bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular markers and pathway analysis of colorectal carcinoma in the Middle East
Authors: Beg Shaham , Siraj Abdul K. , Prabhakaran Sarita , Bu Rong , Al‐Rasheed Maha , Sultana Mehar , Qadri Zeeshan , Al‐Assiri Mohammed , Sairafi Rami , Al‐Dayel Fouad , Al‐Sanea Nasser , Uddin Shahab , Al‐Kuraya Khawla S. 
Published: July 2015

BACKGROUNDColorectal cancer (CRC) is one of the most common cancers in the world. A newly proposed integrated pathway comprising traditional, alternate, and serrated pathways by genetic and epigenetic factors was defined recently and hypothesized to play a role in the pathogenesis of CRC; however, to the authors' knowledge, there is a paucity of information regarding these proposed molecular pathways in different ethnic groups.METHODSMolecular characterization of 770 CRC specimens was performed for microsatellite instability, BRAF, and KRAS by polymerase chain reaction and 500 cases for CpG island methylator phenotype (CIMP) high phenotype by MethyLight technology. Tumors were assigned to different molecular pathways and examined for clinicopathological correlation and survival analysis.RESULTSThe traditional pathway constituted 33.4% of CRC cases, the alternate pathway comprised 11.6%, and the serrated molecular pathway accounted for only 0.8% of Middle Eastern CRC cases. Approximately 54.2% of CRC cases did not qualify to fit into any pathway and thus were designated as an unassigned group. Molecular pathways were found to be significantly associated with tumor site and grade. A subset of cases with an uncategorized pathway demonstrated a significant survival difference (P = .0079).CONCLUSIONSThe serrated pathway was found to account for a very low percentage of the CRC patient cohort in the current study. The unassigned group accounted for the majority of Middle Eastern CRC cases, and therefore methods of CRC pathway analysis might not be applicable to this ethnic group. The current study demonstrates the need to unravel the molecular genetic basis of this disease to further subcategorize these CRC cases. It also identifies a need for further studies on different populations for a better understanding of their exact role and incidence. Cancer 2015;121:3799–3808. © 2015 American Cancer Society.
Uncertainty quantification in virtual surgery hemodynamics predictions for single ventricle palliation
Authors: Schiavazzi D. E. , Arbia G. , Baker C. , Hlavacek A. M. , Hsia T. Y. , Marsden A. L. , Vignon‐Clementel I. E. , of Congenital Hearts Alliance (MOCHA) Investigators The Modeling 
Published: July 2015

SummaryThe adoption of simulation tools to predict surgical outcomes is increasingly leading to questions about the variability of these predictions in the presence of uncertainty associated with the input clinical data. In the present study, we propose a methodology for full propagation of uncertainty from clinical data to model results that, unlike deterministic simulation, enables estimation of the confidence associated with model predictions. We illustrate this problem in a virtual stage II single ventricle palliation surgery example. First, probability density functions (PDFs) of right pulmonary artery (PA) flow split ratio and average pulmonary pressure are determined from clinical measurements, complemented by literature data. Starting from a zero‐dimensional semi‐empirical approximation, Bayesian parameter estimation is used to find the distributions of boundary conditions that produce the expected PA flow split and average pressure PDFs as pre‐operative model results. To reduce computational cost, this inverse problem is solved using a Kriging approximant. Second, uncertainties in the boundary conditions are propagated to simulation predictions. Sparse grid stochastic collocation is employed to statistically characterize model predictions of post‐operative hemodynamics in models with and without PA stenosis. The results quantify the statistical variability in virtual surgery predictions, allowing for placement of confidence intervals on simulation outputs. Copyright © 2015 John Wiley & Sons, Ltd.
The DEEP Project An alternative approach to heterogeneous cluster‐computing in the many‐core era
Authors: Eicker Norbert , Lippert Thomas , Moschny Thomas , Suarez Estela ,   for the DEEP project
Published: July 2015

