bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local and non‐local elasto‐viscoplasticity in strain localization analysis of multiphase geomaterials
Authors: Lazari M. , Sanavia L. , Schrefler B.A. 
Published: July 2015

SummaryIn this paper, rate‐dependent plasticity is employed to regularize, for the scope of mesh independency, the numerical solution in strain localization process of multiphase geomaterials. Towards this goal, the viscoplastic Duvaut–Lions and the viscoplastic Perzyna models are implemented in an existing finite element code for multiphase porous media. Perzyna's model is then extended according to the non‐local approach, allowing for handling weakly rate‐sensitive materials for which viscoplasticity is not sufficient to meet numerical requirements. Assuming quasi‐static and isothermal conditions, the models are validated and applied in the numerical simulation of an undrained plane strain biaxial compression test on initially water‐saturated dense sand taken from the existing literature. An overview of the significant factors such as loading velocity and soil permeability in conjunction with viscosity on the formation of localization pattern is presented. The interaction of the two internal lengths introduced by non‐locality and viscosity is also discussed. Finally, the obtained results are analysed and compared emphasizing the capabilities and shortcomings of each regularization technique. Copyright © 2015 John Wiley & Sons, Ltd.
Vitamin D attenuates proteinuria by inhibition of heparanase expression in the podocyte
Authors: Garsen Marjolein , Sonneveld Ramon , Rops Angelique LWMM , Huntink Suzanne , van Kuppevelt Toin H , Rabelink Ton J , Hoenderop Joost GJ , Berden Jo HM , Nijenhuis Tom , van der Vlag Johan 
Published: July 2015

AbstractThe glomerular filtration barrier consists of podocytes, the glomerular basement membrane, and endothelial cells covered with a glycocalyx. Heparan sulphate (HS) in the glomerular filtration barrier is reduced in patients with proteinuria, which is associated with increased expression of the HS‐degrading enzyme heparanase. Previously, we showed that heparanase is essential for the development of proteinuria in experimental diabetic nephropathy. Vitamin D supplementation reduces podocyte loss and proteinuria in vitro and in vivo. Therefore, we hypothesize that vitamin D reduces proteinuria by reducing glomerular heparanase. Adriamycin‐exposed rats developed proteinuria and showed increased heparanase expression, which was reduced by 1,25‐dihydroxyvitamin D3 (1,25‐D3) treatment. In vitro, adriamycin increased heparanase mRNA in the podocyte, which could be corrected by 1,25‐D3 treatment. In addition, 1,25‐D3 treatment reduced transendothelial albumin passage after adriamycin stimulation. In line with these results, we showed direct binding of the vitamin D receptor to the heparanase promoter, and 1,25‐D3 dose‐dependently reduced heparanase promoter activity. Finally, 1,25‐D3‐deficient 25‐hydroxy‐1α‐hydroxylase knockout mice developed proteinuria and showed increased heparanase, which was normalized by 1,25‐D3 treatment. Our data suggest that the protective effect of vitamin D on the development of proteinuria is mediated by inhibiting heparanase expression in the podocyte. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
A New Reference Material and Safe Sampling of Terrorists Peroxide Explosives by a Non‐Volatile Matrix
Authors: Lubczyk Daniel , Hahma Arno , Brutschy Malte , Siering Carsten , Waldvogel Siegfried R. 
Published: July 2015

AbstractHighly sensitive peroxide based explosives can be dissolved in ionic liquids for a safe handling. These solutions are easy to use and may be applied as powerful odor sources for analytical testing and training purposes. Moreover, the stabilizing effect of the ionic liquids can be exploited for a safe sampling of large quantities of these explosives. Such samples of triacetone triperoxide are long‐term stable, safe, and valid for forensic evaluations.
CASP11 refinement experiments with ROSETTA
Authors: Park Hahnbeom , DiMaio Frank , Baker David 
Published: July 2015

