bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting super-enhancer hierarchy based on chromatin interactions
Authors: Huang Jialiang , Li Kailong , Cai Wenqing , Liu Xin , Zhang Yuannyu , Orkin Stuart H. , Xu Jian , Yuan Guo-Cheng 
Published: June 2017

AbstractRecent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.
Pleistocene climate change and the formation of regional species pools
Authors: Calatayud Joaquín , Rodríguez Miguel Ángel , Molina-Vengas Rafael , Leo María , Hórreo Jose Luís , Hortal Joaquín 
Published: June 2017

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100053). Despite the description of bioregions dates back from the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring bioregions, but the effects of more recent events on these regional biotas are largely unknown. We use a network approach to identify regional and sub-regional faunas of EuropeanCarabusbeetles, and analyse the effects of dispersal barriers, niche similarities and phylogenetic history on their configuration. We identify a transition zone matching the limit of the ice sheets at Last Glacial Maximum. While southern species pools are mostly separated by dispersal barriers, in the north species are mainly sorted by their environmental niches. Strikingly, most phylogenetic structuration ofCarabusfaunas occurred during the Pleistocene. Our results show how extreme recent historical events –such as Pleistocene climate cooling, rather than just deep-time evolutionary processes, can profoundly modify the composition and structure of geographic species pools.
Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated Cyclic AMP Signals
Authors: Getz Michael , Swanson Lee , Sahoo Debashish , Ghosh Pradipta , Rangamani Padmini 
Published: June 2017

AbstractCellular levels of the versatile second messenger, cyclic-(c)AMP are regulated by the antagonistic actions of the canonical G protein→adenylyl cyclase pathway that is initiated by G-protein-coupled receptors (GPCRs) and by phosphodiesterases (PDEs); dysregulated cAMP signaling drives many diseases, including cancers. Recently, an alternative paradigm for cAMP signaling has emerged, in which growth factor-receptor tyrosine kinases (RTKs;e.g., EGFR) access and modulate G proteins via cytosolic guanine-nucleotide exchange modulator (GEM), GIV/Girdin; dysregulation of this pathway is frequently encountered in cancers. Here we present a comprehensive network-based compartmental model for the paradigm of GEM-dependent signaling that reveals unforeseen crosstalk and network dynamics between upstream events and the various feedback-loops that fine-tune the GEM action of GIV, and captures the experimentally determined dynamics of cAMP. The model also reveals that GIV acts a tunable control-valve within the RTK→cAMP pathway; hence, it modulates cAMP via mechanisms distinct from the two most-often targeted classes of cAMP modulators, GPCRs and PDEs.
Standing balance assessment using a head-mounted wearable device
Authors: Salisbury Joseph P. , Keshav Neha U. , Sossong Anthony D. , Sahin Ned T. 
Published: June 2017

AbstractBackground:The presence of accelerometers in smartphones has enabled low-cost balance assessment. Smartglasses, which contain an accelerometer similar to that of smartphones, could provide a safe and engaging platform for virtual and augmented reality balance rehabilitation; however, the validity of head-mounted measurement of balance using smartglasses has not been investigated.Objective:To perform preliminary validation of a smartglasses-based balance accelerometry measure (BAM) compared with previously validated waist-based BAM.Methods:42 healthy individuals (26 male, 16 female; mean age ± SD = 23.8 ± 5.2 years) participated in the study. Following the BAM protocol, each subject performed two trials of six balance stances while accelerometer and gyroscope data were recorded from smartglasses (Google Glass). Test-retest reliability and correlation were determined relative to waist-based BAM as used in the NIH Standing Balance Toolbox.Results:Balance measurements obtained using a head-mounted wearable were highly correlated with those obtained through a waist-mounted accelerometer (Spearman’s rank correlation coefficient = 0.85). Test-retest reliability was high (ICC = 0.85, 95% CI 0.81-0.88), and in good agreement with waist balance measurements (ICC = 0.84, 95% CI 0.80-0.88). Taking into account the total NPL magnitude improved inter-device correlation (0.90) while maintaining test-retest reliability (0.87, 95% CI 0.83-0.90). All subjects successfully completed the study, demonstrating the feasibility of using a head-mounted wearable to assess balance in a healthy population.Conclusion:Balance measurements derived from the smartglasses-based accelerometer were consistent with those obtained using a waist-mounted accelerometer. Given this and the potential for smartglasses in vestibular rehabilitation, the continued development and validation of balance assessment measurements obtained via smartglasses is warranted. This research was funded in part by Department of Defense/Defense Health Program (#W81XWH-14-C-0007, SBIR Phase II contract awarded to TIAX, LLC).
Collaboration between designers and facility managers
Authors: Kalantari Saleh , Shepley Mardelle M. , Rybkowski Zofia K. , Bryant John A. 
Published: June 2017

Purpose
The aim of this study is to focus on the perspectives of facility managers in each region and the different challenges impacting collaboration in each geographical context. This research analyzed obstacles to collaboration between facility managers and architectural designers in three international regions.

