bluuebunny/crossref_metadata_2025_split huggingface dataset:
Speeding up systems biology simulations of biochemical pathways using condor
Authors: Liu Xuan , Taylor Simon J. E. , Mustafee Navonil , Wang Jun , Gao Qian , Gilbert David 
Published: December 2013

SUMMARYSystems biology is a scientific field that uses computational modelling to study biological and biochemical systems. The simulation and analysis of models of these systems typically explore behaviour over a wide range of parameter values; as such, they are usually characterised by the need for nontrivial amounts of computing power. Grid computing provides access to such computational resources. In previous research, we created the grid‐enabled biochemical networks simulation environment to attempt to speed up system biology simulations over a grid (the UK National Grid Service and ScotGrid). Following on from this work, we have created the simulation modelling of the epidermal growth factor receptor microtubule‐associated protein kinase pathway utility, a standalone simulation tool dedicated to the modelling and analysis of the epidermal growth factor receptor microtubule‐associated protein kinase pathway. This builds on experiences from biochemical networks simulation environment by decoupling the simulation modelling elements from the Grid middleware. This new utility enables us to interface with different grid technologies. This paper therefore describes the new SIMAP utility and an empirical investigation of its performance when deployed over a desktop grid based on the high throughput computing middleware Condor. We present our results based on a case study with a model of the mammalian ErbB signalling pathway, a pathway strongly linked to cancer. Copyright © 2013 John Wiley & Sons, Ltd.
Massively multithreaded maxflow for image segmentation on the Cray XMT‐2
Authors: Bokhari Shahid H. , Çatalyürek Ümit V. , Gurcan Metin N. 
Published: December 2013

SUMMARYImage segmentation is a very important step in the computerized analysis of digital images. The maxflow mincut approach has been successfully used to obtain minimum energy segmentations of images in many fields. Classical algorithms for maxflow in networks do not directly lend themselves to efficient parallel implementations on contemporary parallel processors. We present the results of an implementation of Goldberg–Tarjan preflow‐push algorithm on the Cray XMT‐2 massively multithreaded supercomputer. This machine has hardware support for 128 threads in each physical processor, a uniformly accessible shared memory of up to 4 TB and hardware synchronization foreach64 bit word. It is thus well‐suited to the parallelization of graph theoretic algorithms, such as preflow‐push. We describe the implementation of the preflow‐push code on the XMT‐2 and present the results of timing experiments on a series of synthetically generated as well as real images. Our results indicate very good performance on large images and pave the way for practical applications of this machine architecture for image analysis in a production setting. The largest images we have run are 320002pixels in size, which are well beyond the largest previously reported in the literature.Copyright © 2013 John Wiley & Sons, Ltd.
Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence‐Specific Detection of Double‐Stranded DNA
Authors: Doluca Osman , Hale Tracy K. , Edwards Patrick J. B. , González Carlos , Filichev Vyacheslav V. 
Published: December 2013

AbstractInvited for this month’s cover is the group of Dr. Vyacheslav V. Filichev from Massey University, New Zealand and a collaborator from the Instituto de Química Física Rocasalano, CSIC, Spain. The cover picture shows how a DNA strand that forms a highly stable G‐quadruplex can be converted into an efficient DNA triplex‐forming oligonucleotide by incorporating a pyrene intercalator into the sequence. Read the full text of the article at 10.1002/cplu.201300310
Solvent‐Free and Catalysts‐Free Chemistry: A Benign Pathway to Sustainability
Authors: Gawande Manoj B. , Bonifácio Vasco D. B. , Luque Rafael , Branco Paula S. , Varma Rajender S. 
Published: December 2013

