bluuebunny/crossref_metadata_2025_split huggingface dataset:
Existence and amplitude bounds for irrotational water waves in finite depth
Authors: Kogelbauer Florian 
Published: December 2017

We prove the existence of solutions to the irrotational water-wave problem in finite depth and derive an explicit upper bound on the amplitude of the nonlinear solutions in terms of the wavenumber, the total hydraulic head, the wave speed and the relative mass flux. Our approach relies upon a reformulation of the water-wave problem as a one-dimensional pseudo-differential equation and the Newton–Kantorovich iteration for Banach spaces.
This article is part of the theme issue ‘Nonlinear water waves’.
Cerebral White Matter Sex Dimorphism in Alcoholism: A Diffusion Tensor Imaging Study
Authors: Sawyer Kayle S. , Maleki Nasim , Papadimitriou George , Makris Nikos , Oscar-Berman Marlene , Harris Gordon J. 
Published: December 2017

AbstractBackgroundExcessive alcohol consumption is associated with widespread brain damage, including abnormalities in frontal and limbic brain regions. In a prior study of neuronal circuitry connecting the frontal lobes and limbic system structures in abstinent alcoholic men, we demonstrated decreases in white matter fractional anisotropy (FA) on diffusion tensor magnetic resonance imaging (dMRI). In the present study, we examined sex differences in alcoholism-related abnormalities of white matter connectivity.MethodsdMRI scans were acquired from 49 abstinent alcoholic individuals (26 women) and 41 nonalcoholic controls (22 women). Tract-based spatial statistical tools were used to estimate regional FA of white matter tracts and to determine sex differences and their relation to measures of alcoholism history.ResultsSex-related differences in white matter connectivity were observed in association with alcoholism: Compared to nonalcoholic men, alcoholic men had diminished FA in portions of the corpus callosum, the superior longitudinal fasciculi II and III, and the arcuate fasciculus and extreme capsule. In contrast, alcoholic women had higher FA in these regions. Sex differences also were observed for correlations between corpus callosum FA and length of sobriety.ConclusionsSexual dimorphism in white matter microstructure in abstinent alcoholics may implicate underlying differences in the neurobehavioral liabilities for developing alcohol abuse disorders, or for sequelae following abuse.
Leveraging heterogeneity for neural computation with fading memory in layer 2/3 cortical microcircuits
Authors: Duarte Renato , Morrison Abigail 
Published: December 2017

AbstractComplexity and heterogeneity are intrinsic to neurobiological systems, manifest in every process, at every scale, and are inextricably linked to the systems’ emergent collective behaviours and function. However, the majority of studies addressing the dynamics and computational properties of biologically inspired cortical microcircuits tend to assume (often for the sake of analytical tractability) a great degree of homogeneity in both neuronal and synaptic/connectivity parameters. While simplification and reductionism are necessary to understand the brain’s functional principles, disregarding the existence of the multiple heterogeneities in the cortical composition, which may be at the core of its computational proficiency, will inevitably fail to account for important phenomena and limit the scope and generalizability of cortical models. We address these issues by studying the individual and composite functional roles of heterogeneities in neuronal, synaptic and structural properties in a biophysically plausible layer 2/3 microcircuit model, built and constrained by multiple sources of empirical data. This approach was made possible by the emergence of large-scale, well curated databases, as well as the substantial improvements in experimental methodologies achieved over the last few years. Our results show that variability in single neuron parameters is the dominant source of functional specialization, leading to highly proficient microcircuits with much higher computational power than their homogeneous counterparts. We further show that fully heterogeneous circuits, which are closest to the biophysical reality, owe their response properties to the differential contribution of different sources of heterogeneity.
Global optimization approach for circular and chloroplast genome assembly
Authors: François Sebastien , Andonov Rumen , Lavenier Dominique , Djidjev Hristo 
Published: December 2017