SummaryHomogeneous cluster architectures, which used to dominate high‐performance computing (HPC), are challenged today by heterogeneous approaches utilizing accelerator or co‐processor devices. The DEEP (Dynamical Exascale Entry Platform) project is implementing a novel architecture for HPC, in which a standard HPC cluster is directly connected to a so‐called ‘Booster’: a cluster of many‐core processors. By these means heterogeneity is organized differently as in today's standard approach, where accelerators are added to each node of the cluster. In order to adapt application codes to this Cluster‐Booster architecture as seamless as possible, DEEP has developed a complete programming environment. It integrates the offloading functionality given by the Message Passing Interface standard with an abstraction layer based on the task‐based OmpSs programming paradigm. This paper presents the DEEP project with an emphasis on the DEEP programming environment. Copyright © 2015 John Wiley & Sons, Ltd.
Bio‐inspired cost‐aware optimization for data‐intensive service provision
Authors: Wang Lijuan , Shen Jun , Luo Junzhou 
Published: July 2015

SummaryThe use of Big Data and the development of cloud computing have led to greater dependence on data‐intensive services. Each service may actually request or create a large amount of data sets. The scope, number, and complexity of data‐intensive services are all set to soar in the future. To compose these services will be more challenging. Issues of autonomy, scalability, adaptability, and robustness, become difficult to resolve. Bio‐inspired algorithms can overcome the new challenging requirements of data‐intensive service provision. It is useful for the provision of data‐intensive services to explore key features and mechanisms of biological systems and accordingly to add biological mechanisms to services. In this paper, we will discuss single‐objective and multi‐objective data‐intensive service provision problems based on bio‐inspired algorithms. Further, we will propose an ant‐inspired negotiation approach. Finally, this paper points out future research topics. Copyright © 2015 John Wiley & Sons, Ltd.
A novel application classification attack against Tor
Authors: He Gaofeng , Yang Ming , Luo Junzhou , Gu Xiaodan 
Published: July 2015

SummaryTor is a famous anonymous communication system for preserving users' online privacy. It supports TCP applications and packs upper‐layer application data into encrypted equal‐sized cells with onion routing to hide private information of users. However, we note that the current Tor design cannot conceal certain application behaviors. For example, P2P applications usually upload and download files simultaneously, and this behavioral feature is also kept in Tor traffic. Motivated by this observation, we investigate a new attack against Tor, application classification attack, which can recognize application types from Tor traffic. An attacker first carefully selects some flow features such as burst volumes and directions to represent the application behaviors and takes advantage of some efficient machine‐learning algorithm (e.g., Profile Hidden Markov Model) to model different types of applications. Then he or she can use these established models to classify target's Tor traffic and infer its application type. We have implemented the application classification attack on Tor using parallel computing, and our experiments validate the feasibility and effectiveness of the attack. We argue that the disclosure of application type information is a serious threat to Tor users' anonymity because it can be used to reduce the anonymity set and facilitate other attacks. We also present guidelines to defend against application classification attack. Copyright © 2015 John Wiley & Sons, Ltd.
SGAM: strategy‐proof group buying‐based auction mechanism for virtual machine allocation in clouds
Authors: Zhang Yonglong , Li Bin , Huang Zhiqiu , Wang Jin , Zhu Junwu 
Published: July 2015

SummaryWe study the cloud resource auction problem where users can bid for resource bundle containing heterogeneous types of virtual machines, and providers allocate virtual machines to their users through group price model. Compared with fixed price model, which is not always the best approach for trading resources as its economically inefficient and inflexible nature, the group price model possess the better flexibility and monetary benefits for auction participants (e.g., cloud providers and users). The proposed auction mechanism strategy‐proof group buying‐based auction mechanism, which formulates the problem of virtual machine allocation in clouds as a combinatorial auction problem, and holds some important property such as individual rationality, ex‐post budget balance, and truthfulness, meanwhile guaranteeing efficiency in both the provider's revenue and system efficiency. Extensive simulation results show that the proposed mechanism yields the allocation efficiency and computational tractability compared with the mechanism with fixed price model. Copyright © 2015 John Wiley & Sons, Ltd.
Variation of a classical fingerprint of ideal memristor
Authors: Biolek Zdeněk , Biolek Dalibor , Biolková Viera , Kolka Zdeněk 
Published: July 2015