AbstractIn the past decade, alternative benign organic methodologies have become an imperative part of organic syntheses and chemical reactions. The various new and innovative sustainable organic reactions and methodologies using no solvents or catalysts and employing alternative energy inputs such as microwaves, sonication, conventional and room temperature heating conditions, mechanochemical mixing, and high‐speed ball milling are discussed in detail. Environmentally benign and pharmaceutically important reactions such as multicomponent, condensation, and Michael addition reactions; ring opening of epoxides; and oxidation and other significant organic reactions are discussed. An overview of benign reactions through solvent‐ and catalyst‐free (SF–CF) chemistry and a critical perspective on emerging synergies between SF–CF organic reactions are discussed.
On the cutting edge of organ renewal: Identification, regulation, and evolution of incisor stem cells
Authors: Kuang‐Hsien Hu Jimmy , Mushegyan Vagan , Klein Ophir D. 
Published: December 2013

SummaryThe rodent incisor is one of a number of organs that grow continuously throughout the life of an animal. Continuous growth of the incisor arose as an evolutionary adaptation to compensate for abrasion at the distal end of the tooth. The sustained turnover of cells that deposit the mineralized dental tissues is made possible by epithelial and mesenchymal stem cells residing at the proximal end of the incisor. A complex network of signaling pathways and transcription factors regulates the formation, maintenance, and differentiation of these stem cells during development and throughout adulthood. Research over the past 15 years has led to significant progress in our understanding of this network, which includes FGF, BMP, Notch, and Hh signaling, as well as cell adhesion molecules and micro‐RNAs. This review surveys key historical experiments that laid the foundation of the field and discusses more recent findings that definitively identified the stem cell population, elucidated the regulatory network, and demonstrated possible genetic mechanisms for the evolution of continuously growing teeth. genesis 52:79–92. © 2013 Wiley Periodicals, Inc.
Divergence of feeding channels within the soil food web determined by ecosystem type
Authors: Crotty Felicity V. , Blackshaw Rod P. , Adl Sina M. , Inger Richard , Murray Philip J. 
Published: December 2013

AbstractUnderstanding trophic linkages within the soil food web (SFW) is hampered by its opacity, diversity, and limited niche adaptation. We need to expand our insight between the feeding guilds of fauna and not just count biodiversity. The soil fauna drive nutrient cycling and play a pivotal, but little understood role within both the carbon (C) and nitrogen (N) cycles that may be ecosystem dependent. Here, we define the structure of theSFWin two habitats (grassland and woodland) on the same soil type and test the hypothesis that land management would alter theSFWin these habitats. To do this, we census the community structure and use stable isotope analysis to establish the pathway of C and N through each trophic level within the ecosystems. Stable isotope ratios of C and N from all invertebrates were used as a proxy for trophic niche, and community‐wide metrics were obtained. Our empirically derived C/N ratios differed from those previously reported, diverging from model predictions of global C and N cycling, which was unexpected. An assessment of the relative response of the different functional groups to the change from agricultural grassland to woodland was performed. This showed that abundance of herbivores, microbivores, and micropredators were stimulated, while omnivores and macropredators were inhibited in the grassland. Differences between stable isotope ratios and community‐wide metrics, highlighted habitats with similar taxa had differentSFWs, using different basal resources, either driven by root or litter derived resources. Overall, we conclude that plant type can act as a top‐down driver of community functioning and that differing land management can impact on the wholeSFW.
Large crowd modelling: an analysis of the Duisburg Love Parade disaster
Authors: Pretorius Maria , Gwynne Steven , Galea Edwin R. 
Published: December 2013

SummaryGiven the amount of data publically available relating to the incident at the Duisburg Love Parade of 2010, this event is a valuable case study for the development and management of large‐scale crowd circulation and emergency incidents. Here, we study the crowd dynamics associated with a large crowd event similar to that of the Love Parade in Duisburg. The paper discusses the analysis of observations of the incident and explores the application of an evacuation model to investigate similar crowd scenarios. The data‐set produced from this analysis was used to configure the buildingEXODUS model to approximate the original incident to verify whether buildingEXODUS can reliably represent agent actions, the conditions that develop and the impact of these developments upon performance. The model is then used to identify potential alternative crowd management and ingress/egress strategies to prevent the crowd crush incident from occurring. Traditionally, fine mesh evacuation models, such as buildingEXODUS, are not used to investigate high‐density crowd conditions, because the underlying discretisation of space limits the maximum density that can be achieved within the models. In this paper, a novel approach is used to combine the data of pedestrian flow and space utilisation to indicate the onset of potentially dangerous population densities using a fine node model. The analysis demonstrates that the model can capture the key elements of such a large‐scale incident and identify important causal factors. The work demonstrates that the model is broadly able to capture key crowd features if representative assumptions are implemented. Copyright © 2013 John Wiley & Sons, Ltd.
The Impact of Work‐Limiting Disability on Labor Force Participation
Authors: Webber Douglas A. , Bjelland Melissa J. 
Published: December 2013