AbstractWe describe a global optimization approach for genome assembly where the steps of scaffolding, gap-filling, and scaffold extension are simultaneously solved in the framework of a common objective function. The approach is based on integer programming model for solving genome scaffolding as a problem of finding a long simple path in a specific graph that satisfies additional constraints encoding the insert-size information. The optimal solution of this problem allows one to obtain new kind of contigs that we call distance-based contig. We test the algorithm on a benchmark of chloroplasts and compare the quality of the results with recent scaffolders.
Deep Brain Stimulation for Parkinson’s disease changes perception in the Rubber Hand Illusion
Authors: Ding Catherine , Palmer Colin J , Hohwy Jakob , Youssef George J , Paton Bryan , Tsuchiya Naotsugu , Stout Julie C , Thyagarajan Dominic 
Published: December 2017

ABSTRACTParkinson’s disease (PD) alters cortico-basal ganglia-thalamic circuitry and susceptibility to an illusion of bodily awareness, the Rubber Hand Illusion (RHI). Bodily awareness is thought to result from multisensory integration in a predominantly cortical network; the role of subcortical connections is unknown. We studied the effect of modulating cortico-subcortical circuitry on multisensory integration for bodily awareness in PD patients treated with subthalamic nucleus (STN) deep brain stimulation (DBS) using the RHI experiment. Typically, synchronous visuo-tactile cues induce a false perception of touch on the rubber hand as if it were the subject’s hand, whereas asynchronous visuo-tactile cues do not. However, we found that in the asynchronous condition, patients in the off-stimulation state did not reject the RHI as strongly as healthy controls; switching on STN-DBS partially ‘normalised’ their responses. Patients in the off-stimulation state also misjudged the position of their hand, indicating it to be closer to the rubber hand than controls. However, STN-DBS did not affect proprioceptive judgements or subsequent arm movements altered by the perceptual effects of the illusion. Our findings support the idea that the STN and subcortical connections have a key role in multisensory integration for bodily awareness. Decisionmaking in multisensory bodily illusions is discussed.
Tools for engineering coordinated system behaviour in synthetic microbial consortia
Authors: Kylilis Nicolas , Stan Guy-Bart , Polizzi Karen M 
Published: December 2017

AbstractAdvancing synthetic biology to the multicellular level requires the development of multiple orthogonal cell-to-cell communication channels to propagate information with minimal signal interference. The development of quorum sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on reducing signal leakage between systems of cognate AHL/transcription factor pairs. However, the use of non-cognate signals as a design feature has received limited attention so far. Here, we demonstrate the largest library of AHL-receiver devices constructed to date with all cognate and non-cognate chemical signal interactions quantified and we develop a software tool that allows automated selection of orthogonal chemical channels. We use this approach to identify up to four orthogonal channels in silico and experimentally demonstrate the simultaneous use of three channels in co-culture. The development of multiple non-interfering cell-to-cell communication channels will facilitate the design of synthetic microbial consortia for novel applications including distributed bio-computation, increased bioprocess efficiency, cell specialisation, and spatial organisation.
Systemic Inflammation Mediates the Relationship between Obesity and Health Related Quality of Life
Authors: Wilkins Jeffrey , Ghosh Palash , Vivar Juan , Chakraborty Bibhas , Ghosh Sujoy 
Published: December 2017

