bluuebunny/crossref_metadata_2025_split huggingface dataset:
PeatlandAcidobacteriawith a dissimilatory sulfur metabolism
Authors: Hausmann Bela , Pelikan Claus , Herbold Craig W. , Köstlbacher Stephan , Albertsen Mads , Eichorst Stephanie A. , del Rio Tijana Glavina , Huemer Martin , Nielsen Per H. , Rattei Thomas , Stingl Ulrich , Tringe Susannah G. , Trojan Daniela , Wentrup Cecilia , Woebken Dagmar , Pester Michael , Loy Alexander 
Published: October 2017

AbstractSulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However,their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novelAcidobacteriaspecies with the potential for dissimilatory sulfite (dsrAB,dsrC,dsrD,dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABCplusdsrgenes). Surprisingly, the genomes also encodeddsrL, a unique gene of the sulfur oxidation pathway. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, could also operate in reverse for sulfur oxidation as recently shown for other microorganisms.Acidobacteriathat only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties ofAcidobacteriaand the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobicAcidobacteriain wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.
The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes
Authors: Mardones Wladimir , Genova Alex Di , Cortés María Paz , Travisany Dante , Maass Alejandro , Eyzaguirre Jaime 
Published: October 2017

AbstractThe high lignocellulolytic activity displayed by the soft-rot fungusP. purpurogenumhas made it a target for the study of novel lignocellulolytic enzymes. We have obtained a reference genome of 36.2Mb of non-redundant sequence (11,057 protein-coding genes). The 49 largest scaffolds cover 90% of the assembly, and CEGMA analysis reveals that our assembly covers most if not all all protein-coding genes. RNASeq was performed and 93.1% of the reads aligned within the assembled genome. These data, plus the independent sequencing of a set of genes of lignocellulose-degrading enzymes, validate the quality of the genome sequence.P. purpurogenumshows a higher number of proteins with CAZy motifs, transcription factors and transporters as compared to other sequencedPenicillia. These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.
Fibroblasts from metastatic sites induce broad-spectrum drug desensitization via modulation of mitochondrial priming
Authors: Landry Benjamin D. , Leete Thomas , Richards Ryan , Cruz-Gordillo Peter , Ren Gary , Schwartz Alyssa D. , Peyton Shelly R. , Lee Michael J. 
Published: October 2017

ABSTRACTDue to tumor heterogeneity, most believe that effective treatments should be tailored to the features of an individual tumor or tumor subclass. It is still unclear what information should be considered for optimal disease stratification, and most prior work focuses on tumor genomics. Here, we focus on the tumor micro-environment. Using a large-scale co-culture assay optimized to measure drug-induced cell death, we identify tumor-stroma interactions that modulate drug sensitivity. Our data show that the chemo-insensitivity typically associated with aggressive subtypes of breast cancer is not cell intrinsic, but rather a product of tumor-fibroblast interactions. Additionally, we find that fibroblast cells influence tumor drug response in two distinct and divergent manners, which were predicable based on the anatomical origin from which the fibroblasts were harvested. These divergent phenotypes result from modulation of “mitochondrial priming” of tumor cells, caused by secretion of inflammatory cytokines, such as IL6 and IL8, from stromal cells.
Conditional Robust Calibration (CRC): a new computational Bayesian methodology for model parameters estimation and identifiability analysis
Authors: Bianconi Fortunato , Antonini Chiara , Tomassoni Lorenzo , Valigi Paolo 
Published: October 2017

AbstractComputational modeling is a remarkable and common tool to quantitatively describe a biological process. However, most model parameters, such as kinetics parameters, initial conditions and scale factors, are usually unknown because they cannot be directly measured.Therefore, key issues in Systems Biology are model calibration and identifiability analysis, i.e. estimate parameters from experimental data and assess how well those parameters are determined by the dimension and quality of the data.Currently in the Systems Biology and Computational Biology communities, the existing methodologies for parameter estimation are divided in two classes: frequentist methods and Bayesian methods. The first ones are based on the optimization of a cost function while the second ones estimate the posterior distribution of model parameters through different sampling techniques.In this work, we present an innovative Bayesian method, called Conditional Robust Calibration (CRC), for model calibration and identifiability analysis. The algorithm is an iterative procedure based on parameter space sampling and on the definition of multiple objective functions related to each output variables. The method estimates step by step the probability density function (pdf) of parameters conditioned to the experimental measures and it returns as output a subset in the parameter space that best reproduce the dataset.We apply CRC to six Ordinary Differential Equations (ODE) models with different characteristics and complexity to test its performances compared with profile likelihood (PL) and Approximate Bayesian Computation Sequential Montecarlo (ABC-SMC) approaches. The datasets selected for calibration are time course measurements of different nature: noisy or noiseless, real or in silico.Compared with PL, our approach finds a more robust solution because parameter identifiability is inferred by conditional pdfs of estimated parameters. Compared with ABC-SMC, we have found a more precise solution with a reduced computational cost.
Hierarchical Brain Network for Face and Voice Integration of Emotion Expression
Authors: Davies-Thompson Jodie , Elli Giulia V. , Rezk Mohamed , Benetti Stefania , Ackeren Markus van , Collignon Olivier 
Published: October 2017

