bluuebunny/crossref_metadata_2025_split huggingface dataset:
Group IIA secreted phospholipase A2in human serum kills commensal but not clinicalEnterococcus faeciumisolates
Authors: Paganelli Fernanda L. , Leavis Helen L. , He Samantha , van Sorge Nina M. , Payré Christine , Lambeau Gérard , Willems Rob J.L. , Rooijakkers Suzan H.M. 
Published: February 2018

AbstractHuman innate immunity employs cellular and humoral mechanisms to facilitate rapid killing of invading bacteria. The direct killing of bacteria by human serum is mainly attributed to the activity of the complement system that forms pores in Gram-negative bacteria. Although Gram-positive bacteria are considered resistant to serum killing, we here uncover that normal human serum effectively killsEnterococcus faecium.Comparison of a well-characterized collection of commensal and clinicalE. faeciumisolates revealed that human serum specifically kills commensalE. faeciumstrains isolated from normal gut microbiota, but not clinical isolates. Inhibitor studies show that the human group IIA secreted phospholipase A2 (hGIIA), but not complement, is responsible for killing of commensalE. faeciumstrains in human normal serum. This is remarkable since hGIIA concentrations in ‘non-inflamed’ serum were considered too low to be bactericidal against Gram-positive bacteria. Mechanistic studies showed that serum hGIIA specifically causes permeabilization of commensalE. faeciummembranes. Altogether, we find that a normal serum concentration of hGIIA effectively kills commensalE. faeciumand that hGIIA resistance of clinicalE. faeciumcould have contributed to the ability of these strains to become opportunistic pathogens in hospitalized patients.ImportanceHuman normal serum contains antimicrobial components that effective kill invading Gram-negative bacteria. Although Gram-positive bacteria are generally considered resistant to serum killing, here we show that normal human effectively kills the Gram-positiveEnterococcus faeciumstrains that live as commensals in the gut of humans. In contrast, clinicalE. faeciumstrains that are responsible for opportunistic infections in debilitated patients are resistant against human serum. The key factor in serum responsible for killing is group IIA secreted phospholipase A2 (hGIIA) that effectively destabilizes commensalE. faeciummembranes. We believe that hGIIA resistance by clinicalE. faeciumcould have contributed to the ability of these strains to cause opportunistic infections in hospitalized patients. Altogether, understanding mechanisms of immune defense and bacterial resistance could aid in further development of novel anti-infective strategies against medically important multidrug resistant Gram-positive pathogens.
Predicting clinically promising therapeutic hypotheses using tensor factorization
Authors: Yao Jin , Hurle Mark R. , Nelson Matthew R. , Agarwal Pankaj 
Published: February 2018

ABSTRACTDetermining which target to pursue is a challenging and error-prone first step in developing a therapeutic treatment for a disease, where missteps are potentially very costly given the long-time frames and high expenses of drug development. We identified examples of successes and failures of target-indication pairs in clinical trials across 875 targets and 574 disease indications to build a gold-standard data set of 6,140 known clinical outcomes. We used information from Open Targets and others databases that covered 17 different sources of evidence for target-indication association and represented the data as a matrix of 21,437×2,211×17 with over two million non-null values. We designed and executed three benchmarking strategies to examine the performance of multiple machine learning models: Logistic Regression, Elasticnet, Random Forest, Tensor Factorization and Gradient Boosting Machine. With ten-fold cross validation, tensor factorization achieved AUROC=0.82±0.02 and AUPRC=0.71±0.03. Across multiple validation schemes, this was comparable or better than other methods. Tensor factorization is a general form of matrix factorization that has been successfully exploited in recommendation systems that suggest items to users based on their existing preference on a small number of items. Our application, using Bayesian probabilistic modelling, extends the capacity of matrix factorization to model multiple relationships between and among targets and indications. We use the model to show that our predicted probabilities of success correlate with clinical phases, and within clinical phase we can predict which trials are most likely to succeed.
Variations in neuromodulatory chemical signatures define compartments in macaque cortex
Authors: Ward Nicholas J. , Zinke Wolf , Coppola Jennifer J. , Disney Anita A. 
Published: February 2018

