bluuebunny/crossref_metadata_2025 huggingface dataset:
Cortical bone fracture analysis using XFEM – case study
Authors: Idkaidek Ashraf , Jasiuk Iwona
Published: June 2016

We aim to achieve an accurate simulation of human cortical bone fracture using the extended finite element method within a commercial finite element software abaqus. A two‐dimensional unit cell model of cortical bone is built based on a microscopy image of the mid‐diaphysis of tibia of a 70‐year‐old human male donor. Each phase of this model, an interstitial bone, a cement line, and an osteon, are considered linear elastic and isotropic with material properties obtained by nanoindentation, taken from literature.

The effect of using fracture analysis methods (cohesive segment approach versus linear elastic fracture mechanics approach), finite element type, and boundary conditions (traction, displacement, and mixed) on cortical bone crack initiation and propagation are studied. In this study cohesive segment damage evolution for a traction separation law based on energy and displacement is used. In addition, effects of the increment size and mesh density on analysis results are investigated.

We find that both cohesive segment and linear elastic fracture mechanics approaches within the extended finite element method can effectively simulate cortical bone fracture. Mesh density and simulation increment size can influence analysis results when employing either approach, and using finer mesh and/or smaller increment size does not always provide more accurate results. Both approaches provide close but not identical results, and crack propagation speed is found to be slower when using the cohesive segment approach. Also, using reduced integration elements along with the cohesive segment approach decreases crack propagation speed compared with using full integration elements. Copyright © 2016 John Wiley & Sons, Ltd.
A performance analysis of a mimetic finite difference scheme for acoustic wave propagation on GPU platforms
Authors: Otero Beatriz , Francés Jorge , Rodriguez Robert , Rojas Otilio , Solano Freysimar , Guevara‐Jordan Juan
Published: June 2016

Realistic applications of numerical modeling of acoustic wave dynamics usually demand high‐performance computing because of the large size of study domains and demanding accuracy requirements on simulation results. Forward modeling of seismic motion on a given subsurface geological structure is by itself a good example of such applications, and when used as a component of seismic inversion tools or as a guide for the design of seismic surveys, its computational cost increases enormously. In the case of finite difference methods (or any other volumen‐discretization scheme), memory and computing demands rise with grid refinement, which may be necessary to reduce errors on numerical wave patterns and better capture target physical devices. In this work, we present several implementations of a mimetic finite difference method for the simulation of acoustic wave propagation on highly dense staggered grids. These implementations evolve as different optimization strategies are employed starting from appropriate setting of compilation flags, code vectorization by using streaming SIMD extensions Advanced Vector Extensions (AVX), CPU parallelization by exploiting the Open Multi‐Processing framework to the final code parallelization on graphics processing unit platforms. We present and discuss the increasing processing speed up of this mimetic scheme achieved by the gradual implementation and testing of all these performance optimizations. In terms of simulation times, the performance of our graphics processing unit parallel implementations is consistently better than the best CPU version. Copyright © 2016 John Wiley & Sons, Ltd.
A multi‐channel architecture for metadata management in cloud storage systems by binding CPU‐cores to disks
Authors: Duan Hancong , Xiang Xiaoke , Zhang Yulu , Min Geyong , Zhan Wenhan , Lv Pengcheng
Published: June 2016

Metadata operations have become dominant file operations in the storage systems. In the scenarios of read‐more and write‐less of massive small files, the current distributed file systems suffer from the unsatisfying performance and scalability of metadata service because of random disk I/O during metadata operations. In this paper, a highly efficient metadata management architecture for cloud storage systems is proposed. The cluster design significantly improves the scalability of the system. A concept of the disk I/O channel is introduced, which is an independent data storage pipe by binding an independent CPU‐core to each physical disk. In addition, a multi‐channel fast key‐value storage engine is proposed to provide the extremely efficient performance for the underlying storage service, which takes full advantages of multi‐core processors and parallel disks I/O. Besides, a new dynamic load‐balancing strategy is proposed to reduce load thrashing and improve the precision of rebalancing among the clusters. Performance measurements under a variety of benchmarks show that the metadata management is capable of handling the massive small files storage and the performance is improved significantly compared to the existing solutions. Copyright © 2016 John Wiley & Sons, Ltd.
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