ABSTRACTThe brain has separate specialized computational units to process faces and voices located in occipital and temporal cortices. However, humans seamlessly integrate signals from the faces and voices of others for optimal social interaction. How are emotional expressions, when delivered by different sensory modalities (faces and voices), integrated in the brain? In this study, we characterized the brains’ response to faces, voices, and combined face-voice information (congruent, incongruent), which varied in expression (neutral, fearful). Using a whole-brain approach, we found that only the right posterior superior temporal sulcus (rpSTS) responded more to bimodal stimuli than to face or voice alone but only when the stimuli contained emotional expression. Face-and voice-selective regions of interest extracted from independent functional localizers, similarly revealed multisensory integration in the face-selective rpSTS only; further, this was the only face-selective region that also responded significantly to voices. Dynamic Causal Modeling revealed that the rpSTS receives unidirectional information from the face-selective fusiform face area (FFA), and voice-selective temporal voice area (TVA), with emotional expression affecting the connection strength. Our study promotes a hierarchical model of face and voice integration, with convergence in the rpSTS, and that such integration depends on the (emotional) salience of the stimuli.
Hierarchical organization endows the kinase domain with regulatory plasticity
Authors: Creixell Pau , Pandey Jai P. , Palmeri Antonio , Santa-Olalla Marc C. , Ranganathan Rama , Pincus David , Yaffe Michael B. 
Published: October 2017

ABSTRACTThe functional diversity of kinases enables specificity in cellular signal transduction. Yet general rules for how the kinase domain allows the more than 500 members of the human kinome to receive specific regulatory inputs and convey information to appropriate substrates – all while using the common signaling currency of phosphorylation – remain enigmatic. Here, using co-evolution analysis and quantitative live-cell assays, we reveal a deep hierarchical organization of the kinase domain that facilitates the orthogonal evolution of regulatory inputs and substrate outputs while maintaining catalytic function. Three quasi-independent functional units in the kinase domain (known as protein sectors) encode for catalysis, substrate specificity and regulation, and these distinct subdomains are differentially exploited by somatic cancer mutations and harnessed by allosteric inhibitors. We propose that this functional architecture endows the kinase domain with inherent regulatory plasticity.
Mechanics and buckling of biopolymeric shells and cell nuclei
Authors: Banigan Edward J. , Stephens Andrew D. , Marko John F. 
Published: October 2017

AbstractWe study a Brownian dynamics simulation model of a biopolymeric shell deformed by axial forces exerted at opposing poles. The model exhibits two distinct linear force-extension regimes, with the response to small tensions governed by linear elasticity and the response to large tensions governed by an effective spring constant that scales with radius asR−0.25. When extended beyond the initial linear elastic regime, the shell undergoes a hysteretic, temperature-dependent buckling transition. We experimentally observe this buckling transition by stretching and imaging the lamina of isolated cell nuclei. Furthermore, the interior contents of the shell can alter mechanical response and buckling, which we show by simulating a model for the nucleus that quantitatively agrees with our micromanipulation experiments stretching individual nuclei.
Genome-wide homology analysis reveals new insights into the origin of the wheat B genome
Authors: Zhang Wei , Zhang Mingyi , Zhu Xianwen , Cao Yaping , Sun Qing , Ma Guojia , Chao Shiaoman , Yan Changhui , Xu Steven S. , Cai Xiwen 
Published: October 2017

AbstractWheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The ancestors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrassAegilops speltoides(genome SS) has been controversially considered a candidate for the ancestor of the wheat B genome. However, the relationship of theAe. speltoidesS genome with the wheat B genome remains largely obscure, which has puzzled the wheat research community for nearly a century. In the present study, the genome-wide homology analysis identified perceptible homology between wheat chromosome 1B andAe. speltoideschromosome 1S, but not between other chromosomes in the B and S genomes. AnAe. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was identified on the long arm of wheat chromosome 1B (1BL). TheAe. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome in wheat species. Thereby, we conclude thatAe. speltoideshad been involved in the origin of the wheat B genome, but should not be considered an exclusive ancestor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, includingAe. speltoides. These novel findings provide significant insights into the origin and evolution of the wheat B genome, and will facilitate polyploid genome studies in wheat and other plants as well.
Clustering, innovation and hotel competitiveness: evidence from the Colombia destination
Authors: Rodríguez-Victoria Orietha Eva , Puig Francisco , González-Loureiro Miguel 
Published: October 2017

Purpose
This paper aims to explore the relationship between clustering and hotel competitiveness in emerging economy destinations by analyzing potential mediation of the management innovations implemented.