AbstractSubcortical neuromodulatory systems exhibit widespread projections that influence the output of cortical circuits. These modulatory systems have been portrayed as providing global signals to the entirety of cortex based on their widespread innervation. This innervation is not necessarily predictive of the levels of the neuromodulatory molecules that actually provide these signals to cortex. In the present study, we examine tissue concentrations of dopamine, noradrenaline, and serotonin to see how they locally vary across multiple areas of the macaque cortex. Our results indicate that different cortical areas exhibit varying levels of dopamine, noradrenaline, and serotonin. Using cluster analysis, we examine how similar cortical regions are to each other, finding that similarities in neurochemical content are shared by areas that exhibit similar functionality. Altogether, these findings demonstrate that neurochemical signatures vary across cortical regions and help define unique, local neuromodulatory signaling compartments.
Capturing the onset of PRC2-mediated repressive domain formation
Authors: Oksuz Ozgur , Narendra Varun , Lee Chul-Hwan , Descostes Nicolas , LeRoy Gary , Raviram Ramya , Blumenberg Lili , Karch Kelly , Rocha Pedro R. , Garcia Benjamin A. , Skok Jane A. , Reinberg Danny 
Published: February 2018

SummaryPolycomb repressive complex 2 (PRC2) maintains gene silencing by catalyzing methylation of histone H3 at lysine 27 (H3K27me2/3) within chromatin. By designing a system whereby PRC2-mediated repressive domains were collapsed and then reconstructed in an inducible fashion in vivo, a two-step mechanism of H3K27me2/3 domain formation became evident. First, PRC2 is stably recruited by the actions of JARID2 and MTF2 to a limited number of spatially interacting “nucleation sites”, creating H3K27me3-forming polycomb foci within the nucleus. Second, PRC2 is allosterically activated via its binding to H3K27me3 and rapidly spreads H3K27me2/3 both in cis and in far-cis via long-range contacts. As PRC2 proceeds further from the nucleation sites, its stability on chromatin decreases such that domains of H3K27me3 remain proximal, and those of H3K27me2 distal, to the nucleation sites. This study demonstrates the principles of de novo establishment of PRC2-mediated repressive domains across the genome.
“Be here now” – service users’ experiences of a mindfulness group intervention
Authors: Dillon Aiveen , Wilson Charlotte , Jackman Catherine 
Published: February 2018

Purpose
The purpose of this paper is to explore service users’ experiences of a mindfulness group intervention.

Design/methodology/approach
In total, 15 participants with a diagnosis of a mild or moderate intellectual disability and concurrent mental health difficulties were interviewed using semi-structured interviews about their experiences of attending the mindfulness group.

Findings
Thematic analysis was used to interpret the data. The three super ordinate themes that emerged were positive aspects of mindfulness, positive aspects of attending the group and negative aspects of attending the group. There were seven subthemes. The results highlighted that participants found the mindfulness group to be beneficial, partly due to specific aspects of the mindfulness intervention and partly due to the group process. The negative aspects of the group were harder to elicit, and were less specifically related to mindfulness.

Originality/value
Mindfulness-based interventions have emerged as a promising approach for individuals with intellectual disabilities with mental health difficulties. There is currently a lack of research exploring service users with intellectual disabilities about their experiences of mindfulness interventions.
Large-scale dynamic and static simulations of complex-shaped granular materials using parallel three-dimensional discrete element method (DEM) on DoD supercomputers
Authors: Yan Beichuan , Regueiro Richard 
Published: March 2018