Design/methodology/approach
A multi-method approach was used, allowing the researchers to triangulate data from in-depth interviews and a widely distributed survey instrument. The participants included a large cross-selection of facility management professionals in each of the regions under study. The interview data were parsed to identify recurring themes, while the survey data were analyzed statistically to test specific hypotheses.

Findings
Significant differences were found in the culture of the facility management profession in each region. These differences created unique challenges for collaboration, especially in the context of a non-local design team. While the facility management profession was perceived as most established and professional in the UK, rates of collaboration between facility managers and designers were actually much higher in the USA. Collaborations between facility managers and designers were almost non-existent in the Middle East.

Originality/value
While the importance of collaboration between facility managers and designers is increasingly recognized for improving the efficiency of building operations, crucial obstacles continue to limit the scope of this engagement. There has been limited previous research analyzing obstacles to collaboration that are specific to international contexts and non-local design teams. This study helps to fill an important gap in the literature by providing a comparative analysis of collaboration challenges in three international contexts.
Co-creating digital services with and for facilities management
Authors: Lavikka Rita Henriikka , Lehtinen Teemu , Hall Daniel 
Published: June 2017

Purpose
This study aims to increase understanding about the co-creation of digital facilities management (FM) services with and for FM during a construction project.

Design/methodology/approach
The paper reports a case study on the co-creation of a digital facilities management service during the Mission Bay medical center construction project for the University of California, San Francisco. The sub-contractors and the FM team co-created a quick-response (QR) code system for valves on the project. This digital service is now used by the FM team for training purposes and in emergency situations when information on valves and their service areas is quickly needed. Researchers made on-site observations, conducted 84 interviews and reviewed archival data in 2012, 2014 and 2016.

Findings
The findings show that a successful co-creation process consists of three elements: a dialogue between the project parties, the creation of shared context between the project parties and the creation of shared understanding about the FM’s needs and the service providers’ ways of satisfying those needs. The study describes ways to promote these elements.

Originality/value
Previous studies emphasize the need for digital FM but few explain how FM teams can be involved in creating digital services for them. This paper describes how to co-create digital FM services with and for FM in the context of a construction project.
A legal perspective of current challenges of the Spanish residential rental market
Authors: Nasarre-Aznar Sergio , Molina-Roig Elga 
Published: June 2017

PurposeThis paper aims to explain the main difficulties in the Spanish residential rental market becoming a true alternative to home ownership.Design/methodology/approachCurrently, the Spanish rental market only meets temporary housing needs; it is very atomized and lacks professionalism. It does not provide an adequate legal framework to fulfil the parties’ aspirations (i.e. stability, affordability and flexibility for tenants; profitability, security and guarantees to landlords). The analysis of this proposition and the resulting proposal are based on six years of research, which started with the TENLAW European project.FindingsOvercoming these constrains is essential to double the rate of residential leases in Spain and get closer to the European average, thus achieving a true diversification of housing tenures and avoiding future housing bubbles.Practical implicationsThe paper makes a series of recommendations to legislators and policymakers to draft an adequate legal framework aimed at increasing the housing rental market share. This is based on the experience of mature tenancy markets in Europe, such as the German, Swiss and Austrian ones.Social implicationsThe new proposed legal framework will help to transform the tenancy model in Spain into a functional one, making it more stable, affordable and flexible, while increasing safety and profitability for landlords. The model is also applicable, on a more general level, to all Mediterranean European countries.Originality/valueRethinking the regulation of tenancies, in a context of housing crisis and unaffordability (still a reality in many European and worldwide countries) has valuable potential for making this type of tenure more popular and for avoiding future housing bubbles.
The effects of population growth, environmental quality and trade openness on economic growth
Authors: Rahman Mohammad Mafizur , Saidi Kais , Ben Mbarek Mounir 
Published: June 2017

PurposeThe purpose of this paper is to explore the effects of population growth (PG), environmental quality and trade openness on economic growth of major developed and developing countries.Design/methodology/approachThe authors have used the panel unit root and panel co-integration tests over the period 1960-2013. Granger causality test is used to find out the direction of causality between the variables.FindingsThere is a bi-directional relationship between economic growth and trade openness, and a unidirectional relation, running from trade openness to CO2emissions in the three developed countries. PG has a positive effect on economic growth in three developing countries and there exists a bidirectional relationships between CO2emissions and PG and a unidirectional relationship from PG to economic growth and from trade openness to economic growth. Furthermore, there is a unidirectional relationship from PG to economic growth and bidirectional relationships between trade openness and economic growth for the six selected countries.Originality/valueThis is the first comprehensive research that combined the selected three major developed and three major emerging countries of the world to explore the effects of three important variables on economic growth. The authors’ findings will help the policy makers as well as the people of these six countries. this study has shown the aggregate and disaggregate results, so a comparison between the groups of countries is possible. Therefore, this research has significant contributions.
P‐ and S‐wave anisotropy to characterise and quantify damage in media: laboratory experiment using synthetic sample with aligned microcracks
Authors: Ndao Baba , Do Duc‐Phi , Hoxha Dashnor 
Published: June 2017

