bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules
Authors: Wang Wei , Cao Siqin , Zhu Lizhe , Huang Xuhui 
Published: October 2017

The function of complex biomolecular machines relies heavily on their conformational changes. Investigating these functional conformational changes is therefore essential for understanding the corresponding biological processes and promoting bioengineering applications and rational drug design. Constructing Markov State Models (MSMs) based on large‐scale molecular dynamics simulations has emerged as a powerful approach to model functional conformational changes of the biomolecular system with sufficient resolution in both time and space. However, the rapid development of theory and algorithms for constructing MSMs has made it difficult for nonexperts to understand and apply the MSM framework, necessitating a comprehensive guidance toward its theory and practical usage. In this study, we introduce the MSM theory of conformational dynamics based on the projection operator scheme. We further propose a general protocol of constructing MSM to investigate functional conformational changes, which integrates the state‐of‐the‐art techniques for building and optimizing initial pathways, performing adaptive sampling and constructing MSMs. We anticipate this protocol to be widely applied and useful in guiding nonexperts to study the functional conformational changes of large biomolecular systems via the MSM framework. We also discuss the current limitations of MSMs and some alternative methods to alleviate them.WIREs Comput Mol Sci2018, 8:e1343. doi: 10.1002/wcms.1343This article is categorized under:Structure and Mechanism > Computational Biochemistry and BiophysicsTheoretical and Physical Chemistry > Statistical Mechanics
Triangle counting in large networks: a review
Authors: Al Hasan Mohammad , Dave Vachik S. 
Published: October 2017

Counting and enumeration of local topological structures, such as triangles, is an important task for analyzing large real‐life networks. For instance, triangle count in a network is used to compute transitivity—an important property for understanding graph evolution over time. Triangles are also used for various other tasks completed for real‐life networks, including community discovery, link prediction, and spam filtering. The task of triangle counting, though simple, has gained wide attention in recent years from the data mining community. This is due to the fact that most of the existing algorithms for counting triangles do not scale well to very large networks with millions (or even billions) of vertices. To circumvent this limitation, researchers proposed triangle counting methods that approximate the count or run on distributed clusters. In this paper, we discuss the existing methods of triangle counting, ranging from sequential to parallel, single‐machine to distributed, exact to approximate, and off‐line to streaming. We also present experimental results of performance comparison among a set of approximate triangle counting methods built under a unified implementation framework. Finally, we conclude with a discussion of future works in this direction. WIREs Data Mining Knowl Discov 2018, 8:e1226. doi: 10.1002/widm.1226This article is categorized under:

Algorithmic Development > Structure Discovery
Mechanisms of carbon nanotube‐induced pulmonary fibrosis: a physicochemical characteristic perspective
Authors: Duke Katherine S. , Bonner James C. 
Published: October 2017

Carbon nanotubes (CNTs) are engineered nanomaterials (ENMs) with numerous beneficial applications. However, they could pose a risk to human health from occupational or consumer exposures. Rodent models demonstrate that exposure to CNTs via inhalation, instillation, or aspiration results in pulmonary fibrosis. The severity of the fibrogenic response is determined by various physicochemical properties of the nanomaterial such as residual metal catalyst content, rigidity, length, aggregation status, or surface charge. CNTs are also increasingly functionalized post‐synthesis with organic or inorganic agents to modify or enhance surface properties. The mechanisms of CNT‐induced fibrosis involve oxidative stress, innate immune responses of macrophages, cytokine and growth factor production, epithelial cell injury and death, expansion of the pulmonary myofibroblast population, and consequent extracellular matrix accumulation. A comprehensive understanding of how physicochemical properties affect the fibrogenic potential of various types of CNTs should be considered in combination with genetic variability and gain or loss of function of specific genes encoding secreted cytokines, enzymes, or intracellular cell signaling molecules. Here, we cover the current state of the literature on mechanisms of CNT‐exposed pulmonary fibrosis in rodent models with a focus on physicochemical characteristics as principal drivers of the mechanisms leading to pulmonary fibrosis.This article is categorized under:

Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease
Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials
Efficacy and Safety of Pleurodesis Using Platelet‐Rich Plasma and Fibrin Glue in Management of Postoperative Chylothorax After Esophagectomy
Authors: Alamdari Daryoush Hamidi , Asadi Mehdi , Rahim Ahmad Nejad , Maddah Ghodratollah , Azizi Shahariar , Shahidsales Soudabeh , Mehrabibahar Mostafa 
Published: October 2017