A 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

Geographic 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.
T cell derived IL‐10 is dispensable for tolerance induction in a murine model of allergic airway inflammation
Authors: Kunz Stefanie , Dolch Anja , Surianarayanan Sangeetha , Dorn Britta , Bewersdorff Mayte , Alessandrini Francesca , Behrendt Rayk , Karp Christopher L. , Muller Werner , Martin Stefan F. , Roers Axel , Jakob Thilo
Published: June 2016

Regulatory mechanisms initiated by allergen‐specific immunotherapy are mainly attributed to T cell derived IL‐10. However, it has not been shown that T cell derived IL‐10 is required for successful tolerance induction (TI). Here, we analyze cellular sources and the functional relevance of cell type specific IL‐10 during TI in a murine model of allergic airway inflammation. While TI was effective in IL‐10 competent mice, neutralizing IL‐10 prior to tolerogenic treatment completely abrogated the beneficial effects. Cellular sources of IL‐10 during TI were identified by using transcriptional reporter mice as T cells, B cells, and to a lesser extent DCs. Interestingly, TI was still effective in mice with T cell, B cell, B and T cell, or DC‐specific IL‐10 deficiency. In contrast, TI was not possible in mice lacking IL‐10 in all hematopoetic cells, while it was effective in bone marrow (BM) chimera that lacked IL‐10 only in nonhematopoetic cells. Taken together, allergen‐specific tolerance depends on IL‐10 from hematopoetic sources. The beneficial effects of allergen‐specific immunotherapy cannot solely be attributed to IL‐10 from T cells, B cells, or even DCs, suggesting a high degree of cellular redundancy in IL‐10‐mediated tolerance.
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

A 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.
Tartaric acid induced conversion of protopanaxadiol to ginsenosides Rg3 and Rg5 and their in situ recoveries by integrated expanded bed adsorption chromatography
Authors: Huang Dan , Li Yang , Zhang Min , Ruan Shengli , Zhang Hongyang , Wang Yuerong , Hu Ping
Published: June 2016

Panax ginseng has been applied in traditional Chinese medicine for over 2000 years. It is still one of the most popular herbs in recent decades. The prescribed ginseng‐containing medicines consist of protopanaxadiol and protopanaxatriol ginsenosides, which are the major constituents of the herb. Minor ginsenosides at low levels in the herb, such as Rg3 and Rg5, have attracted more rising attention than the major ones. The existing approaches to prepare Rg3 and Rg5 usually rely on either steamed red ginseng as the source or chemical/enzymatic conversion of protopanaxadiol to the targets. It is still highly desirable to effectively achieve such minor components. In this paper, a method integrated extraction of protopanaxadiol and conversion of it to Rg3 and Rg5 has been proposed. Protopanaxadiol was extracted and simultaneously converted to Rg3 and Rg5 by d,l‐tartaric acid. The targets were absorbed by resins on expanded bed adsorption chromatography and were then separated from other ginsenosides in different stages. Compared with conventional methods, the developed process has advantages in shortening time consumption and improving the conversion ratio of protopanaxadiol, which is promising in directly achieving Rg3 and Rg5 from P. ginseng.
Molecularly imprinted polymer for the selective extraction of luteolin from Chrysanthemum morifolium Ramat
Authors: Gao Die , Yang Fengqing , Xia Zhining , Zhang Qihui
Published: June 2016

In this work, luteolin‐imprinted polymers were prepared by noncovalent precipitation polymerization for the first time. Their structural features and morphologies were analyzed by using Fourier transform infrared spectroscopy and scanning electron microscopy, respectively. The adsorption experiments revealed that the luteolin‐imprinted polymers presented high selective recognition property to luteolin. The selectivity experiment showed that the adsorption capacity and selectivity of polymers to luteolin was higher than that of three structural analogs, including quercetin, isorhamnetin, and ombuin. Furthermore, an efficient method based on luteolin‐imprinted polymers coupled with solid‐phase extraction was developed for the pretreatment of luteolin from Chrysanthemum morifolium Ramat. The results demonstrated that the luteolin‐imprinted polymers coupled with solid phase extraction method was proven to be a potentially competitive technique for the separation and enrichment of luteolin in complex samples such as Chinese patent medicines and biological samples.
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

Community 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.
Gut microbiota, diet, and obesity‐related disorders—The good, the bad, and the future challenges
Authors: Portune Kevin J. , Benítez‐Páez Alfonso , Del Pulgar Eva Maria Gomez , Cerrudo Victor , Sanz Yolanda
Published: June 2016