ABSTRACTWe report new Rosetta‐based approaches to tackling the major issues that confound protein structure refinement, and the testing of these approaches in the CASP11 experiment. Automated refinement protocols were developed that integrate a range of sampling methods using parallel computation and multiobjective optimization. In CASP11, we used a more aggressive large‐scale structure rebuilding approach for poor starting models, and a less aggressive local rebuilding plus core refinement approach for starting models likely to be closer to the native structure. The more incorrectly modeled a structure was predicted to be, the more it was allowed to vary during refinement. The CASP11 experiment revealed strengths and weaknesses of the approaches: the high‐resolution strategy incorporating local rebuilding with core refinement consistently improved starting structures, while the low‐resolution strategy incorporating the reconstruction of large parts of the structures improved starting models in some cases but often considerably worsened them, largely because of model selection issues. Overall, the results suggest the high‐resolution refinement protocol is a promising method orthogonal to other approaches, while the low‐resolution refinement method clearly requires further development. Proteins 2016; 84(Suppl 1):314–322. © 2015 Wiley Periodicals, Inc.
Accurate contact predictions using covariation techniques and machine learning
Authors: Kosciolek Tomasz , Jones David T. 
Published: July 2015

ABSTRACTHere we present the results of residue–residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effective sequences, our server achieved an average top‐L/5 long‐range contact precision of 27%. MetaPSICOV method bases on a combination of classical contact prediction features, enhanced with three distinct covariation methods embedded in a two‐stage neural network predictor. Some unique features of our approach are (1) the tuning between the classical and covariation features depending on the depth of the input alignment and (2) a hybrid approach to generate deepest possible multiple‐sequence alignments by combining jackHMMer and HHblits. We discuss the CONSIP2 pipeline, our results and show that where the method underperformed, the major factor was relying on a fixed set of parameters for the initial sequence alignments and not attempting to perform domain splitting as a preprocessing step. Proteins 2016; 84(Suppl 1):145–151. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Innate immune response during herpes simplex virus encephalitis and development of immunomodulatory strategies
Authors: Piret Jocelyne , Boivin Guy 
Published: July 2015

SummaryHerpes simplex viruses are large double‐stranded DNA viruses. These viruses have the ability to establish a lifelong latency in sensory ganglia and to invade and replicate in the CNS. Apart from relatively benign mucosal infections, HSV is responsible for severe illnesses including HSV encephalitis (HSE). HSE is the most common cause of sporadic, potentially fatal viral encephalitis in Western countries. If left untreated, the mortality rate associated with HSE is approximately 70%. Despite antiviral therapy, the mortality is still higher than 30%, and almost 60% of surviving individuals develop neurological sequelae. It is suggested that direct virus‐related and indirect immune‐mediated mechanisms contribute to the damages occurring in the CNS during HSE. In this manuscript, we describe the innate immune response to HSV, the development of HSE in mice knock‐out for proteins of the innate immune system as well as inherited deficiencies in key components of the signaling pathways involved in the production of type I interferon that could predispose individuals to develop HSE. Finally, we review several immunomodulatory strategies aimed at modulating the innate immune response at a critical time after infection that were evaluated in mouse models and could be combined with antiviral therapy to improve the prognosis of HSE. In conclusion, the cerebral innate immune response that develops during HSE is a “double‐edged sword” as it is critical to control viral replication in the brain early after infection, but, if left uncontrolled, may also result in an exaggerated inflammatory response that could be detrimental to the host. Copyright © 2015 John Wiley & Sons, Ltd.
Fish Assemblage and Ecosystem Metabolism Responses to Reconnection of the Bird's Point‐New Madrid Floodway during the 2011 Mississippi River Flood
Authors: Rantala H. , Glover D. , Garvey J. , Phelps Q. , Tripp S. , Herzog D. , Hrabik R. , Crites J. , Whiles M. 
Published: July 2015