PurposeThe purpose of this paper is to extend complex-shaped discrete element method simulations from a few thousand particles to millions of particles by using parallel computing on department of defense (DoD) supercomputers and to study the mechanical response of particle assemblies composed of a large number of particles in engineering practice and laboratory tests.Design/methodology/approachParallel algorithm is designed and implemented with advanced features such as link-block, border layer and migration layer, adaptive compute gridding technique and message passing interface (MPI) transmission of C++ objects and pointers, for high performance optimization; performance analyses are conducted across five orders of magnitude of simulation scale on multiple DoD supercomputers; and three full-scale simulations of sand pluviation, constrained collapse and particle shape effect are carried out to study mechanical response of particle assemblies.FindingsThe parallel algorithm and implementation exhibit high speedup and excellent scalability, communication time is a decreasing function of the number of compute nodes and optimal computational granularity for each simulation scale is given. Nearly 50 per cent of wall clock time is spent on rebound phenomenon at the top of particle assembly in dynamic simulation of sand gravitational pluviation. Numerous particles are necessary to capture the pattern and shape of particle assembly in collapse tests; preliminary comparison between sphere assembly and ellipsoid assembly indicates a significant influence of particle shape on kinematic, kinetic and static behavior of particle assemblies.Originality/valueThe high-performance parallel code enables the simulation of a wide range of dynamic and static laboratory and field tests in engineering applications that involve a large number of granular and geotechnical material grains, such as sand pluviation process, buried explosion in various soils, earth penetrator interaction with soil, influence of grain size, shape and gradation on packing density and shear strength and mechanical behavior under different gravity environments such as on the Moon and Mars.
Accomm: adaptive system for supply network operational planning
Authors: Morales-Alzate Luis Fernando , Solano-Vanegas Clara , Carrillo-Ramos Angela , Montoya-Torres Jairo , Fabregat Ramon , Pavlich-Mariscal Jaime A. 
Published: February 2018

PurposeThis paper aims to presentAccomma software implementation ofÁgora-SN, a supply network (SN) customer-oriented model integrated with an Adaptation Model.Accommserves two purposes: as an experimental validation tool to measure the impact of Adaptation on an agribusinessSNmodel and as a logistic and marketing operations planning assistant.Design/methodology/approachThe design ofAccommis based on the results of theÁgora-SNmodel that comprises the following tasks: to characterize theSNactors’ processes ( composed of multiple first-tier suppliers, a focal company and multiple first-tier customers), identifying the ones oriented to the customer; to integrate these processes into aSNmodel which incorporates a supplier cooperation model; and to provide an adaptation model that implements a customer profile and a context profile to improve order fulfillment.FindingsTo validate theÁgora-SNmodel, a prototypeAccommwas created referred to a real Colombian agribusiness sector company, specifically in the floriculture sector. This prototype was validated through two methods: a usability scale and a set of scenarios that compared the application’s behavior with and without adaptation and cooperation. The application provides a better response to demand when both adaptation and cooperation are enabled.Research limitations/implicationsThis work was tested in an academic environment and was validated by different experts. Further tests in operational real-life environments are required to fully validate the approach.Originality/valueThe main contribution of this work is the integration of Adaptation into aSNmodel as a way to center theSNtoward the customer. As an additional contribution, the validation toolAccommis conceived as an operational planning tool for agribusinessSN.
Recently identified university students navigate dyslexia
Authors: Loveland-Armour Lorraine Anne 
Published: February 2018

Purpose
The purpose of this paper is to capture students’ understandings of dyslexia as a component of identity. Specifically, the journey that students embarked on in order to contribute to self-understanding of learning and how dyslexia contributes to these experiences was examined.

Design/methodology/approach
This qualitative case study explored concepts of social identity theory, how students understood their dyslexia and whether or not labelling theory informed students’ identities through an arts-based phenomenological lens. Eight university students participated in a brief survey, a semi-structured interview and created artefacts representing their dyslexia, which facilitated dialogue about their individual experiences in a higher education context.

Findings
Interpretive phenomenological analysis revealed that student participants associated strongly with the identity of dyslexia; however they did not consider themselves to be part of a dyslexic group. They also discussed different routes that informed their decisions to undergo diagnostic assessments for dyslexia. Students did not report dyslexia identity as a label. Nonetheless, the students expressed that creating an artefact supported them to better understand and communicate their dyslexia.