AbstractAccording to the justification hypothesis, non‐employed individuals may over‐report their level of work limitation, leading to biased census/survey estimates of the prevalence of severe disabilities and the associated labor force participation rate. For researchers studying policies which impact the disabled or elderly (e.g., Supplemental Security Income, Disability Insurance, and Early Retirement), this could lead to significant bias in key parameters of interest. Using the American Community Survey, we examine the potential for both inflated and deflated reported disability status and generate a general index of disability, which can be used to reduce the bias of these self‐reports in other studies. We find that at least 4.8 million individuals have left the labor force because of a work‐limiting disability, at least four times greater than the impact implied by our replication of previous models. Copyright © 2013 John Wiley & Sons, Ltd.
Tips of laparoscopic pancreaticoduodenectomy: superior mesenteric artery first approach (with video)
Authors: Cho Akihiro , Yamamoto Hiroshi , Kainuma Osamu 
Published: December 2013

AbstractIn previous reports of laparoscopic pancreaticoduodenectomy, the Kocher maneuver with a wide mobilization of the right colonic flexure is carried out in the early phase, and dissection of the superior mesenteric artery is performed in the last phase of resection. This report describes laparoscopic superior mesenteric artery first approach, in which the superior mesenteric artery is dissected in the early phase of resection. Through the ligament of Treitz, the retroperitoneum is widely opened and the superior mesenteric artery is isolated just superior to the left renal vein. The periarterial connective tissue and nerve plexuses surrounding the superior mesenteric artery are dissected longitudinally to identify the inferior pancreaticoduodenal artery, which is then tied and divided. The superior mesenteric artery first approach and early ligation of the inferior pancreaticoduodenal artery is considered to be a feasible, safe, and effective method for performing pure laparoscopic pancreaticoduodenectomy.
Optimal cut‐off value for the number of colorectal liver metastases: a project study for hepatic surgery of the Japanese Society of Hepato‐Biliary‐Pancreatic Surgery
Authors: Beppu Toru , Sakamoto Yoshihiro , Hasegawa Kiyoshi , Honda Goro , Tanaka Kuniya , Kotera Yoshihito , Nitta Hiroyuki , Yoshidome Hiroyuki , Hatano Etsuro , Ueno Masaki , Takamura Hiroyuki , Baba Hideo , Kosuge Tomoo , Kokudo Norihiro , Takahashi Keiichi , Endo Itaru , Wakabayashi Go , Miyazaki Masaru , Uemoto Shinji , Ohta Tetsuo , Kikuchi Ken , Takayama Tadatoshi , Yamaue Hiroki , Yamamoto Masakazu , Takada Tadahiro 
Published: December 2013

