of any program. During maintenance activities, developers implement changes (sometimes simultaneously) on artifacts in order to fix bugs and to implement new requirements. To reduce this part of the costs, previous work proposed approaches to identify the artifacts of programs that change together. These approaches analyze historical data, mined from version control systems, and report change patterns, which lead at the causes, consequences, and actors of the changes to source code files. They also introduce so‐called change patterns that describe some typical change dependencies among files. In this paper, we introduce two novel change patterns: the asynchrony change pattern, corresponding to macro co‐changes (MC), that is, of files that co‐change within a large time interval (change periods) and the dephase change pattern, corresponding to dephase macro co‐changes (DC), that is, MC that always happens with the same shifts in time. We present our approach, that we named Macocha, to identify these two change patterns in large programs. We use the k‐nearest neighbor algorithm to group changes into change periods. We also use the Hamming distance to detect approximate occurrences of MC and DC. We apply Macocha and compare its performance in terms of precision and recall with UMLDiff (file stability) and association rules (co‐changing files) on seven systems: ArgoUML, FreeBSD, JFreeChart, Openser, SIP, XalanC, and XercesC developed with three different languages (C, C++, and Java). These systems have a size ranging from 532 to 1693 files, and during the study period, they have undergone 1555 to 23,944 change commits. We use external information and static analysis to validate (approximate) MC and DC found by Macocha. Through our case study, we show the existence and usefulness of these novel change patterns to ease software maintenance and, potentially, reduce related costs. Copyright © 2013 John Wiley & Sons, Ltd.
Channel assignment schemes for cooperative spectrum sensing in multi‐channel cognitive radio networks
Authors: Wang Weiwei , Kasiri Behzad , Cai Jun , Alfa Attahiru S. 
Published: October 2013

AbstractIn this paper, channel assignment for spectrum sensing is studied in multi‐channel cognitive radio (CR) networks to maximize the number of channels satisfying sensing performance (called available channels). Beginning with a nonlinear integer programming problem, we derive the upper bound of optimal value through many‐to‐many assignment problem and then propose three algorithms for both centralized and distributed scenarios. In centralized case, a heuristic scheme is proposed based on the signal‐to‐noise ratios (SNRs) over all primary channels (PCs). Then, a greedy scheme is proposed to reduce the reported information from the CRs. In distributed case, a novel scheme with multi‐round operation is designed following the coalitional game theory. In each round, each CR selects some PCs based on SNRs. Then, the CRs selecting the same channel play coalitional game, and thereby, multiple games are played concurrently over multiple channels. Finally, the best coalition for each channel is chosen among the formed coalitions to perform the cooperative spectrum sensing. The simulation results show that the proposed schemes can significantly increase the number of available channels. Copyright © 2013 John Wiley & Sons, Ltd.
Northern bobwhite response to habitat restoration in eastern oklahoma
Authors: Crosby Andrew D. , Elmore R. Dwayne , Leslie David M. 
Published: October 2013

ABSTRACTIn response to the decline of northern bobwhite (Colinus virginianus; hereafter, bobwhite) in eastern Oklahoma, USA, a cost‐share incentive program for private landowners was initiated to restore early successional habitat. Our objectives were to determine whether the program had an effect on bobwhite occupancy in the restoration areas and evaluate how local‐ and landscape‐level habitat characteristics affect occupancy in both restoration and control areas. We surveyed 14 sample units that received treatment between 2009 and 2011, and 17 sample units that were controls. We used single‐season occupancy models, with year as a dummy variable, to test for an effect of restoration treatment and habitat variables on occupancy. We found no significant treatment effect. Model selection showed that occupancy was best explained by the combination of overstory canopy cover and habitat area at both the local and landscape scales. Moran's I revealed positive spatial autocorrelation in the 1,000–3,000‐m distance band, indicating that the likelihood of bobwhite occupancy increased with proximity to other populations. We show that creating ≥20 ha of habitat within 1–3 km of existing bobwhite populations increases the chance of restoration being successful. © 2013 The Wildlife Society. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
Trauma‐induced malformed antler development in male white‐tailed deer
Authors: Karns Gabriel R. , Ditchkoff Stephen S. 
Published: October 2013