AbstractUnderstanding the ecological function of developed large rivers remains elusive because these systems have long been altered for multiple uses. In particular, floodplains of large rivers, such as the Mississippi River, have been contained behind extensive levees. A historic flood occurred in the lower Mississippi River system during spring of 2011, prompting the US Army Corps of Engineers to activate the Bird's Point‐New Madrid floodway, a 55 000‐ha, agriculturally dominated, leveed area. Water entered the floodway at flows >1 m s−1 through two crevasses created in the upper portion of the levee and exited through a crevasse at the lower end. During the month, the floodway was inundated; we quantified discharge, water chemistry, primary production and fish production in the floodway and the adjacent river. Water entering the floodway was retained <1.3 d, and nutrient concentrations were not elevated in the floodway beyond those in the river, despite expected contributions from a legacy of fertilization. Primary production equaled respiration in the floodway, while the adjacent river was heterotrophic. Gizzard shad and freshwater drum were more abundant in the floodway than the river, while channel catfish were more abundant in the river. Growth rates of young native fishes, normalized for temperature, were the same in the floodway and the river, with the exception of gizzard shad, which grew faster in the floodway. Fish community structure, especially in the lower floodway, was temporally and spatially dynamic. Even though it has been heavily modified for agriculture, the floodway provided benefits, albeit limited, to the Mississippi River. With multifunctional management and strategic planning, systems such as these may provide substantial services such as flood abatement, nutrient transformation and fish production in the Mississippi River basin and potentially reduce nutrient loading downstream in areas such as the Gulf of Mexico. Copyright © 2015 John Wiley & Sons, Ltd.
Structurally Flexible C3‐Symmetric Receptors for Molecular Recognition and Their Self‐Assembly Properties
Authors: Singh Ashutosh S. , Sun Shih‐Sheng 
Published: July 2015

AbstractThe bioinspired design and synthesis of building blocks and their assemblies by the supramolecular approach has ever fascinated scientists to utilize such artificial systems for numerous purposes. Flexibility is a basic feature of natural systems. However, in artificial systems this is difficult to control, especially if there is no preorganization of the component(s) of a system. We have designed and synthesized a series of C3‐symmetric N‐bridged flexible receptors and successfully utilized them to selectively entrap the notorious and toxic nitrate anion in aqueous medium. This was the first report of highest binding affinity for the nitrate anion in aqueous medium. An impressive self‐sorting phenomenon of reversibly formed hydrogen‐bonded capsules, which self‐assembled from flexible tripodal receptors having branches of similar size and bearing the same amide functionality, has been disclosed. Encapsulated nitrate anion has been further utilized for the photochemical [2+2] cycloaddition reaction for the synthesis of strained four‐membered ring structures through dynamic self‐assembly. In this Personal Account, we summarize these results showing the utility of naturally inspired flexibility in artificial systems.
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From Fragmentation to Construction—from Void to Massive: Fascination with Organic Mass Spectrometry and the Synthesis of Novel Three‐Dimensional Polycyclic Aromatic Hydrocarbons
Authors: Kuck Dietmar 
Published: July 2015

AbstractDetailed insights gained from our research into the gas‐phase chemistry of ionized and protonated diphenylalkanes and their congeners, obtained by extended synthesis of isotopically labeled model compounds and mass spectrometry, are presented and merged with those acquired during our development of a new family of polycyclic hydrocarbons, the centropolyindanes. Aside from a Personal Account that describes “two scientific lives in one”, it is demonstrated, on the one hand, how our understanding of organic chemistry can help to shed light on the details of mass spectrometric fragmentation and to unravel, in a more fundamental way, the unimolecular reactivity of gaseous ions. On the other hand, it is shown how unexpected reactivity of related ions in solution, being subject to the very same fundamentals of organic chemistry, can lead to the construction of novel and, in part, unique three‐dimensional polycyclic structures that may contribute to future research in material science. Two such apparently independent fields of organic chemistry may be seen as joint contributions of the art of science.
Developing and using geomorphic condition assessments for river rehabilitation planning, implementation and monitoring
Authors: Fryirs Kirstie A. 
Published: July 2015