AbstractBackgroundThe optimal cut‐off value of the number of colorectal liver metastases (CRLM) to predict prognosis after hepatic resection remains unclear. This study was conducted to determine a suitable cut‐off value.MethodsA total of 727 hepatectomized patients with CRLM were evaluated. We proposed the following optimal cut‐off values: first, a small P‐value for the log‐rank test with no overlapping of the 95% confidence interval (CI) for median survival time using the Kaplan–Meier method and the hazard ratio (HR) using the Cox proportional hazards model and, second, the maximum HR value for accurate separation.ResultsFor disease‐free survival analysis, of the three group separations, A2 (1, 2–4, and ≥5) showed a small P‐value and the largest HR, whereas two group separations, B2, B3 and B4 showed similarly small P‐values, but B4 (1–4, ≥5) indicated the largest HR. Regarding the overall survival analysis, of the three group separations, A2 showed the smallest P‐value, whereas the two group separations, B4 showed similarly small P‐values, with the largest HR.ConclusionsTumor number separation in patients with CRLM after hepatic resection should be performed using the A2 (1, 2–4, and ≥5) or B4 (1–4 and ≥5) classifications.
Continuous vagal IONM prevents recurrent laryngeal nerve paralysis by revealing initial EMG changes of impending neuropraxic injury: A prospective, multicenter study
Authors: Phelan Eimear , Schneider Rick , Lorenz Kerstin , Dralle Henning , Kamani Dipti , Potenza Andre , Sritharan Niranjan , Shin Jenifer , W. Randolph Gregory 
Published: December 2013

Objectives/HypothesisExisting intraoperative neuromonitoring (IONM) formats stimulate the recurrent laryngeal nerve (RLN) intermittently, exposing it to risk for injury in between stimulations. We report electrophysiologic parameters of continuous vagal monitoring, utilizing a novel real‐time IONM format, and relate these parameters to intraoperative surgical maneuvers that delineate nascent adverse but reversible electrophysiologic parameters to prevent nerve injury. These results are correlated with postoperative vocal cord functional outcome.Study DesignProspective multicenter tertiary study.MethodEvoked vagal nerve waveform amplitude and latency changes during 102 thyroidectomies were recorded. Adverse electrophysiologic response was categorized into 1‐concordant amplitude reduction and latency increase events (combined events) and 2‐loss of signal (LOS). Surgical maneuvers were modified when adverse electrophysiologic findings were noted. All patients underwent preoperative and postoperative laryngoscopy; intraoperative electrophysiologic findings were correlated with postoperative laryngeal function.ResultsContinuous vagal monitoring did not result in stimulation‐evoked nerve injury or intraoperative adverse cardiac, pulmonary, or gastrointestinal effects. Both intraoperative combined events and LOS were associated with development of vocal cord paralysis (VCP) (P = 0.001 and P >0.001 respectively). Combined events had a positive predictive value (PPV) of 33%, negative predictive value (NPV) of 97%, and were reversible in 73%. LOS had a PPV of 83%, NPV of 98%, and was reversible in only 17%. Milder combined events and isolated amplitude or latency changes were not associated with VCP.ConclusionsContinuous vagal monitoring is safe and provides real‐time RLN evaluation during surgical maneuvers. Combined events and LOS, both easily identifiable intraoperatively, are related to the development of VCP. A combined event represents a largely reversible electrophysiologic change when the associated surgical maneuver is aborted. If allowed to continue, it can advance to LOS (which typically is significantly less reversible) and to postoperative VCP. Continuous vagal monitoring has utility in identifying real‐time adverse concordant amplitude and latency changes (combined events), which can prompt modification of the associated surgical maneuver and may prevent RLN paralysis during thyroidectomy.Level of Evidence4. Laryngoscope, 124:1498–1505, 2014
Extraction‐free In situ Derivatisation of Timosaponin AIII Using Direct Analysis in Real Time TOF/MS
Authors: Kim Hye Jin , Park Se Ri , Jang Young Pyo 
Published: December 2013

