bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein structure refinement by optimization
Authors: Carlsen Martin , Røgen Peter 
Published: June 2015

ABSTRACTKnowledge‐based protein potentials are simplified potentials designed to improve the quality of protein models, which is important as more accurate models are more useful for biological and pharmaceutical studies. Consequently, knowledge‐based potentials often are designed to be efficient in ordering a given set of deformed structures denoted decoys according to how close they are to the relevant native protein structure. This, however, does not necessarily imply that energy minimization of this potential will bring the decoys closer to the native structure. In this study, we introduce an iterative strategy to improve the convergence of decoy structures. It works by adding energy optimized decoys to the pool of decoys used to construct the next and improved knowledge‐based potential. We demonstrate that this strategy results in significantly improved decoy convergence on Titan high resolution decoys and refinement targets from Critical Assessment of protein Structure Prediction competitions. Our potential is formulated in Cartesian coordinates and has a fixed backbone potential to restricts motions to be close to those of a dihedral model, a fixed hydrogen‐bonding potential and a variable coarse grained carbon alpha potential consisting of a pair potential and a novel solvent potential that are b‐spline based as we use explicit gradient and Hessian for efficient energy optimization. Proteins 2015; 83:1616–1624. © 2015 Wiley Periodicals, Inc.
Significance of urethral fibrosis evaluated by preoperative magnetic resonance imaging as a predictor of continence status after robot‐assisted radical prostatectomy
Authors: Momozono Hiroyuki , Miyake Hideaki , Miyazaki Akira , Fujisawa Masato 
Published: June 2015

AbstractBackgroundThe objective of this study was to assess the impact of urethral fibrosis on the continence status following robot‐assisted radical prostatectomy (RARP).MethodsThe findings of fibrosis of the urethral wall and periurethral tissue in 185 patients undergoing RARP were each divided into grade 0 to 3 based on preoperative T2‐weighted magnetic resonance imaging. Urethral fibrosis was defined as the sum of both grades, and scores ≤ 2 and ≥ 3 were considered as ‘no/mild’ and ‘severe’ fibrosis, respectively.ResultsThe incidences of continence in patients with no/mild fibrosis were significantly higher at 3, 6, and 12 months after RARP than those with severe fibrosis. Furthermore, urethral fibrosis was identified as an independent predictor of the postoperative continence status at 3, 6, and 12 months after RARP.ConclusionsAssessment of urethral fibrosis could be a significant predictor of recovery of the urinary continence status after RARP. Copyright © 2015 John Wiley & Sons, Ltd.
Application of a laser‐guided docking system in robot‐assisted urologic surgery
Authors: Guo Fei , Zhang Chao , Wang Hui‐qing , Sheng Xia , Xiao Liang , Sun Ying‐hao , Yang Bo 
Published: June 2015

AbstractBackgroundThis work explores the clinical significance of a laser‐guided docking system for robot‐assisted urologic surgery.Materials and MethodsBetween July 2013 and June 2014, 40 patients underwent robot‐assisted laparoscopic prostatectomy (RALP), and 32 patients underwent robot‐assisted laparoscopic partial nephrectomy (RAPN) performed by a single surgeon. In the RALP and RAPN groups, the robot was docked in the traditional way in 20 and 16 cases, respectively. A laser guiding system was used in the other cases. The docking time and the time required to adjust the angles were recorded.ResultThe docking time was significantly shorter for the laser‐guided process performed by inexperienced nurses. The time required to adjust the angles was also lower. There were no significant differences between the processes performed by experienced nurses.ConclusionA laser‐guided docking system may simplify and standardize the docking process and shorten the learning curve. Copyright © 2015 John Wiley & Sons, Ltd.
Post‐Spawning Survival and Downstream Passage of Landlocked Atlantic Salmon (Salmo salar) in a Regulated River: Is There Potential for Repeat Spawning?
Authors: Nyqvist D. , Calles O. , Bergman E. , Hagelin A. , Greenberg L. A. 
Published: June 2015

AbstractRepeat salmonid spawners may make large contributions to total recruitment and long term population stability. Despite their potential importance, relatively little is known about this phase of the life history for anadromous populations, and nothing has been reported for landlocked populations. Here, we studied post‐spawning behaviour and survival of landlocked Atlantic salmon in relation to downstream dam passage in the River Klarälven, Sweden. Eight hydropower stations separate the feeding grounds in Lake Vänern from the spawning grounds in the River Klarälven, and no measures to facilitate downstream migration are present in the river. Forty‐nine percent of the salmon survived spawning and initiated downstream migration. Females and small fish had higher post‐spawning survival than males and large fish. The post‐spawners migrated downstream in autumn and spring and remained relatively inactive in the river during winter. Downstream migration speed in the free flowing part of the river was highly variable with a median of 9.30 km/day. Most fish passed the first hydropower station via upward‐opening spill gates after a median residence time in the forebay of 25 min. However, no tagged fish survived passage of all eight hydropower stations to reach Lake Vänern. This result underscores the need for remedial measures to increase the survival of downstream migrating kelts. Copyright © 2015 John Wiley & Sons, Ltd.
The long‐term benefits of organizational resilience through sustainable business practices
Authors: Ortiz‐de‐Mandojana Natalia , Bansal Pratima 
Published: June 2015