Design/methodology/approach
This empirical study is based on hotel-level information from a survey including 131 hotels in 2014. Colombia was chosen as a representative of Colombia, Indonesia, Vietnam, Egypt, Turkey and South Africa (CIVETS) emerging destinations. The relationships were analyzed by structural modeling and partial least squares.

Findings
Clustering has a positive direct impact on hotel competitiveness and innovation, and there is a positive effect of innovation on competitiveness. Therefore, the link between clustering and competitiveness is partially mediated through implementation of management innovations.

Practical implications
Hotels should actively participate in agglomerated destinations and build relationships with established firms by clustering. Interaction with related firms and implementation of management innovations will lead to increased levels of economic competitiveness. Public policymakers should foster collaborative strategic networking in the hospitality industry of emerging economy destinations.

Originality/value
This paper focused on separating the direct and indirect effects of clustering on hotel competitiveness. Implementation of management innovations was considered as an outcome derived from clustering in emerging tourist destinations, using the example of Colombia. Clustering stimulates and eases management innovations within the location, and that combination reinforces the role that cooperating while competing plays in hotel competitiveness for destinations with lagging innovation.
Perfectionism in occupational science students: occupational therapy implications
Authors: Wagner Mary Elizabeth , Causey-Upton Renee 
Published: October 2017

Purpose
The purpose of this study is to categorize perfectionism and determine how perfectionism impacts the occupations and perceived health of students in a Bachelor of Science in Occupational Science program.

Design/methodology/approach
A descriptive study with a survey component was conducted. Participants were categorized as perfectionists or non-perfectionists using the Almost Perfect Scale-Revised (APS-R). Time logs were collected to compare categories of time-use between groups over a one-week period. An online survey was conducted with a sub-sample of the perfectionists.

Findings
More students were categorized as perfectionists (N = 41) than non-perfectionists (N = 3). Both groups spent similar amounts of time engaged in productive, pleasurable and restorative occupations. Some perfectionists reported that perfectionism supported health, but others reported negative impacts on well-being.

Research limitations/implications
This study included a small sample size limited to one Occupational Science program in the USA.

Originality/value
Results demonstrated positive and negative health impacts because of perfectionism. The majority of participants were identified as perfectionists; rigorous academic programs may attract students with perfectionistic qualities. Findings are relevant for Occupational Therapy, as these students will become future occupational therapists after completing a Master’s program in Occupational Therapy and may be susceptible to negative outcomes associated with perfectionism such as workaholism and poor health.
Experiences of men with psychosis participating in a community-based football programme
Authors: Moloney Laura , Rohde Daniela 
Published: October 2017

Purpose
Physical activity is associated with both physical and mental health benefits for people with psychosis. However, mental health services have been criticised for failing to adequately promote physical activities. Occupational Therapy, with its focus on meaningful everyday occupations, is well placed to incorporate physical activity interventions. The purpose of this study was to explore the experiences of men with psychosis participating in an Irish community-based football programme.

Design/methodology/approach
Six men with psychosis participated in qualitative interviews. The interviews were audio-recorded and transcribed verbatim. Interview data were analysed thematically.

Findings
Participants identified many benefits of engaging in the programme. Football became a valued part of weekly routines and fostered re-engagement with previously valued roles. Participants identified improvements in social confidence and motor and process skills, as well as a positive impact on their mental and physical health.

Originality/value
This study highlights the value and meaning of participation in football for men with psychosis, as well as demonstrating the longer-term feasibility of football as a therapeutic medium in Occupational Therapy mental health service provision. Findings could help to promote the routine use of sports interventions to mental health services.
Occupational Therapy embraces the National #Littlethings mental health and wellbeing campaign in Offaly via an Operation Transformation Programme
Authors: Deegan Deirdre , McKiver Eileen 
Published: October 2017

Purpose
In early 2015, an Occupational Therapy led Operation Transformation healthy eating and exercise programme produced results suggestive of the value and need to promote and integrate physical activity interventions into mental health services.

