bluuebunny/crossref_metadata_2025_split huggingface dataset:
FORGe: prioritizing variants for graph genomes
Authors: Pritt Jacob , Chen Nae-Chyun , Langmead Ben 
Published: April 2018

AbstractThere is growing interest in using genetic variants to augment the reference genome into a “graph genome” to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment-score penalty, it also increases both the ambiguity of the reference genome and the cost of storing and querying the genome index. We introduce methods and a software tool called FORGe for modeling these effects and prioritizing variants accordingly. We show that FORGe enables a range of advantageous and measurable trade-offs between accuracy and computational overhead.
Active flow control analysis at the rear of an SUV
Authors: Eulalie Yoann , Fournier Elisabeth , Gilotte Philippe , Holst David , Johnson Shaun , Nayeri Christian Navid , Schütz Thomas , Wieser Dirk 
Published: April 2018

Purpose
This paper aims to present an experimental investigation of an active flow control solution mounted at rear of a sport utility vehicle (SUV) with the objective of drag reduction, thanks to a selection of flow control parameters leading to a pressure increase on the tailgate.

Design/methodology/approach
A flow control design of experiments was conducted with a pulsed jet system mounted on the top and sides of the rear window of the vehicle. The wall pressure, instantaneous velocity and drag were measured with this prototype in a wind tunnel. A dynamic modal decomposition (DMD) analysis of the pressure enables to describe the pressure fluctuations. Fluid dynamic computations show relation between pressure and velocity fields.

Findings
Measurements with this prototype in the wind tunnel revealed small improvements in drag for the best flow control configurations. This small benefit is because of the core of the upper span wise vortex further away from the rear window than the lower span wise vortex. These small improvements in drag were confirmed with pressure measurements on the rear window and tailgate. The DMD analysis of the surface pressure showed a low frequency pendulum oscillation on the lower area of the tailgate, linked with low velocity frequencies in the shear layers near the tailgate.

Originality/value
Experimental and numerical results show interest to increase pressure at bottom of the rear end of this SUV prototype. The dynamic description of the wall pressure shows importance of flow control solutions reducing pressure fluctuations at low frequencies in the lower area of the tailgate.
Distortion reconstruction in S-ducts from wall static pressure measurements
Authors: Grenson Pierre , Garnier Eric 
Published: April 2018

Purpose
This paper aims to report the attempts for predicting “on-the-fly” flow distortion in the engine entrance plane of a highly curved S-duct from wall static pressure measurements. Such a technology would be indispensable to trigger active flow control devices to mitigate the intense flow separations which occur in specific flight conditions.

Design/methodology/approach
Evaluation of different reconstruction algorithms is performed on the basis of data extracted from a Zonal Detached Eddy Simulation (ZDES) of a well-documented S-Duct (Garnier et al., AIAA J., 2015). Contrary to RANS methods, such a hybrid approach makes unsteady distortions available, which are necessary information for reconstruction algorithm assessment.

Findings
The best reconstruction accuracy is obtained with the artificial neural network (ANN) but the improvement compared to the classical linear stochastic estimation (LSE) is minor. The different inlet distortion coefficients are not reconstructed with the same accuracy. KA2 coefficient is finally identified as the more suited for activation of the control device.

Originality/value
LSE and its second-order variant (quadratic stochastic estimation [QSE]) are applied for reconstructing instantaneous stagnation pressure in the flow field. The potential improvement of an algorithm based on an ANN is also evaluated. The statistical link between the wall sensors and 40-Kulite rake sensors are carefully discussed and the accuracy of the reconstruction of the most used distortion coefficients (DC60, RDI, CDI and KA2) is quantified for each estimation technique.
The way we work: linking market orientation with internal workplace solutions
Authors: Piroos Amrina , Neffe Carolin , Lattuch Frank 
Published: April 2018

Purpose
This study aims to reinforce the importance of taking HR beyond administrative activity leading to stronger market orientated performance and the greater use of its people. Many organizations underestimate the effects of deliberately combining market orientation with internal communication demands. As a strategic partner, HR can offer support for designing effective workplace concepts that address such a challenge.