ABSTRACTBackgroundAt the population level, obesity has been reported to be positively associated with low-level chronic inflammation, and negatively associated with several indices of health-related quality of life (HRQOL). It is however not clear if obesity-associated inflammation is partly responsible for the observed negative associations between obesity and HRQOL. The present study investigates this question by testing the hypothesis that systemic inflammation is a mediator of the observed association between obesity and a specific HRQOL index called “healthy days”, as measured via a subset of the CDC HRQOL-4 questionnaire.MethodsDemographic, body mass index (BMI), C-reactive protein (CRP), inflammatory disease status, medication use, smoking, and HRQOL data were obtained from NHANES (2005-2008) and analyzed using sampling-weighted generalized linear models. Both main effects and interaction effects were analyzed to evaluate possible mediator-outcome confounding. Model robustness was tested via sensitivity analysis. Prior to model development, data was subjected to multiple imputation in order to mitigate information loss from survey non-response. Averaged results from the imputed datasets were reported in the form of odds ratios (OR) and confidence intervals (CI).ResultsObesity (BMI >30kg/m2) was positively associated with poor physical healthy days (OR: 1.59, 95% CI: 1.15-2.21) in unadjusted models. ‘Elevated’ and ‘clinically raised’ levels of the inflammation marker CRP were also positively associated with poor physical healthy days (OR= 1.61, 95% CI: 1.23-2.12, and OR= 2.45, 95% CI: 1.84-3.26, respectively); additionally ‘clinically raised’ CRP was positively associated with mental unhealthy days (OR= 1.66, 95% CI: 1.26-2.19). The association between obesity and physical HRQOL was rendered non-significant in models including CRP. Association between ‘elevated’ and ‘clinically raised’ CRP and physical unhealthy days remained significant even after adjustment for obesity or inflammation-modulating covariates (OR= 1.36, 95% CI :1.02-1.82, and OR= 1.75, 95% CI: 1.21-2.54, respectively).ConclusionsSystemic inflammation is a significant mediator of the association between obesity and physical unhealthy days. and is also an independent determinant of physical and mental unhealthy days. Importantly, elevated inflammation below the clinical threshold is also negatively associated with physical healthy days and may warrant more attention from a population health perspective than currently appreciated.
Funmap2: an R package for QTL mapping using longitudinal phenotypes
Authors: Wang Nating , Chu Tinyi , Luo Jiangtao , Wu Rongling , Wang Zhong 
Published: December 2017

AbstractQTL mapping is a powerful tool to infer the complexity of the genetic architecture underlying phenotypic traits, and has been extended to include longitudinal traits measured at multiple temporal/spatial points. Here, we introduce the R packageFunmap2based on the functional mapping framework, which integrates biological prior knowledge into the statistical model. Specifically, the functional mapping framework is engineered to include longitudinal curves that describes the genetic effects, and the covariance matrix of the trait of interest.Funmap2may automatically choose the type of longitudinal curve and covariance matrix by information criterion.Funmap2is available for download athttps://github.com/wzhy2000/Funmap2.
Comparative analysis of kidney organoid and adult human kidney single cell and single nucleus transcriptomes
Authors: Wu Haojia , Uchimura Kohei , Donnelly Erinn , Kirita Yuhei , Morris Samantha A. , Humphreys Benjamin D. 
Published: December 2017

AbstractKidney organoids differentiated from human pluripotent stem cells hold great promise for understanding organogenesis, modeling disease and ultimately as a source of replacement tissue. Realizing the full potential of this technology will require better differentiation strategies based upon knowledge of the cellular diversity and differentiation state of all cells within these organoids. Here we analyze single cell gene expression in 45,227 cells isolated from 23 organoids differentiated using two different protocols. Both generate kidney organoids that contain a diverse range of kidney cells at differing ratios as well as non-renal cell types. We quantified the differentiation state of major organoid kidney cell types by comparing them against a 4,259 single nucleus RNA-seq dataset generated from adult human kidney, revealing immaturity of all kidney organoid cell types. We reconstructed lineage relationships during organoid differentiation through pseudotemporal ordering, and identified transcription factor networks associated with fate decisions. These results define impressive kidney organoid cell diversity, identify incomplete differentiation as a major roadblock for current directed differentiation protocols and provide a human adult kidney snRNA-seq dataset against which to benchmark future progress.
Three classes of response elements for human PRC2 and MLL1/2-trithorax complexes
Authors: Du Junqing , Kirk Brian , Zeng Jia , Ma Jianpeng , Wang Qinghua 
Published: December 2017