Frameworks for assessing geomorphic river condition constitute a core part of the river management process, providing a critical platform for environmental decision‐making and associated actions. The evolution of approaches for assessing the geomorphic (also called physical, morphological, or hydromorphological) condition of rivers has shifted from a design and development phase in the late‐1990s and early 2000s to application and use of approaches for assessment, monitoring, and rehabilitation decision making. In this paper I review the core geomorphic principles that are embedded in more sophisticated, process‐based frameworks, and demonstrate how the information generated through use of these frameworks can be used to guide management choices, change management activities or opt‐out of management activities as part of precautionary river management practice. I propose that a key challenge now faced by geomorphologists and managers is to move beyond the development of more new frameworks, and consolidate efforts to use, test, and adapt existing approaches and datasets to achieve river management visions and objectives framed around improving river condition. WIREs Water 2015, 2:649–667. doi: 10.1002/wat2.1100This article is categorized under:

Water and Life > Conservation, Management, and Awareness
Engineering Water > Planning Water
Examination of the Causes of Instability of Soy Protein Isolate During Storage Through Probing of the Heat‐Induced Aggregation
Authors: Guo Feng‐Xian , Xiong Youling L. , Qin Fang , Jian Hua‐Jun , Huang Xiao‐Lin , Chen Jie 
Published: July 2015

AbstractThis study investigated the mechanism of instability of soy protein isolate (SPI) as influenced by thermal aggregation during SPI preparation. Samples with different degrees of aggregation but similar protein solubility were prepared by heating native SPI (5 % w/v) at 80 or 90 °C for different times before spray‐drying. The samples were then stored at 37 °C for up to 12 weeks and analyzed periodically by atomic force microscopy, gel permeation chromatography, and SDS–PAGE. All SPI samples underwent remarkable protein solubility decreases during the first 8 weeks of storage. The rates of solubility loss were positively correlated with the amounts and/or sizes of soluble aggregates contained in the initial samples (time zero), suggesting their nucleation and activation effects. Solubility tests in SDS–urea solutions and disulfide analysis indicated that non‐covalent interactions were the main driving forces for protein storage instability. Conversely, disulfide bonds and protein carbonyls were abundant in soluble aggregates, and their content increased markedly during storage. This effect suggested that covalent linkages acted as blockers for hydrophobic aggregation.
A Unitary Patent for a (Dis)United Europe: The Long Shadow of History
Authors: Plomer Aurora 
Published: July 2015

AbstractThis article retraces the history of patent harmonization in Europe and reviews the European Union “patent package” and its approval by the Grand Chamber of the Court of Justice of the European Union in the light of this history. The article draws on archived and hitherto unused confidential documents to retrace the key institutions and players in the origins and evolution of the European patent unification movement. The study reveals that the EU project was originally led by the Council of Europe and analyzes the reasons why the EU has struggled to develop a coherent model of integration to facilitate realization of the internal market ever since. The historical legacy suggests that a critical turning point was the creation of the European Patent Organization as the leading engine of patent policy in Europe, an autonomous organization which is not subject to judicial oversight by the EU court or meaningful political scrutiny by the European Union and its members. The article concludes with a case study illustrating how the latent difficulties over the relationship between different European institutions and the jurisdiction of European tribunals and courts are manifested today in the unitary patent and the unified patent court.
Research training, productivity and challenges among trainees of pediatric residency programs across Saudi Arabia
Authors: Alhaider S.A. , Alshehri H.A. , Almedhesh S.A. 
Published: July 2015

Background and objectives:
Research provides skills for lifelong learning and pro-motes patient care. In Saudi Arabia, until recently, research training has not been integrated effectively in postgraduate medical education. The aim of this study was to investigate the factors involved in research training, productivity, challenges, and attitude among trainees in pediatric residency programs across Saudi Arabia.