ABSTRACTThough normal antlers are branched and bilaterally symmetrical, male white‐tailed deer (Odocoileus virginianus) sometimes develop malformed antlers because of various reasons. As management for antler quality has grown more popular in recent years, there has been concern that spike‐on‐one‐side (SOOS) antler configuration has a genetic cause. We hypothesized that the majority of SOOS antlers are the artifact of injuries to the antlerogenic periosteum region. We collected 71 SOOS specimens over 2 hunting seasons (2010–2011 and 2011–2012) in Alabama, USA, and identified probable cause for malformed antler development. We confidently assigned cause to 62% of specimens, and frequency of skull and/or pedicle trauma increased with age classes (yearling, 2.5‐yr‐old, and ≥3.5‐yr‐old M). It was difficult to determine the reason that yearling males developed SOOS antler traits (30%), but ease of prescription increased with male age (76% for ≥3.5‐yr‐old M). Based on the physiology of skull and/or pedicle versus skeletal injuries, we recommended different culling strategies for yearling versus adult male white‐tailed deer according to management objectives. © 2013 The Wildlife Society. © The Wildlife Society, 2013
Emergence of sandflies (Phlebotominae) in Austria, a Central European country
Authors: Poeppl Wolfgang , Obwaller Adelheid G. , Weiler Martin , Burgmann Heinz , Mooseder Gerhard , Lorentz Susanne , Rauchenwald Friedrich , Aspöck Horst , Walochnik Julia , Naucke Torsten J. 
Published: October 2013

Abstract
The possible existence of autochthonous sandfly populations in Central Europe north of the Alps has long been excluded. However, in the past years, sandflies have been documented in Germany, Belgium, and recently, also in Austria, close to the Slovenian border. Moreover, autochthonous human Leishmania and Phlebovirus infections have been reported in Central Europe, particularly in Germany. From 2010 to 2012, sandfly trapping (740 trap nights) was performed at 53 different capture sites in Austria using battery-operated CDC miniature light traps. Sites were chosen on the basis of their climate profile in the federal states Styria, Burgenland, and Lower Austria. Sandfly specimens found were transferred to 70 % ethanol for conservation. Identification was based on morphological characters of the male genitalia and the female spermathecae, respectively. Altogether, 24 specimens, 22 females and 2 males, all identified as Phlebotomus (Transphlebotomus) mascittii Grassi, 1908, were found at six different sampling sites in all three federal states investigated. The highest number of catches was made on a farm in Lower Austria. Altogether, the period of sandfly activity in Austria was shown to be much longer than presumed, the earliest capture was made on July 3rd and the latest on August 28th. Sandflies have been autochthonous in Austria in small foci probably for long, but in the course of global warming, further spreading may be expected. Although P. mascittii is only an assumed vector of Leishmania spp.—data on its experimental transmission capacity are still lacking—the wide distribution of sandflies in Austria, a country thought to be free of sandflies, further supports a potential emergence of sandflies in Central Europe. This is of medical relevance, not only with respect to the transmission of Leishmania spp. for which a reservoir is given in dogs, but also with respect to the phleboviruses.
Activating the expression of bacterial cryptic genes by rpoB mutations in RNA polymerase or by rare earth elements
Authors: Ochi Kozo , Tanaka Yukinori , Tojo Shigeo 
Published: October 2013

Abstract
Since bacteria were found to contain genes encoding enzymes that synthesize a plethora of potential secondary metabolites, interest has grown in the activation of these cryptic pathways. Homologous and heterologous expression of these cryptic secondary metabolite-biosynthetic genes, often “silent” under ordinary laboratory fermentation conditions, may lead to the discovery of novel secondary metabolites. We review current progress on this topic, describing concepts for activating silent genes. We especially focus on genetic manipulation of transcription and translation, as well as the utilization of rare earth elements as a novel method to activate the silent genes. The possible roles of silent genes in bacterial physiology are also discussed.
Actinomycetes biosynthetic potential: how to bridge in silico and in vivo?
Authors: Rebets Yuriy , Brötz Elke , Tokovenko Bogdan , Luzhetskyy Andriy 
Published: October 2013

Abstract
Actinomycetes genome sequencing and bioinformatic analyses revealed a large number of “cryptic” gene clusters coding for secondary metabolism. These gene clusters have the potential to increase the chemical diversity of natural products. Indeed, reexamination of well-characterized actinomycetes strains revealed a variety of hidden treasures. Growing information about this metabolic diversity has promoted further development of strategies to discover novel biologically active compounds produced by actinomycetes. This new task for actinomycetes genetics requires the development and use of new approaches and tools. Application of synthetic biology approaches led to the development of a set of strategies and tools to satisfy these new requirements. In this review, we discuss strategies and methods to discover small molecules produced by these fascinating bacteria and also discuss a variety of genetic instruments and regulatory elements used to activate secondary metabolism cryptic genes for the overproduction of these metabolites.
DNA assembly techniques for next-generation combinatorial biosynthesis of natural products
Authors: Cobb Ryan E , Ning Jonathan C , Zhao Huimin 
Published: October 2013