Design/methodology/approach
Using in-depth interviews, the authors explore aspects of effective workplace designs in high-performing German firms. This work is taken from a wider study of commercial office solutions completed in 2017.

Findings
Workplace designs need to be carefully developed to meet firm-specific needs dedicated to a market orientation strategy.

Originality/value
Practical lessons are drawn for helping HR professionals to better facilitate market orientation and communication needs from inside the organization.
Recovery Colleges; how effective are they?
Authors: Ebrahim Selma , Glascott Angela , Mayer Heidi , Gair Elodie 
Published: April 2018

PurposeRecovery Colleges are education-based mental health resources, utilising practitioner and lived experience expertise, promoting skills to enhance student independence. The purpose of this paper is to evaluate the impact of engagement with a Recovery College in Northern England on student wellbeing.Design/methodology/approachFeedback questionnaires were analysed from 89 students attending the Recovery College. Short Warwick-Edinburgh Mental Wellbeing Scale (SWEMBS) and “Empower Flower” (a measure of personal resources) data for 56 students were compared pre- and post-attendance at courses.FindingsThe SWEMBS and Empower Flower indicated improvements in wellbeing and personal resources pre- to post-attendance at Recovery College courses. Satisfaction with the service was high. Students saw the service as unique, accepting and enabling. Students noted they developed a sense of hope, confidence and aspirations. They related this to practical changes, e.g. increasing work-related activity and decreasing service use.Research limitations/implicationsThis research suggests that there is a need for further evaluation of the unique contribution that Recovery Colleges can make to mental wellbeing, and the mechanisms involved in promoting the process of recovery.Practical implicationsThe Recovery College may be a cost-effective way to provide a supportive recovery-orientated environment which promotes students’ ability to build self-confidence and skills, enabling them to connect with others and progress towards independence and valued goals. This complements more traditional mental health services.Originality/valueThis paper reports on an area of mental health development where there is very limited research, adding valuable data to the literature.
Model theory and observing systems. Notes on the use of models in systems research
Authors: Moe Sverre , Kaivo-oja Jari 
Published: April 2018

Purpose
The purpose of the paper is to present three different contributions to a general model theory which the authors think as relevant to systems research based on systems theory, cybernetics and constructivism. This also implies that the three contributions are shown to be of use both in the study of systems that operate by models, as well as in the practice of designing models.

Design/methodology/approach
The text is conceptual and mainly of a descriptive and referring character. Besides the sections on the three contributions to a model theory, the authors have inserted sections that relate them to systems theory. This is also achieved by the help of some simple models.

Findings
The paper also points to models as important instruments in constructing and selecting information to observing systems, and the authors hope that the text can be helpful in developing better knowledge of how models work.

Originality/value
The text is about observing systems that observe by models, and that is probably a somewhat new perspective. It is hoped that the paper can be inspiring to further studies on this matter.
An analysis of supply chain management research by
topic
Authors: Swanson David , Goel Lakshmi , Francisco Kristoffer , Stock James 
Published: April 2018

Purpose
This paper aims to review logistics and supply chain management topics where
theories have been applied to better understand the supply chain management
(SCM) discipline identity. The purpose is threefold: to identify research
topics in logistics and supply chain management where one or more theories
have been examined; provide commentary on the theories that have been
applied to the various logistics and SCM research topics; and to provide
reference material and direction for future research.

Design/methodology/approach
This structured literature review (SLR) examines research papers in logistics
and SCM from 1991 to 2015 published in eight leading academic journals.
Papers in the data set are grouped by topic and further analyzed in terms of
research method, purpose, year and journal.

Findings
This research categorizes papers by the topics that were studied to
understand important insights about how these topics have been examined by
researchers. Within each topic area, theories that researchers have used to
investigate the topics are identified. This method exposes insights such as:
how topics have evolved over time, which topics have lost prominence, which
topics may be particularly promising for future research and how topics are
treated in the literature.

