bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene co-expression networks in whole blood implicate multiple interrelated molecular pathways in obese asthma
Authors: Croteau-Chonka Damien C. , Chen Zhanghua , Barnes Kathleen C. , Barraza-Villarreal Albino , Celedón Juan C. , James Gauderman W. , Gilliland Frank D. , Krishnan Jerry A. , Liu Andrew H. , London Stephanie J. , Martinez Fernando D. , Millstein Joshua , Naureckas Edward T. , Nicolae Dan L. , White Steven R. , Ober Carole , Weiss Scott T. , Raby Benjamin A. 
Published: August 2017

AbstractBackgroundAsthmatic children who develop obesity have poorer outcomes compared to those that do not, including poorer control, more severe symptoms, and greater resistance to standard treatment. Gene expression networks are powerful statistical tools for characterizing the underpinnings of human disease that leverage the putative co-regulatory relationships of genes to infer biological pathways altered in disease states.ObjectiveThe aim of this study was to characterize the biology of childhood asthma complicated by adult obesity.MethodsWe performed weighted gene co-expression network analysis (WGCNA) of gene expression data in whole blood from 514 adult subjects from the Childhood Asthma Management Program (CAMP). We then performed module preservation and association replication analyses in 418 subjects from two independent asthma cohorts (one pediatric and one adult).ResultsWe identified a multivariate model in which four gene co-expression network modules were associated with incident obesity in CAMP (eachP< 0.05). The module memberships were enriched for genes in pathways related to platelets, integrins, extracellular matrix, smooth muscle, NF-κB signaling, and Hedgehog signaling. The network structures of each of the four obese asthma modules were significantly preserved in both replication cohorts (permutationP= 9.999E-05). The corresponding module gene sets were significantly enriched for differential expression in obese subjects in both replication cohorts (eachP< 0.05).ConclusionsOur gene co-expression network profiles thus implicate multiple interrelated pathways in the biology of an important endotype of obese asthma.Key MessagesWe hypothesized that individuals with asthma complicated by obesity had distinct blood gene expression signatures.Gene co-expression network analysis implicated several inflammatory biological pathways in one form of obese asthma.Capsule SummaryThis work addresses a knowledge gap about the molecular relationship between asthma and obesity, suggesting that an endotype of obese asthma, known as asthma complicated by obesity, is underpinned by coherent biological mechanisms.AbbreviationsCAMPChildhood Asthma Management ProgramWGCNAweighted gene co-expression network analysisAsthma BRIDGEAsthma BioRepository for Integrative Genomic ExplorationGACRSGenetics of Asthma in Costa Rica StudyCHSSouthern California Children’s Health StudyBMIbody mass indexBICBayes Information CriterionHUGOHuman Genome OrganisationPCprincipal componentGSEAgene set enrichment analysisIL-1interleukin-1Hh signalingHedgehog signaling
Deep grey matter volume loss drives disability worsening in multiple sclerosis
Authors: Eshaghi Arman , Prados Ferran , Brownlee Wallace , Altmann Daniel R. , Tur Carmen , Jorge Cardoso M. , De Angelis Floriana , van de Pavert Steven H. , Cawley Niamh , De Stefano Nicola , Laura Stromillo M. , Battaglini Marco , Ruggieri Serena , Gasperini Claudio , Filippi Massimo , Rocca Maria A. , Rovira Alex , Sastre-Garriga Jaume , Vrenken Hugo , Leurs Cyra E , Killestein Joep , Pirpamer Lukas , Enzinger Christian , Ourselin Sebastien , Gandini Wheeler-Kingshott Claudia A.M. , Chard Declan , Thompson Alan J. , Alexander Daniel C. , Barkhof Frederik , Ciccarelli Olga , Ciccarelli Olga 
Published: August 2017