ABSTRACTDamage characterisation in solid media is studied in this work through ultrasonic measurements. A synthetic three‐dimensional printed sample including a system of horizontally aligned microcracks is used. In contrast to other manual fabrication methods presented in the literature, the construction process considered here ensures a better control and accuracy of size, shape, and spatial distribution of the microcrack network in the synthetic sample. The acoustic measurements were conducted through a specific device using triple acoustic sensors, which allows capturing at each incident direction three wave modes. The evolution of the ultrasonic velocities with respect to incident angle accounted for the damage‐induced anisotropy. The experimental results are then compared with some well‐known effective media theories in order to discuss their potential use for the following studies. Finally, we highlighted and compared the accuracy of these theories used for inversion procedure to quantify damage in the medium.
Full waveform inversion of SH‐ and Love‐wave data in near‐surface prospecting
Authors: Dokter E. , Köhn D. , Wilken D. , De Nil D. , Rabbel W. 
Published: June 2017

ABSTRACTWe develop a two‐dimensional full waveform inversion approach for the simultaneous determination of S‐wave velocity and density models from SH ‐ and Love‐wave data. We illustrate the advantages of the SH/Love full waveform inversion with a simple synthetic example and demonstrate the method's applicability to a near‐surface dataset, recorded in the village Čachtice in Northwestern Slovakia. Goal of the survey was to map remains of historical building foundations in a highly heterogeneous subsurface. The seismic survey comprises two parallel SH‐profiles with maximum offsets of 24 m and covers a frequency range from 5 Hz to 80 Hz with high signal‐to‐noise ratio well suited for full waveform inversion. Using the Wiechert–Herglotz method, we determined a one‐dimensional gradient velocity model as a starting model for full waveform inversion. The two‐dimensional waveform inversion approach uses the global correlation norm as objective function in combination with a sequential inversion of low‐pass filtered field data. This mitigates the non‐linearity of the multi‐parameter inverse problem. Test computations show that the influence of visco‐elastic effects on the waveform inversion result is rather small. Further tests using a mono‐parameter shear modulus inversion reveal that the inversion of the density model has no significant impact on the final data fit. The final full waveform inversion S‐wave velocity and density models show a prominent low‐velocity weathering layer. Below this layer, the subsurface is highly heterogeneous. Minimum anomaly sizes correspond to approximately half of the dominant Love‐wavelength. The results demonstrate the ability of two‐dimensional SH waveform inversion to image shallow small‐scale soil structure. However, they do not show any evidence of foundation walls.
Medical therapy for preventing recurrent endometriosis after conservative surgery: a cost‐effectiveness analysis
Authors: Wu B , Yang Z , Tobe RG , Wang Y 
Published: June 2017

ObjectiveTo assess the cost‐effectiveness of different strategies, including gonadotropin‐releasing hormone agonist (GnRH‐a) and oral contraceptive therapy, for the prevention of endometriosis recurrence after conservative surgery.DesignCost‐effectiveness analysis from a health care perspective.SettingA health‐resource‐limited setting in China.PopulationPatients who underwent conservative laparoscopic or laparotomic surgery for endometriosis.MethodsA Markov model was developed for the endometriosis disease course. Clinical data were obtained from published studies. Direct medical costs and resource utilization in the Chinese health care setting were taken into account. The health and economic outcomes were evaluated over a period from treatment initiation to menopause onset. Sensitivity analyses were carried out to test the impact of various parameters and assumptions on the model output.Main outcome measuresQuality‐adjusted life years (QALYs) gained and costs from a health care perspective.ResultsThe incremental cost‐effectiveness ratio of 6‐month GnRH‐a therapy compared with no therapy ranged from $6,185 per QALY in deep endometriosis to $6,425 with peritoneal endometriosis. A one‐way sensitivity analysis showed considerable influential factors, such as remission rates and utility values. Probabilistic sensitivity analysis indicated that 6‐month GnRH‐a therapy is cost‐effective in most cases at a threshold of $7,400/QALY, regardless of the type of endometriosis.ConclusionSix months of therapy with GnRH‐a can be a highly cost‐effective option for the prevention of endometriosis recurrence.Tweetable abstractGonadotropin‐releasing hormone agonist is cost effective for the prevention of endometriosis recurrence.
Impacts of Cellulose Fiber Particle Size and Starch Type on Expansion During Extrusion Processing
Authors: Kallu Sravya , Kowalski Ryan J. , Ganjyal Girish M. 
Published: June 2017