SummaryGradual disappearance of hysteresis with increasing frequency of the exciting signal is considered a classical fingerprint of general memristive systems. The paper analyzes a special version of this fingerprint, when the value of the charge delivered within the half‐period remains constant while the frequency of the sinusoidal current is increasing. Under these conditions, the area of the pinched hysteresis loop of the ideal memristor increases with the square of the frequency. Breaking the rules of this fingerprint indicates reliably that the element analyzed is not an ideal memristor. Copyright © 2015 The Authors International Journal of Circuit Theory and Applications Published by John Wiley & Sons, Ltd.
Contrasting demographic history and gene flow patterns of two mangrove species on either side of theCentralAmericanIsthmus
Authors: Cerón‐Souza Ivania , Gonzalez Elena G. , Schwarzbach Andrea E. , Salas‐Leiva Dayana E. , Rivera‐Ocasio Elsie , Toro‐Perea Nelson , Bermingham Eldredge , McMillan W. Owen 
Published: July 2015

AbstractComparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life‐history traits on diversification of unrelated but co‐distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present‐day marine currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans,Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life‐history traits. We sampled 18 Atlantic and 26 Pacific locations forA. germinans(N = 292) andR. mangle(N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major marine (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of theCentral American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid‐Pleistocene and early Holocene, (3) asymmetric historical migration with higher gene flow from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary gene flow between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life‐history traits of mangrove species, which should have had a strong influence on seed dispersal capability and, thus, population connectivity, we found that vicariant events, climate fluctuations and marine currents have shaped the distribution of genetic diversity in strikingly similar ways.
Prospective study on changes in blood variables in pregnant women at higher risk of peripartum cardiomyopathy
Authors: Umazume Takeshi , Yamada Takahiro , Ishikawa Satoshi , Yamada Takashi , Koyama Takahiro , Furuta Itsuko , Morikawa Mamoru , Yamada Satoshi , Minakami Hisanori 
Published: July 2015

AbstractAimsEchocardiography is necessary for the diagnosis of peripartum cardiomyopathy (PPCM). Multifetal pregnancies (MFP) and hypertensive disorders (HD) are prominent risk factors for PPCM. To determine which blood variables exhibit greater change in a late stage of pregnancy in women with MFP and/or HD compared with women with normotensive singleton pregnancies.Methods and resultsSerum levels of six variables—high‐sensitive troponin I (hs‐TnI), N‐terminal fragment of precursor protein brain‐type natriuretic peptide (NT‐proBNP), myoglobin, creatine kinase‐myocardial band, ferritin, and prolactin—were compared between 29 women with MFP (n = 13) and/or HD (n = 18) and 100 women with normotensive singleton pregnancies (control group). None of 129 women developed PPCM. All variables increased significantly peripartum in both groups. In 29 women with MFP and/or HD, the elevated hs‐TnI and NT‐proBNP levels (median) were significantly higher compared with the control group (5.4 vs. 3.7 pg/mL for hs‐TnI with P = 0.002, 185 vs. 68 pg/mL for NT‐proBNP with P = 0.007), and the prevalence rate of more than 90th percentile value specific for the 129 women was significantly more frequent for hs‐TnI (>12.2 pg/mL; 31% [9/29] vs. 4.0% [4/100], P < 0.001) and tended to be more frequent for NT‐proBNP (>342 pg/mL; 21% [6/29] vs. 7.0%, P = 0.072).ConclusionsBoth hs‐TnI and NT‐proBNP were likely to increase markedly in women with MFP and/or HD. The combination of hs‐TnI and NT‐proBNP may contribute to better selection of candidates for echocardiography.
Depositional development of the Muskeg Lake crevasse splay in the Cumberland Marshes (Canada)
Authors: Toonen Willem H. J. , van Asselen Sanneke , Stouthamer Esther , Smith Norman D. 
Published: July 2015