Originality/value
Despite multiple calls for clarification regarding how theory has been used
in logistics and SCM, the logistics and SCM disciplines continue to grow
without adequate research on how theory has been used to examine SCM topics.
This SLR therefore provides a broad compilation of logistics and SCM
research that uses named theories and that is organized by SCM topic to
better understand the SCM discipline.
Keystone taxa predict compositional change in microbial communities
Authors: Herren Cristina M. , McMahon Katherine D. 
Published: April 2018

SummaryThe influence of biotic interactions on microbial community assembly is intensely debated. We hypothesized that keystone taxa, which influence community assembly through strong biotic interactions, are important for regulating microbial community composition. While highly connected microbes have been identified, evidence that these taxa act as keystones is lacking, because keystone status requires influence on whole‐community dynamics. We address this gap, showing that small subsets of highly connected keystone taxa (generally 1%–5% of richness) can be optimal predictors of whole‐community compositional change. In three long‐term data sets, greater connectivity due to the presence of keystone taxa corresponded to lower compositional turnover. We further hypothesized that the influence of keystone taxa would be diminished when environmental disturbance was a strong driver of compositional change. We used two case studies of reference and disturbed communities to investigate how biotic and abiotic forces interact to shape community composition. Most of the same taxa were present in both the reference and disturbed communities, but keystone taxa had much greater explanatory power in the reference communities. Our results suggest that greater biotic connectivity arising from the presence of keystone taxa is stabilizing to community composition, and that keystone taxa can be good indicators of pending community shifts.
China's Urban Speed Machine: The Politics of Speed and Time in a Period of Rapid Urban Growth
Authors: Chien Shiuh‐shen , Woodworth Max D. 
Published: April 2018

AbstractChina's urban transformation since 1978 is notable for both its scale and speed. Focusing on the dimension of speed, we propose the concept of the ‘urban speed machine’ to assess its role in shaping the politics and political economy of Chinese urbanization. We argue that in China speed must not be understood merely by means of measurable outcomes of change, but rather that speed is an essential and vital element embedded within China's specific processes and mechanisms driving urban growth. In this sense, speed is constantly at the forefront of local cadres’ considerations, since moving fast to achieve urban growth is an expression of political imperatives and pervasive city‐based accumulation strategies. The Chinese urban speed machine, as we conceive it, mainly involves three state‐dominated institutional arenas: the Communist party's personnel review system, the planning mechanism and local finance. We also discuss regional variability vis‐à‐vis the nature of speed in urbanization and in the differing responses to problems of fast‐city growth in recent years. This article's core contributions are to clarify the paramount importance of speed in the political economy of urban growth and illuminate a relational understanding of the politics of speed in China's urban change.
Secondary Hyperparathyroidism and Protein‐Energy Wasting in End‐Stage Renal Disease
Authors: Komaba Hirotaka , Fukagawa Masafumi 
Published: April 2018

AbstractProtein‐energy wasting (PEW), a syndrome involving adverse changes in nutrition and body composition, is a serious problem associated with morbidity and mortality in patients with end‐stage renal disease (ESRD). The pathogenesis of PEW is multifactorial, and the underlying mechanisms are not fully understood. However, recent translational work has provided compelling evidence for a causal role of parathyroid hormone (PTH) in the pathogenesis of adipose tissue browning and increased energy expenditure, a critical component of PEW in ESRD. These results provide a biological explanation for the clinical association between secondary hyperparathyroidism (SHPT) and PEW in hemodialysis patients and may serve as an additional rationale for treating SHPT. Large‐scale clinical and epidemiological studies should determine the clinical significance of SHPT as a contributor to PEW and establish the optimal management of SHPT to ameliorate PEW.
Pour Guess: The Effect of Glass Shape and an Ice Substitute on Alcohol Pouring and Estimation
Authors: Knibb Graeme , Jones Andrew , Christiansen Paul 
Published: April 2018