AbstractObjective of this study was to understand the impacts of cellulose fiber with different particle size distributions, and starches with different molecular weights, on the expansion of direct expanded products. Fiber with 3 different particle size distributions (<125, 150 to 250, 300 to 425 μm) and 4 types of starches representing different amylose contents (0%, 23%, 50%, and 70%) were investigated. Feed moisture content (18 ± 0.5 % w.b) and extruder temperature (140 °C) were kept constant and only the extruder screw speed was varied (100, 175, and 250 rpm) to achieve different specific mechanical energy inputs. Fiber particle size and starch type significantly influenced the various product parameters. In general, the smaller fiber particle size resulted in extrudate with higher expansion ratio. Starch with an amylose: amylopectin ratio of 23:77 resulted in highest expansion compared to the other starches, when no fiber was added. Interestingly, starch with 50:50, amylose: amylopectin ratio in combination with smaller fiber particles resulted in product with significantly greater expansion than the control starch extrudates. Aggregation of fiber and shrinkage of surface was observed in the Scanning Electron Microscope images at 10% fiber level. The results suggest the presence of active interactions between the cellulose fiber particles and corn starch molecules during the expansion process. A better understanding of these interactions can help in the development of high fiber extruded products with better expansion.
First report on a novel Nigrospora sphaerica isolated from Catharanthus roseus plant with anticarcinogenic properties
Authors: Ayob Farah Wahida , Simarani Khanom , Zainal Abidin Nurhayati , Mohamad Jamaludin 
Published: June 2017

SummaryThis paper reports on the vinca alkaloid produced by a novel Nigrospora sphaerica isolated from Catharanthus roseus. Through liquid chromatography–mass spectrometry (LCMS), only the crude mycelia extract of this fungus was positive for determination of vinblastine. This vinca alkaloid was then purified by using high‐performance liquid chromatography (HPLC) and tested for cytotoxicity activity using MTT assays. The breast cell line cancer (MDA‐MB 231) was treated with a purified vinblastine which was intracellulary produced by N. sphaerica. The purified vinblastine from extracted leaf of C. roseus was used as a standard comparison. A positive result with a value of half maximal inhibitory concentration (IC50) of > 32 μg ml−1 was observed compared with standard (IC50) of 350 μg ml−1 only. It showed that a vinblastine produced by N. sphaerica has a high cytotoxicity activity even though the concentration of vinblastine produced by this endophytic fungus was only 0.868 μg ml−1.
Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota
Authors: Danchin Antoine , Braham Sherazade 
Published: June 2017

SummaryMicrobial communities thrive in a number of environments. Exploration of their microbiomes – their global genome – may reveal metabolic features that contribute to the development and welfare of their hosts, or chemical cleansing of environments. Yet we often lack final demonstration of their causal role in features of interest. The reason is that we do not have proper baselines that we could use to monitor how microbiota cope with key metabolites in the hosting environment. Here, focusing on animal gut microbiota, we describe the fate of cobalamins – metabolites of the B12 coenzyme family – that are essential for animals but synthesized only by prokaryotes. Microbiota produce the vitamin used in a variety of animals (and in algae). Coprophagy plays a role in its management. For coprophobic man, preliminary observations suggest that the gut microbial production of vitamin B12 plays only a limited role. By contrast, the vitamin is key for structuring microbiota. This implies that it is freely available in the environment. This can only result from lysis of the microbes that make it. A consequence for biotechnology applications is that, if valuable for their host, B12‐producing microbes should be sensitive to bacteriophages and colicins, or make spores.
Small‐ and large‐scale heterogeneity in genetic variation across the collard flycatcher genome: implications for estimating genetic diversity in nonmodel organisms
Authors: Ingvarsson Pär K. , Wang Jing 
Published: June 2017

Population genetic studies in nonmodel organisms are often hampered by a lack of reference genomes that are essential for whole‐genome resequencing. In the light of this, genotyping methods have been developed to effectively eliminate the need for a reference genome, such as genotyping by sequencing or restriction site‐associated DNA sequencing (RAD‐seq). However, what remains relatively poorly studied is how accurately these methods capture both average and variation in genetic diversity across an organism's genome. In this issue of Molecular Ecology Resources, Dutoit et al. (2016) use whole‐genome resequencing data from the collard flycatcher to assess what factors drive heterogeneity in nucleotide diversity across the genome. Using these data, they then simulate how well different sequencing designs, including RAD sequencing, could capture most of the variation in genetic diversity. They conclude that for evolutionary and conservation‐related studies focused on the estimating genomic diversity, researchers should emphasize the number of loci analysed over the number of individuals sequenced.