AbstractIntroductionChylothorax is by definition a collection of lymphatic fluids in the pleural cavity because of leakage from main thoracic duct or its tributaries. It is an uncommon but serious postoperative complication in esophageal cancer patients. There is no standard therapeutic algorithm for chylothorax because no prospective or randomized trials have yet been performed to evaluate the available treatment options. The aim of this study was to evaluate the efficacy of pleurodesis with a combination of platelet‐rich plasma (PRP) and fibrin glue to the treatment of chylothorax after trans‐hiatal esophagectomy.Materials and methodsWe randomly allocated 52 consecutive esophageal cancer patients with postoperative chylothorax who did not respond to conservative management to either PRP fibrin glue pleurodesis or surgical thoracic duct ligation. 26 patients in each group were treated with PRP fibrin glue pleurodesis or surgical thoracic duct ligation in order to control chylothorax. Perioperative data, including success rate and complications of both interventions, were analyzed.ResultsTwo groups were similar in terms of patients’ demographics and tumor characteristics. All 26 patients in pleurodesis group (100%) and 20 patients in surgery group (76.9%) were successfully treated (p = 0.009). Seven patients (26.92%) in pleurodesis group required a second application of PRP fibrin glue after a week. The mean length of hospital stay was 53.50 ± 16.662 days in surgery group and 36.04 ± 8.224 days in pleurodesis group (p < 0.001). Although mortality rate in surgery group was higher than pleurodesis group, it was not statistically significant (p = 0.1621). There was no significant difference in complications between two groups either. No serious side effect occurred with PRP fibrin glue application.ConclusionIn conclusion, pleurodesis using PRP and fibrin glue for chylothorax after trans‐hiatal esophagectomy was associated with significantly increased success rate, decreased ICU stay, decreased overall hospital stay, and decreased mortality compared with surgical thoracic duct ligation. No patient after PRFG required additional intervention including surgery. Thus, given the improved outcomes with PRFG pleurodesis, this technique may be considered in all patients with postoperative chylothorax after or during conservative management and before proceeding to more invasive interventions.
Extracellular Vesicles: Biomarkers, Therapeutics, and Vehicles in the Visual System
Authors: van der Merwe Yolandi , Steketee Michael B. 
Published: October 2017

Abstract

Purpose
We discuss recent advances in extracellular vesicle (EV) technology as biomarkers, therapeutics, and drug delivery vehicles in the visual system with an emphasis on the retina.

Recent Findings
Retinal cell-type specific EVs can be detected in the blood and in the aqueous humor and EV miRNA cargoes can be used diagnostically to predict retinal disease progression. Studies have now shown EVs can deliver bioactive miRNA and AAV cargoes to the inner retinal cell layers and, in some models, improve retinal ganglion cell (RGC) survival and axon regeneration.

Summary
EV molecular profiles and cargoes are attractive biomarkers for retinal and optic nerve disease and trauma and EVs offer a safe and tunable platform for delivering therapies to ocular tissues. However, EVs are heterogeneous by nature with variable lipid membranes, cargoes, and biologic effects, warranting stringent characterization to understand how heterogeneous EV populations modulate positive tissue remodeling.
Inspiration From the Classroom: A Mixed Method Case Study of Interdisciplinary Sustainability Learning in Higher Education
Authors: Noy Sue , Patrick Rebecca , Capetola Teresa , McBurnie Janine 
Published: October 2017

AbstractWithin higher education there is widespread support for developing students’ interdisciplinary skills. Despite this, evidence for, and practice of, cross-faculty interdisciplinary sustainability learning remains in its infancy. Recent articles have shown that Australia is no exception. This article provides a case study of interdisciplinary learning and teaching within a cross-faculty Education for Sustainability (EfS) undergraduate subject involving science, arts, business, and health students at an Australian university. A description of the subject and its theoretical context provides a platform for presenting the findings of a mixed method enquiry into how pedagogy supports interdisciplinary sustainability learning. The sequential explanatory research design involved a post-subject quantitative survey analysed using SPSS, augmented by qualitative student journal data (n = 67) using phenomenological analysis within NVivo. The study found that students, regardless of discipline background, valued the processes and pedagogy used to promote interdisciplinary collaboration and awareness. The experience left students feeling more skilled and confident of their ability to contribute to future interdisciplinary sustainability collaboration. This case study, replete with a subject description, theoretical context for an innovative pedagogical approach and study results, provides higher education professionals with a template for deliberative curriculum and pedagogy that promote interdisciplinary knowledge, skills and confidence that may contribute to transformative learning that supports EfS goals. The article presents a strong case for future EfS curriculum frameworks and strategic education policy to include deliberative interdisciplinary pedagogy. It also challenges higher education institutions to create flexible systems that facilitate cross-faculty interdisciplinary learning that is necessary for preparing students for the future.
Educating good decisions
Authors: PETERS ELLEN 
Published: October 2017