AbstractObjectiveGrey matter (GM) atrophy occurs in all multiple sclerosis (MS) phenotypes. We investigated whether there is a spatiotemporal pattern of GM atrophy that is associated with faster disability accumulation in MS.MethodsWe analysed 3,604 brain high-resolution T1-weighted MRI scans from 1,417 participants: 1,214 MS patients (253 clinically-isolated syndrome[CIS], 708 relapsingremitting[RRMS], 128 secondary-progressive[SPMS], 125 primary-progressive[PPMS]), over an average follow-up of 2.41 years (standard deviation[SD]=1.97), and 203 healthy controls (HCs) [average follow-up=1.83 year, SD=1.77], attending 7 European centres. Disability was assessed with the Expanded-Disability Status Scale (EDSS). We obtained volumes of the deep GM (DGM), temporal, frontal, parietal, occipital and cerebellar GM, brainstem and cerebral white matter. Hierarchical mixed-models assessed annual percentage rate of regional tissue loss and identified regional volumes associated with time-to-EDSS progression.ResultsSPMS showed the lowest baseline volumes of cortical GM and DGM. Of all baseline regional volumes, only that of the DGM predicted time-to-EDSS progression (hazard ratio=0.73, 95% CIs 0.65, 0.82;p<0.001): for every standard deviation decrease in baseline DGM volume, the risk of presenting a shorter time to EDSS worsening during follow-up increased by 27%. Of all longitudinal measures, DGM showed the fastest annual rate of atrophy, which was faster in SPMS (-1.45%), PPMS (-1.66%), and RRMS (-1.34%) than CIS (-0.88%) and HCs (-0.94%)[p<0.01]. The rate of temporal GM atrophy in SPMS (-1.21%) was significantly faster than RRMS (-0.76%), CIS (-0.75%), and HCs (-0.51%). Similarly, the rate of parietal GM atrophy in SPMS (-1.24-%) was faster than CIS (-0.63%) and HCs (-0.23%) (all p values <0.05). Only the atrophy rate in DGM in patients was significantly associated with disability accumulation (beta=0.04,p<0.001).InterpretationThis large multi-centre and longitudinal study shows that DGM volume loss drives disability accumulation in MS, and that temporal cortical GM shows accelerated atrophy in SPMS than RRMS. The difference in regional GM atrophy development between phenotypes needs to be taken into account when evaluating treatment effect of therapeutic interventions.
Mouse hepatitis virus nsp14 exoribonuclease activity is required for resistance to innate immunity
Authors: Case James Brett , Li Yize , Elliott Ruth , Lu Xiaotao , Graepel Kevin W. , Sexton Nicole R. , Smith Everett Clinton , Weiss Susan R. , Denison Mark R. 
Published: August 2017

ABSTRACTCoronaviruses (CoV) are positive-sense RNA viruses that infect numerous mammalian and avian species and are capable of causing severe and lethal disease in humans. CoVs encode several innate immune antagonists that interact with the host innate immune response to facilitate efficient viral replication. CoV non-structural protein 14 (nsp14) encodes 3'-to-5' exoribonuclease activity (ExoN), which performs a proofreading function and is required for high-fidelity replication. Outside of the orderNidovirales, arenaviruses are the only RNA viruses that encode an ExoN, which functions to degrade dsRNA replication intermediates. In this study, we tested the hypothesis that CoV ExoN may also function to antagonize the innate immune response. We demonstrate that viruses lacking ExoN activity [ExoN(-)] are sensitive to cellular pretreatment with interferon beta (IFN-β) in a dose-dependent manner. In addition, ExoN(-) virus replication was attenuated in wild-type bone marrow-derived macrophages (BMMs) and partially restored in interferon alpha/beta receptor deficient (IFNAR-/-) BMMs. ExoN(-) virus replication did not result in IFN-β gene expression, and in the presence of an IFN-β-mediated antiviral state, ExoN(-) viral RNA levels were not substantially reduced relative to untreated. However, ExoN(-) virus generated from IFN-β pretreated cells had reduced specific infectivity and decreased relative fitness, suggesting that ExoN(-) virus generated during an antiviral state is less viable to establish a subsequent infection. Overall, our data suggest MHV ExoN activity is required for resistance to the innate immune response and antiviral mechanisms affecting the viral RNA sequence and/or an RNA modification act on viruses lacking ExoN activity.
Ecophylogenetics Reveals the Evolutionary Associations between Mammals and their Gut Microbiota
Authors: Gaulke Christopher A. , Arnold Holly K. , Kembel Steven W. , O’Dwyer James P. , Sharpton Thomas J. 
Published: August 2017