AbstractCrevasse splays are common geomorphological features in alluvial and deltaic floodplains. Although crevasse splays can develop into full avulsions, thereby transforming large areas of floodbasins, little is known about their sedimentary and geomorphological development at the decadal scale and their avulsion potential. We used aerial photography and lithological cross‐sections to reconstruct crevasse‐splay formation in the largely unmanaged floodplain of the Saskatchewan River in the Cumberland Marshes (Saskatchewan, Canada). Based on surface geomorphology and subsurface deposits, various stages of crevasse‐splay development were described which were linked to both external forcing and internal morphodynamics. Initial splay deposition, following a levee breach during a large flood, occurred as a broad but relatively thin sandy sheet in a down‐basin direction in the receiving backswamp area. In a next phase, these primary crevasse‐splay deposits blocked local down‐basin flow, thereby forcing the crevasse‐splay channel in a direction perpendicular to the parent channel and original floodbasin gradient. This created an asymmetrical splay sequence composition, which differs in appearance from more commonly observed dendritic crevasse splays. It is concluded that sedimentation patterns in the splay have been influenced by inherited effects of previously formed deposits. Feedbacks of the original floodbasin gradient and earlier stages of splay formation are suggested as prominent mechanisms in creating the current morphology, orientation, and architecture of its deposits. Copyright © 2015 John Wiley & Sons, Ltd.
Sublethal effects of multiwalled carbon nanotube exposure in the invertebrate Daphnia magna
Authors: Stanley Jacob K. , Laird Jennifer G. , Kennedy Alan J. , Steevens Jeffery A. 
Published: July 2015

Abstract

Carbon nanotubes were previously demonstrated to accumulate on the carapace and in the gut of daphnids in aquatic exposures. The purpose of the present study was to assess the effects of multiwalled carbon nanotube (MWCNT) exposure on the sublethal Daphnia magna endpoints swimming behavior, algal feeding, growth, and reproduction and to determine the relative magnitude of difference between lethal and sublethal toxicity thresholds in 48-h and 14-d exposures. A stable dispersion of MWCNTs was prepared using 100 mg/L natural organic matter (NOM), and all treatments were compared statistically to a NOM control. The swimming behavior endpoints of mean velocity and total distance moved were determined using digital tracking software. For the acute (48-h) exposure, a 50% lethal concentration (LC50) of 29.3 (23.6–36.3) mg/L and a 50% effective concentration (EC50) of 6.7 mg/L in the swimming velocity endpoint were determined. When swimming response was nonmonotonic below 2 mg/L, consistent reductions in velocity were observed at 6.9 mg/L and above. Median effect concentrations were lower in the chronic (14-d) bioassay. The 14-d LC50 was 4.3 mg/L (3.3–5.6 mg/L), and the reproduction EC50 was 5.0 mg/L. Lowest-observed-effect concentrations for survival and reproduction were 5.4 mg/L and 1.7 mg/L, respectively. Significantly fewer (23.1%) algal cells were consumed in the 3.9-mg/L treatment relative to the control. No significant effects on swimming behavior were observed for the 14-d bioassay. Less traditional sublethal endpoints such as swimming behavior and feeding rate may be especially important to assess for MWCNTs and other materials expected to be more physically than chemically toxic through mechanisms such as gut clogging. Environ Toxicol Chem 2016;35:200–204. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and is in the public domain in the United States of America.
Temporality of perception during the consumption of French grape brandies with different aging times in relation with aroma compound release
Authors: Fiches Guillaume , Saint Eve Anne , Jourdren Solenne , Déléris Isabelle , Brunerie Pascal , Souchon Isabelle 
Published: July 2015