AbstractCan we educate decision-makers to make better decisions? In the present paper, I argue that we can in at least two broad ways: (1) teaching concrete knowledge about a specific decision or decision type; and (2) teaching more abstract decision-making competencies that are thought to lead to better decisions. Teaching knowledge can be done using decision aids and similar techniques that provide important information about a specific choice (e.g. a medical treatment option). In these cases, information presented using evidence-based techniques to improve comprehension and use of information will have greater effects on judgements and choices. Teaching more abstract decision competencies, on the other hand, involves formal schooling (with the bulk of formal education falling during childhood) or training in a specific competency that is important to decision processes and outcomes; I use numeracy interventions as an exemplar.
Behavioural public policy: the constitutional approach
Authors: HARGREAVES HEAP SHAUN P. 
Published: October 2017

AbstractOne interpretation of the evidence on how people actually behave is that they sometimes/often do not have well-defined preferences. Although this makes public policy based on preference satisfaction problematic, it does not count against policy intervention per se. This paper argues instead that it shifts the object of intervention to the rules that constrain and enable action (away from the outcomes arising from those actions). This is the constitutional approach to public policy. Drawing on the constitutional tradition in political theory that values individuals for their individuality, the paper develops an argument for a basic income and a constitutionally constrained tax system. The key feature of this system is its simplicity. This should appeal on behavioural grounds to anyone who is concerned with using the tax and benefit system in public policy and not just those who are persuaded by the argument here for the constitutional approach to public policy.
Behavioural economics, consumer behaviour and consumer policy: state of the art
Authors: REISCH LUCIA A. , ZHAO MIN 
Published: October 2017

AbstractCounter to the traditional assumption of neoclassical economics that individuals are rationalHomo oeconomicithat always seek to maximize their utility and follow their ‘true’ preferences, research in behavioural economics has demonstrated that people's judgements and decisions are often subject to systematic biases and heuristics, and are strongly dependent on the context of the decision. In this article, we briefly review the transition of research from neoclassical economics to behavioural economics, and discuss how the latter has influenced research in consumer behaviour and consumer policy. In particular, we discuss the impacts of key principles such as status quo bias, the endowment effect, mental accounting and the sunk-cost effect, other heuristics and biases related to availability, salience, the anchoring effect and simplicity rules, as well as the effects of other supposedly irrelevant factors such as music, temperature and physical markers on consumers’ decisions. These principles not only add significantly to research on consumer behaviour – they also offer readily available practical implications for consumer policy to nudge behaviour in beneficial directions in consumption domains including financial decision making, product choice, healthy eating and sustainable consumption.
Statistics of turbulence in the energy-containing range of Taylor–Couette compared to canonical wall-bounded flows
Authors: Krug Dominik , Yang Xiang I. A. , de Silva Charitha M. , Ostilla-Mónico Rodolfo , Verzicco Roberto , Marusic Ivan , Lohse Detlef 
Published: October 2017

Considering structure functions of the streamwise velocity component in a framework akin to the extended self-similarity hypothesis (ESS), de Silva et al. (J. Fluid Mech., vol. 823, 2017, pp. 498–510) observed that remarkably the large-scale (energy-containing range) statistics in canonical wall-bounded flows exhibit universal behaviour. In the present study, we extend this universality, which was seen to encompass also flows at moderate Reynolds number, to Taylor–Couette flow. In doing so, we find that also the transversal structure function of the spanwise velocity component exhibits the same universal behaviour across all flow types considered. We further demonstrate that these observations are consistent with predictions developed based on an attached-eddy hypothesis. These considerations also yield a possible explanation for the efficacy of the ESS framework by showing that it relaxes the self-similarity assumption for the attached-eddy contributions. By taking the effect of streamwise alignment into account, the attached-eddy model predicts different behaviour for structure functions in the streamwise and in the spanwise directions and that this effect cancels in the ESS framework – both consistent with the data. Moreover, it is demonstrated here that also the additive constants, which were previously believed to be flow dependent, are indeed universal at least in turbulent boundary layers and pipe flow where high Reynolds number data are currently available.
New treebank or repurposed? On the feasibility of cross-lingual parsing of Romance languages with Universal Dependencies
Authors: GARCIA MARCOS , GÓMEZ-RODRÍGUEZ CARLOS , ALONSO MIGUEL A. 
Published: October 2017