AbstractA tantalizing hypothesis posits that mammals coevolved with their gut microbiota. Unfortunately, the limited resolution of microbial taxonomy hinders the exploration of this hypothesis and specifically challenges the discovery of gut microbes that are linked to mammalian evolution. To address this, we developed a novel approach that groups microbes into new, more meaningful taxonomic units based on their common ancestry and ecological redundancy. Treating mammalian lineages as different ecosystems, we quantified the distribution of these microbial taxa across mammals. Our analysis discovered monophyletic clades of gut bacteria that are unexpectedly prevalent, or conserved, across all mammals, as well as conserved clades that are exclusive to particular mammalian lineages. These clades often manifest phylogenetic patterns indicating that they are subject to selection. Lineage - specific changes in clade conservation, including a human-accelerated loss of conserved clades, suggest that mammalian evolution associates with a change in the selective regimes that act on gut microbiota. Collectively, these results point to the existence of microbes that possess traits that facilitate their dispersion or survival in the mammalian gut, possibly because they are subject to host selection. Ultimately, our analysis clarifies the relationship between the diversification of the gut microbiome and mammalian evolutionary history.
Towards physical principles of biological evolution
Authors: Katsnelson Mikhail I. , Wolf Yuri I. , Koonin Eugene V. 
Published: August 2017

AbstractBiological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in “emergent phenomena”. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice for adequate modeling of the biological level of complexity, and new developments within physics itself are likely to be required.
Heat dissipation analysis of continuously-moving plate undergoing thermal processing using Laplace Adomian decomposition method
Authors: Chen Cha’o Kuang , Chang Yu-Shen , Liu Chin-Chia , Chen Bang-Shiuh 
Published: August 2017

Purpose
This paper aims to use the Laplace Adomian decomposition method (LADM) to investigate the effects of thermal convection, thermal conduction, surface emissivity and thermal radiation on the heat dissipated by a continuously moving plate undergoing thermal processing.

Design/methodology/approach
In performing the analysis, it is assumed that the thermal conductivity and surface emissivity of the plate are both temperature-dependent. The accuracy of the LADM solutions is confirmed by comparing the results obtained for the temperature distribution within the plate with those reported in the literature based on the differential transformation method.

Findings
It is shown that the heat dissipated from the plate reduces as the Peclet number increases. By contrast, the dissipated heat increases as any one of the non-dimensionalized parameters of the system, i.e. Nc, Nr and B, increases. In addition, the temperature drop along the length of the plate reduces as parameter A increases owing to a more rapid heat transfer.

Originality/value
The results provide a useful source of reference for the choice of suitable materials and cooling fluids in a variety of practical applications.
An improved artificial bee colony algorithm for robust design of power system stabilizers
Authors: Guesmi Tawfik , Alshammari Badr M. 
Published: August 2017

Purpose
Low-frequency oscillations of 0.1 to 3 Hz are prejudicial to the power system stability. Within this context, this study aims to present an improved artificial bee colony (ABC)-based algorithm for optimal setting of multimachine power system stabilizers (PSSs) under several loading conditions simultaneously.

Design/methodology/approach
The proposed approach symbolized by GCABC incorporates the grenade explosion technique and the Cauchy operator in the employed bee and onlooker bee phases to avoid random search. The parameters of the grenade explosion method and Cauchy operator based ABC(GCABC)-based PSSs (GCABC-PSSs) are tuned to place all undamped and lightly damped electromechanical modes in a prespecified zone in the s-plan.