Diet has been shown to be a major factor in modulating the structure of the mammalian gut microbiota by providing specific nutrient sources and inducing environmental changes (pH, bile acids) in the gut ecosystem. Long‐term dietary patterns and short‐term interventions have been shown to induce changes in gut microbiota structure and function, with several studies revealing metabolic changes likely resulting from the host microbiota cross‐talk, which ultimately could influence host physiology. However, a more precise identification of the specific dietary patterns and food constituents that effectively modulate the gut microbiota and bring a predictable benefit to the host metabolic phenotype is needed to establish microbiome‐based dietary recommendations. Here, we briefly review the existing data regarding gut microbiota changes induced by different macronutrients and the resulting metabolites produced via their respective fermentation, including their potential effects on obesity and associated metabolic disorders. We also discuss major limitations of current dietary intervention studies as well as future needs of applying cutting‐edge “omic” techniques and of progressing in functional microbiota gene discovery to establish robust causal relationships between the dietary microbiota induced changes and metabolic health or disease.
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

Scope

Olive 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 results

In 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.

Conclusions

These 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

Introduction

Repetitive 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

This 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

Alcohol‐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.
Epigenetic regulation of neural N‐glycomics
Authors: Kizuka Yasuhiko , Nakano Miyako , Miura Yuki , Taniguchi Naoyuki
Published: June 2016

Glycan expression is tightly regulated in a cell‐type‐specific manner, which is essential for the diverse functions of glycans. In particular, neural cells such as neurons and astrocytes are known to express unique functional glycans not found in other cells, and these glycans play critical roles in high‐order brain functions and various neurological disorders. However, little is known about how the expression of these neural glycans is established and maintained. Here, we investigated which glycans are expressed in each primary neural cell and how epigenetics contributes to the expression of neural glycans. We first isolated primary neurons, astrocytes, and fibroblasts from mouse embryos and carried out N‐glycomic and glycosyltransferase (GlycoT)‐transcriptomic analyses to identify N‐glycans specific to a particular neural cell type and to clarify the underlying transcriptional basis. We next treated the cells with epigenetic drugs (5‐aza‐2′‐deoxycytidine (5‐aza) and trichostatin A (TSA)) and characterized the changes in GlycoT‐transcriptomes and N‐glycomes. We found that the N‐glycomes in neurons were highly stable and resistant to epigenetic stimulation. In contrast, astrocytes showed dynamic N‐glycan changes after treatment, such as a shift in the linkages of sialic acid. These results provide novel insights into how the expression of neural glycans is maintained and epigenetically regulated.
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

Substrate 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

Protein–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

The 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.
Teaching Poetry inTESOLTeacher Education: Heightened Attention to Language as Well as to Cultural and Political Critique Through Poetry Writing
Authors: Cahnmann‐Taylor Melisa , Bleyle Susan , Hwang Yohan , Zhang Kuo
Published: June 2016

Teachers of World English are no longer charged with teaching a fixed set of grammar rules and lexical choices but with teaching creative ways to navigate varieties of English and other world languages according to a wide set of contextual variables. Although there is a great deal of advocacy for teaching creativity and strategy inTESOLclassrooms (Richards, 2013), there is little documentation regarding how preservice teachers themselves exercise their own abilities as creative language users. How might students enrolled in aTESOLteacher preparation program respond to a course specifically designed to tap into prospectiveTESOLteachers' own creativity? In this article the authors present research documenting the implementation of poetry writing courses as part of aTESOLteacher preparation program in the southeastern United States that has attracted increasing numbers of native‐Chinese‐speaking students. Through qualitative analysis of students' poems, interviews, and classroom observations, we describe the ways in which the poetry writing offeredintellectual tools of inquiry(Johnson, 2006), heightening students' attention to the nuances and aesthetics of language (English and Chinese) as well as to articulations of “East‐West” learner identity and political critique seldom documented inTESOLteacher preparation scholarship.
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

Objective

Victims 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.

Methods

Secondary 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.

Results

Approximately 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.

