bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural network‐based multi‐agent approach for scheduling in distributed systems
Authors: Ezugwu Absalom E. , Frincu Marc E. , Adewumi Aderemi O. , Buhari Seyed M. , Junaidu Sahalu B. 
Published: June 2016

SummaryA distributed system consists of a collection of autonomous heterogeneous resources that provide resource sharing and a common platform for running parallel compute‐intensive applications. The different application characteristics combined with the heterogeneity and performance variations of the distributed system make it difficult to find the optimal set of needed resources. When deployed, user applications are usually handled by application domain experts or system administrators who depending on the infrastructure provide a scheduling strategy for selecting the best candidate resource over a set of available resources. However, the provided strategy is usually generic, aimed at handling a wide array of applications and does not take into consideration specific application resource requirements. As such, an intelligent method for selecting the best resources based on expert knowledge is needed. In this paper, we propose a neural network‐based multi‐agent resource selection technique capable of mimicking the services of an expert user. In addition, to cope with the geographical distribution of the underlying system, we employ a multi‐agent coordination mechanism. The proposed neural network‐based scheduling framework combined with the multi‐agent intelligence is a unique approach to efficiently deal with the resource selection problem. Results run on a simulated environment show the efficiency of our proposed method. Several scheduling simulations were conducted to compare the performance of some conventional resource selection methods against the proposed agent‐based neural network technique. The results obtained indicate that the agent‐based approach outperformed the classical algorithms by reducing the amount of time required to search for suitable resources irrespective of the resource size. Copyright © 2016 John Wiley & Sons, Ltd.
Ocean warming expands habitat of a rich natural resource and benefits a national economy
Authors: Jansen Teunis , Post Søren , Kristiansen Trond , Óskarsson Guðmundur J. , Boje Jesper , MacKenzie Brian R. , Broberg Mala , Siegstad Helle 
Published: June 2016

AbstractGeographic redistribution of living natural resources changes access and thereby harvesting opportunities between countries. Internationally shared fish resources can be sensitive to shifts in the marine environment and this may have great impact on the economies of countries and regions that rely most heavily on fisheries to provide employment and food supply. Here we present a climate change‐related biotic expansion of a rich natural resource with substantial economic consequences, namely the appearance of northeast Atlantic mackerel (Scomber scombrus) in Greenlandic waters. In recent years, the summer temperature has reached record highs in the Irminger Current, and this development has expanded the available and realized mackerel habitat in time and space. Observations in the Irminger Current in east Greenland in 2011 of this temperature‐sensitive epipelagic fish were the first records so far northwest in the Atlantic. This change in migration pattern was followed by a rapid development of a large‐scale fishery of substantial importance for the national economy of Greenland (23% of Greenland's export value of all goods in 2014). A pelagic trawl survey was conducted in mid‐summer 2014 and the results showed that the bulk of ~1 million Mg (=t) of mackerel in the Irminger Current in southeast Greenland were located in the relatively warm (>8.5°C) surface layer. Mackerel was also observed in southwest Greenland. Finally, 15 CMIP5 Earth System Model projections of future marine climate were used to evaluate the epipelagic environment in Greenland. These projections for moderate and high CO2 emission scenarios (representative concentration pathways [RCP] 4.5 and 8.5) suggest how the available mackerel habitat may expand further in space and time. Overall, our results indicate that, if the stock remains large, productive, and continues its current migration pattern, then climate change has provided Greenland with a new unique opportunity for commercial exploitation. However, positive cases like this should not be cherry‐picked and misused as arguments against timely and effective mitigation of climate change.
Numerical modelling of alternate bar formation, development and sediment sorting in straight channels
Authors: Qian Honglu , Cao Zhixian , Liu Huaihan , Pender Gareth 
Published: June 2016