AbstractDistilled beverages are appreciated by consumers for their aromatic richness and changes during product consumption, but mechanisms still remain unclear. In this context, the objective of the present study was to better understand the origin of temporal perception by a combined approach (dynamic sensory and instrumental) during the consumption of brandies with different aging and known to have different qualities. The five brandies were significantly perceived differently according to sensory profile results. Temporal sensory results showed common perception sequences between products in terms of taste and trigeminal sensations whereas different aromatic sequences were highlighted between products after they were spat out, depending mainly on their aging. Releases over consumption of some aroma compounds specific of brandy flavour were measured in panelist's nose by proton transfer reaction‐mass spectrometry. In all cases, similar release patterns were observed, although higher intensities were observed for esters in aged brandies, where they were at higher levels. It is therefore proposed that quantitative differences and not specific release patterns are at the origin of the observed pattern of temporal dominance of sensations. Aroma compounds from wood could also be possible at the origin of aromatic interactions with other perceptions, changing brandy overall perception. Copyright © 2015 John Wiley & Sons, Ltd.
An adaptive finite element method for the modeling of the equilibrium of red blood cells
Authors: Laadhari Aymen , Saramito Pierre , Misbah Chaouqi 
Published: July 2015

SummaryThis contribution is concerned with the numerical modeling of an isolated red blood cell (RBC), and more generally of phospholipid membranes. We propose an adaptive Eulerian finite element approximation, based on the level set method, of a shape optimization problem arising in the study of RBCs. We simulate the equilibrium shapes that minimize the elastic bending energy under prescribed constraints of fixed volume and surface area. An anisotropic mesh adaptation technique is used in the vicinity of the cell membrane to enhance the robustness of the method. Efficient time and spatial discretizations are considered and implemented. We address in detail the main features of the proposed method, and finally we report several numerical experiments in the two‐dimensional and the three‐dimensional axisymmetric cases. The effectiveness of the numerical method is further demonstrated through numerical comparisons withsemi‐analyticalsolutions provided by a reduced order model. Copyright © 2015 John Wiley & Sons, Ltd.
Identifying Demand Responses to Illegal Drug Supply Interdictions
Authors: Cunningham Scott , Finlay Keith 
Published: July 2015

SummarySuccessful supply‐side interdictions into illegal drug markets are predicated on the responsiveness of drug prices to enforcement and the price elasticity of demand for addictive drugs. We present causal estimates that targeted interventions aimed at methamphetamine input markets (‘precursor control’) can temporarily increase retail street prices, but methamphetamine consumption is weakly responsive to higher drug prices. After the supply interventions, purity‐adjusted prices increased then quickly returned to pre‐treatment levels within 6–12 months, demonstrating the short‐term effects of precursor control. The price elasticity of methamphetamine demand is −0.13 to −0.21 for self‐admitted drug treatment admissions and between −0.24 and −0.28 for hospital inpatient admissions. We find some evidence of a positive cross‐price effect for cocaine, but we do not find robust evidence that increases in methamphetamine prices increased heroin, alcohol, or marijuana drug use. This study can inform policy discussions regarding other synthesized drugs, including illicit use of pharmaceuticals. Copyright © 2015 John Wiley & Sons, Ltd.
Methoxetamine‐related deaths in the UK: an overview
Authors: Chiappini Stefania , Claridge Hugh , Corkery John M. , Goodair Christine , Loi Barbara , Schifano Fabrizio 
Published: July 2015

ObjectiveThe goal of this study is to provide an update on the data given on methoxetamine (MXE)‐related fatalities that occurred in 2011–2013, presented at the Second International Conference on Novel Psychoactive Substances.MethodsFatalities involving MXE were extracted from the database of the National Programme on Substance Abuse Deaths, which receives information on drug‐related deaths from Coroners in the UK and Islands (Isle of Man, Jersey, Guernsey) and other data suppliers.ResultsEight cases, received by 3 September 2013, in which MXE was found at post‐mortem and/or directly implicated in the death and/or mentioned in the Coroner's verdict are described. The median age at death was 27 years, with the majority of White ethnicity (6/8) and male (7/8). MXE was used together with other substances in 7/8 cases. MXE was found at post‐mortem in all cases, directly implicated in the deaths of four and likely to have had an influence in two.ConclusionsMore research needs to be conducted into its health effects and toxicity potential. Health care professionals should be made aware of the potential health harms of MXE, in order to develop early intervention measures and minimise the number of MXE‐related poisonings and fatalities. Copyright © 2015 John Wiley & Sons, Ltd.