Design/methodology/approach
In all, 41 clients with various mental illness diagnoses participated in the eight-week Operation Transformation programme. The outcome measures involved weekly weigh-ins and an end of programme evaluation form.

Findings
The quantifiable benefits – a total weight loss of nine stone ten and a half pounds – were mirrored in equally impressive qualitative impacts. Participants’ feedback via anonymous evaluation forms, echoed the findings of the articles appraised in the literature, including improvements in mood and energy levels, better sleep and increased motivation.

Practical implications
The organisers will benefit from lessons learned in this first experience, including overcoming logistical and organisational difficulties experienced in enabling clients’ full participation.

Originality/value
The evidence base points to the successful benefits of physical activity in promoting positive mental health. Occupational Therapists have a unique opportunity to drive forward the message of promoting physical activity via meaningful occupations.
A spatial analysis of suicide rates in Tennessee
Authors: Difurio Ferdinand Gabriel , Lewis Willis 
Published: October 2017

PurposeSuicide rates at the county level may be influenced by various macro-level factors emanating from surrounding communities. The purpose of this paper is to measure the extent of geographic spillover effects from socioeconomic factors on suicide rates.Design/methodology/approachUsing county level, panel data over the years 2002-2007, a spatial dependence function is applied to measure how socioeconomic factors within surrounding counties may influence suicide rates in neighboring, adjacent counties in the state of TN.FindingsA negative correlation is identified between divorce and suicide rates within each county, which seems to contradict traditional beliefs that these variables move together. Also contrary to expectations, unemployment and suicide are not significantly related within counties. When the analysis measures the spillover effects of surrounding communities, county-level variables such as income, crime, and church density are significant. And although the signs on income and crime are consistent with past findings, church density counters research expectations.Practical implicationsThese results suggest that certain socioeconomic factors influence suicide in surrounding communities, while others do not. Incorporating spatial analysis into future research on suicide and mental health may assist practitioners with suicide prevention. Appropriate prevention policies should be designed and implemented at the local or regional level. Regional differences make broad policies based on national data inappropriate for local areas that differ from national norms.Originality/valueStudies on the external links to suicide and suicide rates have made significant contributions to raise the understanding about mental health issues. Very few, however, have directly employed research methods to capture spillover effects when the study encompasses spatial elements.
Beyond the equal-weight framework of the Social Progress Index
Authors: Jitmaneeroj Boonlert 
Published: October 2017

Purpose
Although the Social Progress Index offers a thorough overview of the top-ranked countries with a highly developed social performance, it assigns the same weight to all component scores, implying that each component has identical and independent contribution to the SPI. By removing these flawed assumptions, the purpose of this paper is to examine the causal relationships among component scores and identify the critical components for reform priorities.

Design/methodology/approach
The authors propose an alternative approach to exploring the causal relationships and prioritizing the underlying components of the SPI. The four-step methodology comprises cluster analysis, data mining, partial least square path modeling, and importance-performance matrix analysis.

Findings
The authors find evidence of causal interrelations between the 12 components of the SPI. To accelerate social progress, the authors suggest that policy makers should allocate resources in order of priority to personal freedom and choice, personal rights, access to advanced education, water and sanitation, access to information and communications, tolerance and inclusion, personal safety, shelter, ecosystem sustainability, nutrition and basic medical care, health and wellness, and, finally, access to basic knowledge.

Practical implications
Policy makers in government, business, and civil society should become aware of causal relationships among the 12 components of the SPI and select an appropriate methodology to prioritize areas where social improvement is most needed.

Originality/value
Allowing for unequal weighting and causal relationships between component scores of the SPI, the authors’ methodology is the first attempt to offer a concrete way to identify which areas of social progress should constitute priorities for policy reforms.
Efficiency of banks in Southeast Asia: Indonesia, Malaysia, Philippines and Thailand
Authors: Mohd Khan Shazida Jan , Samsudin Shamzaeffa , Islam Rabiul 
Published: October 2017

Purpose
The purpose of this paper is to use the concept of meta-frontiers data envelopment analysis (DEA) to compare the technical efficiencies of banks in selected Southeast Asia countries in the periods of 1998-2012.

Design/methodology/approach
The authors evaluate bank efficiency in Indonesia, Malaysia, Thailand and the Philippines by means of DEA, and the authors employ a meta-frontiers approach to calculate efficiency scores in a cross-country setting.

Findings
The analysis shows that even there are some similarities in the process of financial reforms undertaken in the selected countries, the observed efficiency levels of banks vary substantially across the market.

Originality/value
It is crucial to take into consideration of different technologies in explaining the efficiency differences.