ABSTRACTIntroductionDirect analysis in real time (DART) TOF/MS has been used for mass information of various non‐polar phytochemicals in raw material with no sample preparation. However, low ionisation efficiency for polar compounds including glycosides limits its extensive use in the field of phytochemical analysis.ObjectiveIn order to develop a direct analysis method for polar glycosides using in situ derivatisation, which improves ionisation efficiency of hydrophilic glycosides.MethodAnemarrhena Rhizoma was used as a model plant targeting on Timosaponin AIII utilising a Dip‐It module. Permethylation was applied to the powdered raw material with tetramethylammonium hydroxide in front of a DART ion source. Also, DART TOF/MS combined with permethylation was applied to timosaponin AIII standard solution to obtain the limit of detection (LOD).ResultsIn situ methylation of timosaponin AIII and Anemarrhena Rhizoma raw material were successfully used to ionise the glycoside. The LOD was found to be in the range of 2.4–4.8 ng for permethylated timosaponin AIII and this level is four times higher than the range of the underivatisation analysis. Direct analysis of permethylated timosaponin from Anemarrhena Rhizoma was also successfully performed.ConclusionA simple and quick derivatisation method with tetramethylammonium hydroxide was developed for the direct identification of a hydrophilic saponin from the plant tissue. Better ionisation efficiency conferred by in situ permethylation enabled ionisation of whole molecules of timosaponin AIII from the plant tissue. This simple analytical method will provide a solution to reduce tedious sample preparation steps, not only for non‐polar but also hydrophilic natural products directly from the tissue. Copyright © 2013 John Wiley & Sons, Ltd.
Biomimetic protein‐based elastomeric hydrogels for biomedical applications
Authors: Whittaker Jasmin , Balu Rajkamal , Choudhury Namita R. , Dutta Naba K. 
Published: December 2013

AbstractIn recent years, protein‐based elastomeric hydrogels have gained increased research interest in biomedical applications for their remarkable self‐assembly behaviour, tunable 3D porous structure, high resilience (elasticity), fatigue lifetime (durability), water uptake, excellent biocompatibility and biological activity. The proteins and polypeptides can be derived naturally (animal or insect sources) or by recombinant (bacterial expression) routes and can be crosslinked via physical or chemical approaches to obtain elastomeric hydrogels. Here we review and present the recent accomplishments in the synthesis, fabrication and biomedical applications of protein‐based elastomeric hydrogels such as elastin, resilin, flagelliform spider silk and their derivatives. © 2013 Society of Chemical Industry
Segregation indices for disease clustering
Authors: Ceyhan Elvan 
Published: December 2013

AbstractSpatial clustering has important implications in various fields. In particular, disease clustering is of major public concern in epidemiology. In this article, we propose the use of two distance‐based segregation indices to test the significance of disease clustering among subjects whose locations are from a homogeneous or an inhomogeneous population. We derive the asymptotic distributions of the segregation indices and compare them with other distance‐based disease clustering tests in terms of empirical size and power by extensive Monte Carlo simulations. The null pattern we consider is the random labeling (RL) of cases and controls to the given locations. Along this line, we investigate the sensitivity of the size of these tests to the underlying background pattern (e.g., clustered or homogenous) on which the RL is applied, the level of clustering and number of clusters, or to differences in relative abundances of the classes. We demonstrate that differences in relative abundances have the highest influence on the empirical sizes of the tests. We also propose various non‐RL patterns as alternatives to the RL pattern and assess the empirical power performances of the tests under these alternatives. We observe that the empirical size of one of the indices is more robust to the differences in relative abundances, and this index performs comparable with the best performers in literature in terms of power. We illustrate the methods on two real‐life examples from epidemiology. Copyright © 2013 John Wiley & Sons, Ltd.
Multi‐state models for colon cancer recurrence and death with a cured fraction
Authors: Conlon A.S.C. , Taylor J.M.G. , Sargent D.J. 
Published: December 2013

AbstractIn cancer clinical trials, patients often experience a recurrence of disease prior to the outcome of interest, overall survival. Additionally, for many cancers, there is a cured fraction of the population who will never experience a recurrence. There is often interest in how different covariates affect the probability of being cured of disease and the time to recurrence, time to death, and time to death after recurrence. We propose a multi‐state Markov model with an incorporated cured fraction to jointly model recurrence and death in colon cancer. A Bayesian estimation strategy is used to obtain parameter estimates. The model can be used to assess how individual covariates affect the probability of being cured and each of the transition rates. Checks for the adequacy of the model fit and for the functional forms of covariates are explored. The methods are applied to data from 12 randomized trials in colon cancer, where we show common effects of specific covariates across the trials. Copyright © 2013 John Wiley & Sons, Ltd.