AbstractA two‐dimensional shallow water hydro‐sediment‐morphodynamic model is applied to investigate alternate bar formation, development and sediment sorting in straight channels. The model is coupled, explicitly incorporating the flow–sediment–bed interactions by using the full mass and momentum conservation equations, which are numerically solved by a well‐balanced version of the finite volume Slope Limiter Centred (SLIC) scheme. The model is first tested against a flume experiment on alternate bars formed over a uniform sediment bed, which clearly exhibits processes of bar formation, migrating and finally approaching an equilibrium state. Then it is applied to another flume experiment on alternate bars due to non‐uniform sediment transport. The computational results are evaluated, with a focus on the longitudinal and vertical sediment sorting. It is argued for the first time that the inconsistent sediment sorting patterns observed in previous studies are determined by different sediment transport conditions, i.e. full versus partial transport. When a condition of full transport is achieved, under which all size fractions are fully mobilized and transported, the longitudinal surface sediment shows a sorting pattern of coarse‐on‐head and fine‐in‐pool, and the vertical substrate sediment exhibits an immobile‐fine‐coarse structure upwards. In contrast, for a partial transport condition, under which only finer fraction participates in the transport process, an opposite longitudinal pattern (i.e. fine‐on‐head and coarse‐in‐pool) and a different vertical structure (i.e. immobile‐coarse‐fine) are observed. Concurrently, numerical experiments with specified conditions show that the critical aspect ratio for the formation of migrating alternate bars is approximately equal to 12. With the increase of the aspect ratio, the bar length grows gradually, while the bar height increases rapidly for moderate values of the aspect ratio and then keeps nearly stable. The bar celerity, however, is weakly sensitive to the variation of this ratio. Copyright © 2016 John Wiley & Sons, Ltd.
Legumes Functional Group Promotes Soil Organic Carbon and Nitrogen Storage by Increasing Plant Diversity
Authors: Wu Gao‐Lin , Liu Yu , Tian Fu‐Ping , Shi Zhi‐Hua 
Published: June 2016

AbstractCommunity composition strongly affected the soil C and N storages. However, the influences of community composition on native grassland remain poorly understood. The purpose of this study is to investigate the ability of plant communities including how legumes affect the soil C and N storages in the semi‐arid grassland. Experimental grassland communities were separated by whether or not containing legumes. We measured soil C and N storages and determined above‐ground and below‐ground biomass, litter biomass, plant species richness, and species diversity to understand the mechanisms underlying the changes of soil C and N storages and to determine the relationship of species diversity and productivity. The results showed that legumes increased above‐ground and below‐ground biomass and C and N storages. Soil C and N storages were significantly and positively related to above‐ground and below‐ground biomass, litter biomass, plant species richness, and diversity in the presence of legumes. The presence of legumes increased soil C and N simultaneously but not synchronously, which resulting in a higher C:N ratio. This study indicated that legumes increased soil C and N storages possibly through increasing biomass and soil C and N inputs. The increases are mediated by plant diversity and plant functional complementarity. We suggest that the combination of legumes‐grass species may greatly enhance ecosystem services such as soil C and N storages, productivity, and diversity in semi‐arid grassland. Copyright © 2016 John Wiley & Sons, Ltd.
Hydroxytyrosol mildly improve cognitive function independent of APP processing in APP/PS1 mice
Authors: Peng Yunhua , Hou Chen , Yang Ziqi , Li Caixia , Jia Liyan , Liu Jing , Tang Ying , Shi Le , Li Yongqin , Long Jiangang , Liu Jiankang 
Published: June 2016

ScopeOlive products, the hallmark of Mediterranean diet, are associated with reduced risk of mild cognitive impairment and Alzheimer's disease (AD). We and other groups have shown that hydroxytyrosol (HT), a bioactive compound of olive products, ameliorates oxidative stress, mitochondrial dysfunction, and neural toxicity. However, whether HT in Mediterranean diet acts as a functional ingredient in delaying AD pathogenesis remains unclear.Methods and resultsIn the present study, APP/PS1 mice, an animal model of AD, were administrated for 6 months with 5 mg/kg/day of HT, a comparable level of HT in daily Mediterranean diet. HT improved electroencephalography activity and marginally benefited cognitive behavior of transgenic mice. In addition, HT treatment ameliorated mitochondrial dysfunction, reduced mitochondrial carbonyl protein, enhanced superoxide dismutase 2 expression, reversed the phase 2 enzyme system and reduced the levels of brain inflammatory markers, but had no effect on brain β‐amyloid (Aβ) accumulation in APP/PS1 mice.ConclusionsThese results suggest that HT may represent as a functional ingredient in Mediterranean diet in ameliorating AD‐involved neuronal impairment via modulating mitochondrial oxidative stress, neuronal inflammation, and apoptosis without affecting APP processing.
Repetitive nerve stimulation cutoff values for the diagnosis of myasthenia gravis
Authors: Abraham Alon , Alabdali Majed , Alsulaiman Abdulla , Breiner Ari , Barnett Carolina , Katzberg Hans D. , Lovblom Leif E. , Bril Vera 
Published: June 2016