Conclusions

Most 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

Understanding 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.
Development of the Personal Responsibility Scale for adolescents
Authors: Mergler Amanda , Shield Paul
Published: June 2016

Increasing interest by policy makers and educators in enhancing the non‐cognitive factors that impact on the wellbeing of young people across the school years requires valid and reliable measurement scales. This paper reports the psychometric development of the Personal Responsibility Scale drawing on a preliminary 34‐item measure developed using data from focus groups with secondary students in Australia. This scale was then administered to 513 students across Years 9–12. Exploratory factor analysis identified three factors, ‘personal accountability’, ‘behavioural and emotional control’, and ‘cognitive control’. Structural equation modelling was used to examine the congeneric measurement models for these factors. The multidimensional nature of the personal responsibility construct was then examined through multilevel confirmatory factor analysis. These analyses supported a three‐factor structure to propose a final 15‐item scale. Additional validation requirements, future research possibilities, and implications of this study are addressed.
Changes of junctions of endothelial cells in coronary sclerosis: A review
Authors: Zhang Li‐Zi , Lei Sun
Published: June 2016

Atherosclerosis, the major cause of cardiovascular diseases, has been a leading contributor to morbidity and mortality in the United States and it has been on the rise globally. Endothelial cell–cell junctions are critical for vascular integrity and maintenance of vascular function. Endothelial cell junctions dysfunction is the onset step of future coronary events and coronary artery disease.
Characteristics and risk factors of hospital acquired — Methicillin-resistant Staphylococcus aureus (HA-MRSA) infection of pediatric patients in a tertiary care hospital in Riyadh, Saudi Arabia
Authors: Alrabiah Khalid , Al Alola Sulaiman , Al Banyan Esam , Al Shaalan Mohammad , Al Johani Sameera
Published: June 2016

Background and objectives:

The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) infections has been steadily increasing. These infections are considered to be either hospital-acquired MRSA (HA-MRSA) or community-acquired MRSA (CA-MRSA). Children are at higher risk of infection than adults. HA-MRSA has been reported to have more serious outcomes than CA-MRSA. However, there are not enough studies in Saudi Arabia to study the characteristics of HA-MRSA in children. We aim to describe the characteristics of HA-MRSA infection, including risk factors, culture site, clinical manifestations, complications, and outcomes among pediatric patients in a tertiary care hospital in Riyadh, Saudi Arabia.

Design and settings:

This is a retrospective chart review study. It was conducted in King Abdu-laziz medical city in Riyadh.

Patients and methods:

The study included all patients 14 years of age or younger who were culture-positive from any site in the body during the period from January 1,2009 to December 31,2011. The time of culture compared to admission time was used to differentiate between CA-MRSA (within 72 h of admission) and HA-MRSA (more than 72 h after admission). The final sample size was 39 patients.

Results:

We found HA-MRSA to be more common in males and those with risk factors such as previous surgery and previous hospitalization. Patients had a high Pediatric intensive care unit (PICU) admission rate and were commonly septic with positive blood cultures. Seventy-four percent of patients fully recovered, 10% recovered with complications and 15% died.

Conclusion:

HA-MRSA is an infection that can cause serious complications and a high rate of PICU admissions. Clinical manifestations such as shock are associated with higher mortality and morbidity rates. Special care should be given to those admitted to PICU, as they have high rates of mortality and morbidity.
Function and expression study uncovered hepatocyte plasma membrane ecto-ATP synthase as a novel player in liver regeneration
Authors: Taurino Federica , Giannoccaro Caterina , Sardanelli Anna Maria , Cavallo Alessandro , De Luca Elisa , Santacroce Salvatore , Papa Sergio , Zanotti Franco , Gnoni Antonio
Published: June 2016

ATP synthase, canonically mitochondrially located, is reported to be ectopically expressed on the plasma membrane outer face of several cell types. We analysed, for the first time, the expression and catalytic activities of the ecto- and mitochondrial ATP synthase during liver regeneration. Liver regeneration was induced in rats by two-thirds partial hepatectomy. The protein level and the ATP synthase and/or hydrolase activities of the hepatocyte ecto- and mitochondrial ATP synthase were analysed on freshly isolated hepatocytes and mitochondria from control, sham-operated and partial hepatectomized rats. During the priming phase of liver regeneration, 3 h after partial hepatectomy, liver mitochondria showed a marked lowering of the ATP synthase protein level that was reflected in the impairment of both ATP synthesis and hydrolysis. The ecto-ATP synthase level, in 3 h partial hepatectomized hepatocytes, was decreased similarly to the level of the mitochondrial ATP synthase, associated with a lowering of the ecto-ATP hydrolase activity coupled to proton influx. Noteworthily, the ecto-ATP synthase activity coupled to proton efflux was completely inhibited in 3 h partial hepatectomized hepatocytes, even in the presence of a marked intracellular acidification that would sustain it as in control and sham-operated hepatocytes. At the end of the liver regeneration, 7 days after partial hepatectomy, the level and the catalytic activities of the ecto- and mitochondrial ATP synthase reached the control and sham-operated values. The specific modulation of hepatocyte ecto-ATP synthase catalytic activities during liver regeneration priming phase may modulate the extracellular ADP/ATP levels and/or proton influx/efflux trafficking, making hepatocyte ecto-ATP synthase a candidate for a novel player in the liver regeneration process.
Lachesana tarabaevi, an expert in membrane-active toxins
Authors: Kuzmenkov Alexey I. , Sachkova Maria Y. , Kovalchuk Sergey I. , Grishin Eugene V. , Vassilevski Alexander A.
Published: June 2016