Findings
Simulation results based on eigenvalue analysis and nonlinear time-domain simulation show the potential and the dominance of the proposed controllers GCABC-PSSs in the improvement of the system stability under several disturbances and large set of operating points compared with the classical ABC method and genetic algorithm-based PSSs.

Originality/value
The novelty of the study is to efficiently implement a new optimization method called GCABC for an optimum design of PSSs. The design problem is formulated as a multi-objective optimization problem. In addition, all PSS parameters have been included in the space research.
Implementing a collaborative mental health care model: the MHPN
Authors: Gibbs Chris , Murphy Barbara , Ratnaike Deepika , Hoppe Kate , Lovelock Harry 
Published: August 2017

Purpose
The purpose of this paper is to describe the development and experience of the Mental Health Professionals’ Network (MHPN) in building and supporting a national interdisciplinary professional development platform in community mental health to enhance practitioner response to the needs of consumers.

Design/methodology/approach
The key components of the MHPN model are described highlighting effective ways of engaging practitioners and supporting interdisciplinary practice. The MHPN has two key programs – Face-to-Face Interdisciplinary Practitioner Networks and an Online Professional Development Program.

Findings
The MHPN model has had significant uptake in communities across Australia and continues to grow. Practitioners report positive outcomes in engaging with other practitioners, improving their professional knowledge and having gained increased confidence in the provision of mental health care to patients.

Practical implications
The progress and learnings to date offer some useful insights that can be applied to other settings to support integrated care for patients with mental health problems through enhancing collaborative care among practitioners at the primary care level.

Originality/value
MHPN is a unique, national, successful platform delivering opportunities for interdisciplinary professional development in the primary mental health sector. The model is cost effective, practitioner driven, and transferable to other settings.
The role of job dedication in organizational citizenship behavior performance
Authors: Muldoon Jeffrey , Keough Shawn M. , Liguori Eric W. 
Published: August 2017

PurposeThis paper aims to attempt to clarify differences between organizational citizenship behaviors (OCBs) and attitudes as well as explore job dedication’s role regarding OCBs. Using social exchange theory, job dedication is hypothesized to mediate the relationship between leader-member exchange (LMX) and OCBs.Design/methodology/approachHierarchical regression analysis was performed on data obtained from 190 supervisor/subordinate dyads from a number of firms to test the study hypotheses.FindingsResults indicate that job dedication fully mediates the relationship between LMX and OCBs directed toward individuals and the organization, thus playing a role in the production of OCBs.Research limitations/implicationsDue to non-employment of an experimental design, causality cannot be determined. If managers use signals to determine performance, then scholars need to conduct further research to determine what the cues are.Practical implicationsManagers need to spend time in determining and care whether what they are actually measuring is accurate in terms of spontaneous behaviors performance.Originality/valueFirst, this study has developed an explanation as to how managers can use job dedication as a means to track the behaviors of multiple subordinates based on social exchange theory. Second, this study provides empirical evidence of the mediating role job dedication plays on mediating the LMX/OCBs relationship.
Design workshops in the age of climate change
Authors: De Waegemaeker Jeroen , Kerselaers Eva , Van Acker Maarten , Rogge Elke 
Published: August 2017