SummaryPolycomb group (PcG) and trithorax group (TrxG) proteins are essential for maintaining epigenetic memory in both embryonic stem cells and differentiated cells. To date, how they are localized to hundreds of specific target genes within a vertebrate genome had remained elusive. Here, by focusing on shortcis-acting DNA elements of single functions, we discovered, for the first time, to our knowledge, three classes of response elements in human genome: PcG response elements (PREs), MLL1/2-TrxG response elements (TREs) and PcG/TrxG response elements (P/TREs). We further demonstrated that, in contrast to their proposed roles in recruiting PcG proteins to PREs, YY1 and CpG islands are specifically enriched in TREs and P/TREs, but not in PREs. The three classes of response elements as unraveled in this study open new doors for a deeper understanding of PcG and TrxG mechanisms in vertebrates.
Can prospect theory explain the disposition effect? An analysis based on value function
Authors: Liu Xiaotian , Zhang Huayue , Zhao Shengmin 
Published: December 2017

Purpose
The prospect theory is potentially an essential ingredient in modeling the disposition effect. However, many scholars have tried to explain the disposition effect with the help of prospect theory and they came to opposite conclusions. The purpose of this paper is to examine the impact of value function of the prospect theory on predicting the disposition effect.

Design/methodology/approach
Lagrange multiplier optimization and dynamic programming method are used to solve the representative investor’s optimal portfolio choice problem. Furthermore, numerical simulation is used to compare the prediction ability of different types of value function.

Findings
The authors support that the value function has a crucial role in predicting the disposition effect with prospect theory, i.e. the curvature and boundedness of the value function may influence the performance of applying the prospect theory in the disposition effect. They conclude that a piecewise negative exponential value function can predict the disposition effect, while others like the piecewise power value function may not.

Originality/value
Extant literature about modeling the disposition effect with the prospect theory mostly focus on the time when gain-loss utility occurs or the selection of reference point. This paper based on the value function properties provides a new perspective in analyzing the crucial role that value function has in predicting financial market anomalies.
Investor recognition and stock returns: evidence from China
Authors: Zhu Hongquan , Jiang Lingling 
Published: December 2017

Purpose
Merton’s model of capital market equilibrium under incomplete information predicts that contemporaneous stock returns are positively related to investor recognition and that future stock returns are negatively related to investor recognition. The purpose of this paper is to empirically investigate whether Merton’s theory holds true for the Chinese stock market.

Design/methodology/approach
This paper proposes the degree of shareholder base growth (SBG) as a proxy for investor recognition and examines the relationship between investor recognition and stock returns through a univariate analysis and Fama-Macbeth cross-sectional regressions based on A-Share listed firms.

Findings
The results show that investor recognition is nonlinearly and positively related to contemporaneous stock returns and is negatively related to future stock returns in contrast to the conclusions of Merton’s theory. A long-short trading strategy that involves buying stocks with the lowest SBG rate and that sells stocks with the highest SBG rate will earn an average monthly return of 3.615 percent.

Research limitations/implications
Though Merton’s theory is not fully reflected in the Chinese stock market, investor recognition is considered an important risk factor in the Chinese stock market.

Originality/value
No works have yet investigated the validity of Merton’s “investor cognition hypothesis” in relation to the Chinese stock market. This paper strives to fill this gap.
Does a unique “T+1 trading rule” in China incur return difference between daytime and overnight periods?
Authors: Diao Xundi , Qiu Hongyang , Tong Bin 
Published: December 2017

Purpose
The purpose of this paper is to examine the difference between the daytime (open-to-close) and overnight (close-to-open) returns of CSI 300 index and its derivative futures.

Design/methodology/approach
The paper explores the difference between the daytime and overnight time returns by using nonparametric techniques. Moreover, investigation on some factors such as short selling, trading rules, risks are made to seek the sources of the day and night effects based on a large number of empirical analysis. In the end, further analyses on daytime and overnight returns are given by the use of high-frequency data and linear regression technique.