Research summary: Prior work on the benefits of business sustainability often applies short‐term causal logic and data analysis. In this article, we argue that the social and the environmental practices (SEPs) associated with business sustainability not only contribute to short‐term outcomes, but also to organizational resilience, which we define as the firm's ability to sense and correct maladaptive tendencies and cope positively with unexpected situations. Because organizational resilience is a latent, path‐dependent construct, we assess it through the long‐term outcomes, including improved financial volatility, sales growth, and survival rates. We tested these hypotheses with data from 121 U.S.‐based matched‐pairs (242 individual firms) over a 15‐year period. We also tested, but did not find support for, the relationship between SEPs and short‐term financial performance.Managerial summary: Most managers look for short‐term financial benefits to justify socially responsible or sustainable practices. In this article, we argue that such practices also help firms become more resilient, which helps them avoid crises and bounce back from shocks. However, it is difficult to measure the avoidance of shocks, so we analyzed long‐term outcomes. We show that firms that adopt responsible social and environmental practices, relative to a carefully matched control group, have lower financial volatility, higher sales growth, and higher chances of survival over a 15‐year period; yet, we were unable to find any differences in short‐term profits. We hope this research provides good reasons for firms to practice sustainability beyond the pursuit of short‐term profits. Copyright © 2015 John Wiley & Sons, Ltd.
Acceptable risks to persons associated with building structures
Authors: Tanner Peter , Hingorani Ramon 
Published: June 2015

AbstractIn routine engineering practice, the risks associated with safety considerations addressed when designing new or assessing existing structures are not quantified and the corresponding acceptance criteria may diverge widely. Although the use of explicit risk analysis methods to quantify structural safety would therefore deliver significant benefits, the implementation of such methods is hindered by a series of technical and administrative obstacles.The present study explores methods and tools for the practical application of explicit risk analysis methods. Structure‐related risks to persons are established on the grounds of the probability of structural failure and its consequences in terms of loss of human life. The procedure adopted is applied to a representative set of building structures. Acceptance criteria for risks to persons associated with such structures are deduced from the findings. These criteria provide a rational basis for decision‐making in structural engineering. They may be used in explicit risk analysis or as a basis for the consistent calibration of simplified models for determining partial factors in the design of new or assessment of existing structures.
Assessing and updating the reliability of concrete bridges subjected to spatial deterioration – principles and software implementation
Authors: Schneider Ronald , Fischer Johannes , Bügler Maximilian , Nowak Marcel , Thöns Sebastian , Borrmann André , Straub Daniel 
Published: June 2015

AbstractInspection and maintenance of concrete bridges is a major cost factor in transportation infrastructure, and there is significant potential for using information gained during inspection to update predictive models of the performance and reliability of such structures. In this context, this paper presents an approach for assessing and updating the reliability of prestressed concrete bridges subjected to chloride‐induced reinforcement corrosion. The system deterioration state is determined based on a Dynamic Bayesian Network (DBN) model that considers the spatial variability of the corrosion process. The overall system reliability is computed by means of a probabilistic structural model coupled with the deterioration model. Inspection data are included in the system reliability calculation through Bayesian updating on the basis of the DBN model. As proof of concept, a software prototype is developed to implement the method presented here. The software prototype is applied to a typical highway bridge and the influence of inspection information on the system deterioration state and the structural reliability is quantified taking into account the spatial correlation of the corrosion process. This work is a step towards developing a software tool that can be used by engineering practitioners to perform reliability assessments of ageing concrete bridges and update their reliability with inspection and monitoring data.
Safety assessment of punching shear failure according to the level of approximation approach
Authors: Belletti Beatrice , Pimentel Mário , Scolari Matteo , Walraven Joost C. 
Published: June 2015