AbstractNatural product scaffolds remain important leads for pharmaceutical development. However, transforming a natural product into a drug entity often requires derivatization to enhance the compound’s therapeutic properties. A powerful method by which to perform this derivatization is combinatorial biosynthesis, the manipulation of the genes in the corresponding pathway to divert synthesis towards novel derivatives. While these manipulations have traditionally been carried out via restriction digestion/ligation-based cloning, the shortcomings of such techniques limit their throughput and thus the scope of corresponding combinatorial biosynthesis experiments. In the burgeoning field of synthetic biology, the demand for facile DNA assembly techniques has promoted the development of a host of novel DNA assembly strategies. Here we describe the advantages of these recently developed tools for rapid, efficient synthesis of large DNA constructs. We also discuss their potential to facilitate the simultaneous assembly of complete libraries of natural product biosynthetic pathways, ushering in the next generation of combinatorial biosynthesis.
Antioxidant Property, Thymoquinone Content and Chemical Characteristics of Different Extracts from Nigella sativa L. Seeds
Authors: Solati Zeinab , Baharin Badlishah Sham , Bagheri Hossein 
Published: October 2013

AbstractIn this study, Nigella sativa L. seeds were extracted using supercritical carbon dioxide (SC‐CO2) and Soxhlet. Chemical characteristics, fatty acid composition, antioxidant activity and thymoquinone content of N. sativa L. extracts obtained through different methods were investigated and compared. It was revealed that antioxidant activity and thymoquinone content could be significantly different for SC‐CO2 and Soxhlet extracts. The results for fatty acid composition indicated that linoleic acid, palmitic acid and oleic acid were the main fatty acids in both extracts. The SC‐CO2 extraction could provide an extract with higher quality and antioxidant activity compared to Soxhlet extraction method and can be considered a more appropriate method for attaining a high‐quality extract.
Prognostic value of age and Wassel classification in the reconstruction of thumb duplication
Authors: Cabrera González Marisa , Pérez López Laura M. , Martínez Soto Gino , Gutiérrez de la Iglesia Diego 
Published: October 2013

Background Various surgical techniques for thumb duplication have been described. The main goal in thumb reconstruction is to achieve optimal function, stability, and shape. Few publications have quantified the functional results of each surgical option and factors that may affect these outcomes. Methods We performed a retrospective review during the period from 1990 to 2011 of 115 surgery patients, 99 of whom had a mean postoperative follow-up of 44.1 months. They were classified according to the Wassel classification. We assessed the surgical technique, functional results, and complications, and evaluated the probable prognostic value of age and Wassel classification. Results This case series comprised mainly female patients (62 %) and the right hand (74 %), with a mean age at operation of 20 months. The most common group was Wassel type IV (54 %). On the basis of the Tada scoring system, we obtained 91 good results (91 %). Complications occurred in 27 patients (27 %), mainly instability and axis deformation. In a comparison of preoperative factors (age at the time of surgery and Wassel classification) with the final results (Tada score and complications), the association between older age at surgery and complications ( p = 0.0001) and Wassel types III and IV and complications ( p = 0.0210 and p = 0.0095) was statistically significant. Conclusions Following the basic concepts of anatomical reconstruction, we obtained good results in most patients. The main complications were instability and axial deformity. These were most common in patients who underwent operations at an age of more than 12 months, and patients with Wassel types III and IV deformities.
Why does the impact of multidisciplinary pain management on quality of life differ so much between chronic pain patients?
Authors: Vartiainen P. , Heiskanen T. , Roine R.P. , Kalso E. 
Published: October 2013

Abstract

Aims
To assess the change in quality of life and factors predicting this change in 1425 chronic pain patients treated in a multidisciplinary pain clinic.

Methods
This is an observational follow-up study using the 15D generic health-related quality of life (HRQoL) instrument. Patients filled in the HRQoL questionnaire at baseline, and 6 and 12 months after discharge. To assess if mental factors predicted treatment success, the changes in the overall 15D score were compared and related to the baseline variables of depression and distress. The group of patients, who scored 4 or 5 on the 1–5 scale for the depression and distress dimensions of the 15D instrument, were considered mentally distressed (N =199). They were compared with the non-distressed patients (i.e. those who scored 1; N = 401).

Results
Pain was associated to depression and distress: 85.4% of mentally distressed patients scored 4 or 5 also on the discomfort and symptoms dimension, vs. 51.4% of the non-distressed (p < 0.001). The mean 15D score of the mentally distressed patients improved statistically significantly more (from 0.572 to 0.636, N =141) during the first six months after treatment compared with the 15D of those who were not mentally distressed, who improved only marginally (0.790–0.803, N = 294; p < 0.001).

Conclusions
Patients with more severe depression or distress at baseline appear to gain more from the treatment than those who have less mental distress. In our ongoing study more baseline factors will be evaluated to assess their effect on the success of treatment.