ABSTRACTIntroductionRepetitive nerve stimulation (RNS) showing ≥ 10% decrement is considered the cutoff for myasthenia gravis (MG), but this has never been validated. The objective of this study was to find an optimal validated cutoff value for decrement on RNS. Methods: We performed retrospective chart review of patients who had electrophysiological assessment for possible MG from 2013 to 2015. Results: A total of 122 patients with MG and 182 controls were identified. RNS sensitivities for generalized and ocular MG using the traditional ≥10% cutoff value were 46% and 15%, respectively, for frontalis recordings, and 35% and 19%, respectively, for nasalis recordings. Using a decrement cutoff value of 7% for frontalis and 8% for nasalis increased the sensitivities by 6–11%, with specificities of 95–96%. Conclusions: For RNS in facial muscles, we suggest a cutoff value of 7–8%, which increases test sensitivity by 6–11%, while preserving high specificity for the diagnosis of MG. Muscle Nerve, 2016 Muscle Nerve 55: 166–170, 2017
A new monolithic Newton‐multigrid‐based FEM solution scheme for large strain dynamic poroelasticity problems
Authors: Obaid A. , Turek St. , Heider Y. , Markert B. 
Published: June 2016

SummaryThis paper presents a new efficient monolithic finite element solution scheme to treat the set of PDEs governing a 2D, biphasic, saturated theory of porous media model with intrinsically coupled and incompressible solid and fluid constituents for infinitesimal and large elastic deformation. Our approach, which inherits some of its techniques from CFD, is characterized by the following aspects: (1) it only performs operator evaluation with no additional Gateaux derivatives. In particular, the computations of the time‐consuming material tangent matrix are not involved here; (2) it solves the non‐linear dynamic problem with no restriction on the strength of coupling; (3) it is more efficient than the linear uvp solver discussed in previous works; (4) it requires weaker derivatives, and hence, lower‐order FE can be tested; and (5) the boundary conditions are reduced, solution independent and more convenient to apply than in the old uvp formulation. For the purpose of validation and comparison, prototypical simulations including analytical solutions are carried out, and at the end, an adaptive time stepping procedure is introduced to handle the rapid change in the numbers of nonlinear iterations that may occur. Copyright © 2016 John Wiley & Sons, Ltd.
Dysregulation of hepatic cAMP levels via altered Pde4b expression plays a critical role in alcohol‐induced steatosis
Authors: Avila Diana V , Barker David F , Zhang JingWen , McClain Craig J , Barve Shirish , Gobejishvili Leila 
Published: June 2016

AbstractAlcohol‐induced hepatic steatosis is a significant risk factor for progressive liver disease. Cyclic adenosine monophosphate (cAMP) signalling has been shown to significantly regulate lipid metabolism; however, the role of altered cAMP homeostasis in alcohol‐mediated hepatic steatosis has never been studied. Our previous work demonstrated that increased expression of hepatic phosphodiesterase 4 (Pde4), which specifically hydrolyses and decreases cAMP levels, plays a pathogenic role in the development of liver inflammation/injury. The aim of this study was to examine the role of PDE4 in alcohol‐induced hepatic steatosis. C57BL/6 wild‐type and Pde4b knockout (Pde4b−/−) mice were pair‐fed control or ethanol liquid diets. One group of wild‐type mice received rolipram, a PDE4‐specific inhibitor, during alcohol feeding. We demonstrate for the first time that an early increase in PDE4 enzyme expression and a resultant decrease in hepatic cAMP levels are associated with the significant reduction in carnitine palmitoyltransferase 1A (Cpt1a) expression. Notably, alcohol‐fed (AF) Pde4b−/− mice and AF wild‐type mice treated with rolipram had significantly lower hepatic free fatty acid content compared with AF wild‐type mice. Importantly, PDE4 inhibition in alcohol‐fed mice prevented the decrease in hepatic Cpt1a expression via the Pparα/Sirt1/Pgc1α pathway. These results demonstrate that the alcohol‐ induced increase in hepatic Pde4, specifically Pde4b expression, and compromised cAMP signalling predispose the liver to impaired fatty acid oxidation and the development of steatosis. Moreover, these data also suggest that hepatic PDE4 may be a clinically relevant therapeutic target for the treatment of alcohol‐induced hepatic steatosis. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
BiPPred: Combined sequence‐ and structure‐based prediction of peptide binding to the Hsp70 chaperone BiP
Authors: Schneider Markus , Rosam Mathias , Glaser Manuel , Patronov Atanas , Shah Harpreet , Back Katrin Christiane , Daake Marina Angelika , Buchner Johannes , Antes Iris 
Published: June 2016