AbstractThe fib Model Code for Concrete Structures 2010 introduced the concept of levels of approximation (LoA) as a strategy for simplifying the procedures involved in preliminary design stages or the design of non‐critical structural elements while still providing the tools for engineers to use state‐of‐the‐art techniques in the assessment of existing structures or in the advanced stages of design for critical structural elements. In this paper, this concept is applied to the determination of the punching shear resistance of reinforced concrete slabs. A procedure is validated for the highest LoA involving non‐linear finite element analysis (NLFEA) with multi‐layered shell elements and the critical shear crack theory (CSCT). The safety format proposed for use in the safety verification assisted by NLFEA is based on the definition of a global resistance safety factor. A semi‐probabilistic approach is followed, based on the assumption of a lognormal distribution for the resistance and on an estimate of its coefficient of variation. This approach is validated by means of a comparison with the results from a probabilistic analysis.The LoA approach is initially applied to the study of statically determinate slabs supported on one column to verify the effectiveness of the procedure presented here compared with other validated methods available in the literature. The paper concludes with a case study illustrating the application of the proposed procedure to a bridge deck slab and highlighting the benefits of using a higher LoA.
Monitoring‐based performance assessment of rail‐bridge interaction based on structural reliability
Authors: Strauss Alfred , Karimi Saeed , Kopf Fritz , Capraru Catalin , Bergmeister Konrad 
Published: June 2015

AbstractFor today's railways, the continuous welded rail, which enhances driving dynamics and comfort for passengers, is often the construction method of choice. However, bridges and viaducts, which can be seen as singularities in the railway substructure, still pose a few unsolved problems; the bridge structure deforms under the impacts of thermal variation, creep, shrinkage, train passage and braking. The track‐bridge interaction is an important parameter in railway bridge design. Measurement campaigns and research projects have been performed to investigate the interaction process and learn how to predict longitudinal forces in the rail and the concrete slab track. For the construction of long bridges on high‐speed railway lines, new computational tools, monitoring systems and enhanced verification methods for tolerable rail stresses on bridges had to be developed. In order to take the modified stiffness conditions and recent findings on rail resistance into account, the verification schemes and safety concepts based on monitoring data have to be revised and performance‐based methods need to be developed. The target of this article is to present monitoring‐ and reliability‐based assessment methods for the concrete structure‐rail interaction using monitoring and non‐linear analysis techniques.
Economic and human safety reliability levels for existing structures
Authors: Steenbergen Raphaël D. J. M. , Sýkora Miroslav , Diamantidis Dimitris , Holický Milan , Vrouwenvelder Ton 
Published: June 2015

AbstractSpecifying the target reliability levels is one of the key issues in the assessment of existing structures. For a majority of existing buildings and infrastructures, the design life has been reached or will be reached in the near future. These structures need to be reassessed in order to verify their safety. Eurocodes provide a general basis primarily intended for the design of new structures, but the basic principles can be used for assessing existing buildings, too. Reliability levels are generally based on both economic optimization and criteria for human safety. In this study, both methods are elaborated for existing structures. It appears that the requirement for the same target reliability for existing and new structures is uneconomical. Further, cost optimization seems to yield rather low reliability levels and human safety criteria often become the critical factor. The study concludes with practical guidelines for establishing reliability indices for existing structures linked to Eurocode principles.
A Personal History of Quadruplex–Small Molecule Targeting
Authors: Neidle Stephen 
Published: June 2015

AbstractThe story behind some of the early studies in the laboratory of Stephen Neidle on quadruplex‐binding small molecules and the structural studies on quadruplexes and their complexes is presented and discussed in the context of his earlier work on drug–DNA interactions. More recent studies and future directions in the rational design of small molecules targeting telomeric and gene promoter quadruplexes are also described.
Chronic exposure to manganese sulfate leads to adverse dose‐dependent effects on the neurobehavioral ability of rats
Authors: Su Cheng , Chen Kangcheng , Zou Yunfeng , Shen Yuefei , Xia Bing , Liang Guiqiang , Lv Yingnan , Wang Fenfen , Huang Damin , Yang Xiaobo 
Published: June 2015

ABSTRACTManganese sulfate is the main combustion product of methylcyclopentadienyl manganese tricarbonyl (MMT). Currently, little is known about the neurobehavioral consequences of chronic manganese sulfate exposure. In this study, rats were treated with 0, 5.0, 10.0, and 20.0 mg/kg MnSO4·H2O for 24 consecutive weeks via intraperitoneal injection. During the treatment period, spatial learning‐memory ability was measured using the Morris water maze (MWM). At the end of the exposure period, spontaneous motor behavior and emotional status, hippocampal histologic changes, and Hsp70 mRNA levels were measured using the open‐field test (OFT), hematoxylin‐eosin staining and real‐time quantitative PCR (RT‐PCR), respectively. A dose‐dependent decrease was noted in the spatial learning‐memory ability and the spontaneous activities of rats (P < 0.05), and negative emotions differed significantly between the exposed groups and the control group (P < 0.05). Moreover, overt morphological changes in the hippocampuses of the exposed rats were detected. Cellular degeneration and death were also found. The Hsp70 mRNA levels of the hippocampal areas in the 20.0 mg/kg group (1.567 ± 0.236) were significantly increased compared with the control group (P < 0.05). These results suggest that chronic exposure to manganese sulfate can have adverse dose‐dependent effects on rats' neurobehavioral ability, and the mechanism of abnormal hippocampal Hsp70 expression needs to be further explored. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1571–1579, 2016.
Quality assurance and its impact on ovarian visualization rates in the multicenter United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS)
Authors: Sharma A. , Burnell M. , Gentry‐Maharaj A. , Campbell S. , Amso N. N. , Seif M. W. , Fletcher G. , Brunell C. , Turner G. , Rangar R. , Ryan A. , Jacobs I. , Menon U. 
Published: June 2015