BackgroundResearch suggests that people are poor at estimating the amount of alcohol they have served themselves. Glass shape, the presence of ice, and alcohol consumption may influence the amount of alcohol people pour and estimate they have poured. The aim of these studies was to examine whether these factors would affect pouring behavior, in the laboratory and in real‐world environments.MethodsAcross 4 studies, 1 laboratory study and 3 conducted during public engagement events, we tested the effect of glass shape (straight sided highball and tumbler glasses) and, using an ice substitute (whiskey stones), the effect of ice on pouring and estimating a self‐defined typical drink. We also assessed the association between alcohol consumption and pouring accuracy.ResultsOverall, participants consistently overestimated their typical serving of alcohol, and poured more than 1 U.K. unit when pouring into an empty glass. Findings demonstrate no credible effect of glass shape or ice substitute on alcohol unit estimation or the amount of a typical serving. However, while alcohol consumption was not related to accuracy, the presence of an ice substitute improved accuracy when pouring a single U.K. unit.ConclusionsGiven that participants overestimated the amount of alcohol in their typical alcoholic drink, self‐report measures of alcohol consumption may be overstating the amount of alcohol individuals consume. Additionally, the presence of ice may improve accuracy when pouring standard servings (U.K. units) of alcohol. Therefore, self‐report measures may be improved if the presence of ice is considered.
Genotype–phenotype relationship and risk stratification in loss‐of‐function SCN5A mutation carriers
Authors: Robyns Tomas , Nuyens Dieter , Vandenberk Bert , Kuiperi Cuno , Corveleyn Anniek , Breckpot Jeroen , Garweg Christophe , Ector Joris , Willems Rik 
Published: April 2018

IntroductionLoss‐of‐function (LoF) mutations in the SCN5A gene cause multiple phenotypes including Brugada Syndrome (BrS) and a diffuse cardiac conduction defect. Markers of increased risk for sudden cardiac death (SCD) in LoF SCN5A mutation carriers are ill defined. We hypothesized that late potentials and fragmented QRS would be more prevalent in SCN5A mutation carriers compared to SCN5A‐negative BrS patients and evaluated risk markers for SCD in SCN5A mutation carriers.MethodsWe included all SCN5A loss‐of‐function mutation carriers and SCN5A‐negative BrS patients from our center. A combined arrhythmic endpoint was defined as appropriate ICD shock or SCD.ResultsLate potentials were more prevalent in 79 SCN5A mutation carriers compared to 39 SCN5A‐negative BrS patients (66% versus 44%, p = .021), while there was no difference in the prevalence of fragmented QRS. PR interval prolongation was the only parameter that predicted the presence of a SCN5A mutation in BrS (OR 1.08; p < .001). Four SCN5A mutation carriers, of whom three did not have a diagnostic type 1 ECG either spontaneously or after provocation with a sodium channel blocker, reached the combined arrhythmic endpoint during a follow‐up of 44 ± 52 months resulting in an annual incidence rate of 1.37%.ConclusionLP were more frequently observed in SCN5A mutation carriers, while fQRS was not. In SCN5A mutation carriers, the annual incidence rate of SCD was non‐negligible, even in the absence of a spontaneous or induced type 1 ECG. Therefore, proper follow‐up of SCN5A mutation carriers without Brugada syndrome phenotype is warranted.
Effect of humic acids on intestinal viscosity, leaky gut and ammonia excretion in a 24 hr feed restriction model to induce intestinal permeability in broiler chickens
Authors: Maguey‐Gonzalez Jesús A. , Michel Matias A. , Baxter Mikayla F.A. , Tellez Guillermo , Moore Philip A. , Solis‐Cruz Bruno , Hernández‐Patlan Daniel , Merino‐Guzman Rubén , Hernandez‐Velasco Xochitl , Latorre Juan D. , Hargis Billy M. , Gomez‐Rosales Sergio , Tellez‐Isaias Guillermo 
Published: April 2018