Originality/value
Although visual methods are increasingly prevalent in educational research, they are not typical in the field of dyslexia in higher education. This research therefore engaged students in active self-reflection which provided valuable insight into the nature and diversity of the experiences that can emerge from identification of dyslexia at university.
Because access matters: an institutional case study
Authors: Peck Catherine , Bouilheres Frederique , Brown Melanie , Witney Carol 
Published: February 2018

Purpose
The purpose of this paper is to overview an institution wide accessibility project undertaken at the Vietnam locations of a transnational Australian university, and the significance of this initiative in symbolising the organisation’s commitment to inclusion and diversity. The project implemented universal accessibility standards for learning materials across all courses delivered at the university. This facilitated an easier in-class and online learning experience for students with a broad range of print disabilities, visual or hearing impairments, and a range of other learning differences or disabilities.

Design/methodology/approach
The implementation of this project entailed three concurrent streams of activity which the authors describe in this paper. These included development of accessibility standards and processes for conversion of the existing learning materials, a sustained awareness raising campaign for staff and students, and integration of the accessibility standards into induction, support and development activities.

Findings
The process of establishing the technical foundations for inclusion through a focus on accessibility prompted rich dialogue with staff and students around inclusive practices. Many staff working in professional and non-teaching roles voluntarily adopted the standards to promote an inclusive workplace. Capability building activities for high school teachers were also conducted for the Vietnamese Department of Education & Training.

Originality/value
The approach outlined in this case is highly transferable, and provides a practical roadmap for achieving accessibility and promoting an inclusive environment. The strategies described through the lens of Kotter’s (1996) process for leading change in this paper can be applied by higher education institutions internationally.
Disability disclosure: categorical and cultural difficulties HETL Scotland 2017
Authors: Soorenian Armineh 
Published: February 2018

Purpose
The purpose of this paper is to analyze a group of disabled students’ views and feelings on disclosing the nature of their impairments by applying via Universities and Colleges Admissions Service (UCAS, 2016), using a numerical coding system. The adequacy of “disability” categories on both university and UCAS forms, and related sensitive issues will be central to this paper.

Design/methodology/approach
Thus, the author will visit the debates surrounding the two contrasting models of “disability”, namely, the individual medical and the social model of “disability”. The associated advantages and disadvantages that are ensued will be examined.

Findings
This paper will conclude by offering inclusive solutions to disclosure, which are sensitive to both impairment and cultural-related issues and encourage disclosure from students with a wide range of impairments. The benefits of all-encompassing inclusive practice and the resulting wider implications for the student population at large will, therefore, be highlighted.

Originality/value
There is an acute shortage of similar kinds of research conducted on disabled international students’ experiences of disclosure, which make the current work timely and original.
Firm‐Level Analysis Using the ABS’ Business Longitudinal Analysis Data Environment (BLADE)
Authors: Hansell David , Rafi Bilal 
Published: March 2018

AbstractThe Australian Bureau of Statistics’ (ABS) Business Longitudinal Analysis Data Environment (BLADE) is the most comprehensive firm‐level statistical asset in Australia. This short overview provides readers a window into what data sources are used, how they are integrated, current and future applications and how these can contribute to evidence‐based policy making in Australia. At present, direct access is limited to staff directly employed by the Australian Statistician or through secondment.
Of Lambkins And Piglets In Old English And Beyond
Authors: Stiles Patrick V. 
Published: February 2018