ABSTRACTObjectiveTo describe the quality assurance (QA) processes and their impact on visualization of postmenopausal ovaries in the ultrasound arm of a multicenter screening trial for ovarian cancer.MethodsIn the United Kingdom Collaborative Trial of Ovarian Cancer Screening, 50 639 women aged 50–74 years were randomized to the ultrasound arm and underwent annual transvaginal ultrasound (TVS) examinations. QA processes were developed during the course of the trial and included regular monitoring of the visualization rate (VR) of the right ovary. Non‐subjective factors identified previously as impacting on VR of the right ovary were included in a generalized estimating equation model for binary outcomes to enable comparison of observed vs adjusted VR between individual sonographers who had undertaken > 1000 scans during the trial and comparison between centers. Observed and adjusted VRs of sonographers and centers were ranked according to the highest VR. Analysis of annual VRs of sonographers and those of the included centers was undertaken.ResultsBetween June 2001 and December 2010, 48 230 of 50 639 women attended one of 13 centers for a total of 270 035 annual TVS scans. One or both ovaries were seen in 228 145 (84.5%) TVS scans. The right ovary was seen on 196 426 (72.7%) of the scans. For the 78 sonographers included in the model, the median difference between observed and adjusted VR was −0.7% (range, −7.9 to 5.9%) and the median change in VR rank after adjustment was 3 (range, 0–18). For the 13 centers, the median difference between observed and adjusted VR was −0.5% (range, −2.2 to 1%), with no change in ranking after adjustment. The median adjusted VR was 73% (interquartile range (IQR), 65–82%) for sonographers and 74.7% (IQR, 67.1–79.0%) for centers. Despite the increasing age of the women being scanned, there was a steady decrease in the number of sonographers with VR < 60% (21.4% in 2002 vs 2.0% in 2010) and an increase in sonographers with VR > 80% (14.3% in 2002 vs 40.8% in 2010). The median VR of the centers increased from 65.5% (range, 55.7–81.0%) in 2001 to 80.3% (range, 74.5–90.9%) in 2010.ConclusionsA robust QA program can improve visualization of postmenopausal ovaries and is an essential component of ultrasound‐based ovarian cancer screening trials. While VR should be adjusted for non‐subjective factors that impact on ovarian visualization, subjective factors are likely to be the largest contributors to differences in VR. © 2015 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd. on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.
Evaluating the reliability of field identification and morphometric classifications for carnivore scats confirmed with genetic analysis
Authors: Lonsinger Robert C. , Gese Eric M. , Waits Lisette P. 
Published: June 2015

ABSTRACTScat surveys are commonly used to monitor carnivore populations. Scats of sympatric carnivores can be difficult to differentiate and field‐based identification can be misleading. We evaluated the success of field‐based species identification for scats of 2 sympatric carnivores—coyotes (Canis latrans) and kit foxes (Vulpes macrotis). We conducted scat surveys in the Great Basin desert of Utah, USA, during the winter and summer of 2013, and we detected 1,680 carnivore scats. We classified scats based on field identification, recorded morphometric measurements, and collected fecal DNA samples for molecular species identification. We subsequently evaluated the classification success of field identification and the predictive power of 2 nonparametric classification techniques—k‐nearest neighbors and classification trees—based on scat measurements. Overall, 12.2% of scats were misclassified by field identification, but misclassifications were not equitable between species. Only 7.1% of the scats identified as coyote with field identification were misclassified, compared with 22.9% of scats identified as kit fox. Results from both k‐nearest neighbor and classification‐tree analyses suggest that morphometric measurements provided an objective alternative to field identification that improved classification of rarer species. Overall misclassification rates for k‐nearest neighbor and classification‐tree analyses were 11.7% and 7.5%, respectively. Using classification trees, misclassification was reduced for kit foxes (8.5%) and remained similar for coyotes (7.2%), relative to field identification. Although molecular techniques provide unambiguous species identification, classification approaches may offer a cost‐effective alternative. We recommend that monitoring programs employing scat surveys utilize molecular species identification to develop training data sets and evaluate the accuracy of field‐based and statistical classification approaches. © 2015 The Wildlife Society.