Findings
The authors show that the daytime returns of CSI 300 index are no less than its overnight returns, while the daytime returns of CSI 300 index futures are no more than its overnight returns, even after removing the heteroscedasticity of the researched time series. Specifically, the PM returns (13:05 to close) play a quite important role in the intra-day time. The findings also suggest that the unique “T+1 trading rule” in China may be a reason that incurs the lower opening price in the morning and the higher closing price in the afternoon, resulting in the statistically significant differences between the daytime and overnight returns.

Practical implications
The findings are of great importance for investors to decide when to buy and sell stock and futures portfolios in Chinese financial markets.

Originality/value
This study empirically analyzes why there the higher daytime returns and the lower overnight returns exist in the Chinese stock markets from different aspects and contributes the existing literature on day and night effects because of periodic market closures.
Implementation fidelity of a voluntary sector-led diabetes education programme
Authors: Kok Michele S.Y. , Jones Mat , Solomon-Moore Emma , Smith Jane R. 
Published: December 2017

Purpose
The quality of voluntary sector-led community health programmes is an important concern for service users, providers and commissioners. Research on the fidelity of programme implementation offers a basis for assessing and further enhancing practice. The purpose of this paper is to report on the fidelity assessment of Living Well Taking Control (LWTC) – a voluntary sector-led, community-based education programme in England focussing on the prevention and management of type 2 diabetes.

Design/methodology/approach
This fidelity of implementation (FoI) study was conducted with the Devon-based LWTC programme. A fidelity checklist was developed to analyse audio records of group-based lifestyle education sessions – implementation was rated in terms of adherence to protocol and competence in delivery; the influence of wider contextual factors was also assessed. Kappa statistics (κ) were used to test for inter-rater agreement. Course satisfaction data were used as a supplementary indicator of facilitator competence.

Findings
Analysis of 28 sessions, from five diabetes prevention and two diabetes management groups (total participants, n=49), yielded an overall implementation fidelity score of 77.3 per cent for adherence (moderate inter-rater agreement, κ=0.60) and 95.1 per cent for competence (good inter-rater agreement, κ=0.71). The diabetes prevention groups consistently achieved higher adherence scores than the diabetes management groups. Facilitator competence was supported by high participant satisfaction ratings.

Originality/value
An appropriate level of implementation fidelity was delivered for the LWTC group-based education programme, which provides some confidence that outcomes from the programme reflected intervention effectiveness. This study demonstrates the viability of assessing the FoI in a voluntary sector-led public health initiative and the potential of this method for assuring quality and informing service development.
Consumer engagement in online brand communities: a solicitation of congruity theory
Authors: Islam Jamid Ul , Rahman Zillur , Hollebeek Linda D. 
Published: December 2017

Purpose
The purpose of this paper is threefold: first, to study the influence of self-brand image congruity and value congruity on consumer engagement in online brand communities (OBCs); second to test whether gender moderates this effect; and third, it also examines the role of consumer engagement as a driver of brand loyalty.

Design/methodology/approach
Using an online questionnaire, 443 responses were collected from consumers who are members of at least one OBC on Facebook. Structural equation modeling was used to analyze the data.

Findings
The results revealed that both self-brand image congruity and value congruity significantly affect consumer engagement. A positive effect of consumer engagement on brand loyalty was also attained. Third, the results revealed that gender did not moderate the examined relationships.

Practical implications
This research integrates and broadens existing explanations of different congruity effects on consumer engagement. This study thus suggests the value of developing their OBCs to exhibit congruence with customers’ self-image and value, which in turn, will contribute to the development of brand loyalty.

Originality/value
This research applies congruity theory to examine the impact of self-brand image- and value congruity on consumer engagement in OBCs. Through the establishment of this novel theoretical link, this study furthers insight into the domain of social media marketing.