ABSTRACTSubstrate binding to Hsp70 chaperones is involved in many biological processes, and the identification of potential substrates is important for a comprehensive understanding of these events. We present a multi‐scale pipeline for an accurate, yet efficient prediction of peptides binding to the Hsp70 chaperone BiP by combining sequence‐based prediction with molecular docking and MMPBSA calculations. First, we measured the binding of 15mer peptides from known substrate proteins of BiP by peptide array (PA) experiments and performed an accuracy assessment of the PA data by fluorescence anisotropy studies. Several sequence‐based prediction models were fitted using this and other peptide binding data. A structure‐based position‐specific scoring matrix (SB‐PSSM) derived solely from structural modeling data forms the core of all models. The matrix elements are based on a combination of binding energy estimations, molecular dynamics simulations, and analysis of the BiP binding site, which led to new insights into the peptide binding specificities of the chaperone. Using this SB‐PSSM, peptide binders could be predicted with high selectivity even without training of the model on experimental data. Additional training further increased the prediction accuracies. Subsequent molecular docking (DynaDock) and MMGBSA/MMPBSA‐based binding affinity estimations for predicted binders allowed the identification of the correct binding mode of the peptides as well as the calculation of nearly quantitative binding affinities. The general concept behind the developed multi‐scale pipeline can readily be applied to other protein‐peptide complexes with linearly bound peptides, for which sufficient experimental binding data for the training of classical sequence‐based prediction models is not available. Proteins 2016; 84:1390–1407. © 2016 Wiley Periodicals, Inc.
Great interactions: How binding incorrect partners can teach us about protein recognition and function
Authors: Vamparys Lydie , Laurent Benoist , Carbone Alessandra , Sacquin‐Mora Sophie 
Published: June 2016

ABSTRACTProtein–protein interactions play a key part in most biological processes and understanding their mechanism is a fundamental problem leading to numerous practical applications. The prediction of protein binding sites in particular is of paramount importance since proteins now represent a major class of therapeutic targets. Amongst others methods, docking simulations between two proteins known to interact can be a useful tool for the prediction of likely binding patches on a protein surface. From the analysis of the protein interfaces generated by a massive cross‐docking experiment using the 168 proteins of the Docking Benchmark 2.0, where all possible protein pairs, and not only experimental ones, have been docked together, we show that it is also possible to predict a protein's binding residues without having any prior knowledge regarding its potential interaction partners. Evaluating the performance of cross‐docking predictions using the area under the specificity‐sensitivity ROC curve (AUC) leads to an AUC value of 0.77 for the complete benchmark (compared to the 0.5 AUC value obtained for random predictions). Furthermore, a new clustering analysis performed on the binding patches that are scattered on the protein surface show that their distribution and growth will depend on the protein's functional group. Finally, in several cases, the binding‐site predictions resulting from the cross‐docking simulations will lead to the identification of an alternate interface, which corresponds to the interaction with a biomolecular partner that is not included in the original benchmark. Proteins 2016; 84:1408–1421. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Bending resistance and cyclic fatigue of a new heat‐treated reciprocating instrument
Authors: Silva Emmanuel João Nogueira Leal , Rodrigues Cristiane , Vieira Victor Talarico Leal , Belladonna Felipe Gonçalves , De‐Deus Gustavo , Lopes Hélio Pereira 
Published: June 2016