AbstractThe purpose of this study was to evaluate the effect of humic acids (HA) on intestinal viscosity, leaky gut and ammonia excretion in a 24 hr feed restriction (FR) model to induce intestinal permeability in chickens. One‐day‐old male Cobb‐Vantress broilers were randomly allocated to one of two groups (n = 25 chickens), with or without 0.2% of isolated HA from worm‐compost, and placed in brooder batteries. Chicks had ad libitum access to water and feed for 14 days. Intestinal permeability was induced by 24 hr FR starting at 14 days. At 15 days of age, chickens in both groups were given an appropriate dose of fluorescein isothiocyanate dextran (FITC‐d) by oral gavage. Intestine and liver samples were also collected to evaluate viscosity and bacterial translocation (BT), respectively. An increase (p < .05) in intestinal viscosity was observed in the experimental group consuming 0.2% of HA and was confirmed in a published in vitro digestion model that simulates the chemical and physical conditions of the crop, proventriculus and intestine of chickens. Furthermore, the treated group also showed a significant reduction in FITC‐d, liver BT and ammonia in the manure. These results suggest that HA have a positive impact in intestinal integrity in chickens.
Phenotypic and functional analysis of bovine peripheral blood dendritic cells before parturition by a novel purification method
Authors: Zhuang Tao , Urakawa Megumi , Sato Hidetoshi , Sato Yuko , Taguchi Teruaki , Umino Tsuyoshi , Katto Shiro , Tanaka Koutaro , Yoshimura Kozue , Takada Naokazu , Kobayashi Hiroko , Ito Megumi , Rose Michael T. , Kiku Yoshio , Nagasawa Yuya , Kitazawa Haruki , Watanabe Kouichi , Nochi Tomonori , Hayashi Tomohito , Aso Hisashi 
Published: April 2018

AbstractDendritic cells (DCs) are specialized antigen presenting cells specializing in antigen uptake and processing, and play an important role in the innate and adaptive immune response. A subset of bovine peripheral blood DCs was identified as CD172a+/CD11c+/MHC (major histocompatibility complex) class II+ cells. Although DCs are identified at 0.1%–0.7% of peripheral blood mononuclear cells (PBMC), the phenotype and function of DCs remain poorly understood with regard to maintaining tolerance during the pregnancy. All cattle used in this study were 1 month before parturition. We have established a novel method for the purification of DCs from PBMC using magnetic‐activated cell sorting, and purified the CD172a+/CD11c+ DCs, with high expression of MHC class II and CD40, at 84.8% purity. There were individual differences in the expressions of CD205 and co‐stimulatory molecules CD80 and CD86 on DCs. There were positive correlations between expression of cytokine and co‐stimulatory molecules in DCs, and the DCs maintained their immune tolerance, evidenced by their low expressions of the co‐stimulatory molecules and cytokine production. These results suggest that before parturition a half of DCs may be immature and tend to maintain tolerance based on the low cytokine production, and the other DCs with high co‐stimulatory molecules may already have the ability of modulating the T‐cell linage.
Pharmacokinetics, safety and tolerability of OBE022, a selective prostaglandin F2α receptor antagonist tocolytic: A first‐in‐human trial in healthy postmenopausal women
Authors: Pohl Oliver , Marchand Line , Gotteland Jean‐Pierre , Coates Simon , Täubel Jörg , Lorch Ulrike 
Published: April 2018

AimsPreterm birth remains a significant risk for later disability. The selective inhibition of the prostaglandin F2α receptor has significant advantages for a tocolytic. The prodrug OBE022 and its metabolite OBE002 are novel prostaglandin F2α receptor antagonists under development for treating preterm labour.MethodsWe performed a prospective, first in human, Phase I, dose escalation, placebo‐controlled, randomized trial at a clinical trial site in the UK. Placebo, single ascending doses of 10, 30, 100, 300, 1000 or 1300 mg, and multiple ascending doses over 7 days of 100, 300 or 1000 mg day–1; were administered to postmenopausal female volunteers. Food interaction was additionally evaluated.ResultsSubjects tolerated OBE022 well at all single and multiple doses. No clinically relevant changes in safety parameters were shown and there were no serious adverse events. Observations showed that prodrug OBE022 was readily absorbed and rapidly converted into its equally active stable metabolite OBE002. The plasma level of OBE002 rose with increasing doses, reaching exposure levels that were anticipated to be clinically relevant within 1 h following administration. There was no clinically significant food interaction, with peak exposures reduced to 80% and area under the curve staying bioequivalent. The mean half‐life of OBE002 ranged between 8 and 11 h following administration of a single dose and 22–29 h after multiple doses.ConclusionsAdministration of OBE022 was safe and had favourable pharmacokinetic characteristics and no clinically relevant interaction with food. Our results allow further investigation of OBE022 in preterm labour patients.