Materials and methods:
This is a cross-sectional, multicenter study using a questionnaire de-signed to assess several aspects of research training among trainees of the national pediatric residency program in Saudi Arabia from September to December 2013.

Results:
Eighty-three residents from seven training centers participated (response rate of 65.5%). Ninety percent of participants agreed that research training must be mandated in each residency program. The majority of participants (85.5-89.2%) agree that research is beneficial because it improves patient care, enhances the pursuit of academic careers, and improves fellowship acceptance rates and success. More than half (51.8%) of participants believe that research training will interfere with their efforts to become a medical expert in their fields. The survey indicated low research involvement by trainees, with 86.7% of participants having never published scientific manuscripts. The majority of participants (73.5%) reported a lack of regular, structured research activity in their training curriculum. The main challenge in research training was the lack of protected time (according to 86.7% of respondents). The ma-jority of participants (85.6%) agreed that training in research methodologies represents their top educational need.

Conclusion:
This study represents a "needs assessment” phase in the development of a research training curriculum for the Saudi pediatric residency program. The majority of participating residents have a positive attitude toward research. Research productivity and training were found to be low. A dedicated research curriculum within the residency program represents an effective and evidence-based solution.
Types of Injury in Inter-State Reparation Claims: A Guide for the International Criminal Court
Authors: Abtahi Hirad 
Published: July 2015

Abstract
In determining “the scope and extent of any damage, loss and injury to, or in respect of, victims” under article 75(1) of the International Criminal Court (“ICC”) Statute, the ICC will progressively lay the foundation of reparations in international criminal justice. In the process of establishing the typology of harms sustained by natural and—under some qualifications—legal persons, inter-state claims practice may prove to be of assistance to the judges in light of the particular circumstances of each case. In addition, such an exercise illuminates how the doctrinal methods adopted in public international law scholarship categorize and describe the harms that have given rise to reparation claims during both war and peacetime.
Non-targeted lipidomics of CSF and frontal cortex grey and white matter in control, mild cognitive impairment, and Alzheimer’s disease subjects
Authors: Wood Paul L. , Barnette Brooke L. , Kaye Jeffrey A. , Quinn Joseph F. , Woltjer Randall L. 
Published: July 2015

ObjectiveWe undertook a non-targeted lipidomics analysis of post-mortem cerebrospinal fluid (CSF), frontal cortex grey matter, and subjacent white matter to define potential biomarkers that distinguish cognitively intact subjects from those with incipient or established dementia. Our objective was to increase our understanding of the role of brain lipids in pathophysiology of aging and age-related cognitive impairment.MethodsLevels of 650 individual lipids, across 26 lipid subclasses, were measured utilising a high-resolution mass spectrometric analysis platform.ResultsMonoacylglycerols (MAG), diacylglycerols (DAG), and the very-long-chain fatty acid 26:0 were elevated in the grey matter of the mild cognitive impairment (MCI) and old dementia (OD) cohorts. Ethanolamine plasmalogens (PlsEtn) were decreased in the grey matter of the young dementia (YD) and OD cohorts while and phosphatidylethanolamines (PtdEth) were lower in the MCI, YD and OD cohorts. In the white matter, decrements in sulphatide levels were detected in the YD group, DAG levels were elevated in the MCI group, and MAG levels were increased in the YD and OD groups.ConclusionThe parallel changes in grey matter MAGs and DAGs in the MCI and OD groups suggest that these two cohorts may have a similar underlying pathophysiology; consistent with this, MCI subjects were more similar in age to OD than to YD subjects. While PlsEtn and phosphatidylethanolamine were decreased in the YD and OD groups they were unaltered in the MCI group indicating that alterations in plasmalogen synthesis are unlikely to represent an initiating event in the transition from MCI to dementia.