SummaryThe current study aimed to evaluate the bending resistance and the cyclic fatigue life of a new heat‐treated reciprocating instrument (ProDesign R). Untreated ProDesign R, Reciproc R25, and WaveOne Primary instruments were used as reference instruments for comparison. The bending resistance was performed in ten instruments of each system by using a universal testing machine and a proper apparatus. The cyclic fatigue resistance was tested measuring the number of cycles to failure in an artificial stainless steel canal. Scanning electron microscopy analysis was performed to determine the mode of fracture and possible deformations at the helical shaft. Statistical analysis was performed by using parametric methods; one‐way analysis of variance plus post hoc pair‐wise Tukey test for multiple comparisons (p < 0.05). Untreated ProDesign R presented significantly higher bending resistance than the other tested systems (p < 0.05). No differences were observed between ProDesign R and Reciproc files regarding the bending resistance (p > 0.05). Moreover, ProDesign R revealed a significantly longer cyclic fatigue life (p < 0.05). In contrast, Untreated ProDesign R and WaveOne instruments presented significantly lower cyclic fatigue life than Reciproc (p < 0.05). The new heat‐treated reciprocating instrument ProDesign R have higher cyclic fatigue resistance than Untreated ProDesign R, Reciproc, and WaveOne instruments. ProDesign R and Reciproc were significantly more flexible than Untreated ProDesign R and WaveOne files. SCANNING 38:837–841, 2016. © 2016 Wiley Periodicals, Inc.
Child abuse and the prevalence of suicide attempts among those reporting suicide ideation
Authors: Martin Michael S. , Dykxhoorn Jennifer , Afifi Tracie O. , Colman Ian 
Published: June 2016

AbstractObjectiveVictims of child abuse may be at increased risk of acting on suicide ideation, although this has not been empirically tested. We estimated the risk of suicide attempts associated with child abuse among individuals who reported suicide ideation.MethodsSecondary analysis of data from the population-based Canadian Community Health Survey Mental Health (n = 828). This population-based survey included various structured questionnaires, including the Composite International Diagnostic Interview to assess mental illness and suicidal thoughts and behaviours.ResultsApproximately 80 % of those who attempted suicide had a history of child abuse. Poor mental health, financial difficulties, poor coping skills, and reporting a suicide plan were also associated with an increased prevalence of attempting suicide; adjusted for these factors, child abuse was associated with a 1.77-fold increased prevalence (95 % CI 0.93, 3.36) of suicide attempts.ConclusionsMost individuals who attempt suicide experience child abuse, and worse health and social functioning. Adopting a life-course perspective to understand trajectories of suicide risk factors may inform prevention and treatment.
Climatic and geographic effects on the spatial genetic pattern of a landbird species (Alectoris rufa) on the Iberian Peninsula
Authors: Ferrero María Ester , Blanco‐Aguiar Jose Antonio , Dávila José Antonio 
Published: June 2016

AbstractUnderstanding the spatial pattern of genetic diversity may be pivotal to adaptive conservation management of a given taxon. The red‐legged partridge (Alectorisrufa, Linnaeus 1758) is naturally widely distributed from the Mediterranean to humid temperate zones. According to a recent study, the genetic structure of this species comprises five clusters, three of which are in the Iberian Peninsula (glacial refugia). Partridge demographic expansion events and climatic shifts during Pleistocene glaciations have been used to test the hypotheses concerning Iberian red‐legged partridge distribution. We tested the existence of climatic and geographic relationships on genetic diversity/distances. We employed markers from two different genetic systems, such as part of the mitochondrial DNA control region (n = 113) and 20 species‐specific microsatellite DNA loci (n = 377), including climatic and geographic factors from the 14 Iberian localities where A. rufa populations were sampled. Our results showed a mitochondrial genetic diversity pattern associated with a thermic gradient, and a decrease of genetic diversity in peripheral populations that concurred with the ‘abundant centre’ hypothesis. Overall, current climatic variables reliably described genetic variation and differentiation in the red‐legged partridge, which may be a result of local species adaptation.