PurposeAs policy makers address the issue of climate adaptation, they are confronted with climate-specific barriers: a long-term horizon and a high degree of uncertainty. These barriers also hamper the development of spatial planning for climate adaptation. So how can spatial planners encompass these barriers and steer the general debate on climate adaptation? The paper aims to discuss these issues.Design/methodology/approachThis research analyzes the strengths and weaknesses of an international design workshop on climate adaptation, and drought issues in particular. Design workshops are originally an educational setting but they are increasingly employed as a tool to explore alternative futures on a complex, real-life design problem. The case study illustrates how climate-specific barriers emerged throughout the design workshop and clarifies how they were encompassed by the participating design students.FindingsThe research clarifies the added value of a design workshop on climate adaptation. The paper highlights specific promising characteristics of the design workshop: the visualization of future adaptation challenges and the current water system, the focus on a regional project instead of sectoral adjustments and the integration of the adaptation challenge with other socio-economic goals. In the case study Flanders, however, the necessary participation of climate experts and policy makers of other domains proved challenging.Originality/valueThe paper argues that a design workshop has the potential to enrich the debate and policy work on climate adaptation. In many countries with low-planning tradition, however, additional tools are needed to help set the “adaptation agenda.”
A decision support tool to mitigate decision-making problems faced by a building design team
Authors: Singhaputtangkul Natee 
Published: August 2017

Purpose
There are a number of decision-making problems encountered by a building design team. This issue is apparent in assessment of building envelope materials and designs in the early design stage. The purpose of this paper is to develope a decision support tool based on a quality function deployment (QFD) approach integrated with a knowledge management system (KMS) and fuzzy theory to facilitate a building design team to simultaneously mitigate the decision-making problems when assessing the building envelope materials and designs for the first instance.

Design/methodology/approach
This study engaged a design team comprising three decision makers (DMs) to test the developed decision support tool through a case study of a representative building project. The study employed deductive qualitative data analysis with use of a framework analysis approach to analyze perspectives of the DMs after completing the case study through a semi-structured interview.

Findings
A mapping diagram derived qualitatively from the framework analysis suggested that the tool can help mitigate the identified decision-making problems as a whole.

Originality/value
Practical contributions of using the decision support tool include achievement of a more efficient design and construction management, and higher productivity of a project. In terms of academic contributions, this study expands capabilities of a conventional decision support system, KMS, and QFD tool to handle decision-making problems.
Macrobioerosion and Microbioerosion in Marine Molluscan Shells from Holocene and Modern Beaches (39°–40°S, South of Buenos Aires Province, Argentina)
Authors: CHARÓ Melisa P. , CAVALLOTTO Jose L. , ACEÑOLAZA Guillermo 
Published: August 2017

AbstractThe marine sediments of the area of Verde Peninsula – Jabali Island (39°28′S/62°19′W–40°28′S/62°11′W) Holocene in age (3–2 ky), and modern beaches contain a significant amount of bioeroded mollusc shells. Fifteen sites were analyzed, in which 20.11% of the mollusc shells (2168 valves) presented bioerosion traces, in 54 species (30 bivalves and 24 gastropods). Fourteen ichnogenera were reported: Entobia, Maeandropolydora, Iramena, Caulostrepsis, Pennatichnus, Pinaceocladichnus, Trypanites, and Gastrochaenolites (Domichnia), Gnathichnus and Radulichnus (Pascichnia), Finichnus and Centrichnus (Fixichnia), Oichnus (Praedicnia) (macrobioerosion), y Semidendrina (microbioerosion), the latter is first reported in mollusc shells in Argentina. Eleven ichnospecies were identified Finichnus peristroma, Maeandropolydora sulcans, Gnathichnus pentax, Pinaceocladichnus onubensis, Caulostrepsis taeniola, Centrichnus eccentricus, Radulichnus inopinatus, Oichnus simplex, Oichnus paraboloides, Oichnus gradatus, and Gastrochaenolites torpedo (lithic remains). The dominant ichnogenera in the Holocene deposits are Iramena, Entobia and Oichnus. The same ichnogenera are constant with different abundance in the modern beaches, and increasing representation of Pinaceocladichnus and Pennatichnus. The dominant ichnofacies in the Holocene deposits is Trypanites, revealing a benthonic marine community composed of cheilostome bryzoans, clionaid sponges, predator gastropods, regular echinoids, polychaete annelids, bivalves, thallophytas and fungi. Generally, the area was described as a sublittoral, low‐energy, stable environment with high rate of oxygenation, and sandy bottoms, with rocky bottoms at Villalonga locality.