In the present study, we show that venom of the ant spider Lachesana tarabaevi is unique in terms of molecular composition and toxicity. Whereas venom of most spiders studied is rich in disulfide-containing neurotoxic peptides, L. tarabaevi relies on the production of linear (no disulfide bridges) cytolytic polypeptides. We performed full-scale peptidomic examination of L. tarabaevi venom supported by cDNA library analysis. As a result, we identified several dozen components, and a majority (∼80% of total venom protein) exhibited membrane-active properties. In total, 33 membrane-interacting polypeptides (length of 18–79 amino acid residues) comprise five major groups: repetitive polypeptide elements (Rpe), latarcins (Ltc), met-lysines (MLys), cyto-insectotoxins (CIT) and latartoxins (LtTx). Rpe are short (18 residues) amphiphilic molecules that are encoded by the same genes as antimicrobial peptides Ltc 4a and 4b. Isolation of Rpe confirms the validity of the iPQM (inverted processing quadruplet motif) proposed to mark the cleavage sites in spider toxin precursors that are processed into several mature chains. MLys (51 residues) present ‘idealized’ amphiphilicity when modelled in a helical wheel projection with sharply demarcated sectors of hydrophobic, cationic and anionic residues. Four families of CIT (61–79 residues) are the primary weapon of the spider, accounting for its venom toxicity. Toxins from the CIT 1 and 2 families have a modular structure consisting of two shorter Ltc-like peptides. We demonstrate that in CIT 1a, these two parts act in synergy when they are covalently linked. This finding supports the assumption that CIT have evolved through the joining of two shorter membrane-active peptides into one larger molecule.
Comparative genome-scale modelling of
Staphylococcus aureus
strains identifies strain-specific metabolic capabilities linked to pathogenicity
Authors: Bosi Emanuele , Monk Jonathan M. , Aziz Ramy K. , Fondi Marco , Nizet Victor , Palsson Bernhard Ø.
Published: June 2016

Significance

Comparative analysis of multiple strains within a species is a powerful way to uncover pathoadaptive genetic acquisitions. Hundreds of genome sequences are now available for the human pathogen
Staphylococcus aureus,
mostly known for its antibiotic-resistant variants that threaten the emergence of panresistant superbugs. In this study, genome-scale models of metabolism are used to analyze the shared and unique metabolic capabilities of this pathogen and its strain-specific variants. The models are used to distinguish
S. aureus
strains responsible for severe infections based solely on growth capabilities and presence of different virulence factors. The results identify metabolic similarities and differences between
S. aureus
strains that provide insights into the epidemiology of
S. aureus
and may help to combat its spread.
bdvis: visualizing biodiversity data in R
Authors: Barve Vijay , Otegui Javier
Published: June 2016

Summary: Biodiversity studies are relying increasingly on primary biodiversity records (PBRs) for modelling and analysis. Because biodiversity data are frequently ‘harvested’—i.e. not collected by the researcher for that particular study, but obtained from data aggregators such as the Global Biodiversity Information Facility—researchers need to be aware of strengths and weaknesses of their data before they venture into further analysis. R is becoming a lingua franca of data exploration and analysis. Here, we describe an R package, bdvis, which facilitates efforts to understand the gaps and strengths of PBR data with quick and useful visualization functions.

Availability and Implementation: The full code of the R package bdvis, along with instructions on how to install and use it, is available via CRAN – The Comprehensive R Archive Network (http://cran.r-project.org/web/packages/bdvis/index.html) and in the corresponding author’s main GitHub repository: http://www.github.com/vijaybarve/bdvis. The source code is licensed under CC0

Contact:  vijay.barve@gmail.com