AbstractThis paper addresses the feasibility of cross-lingual parsing with Universal Dependencies (UD) between Romance languages, analyzing its performance when compared to the use of manually annotated resources of the target languages. Several experiments take into account factors such as the lexical distance between the source and target varieties, the impact of delexicalization, the combination of different source treebanks or the adaptation of resources to the target language, among others. The results of these evaluations show that the direct application of a parser from one Romance language to another reaches similar labeled attachment score (LAS) values to those obtained with a manual annotation of about 3,000 tokens in the target language, and unlabeled attachment score (UAS) results equivalent to the use of around 7,000 tokens, depending on the case. These numbers can noticeably increase by performing a focused selection of the source treebanks. Furthermore, the removal of the words in the training corpus (delexicalization) is not useful in most cases of cross-lingual parsing of Romance languages. The lessons learned with the performed experiments were used to build a new UD treebank for Galician, with 1,000 sentences manually corrected after an automatic cross-lingual annotation. Several evaluations in this new resource show that a cross-lingual parser built with the best combination and adaptation of the source treebanks performs better (77 percent LAS and 82 percent UAS) than using more than 16,000 (for LAS results) and more than 20,000 (UAS) manually labeled tokens of Galician.
Trade Measures to Prevent Illegal Fishing and the WTO: An Analysis of the Settled Faroe Islands Dispute
Authors: AULD KATHLEEN 
Published: October 2017

AbstractThere has been increasing litigation in the WTO on environmental issues in recent years, much of it about fishing. Two cases,Chile–SwordfishandFaroes–Herring, brought to light the potential for conflict between trade and fisheries law through the imposition of port state measures by WTO members to prevent illegal, unreported, and unregulated (IUU) fishing, although both cases were settled before reaching Panel stage. Port state measures aim to combat IUU fishing by allowing countries to close their ports to IUU fish. This includes using trade measures and trade-related measures, such as import bans and transshipment bans, which may violate WTO law. The potential for conflict is even more acute now that the Port State Measures Agreement (PSMA) has come into force. This paper takes as its studyFaroes–Herring, where the Faroes challenged certain EU regulations aimed at preventing IUU fishing through the use of port state measures. It examines whether these regulations comply with WTO law, and makes recommendations as to how a Panel or Appellate Body can resolve this type of dispute. Specifically, it focuses on ways in which international fisheries law can be incorporated in this process to avoid a conflict between international trade and fisheries law.
Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea
Authors: Kalenitchenko Dimitri , Le Bris Nadine , Dadaglio Laetitia , Peru Erwan , Besserer Arnaud , Galand Pierre E 
Published: October 2017

Abstract
Wood-fall ecosystems host chemosynthetic bacteria that use hydrogen sulfide as an electron donor. The production of hydrogen sulfide from decaying wood in the deep-sea has long been suspected to rely on the activity of wood-boring bivalves, Xylophaga spp. However, recent mesocosm experiments have shown hydrogen sulfide production in the absence of wood borers. Here, we combined in situ chemical measurements, amplicon sequencing and metagenomics to test whether the presence of Xylophaga spp.-affected hydrogen sulfide production and wood microbial community assemblages. During a short-term experiment conducted in a deep-sea canyon, we found that wood-fall microbial communities could produce hydrogen sulfide in the absence of Xylophaga spp. The presence of wood borers had a strong impact on the microbial community composition on the wood surface but not in the wood centre, where communities were observed to be homogeneous among different samples. When wood borers were excluded, the wood centre community did not have the genetic potential to degrade cellulose or hemicellulose but could use shorter carbohydrates such as sucrose. We conclude that wood centre communities produce fermentation products that can be used by the sulfate-reducing bacteria detected near the wood surface. We thus demonstrate that microorganisms alone could establish the chemical basis essential for the recruitment of chemolithotrophic organisms in deep-sea wood falls.
Designing solid-liquid interphases for sodium batteries
Authors: Choudhury Snehashis , Wei Shuya , Ozhabes Yalcin , Gunceler Deniz , Zachman Michael J. , Tu Zhengyuan , Shin Jung Hwan , Nath Pooja , Agrawal Akanksha , Kourkoutis Lena F. , Arias Tomas A. , Archer Lynden A. 
Published: October 2017

AbstractSecondary batteries based on earth-abundant sodium metal anodes are desirable for both stationary and portable electrical energy storage. Room-temperature sodium metal batteries are impractical today because morphological instability during recharge drives rough, dendritic electrodeposition. Chemical instability of liquid electrolytes also leads to premature cell failure as a result of parasitic reactions with the anode. Here we use joint density-functional theoretical analysis to show that the surface diffusion barrier for sodium ion transport is a sensitive function of the chemistry of solid–electrolyte interphase. In particular, we find that a sodium bromide interphase presents an exceptionally low energy barrier to ion transport, comparable to that of metallic magnesium. We evaluate this prediction by means of electrochemical measurements and direct visualization studies. These experiments reveal an approximately three-fold reduction in activation energy for ion transport at a sodium bromide interphase. Direct visualization of sodium electrodeposition confirms large improvements in stability of sodium deposition at sodium bromide-rich interphases.