AbstractIt is suggested that the Old English adjectives ge‐ēan and ge‐cealf, each attested once in the same passage, could refer not only to pregnant livestock but also to mothers with their newborn young (as proposed by Osthoff in 1895). The twice occurring sequence gefearh sugu, which is usually taken to be a compound, is here analysed as consisting of a third such adjective used attributively before the noun; as the feminine nominative singular of a heavy‐syllabled adjective, it is endingless. This appears to be a return to an earlier view. A fourth example, ge‐fol, recorded once, is also discussed. The formation of these adjectives is briefly treated, as is the PGmc noun *auna‐ “lamb” presupposed by the first adjective, together with its presumed relationship to Latin agnus and further cognates. Evidence for the derived class II weak verb *aunôn (reflected in OEēanian*) in the Germanic languages is presented.
Management of distal radius fractures in the emergency department: A long‐term functional outcome measure study with the Disabilities of Arm, Shoulder and Hand (DASH) scores
Authors: Barai Avijit , Lambie Bruce , Cosgrave Conor , Baxter Joanne 
Published: February 2018

AbstractObjectiveDistal radius fracture (DRF) is a common presentation to the ED. However, little is known about the long‐term functional outcome of these patients following their initial management in the ED.MethodsIn order to evaluate the long‐term functional outcome of DRF, we collected the Disabilities of Arm, Shoulder and Hand (DASH) scores from the patients who attended our ED with DRF between January 2014 and June 2015. We divided the patients into two groups based on their overall management: (i) conservative group who did not have any surgical interventions; and (ii) open reduction internal fixation (ORIF) group who needed surgical interventions in the theatre. Multiple linear regression models were used to identify the statistically significant predictor variables.ResultsOut of the 229 patients whom we contacted, 128 patients responded. The response rate was 56%. The majority of the patients belonged to the conservative group (n = 87, 75%), while one‐quarter of the patients were in the ORIF group (n = 29, 25%). DASH score was higher in the ORIF group (median = 12.1, 95% confidence interval 5.6–25) than the conservative group (median = 6, 95% confidence interval 1.7–16.4). This difference between the groups was statistically significant (unadjusted P = 0.017, Wilcoxon test). Multiple linear regression models revealed that the management group and age of the patients were significant predictors for DASH score.ConclusionConservative management had lower DASH scores signifying better functional outcomes. Further prospective multicentre studies may be suggested to assess the generalisability of the study.
A survey of tobacco dependence treatment guidelines content in 61 countries
Authors: Nilan Kapka , McNeill Ann , Murray Rachael L. , McKeever Tricia M. , Raw Martin 
Published: February 2018

AbstractAimsTo assess tobacco dependence treatment guidelines content in accordance with Article 14 of the World Health Organization (WHO) Framework Convention on Tobacco Control (FCTC) and its guidelines, and association between content and country income level.DesignCross‐sectional study.SettingOn‐line survey from March to July 2016.ParticipantsContacts in 77 countries, including 68 FCTC Parties, six Signatories and three non‐Parties which had indicated having guidelines in previous surveys, or had not been surveyed before.MeasurementsA nine‐item questionnaire on guidelines content, key recommendations, writing and dissemination.FindingsWe received responses from contacts in 63 countries (82%); 61 had guidelines. The majority are for doctors (93%), primary care (92%) and nurses (75%). All recommend brief advice, 82% recording tobacco use in medical notes, 98% nicotine replacement therapy (NRT), 61% quitlines, 31% text messaging and 87% intensive specialist support, and 54% stress the importance of health‐care workers not using tobacco. Only 57% have a dissemination strategy, and 62% have not been updated for 5 or more years. Compared with high‐income countries, quitlines are less likely to be recommended in upper middle‐income countries guidelines [odds ratio (OR) = 0.15, 95% confidence interval (CI) = 0.04–0.61] and intensive specialist support in lower middle‐income countries guidelines (OR = 0.01, 95% CI = 0.00–0.20). Guidelines updating is associated positively with country income level (P = 0.027).ConclusionsAlthough most tobacco dependence treatment guidelines in the 61 countries assessed in 2016 follow the World Health Organization's Framework Convention on Tobacco Control Article 14 recommendations and do not differ significantly by income level, improvements are needed in keeping guidelines up‐to‐date, applying good writing practices and developing a dissemination strategy.