bluuebunny/crossref_metadata_2025 huggingface dataset:
Monte Carlo sampling for stochastic weight functions
Authors: Frenkel Daan , Schrenk K. Julian , Martiniani Stefano
Published: June 2017

Significance

Markov chain Monte Carlo is the method of choice for sampling high-dimensional (parameter) spaces. The method requires knowledge of the weight function (or likelihood function) determining the probability that a state is observed. However, in many numerical applications the weight function itself is fluctuating. Here, we present an approach capable of tackling this class of problems by rigorously sampling states proportionally to the average value of their fluctuating likelihood. We demonstrate that the method is capable of computing the volume of a basin of attraction defined by stochastic dynamics as well as being an efficient method to identify a transition state along a known reaction coordinate. We briefly discuss how the method might be extended to experimental settings.
The Elicitor Protein AsES Induces a Systemic Acquired Resistance Response Accompanied by Systemic Microbursts and Micro–Hypersensitive Responses in Fragaria ananassa
Authors: Hael-Conrad Verónica , Perato Silvia Marisa , Arias Marta Eugenia , Martínez-Zamora Martín Gustavo , Di Peto Pía de los Ángeles , Martos Gustavo Gabriel , Castagnaro Atilio Pedro , Díaz-Ricci Juan Carlos , Chalfoun Nadia Regina
Published: June 2017

The elicitor AsES (Acremonium strictum elicitor subtilisin) is a 34-kDa subtilisin-like protein secreted by the opportunistic fungus Acremonium strictum. AsES activates innate immunity and confers resistance against anthracnose and gray mold diseases in strawberry plants (Fragaria × ananassa Duch.) and the last disease also in Arabidopsis. In the present work, we show that, upon AsES recognition, a cascade of defense responses is activated, including: calcium influx, biphasic oxidative burst (O2⋅− and H2O2), hypersensitive cell-death response (HR), accumulation of autofluorescent compounds, cell-wall reinforcement with callose and lignin deposition, salicylic acid accumulation, and expression of defense-related genes, such as FaPR1, FaPG1, FaMYB30, FaRBOH-D, FaRBOH-F, FaCHI23, and FaFLS. All these responses occurred following a spatial and temporal program, first induced in infiltrated leaflets (local acquired resistance), spreading out to untreated lateral leaflets, and later, to distal leaves (systemic acquired resistance). After AsES treatment, macro-HR and macro–oxidative bursts were localized in infiltrated leaflets, while micro-HRs and microbursts occurred later in untreated leaves, being confined to a single cell or a cluster of a few epidermal cells that differentiated from the surrounding ones. The differentiated cells initiated a time-dependent series of physiological and anatomical changes, evolving to idioblasts accumulating H2O2 and autofluorescent compounds that blast, delivering its content into surrounding cells. This kind of systemic cell-death process in plants is described for the first time in response to a single elicitor. All data presented in this study suggest that AsES has the potential to activate a wide spectrum of biochemical and molecular defense responses in F. ananassa that may explain the induced protection toward pathogens of opposite lifestyle, like hemibiotrophic and necrotrophic fungi.
Using a Simulation of a Frustrated Faculty Member During Department Chair Searches: A Proof of Concept Project
Authors: Shapiro Daniel E. , Abbott Lisa M. , Wolpaw Daniel R. , Green Michael J. , Levi Benjamin H.
Published: June 2017

Problem

Vitae reviews, interviews, presentations, and reference checks are typical components of searches used to screen and select new department chairs/heads, but these strategies may fail to identify leaders who can communicate effectively with faculty in common, tense situations.

Approach

Between May 2015 and November 2016, the authors piloted simulation scenarios in four department chair searches at Penn State College of Medicine/Penn State Health to assess candidates’ skill at handling common, challenging situations with faculty members. In the scenarios, a frustrated faculty member complains that he/she has too little time for academic pursuits. Candidates were provided the scenario approximately two weeks in advance. They were asked to explain their goals prior to the 10-minute simulation, do the simulation, and then debrief with the search committees, who observed the interactions.

Outcomes

Approximately two-thirds (20/29; 69.0%) of candidates were judged to have successfully passed the simulation and were ultimately advanced. In most cases, the simulations revealed wide variation in candidates’ style, substance, and even underlying values that were not otherwise identified through the other parts of the recruitment and screening process. In some cases, candidates who performed well during group and individual interviews did poorly during simulations.

Next Steps

The authors will build a larger pool of simulation scenario cases, create a rubric, and formally measure interrater reliability. They will study whether the strategy successfully identifies chairs who will be skilled at navigating common faculty challenges, and if this skill results in greater faculty satisfaction, engagement, and retention.
CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology
Authors: Cankorur-Cetinkaya Ayca , Dias Joao M. L. , Kludas Jana , Slater Nigel K. H. , Rousu Juho , Oliver Stephen G. , Dikicioglu Duygu
Published: June 2017

Multiple interacting factors affect the performance of engineered biological systems in synthetic biology projects. The complexity of these biological systems means that experimental design should often be treated as a multiparametric optimization problem. However, the available methodologies are either impractical, due to a combinatorial explosion in the number of experiments to be performed, or are inaccessible to most experimentalists due to the lack of publicly available, user-friendly software. Although evolutionary algorithms may be employed as alternative approaches to optimize experimental design, the lack of simple-to-use software again restricts their use to specialist practitioners. In addition, the lack of subsidiary approaches to further investigate critical factors and their interactions prevents the full analysis and exploitation of the biotechnological system. We have addressed these problems and, here, provide a simple‐to‐use and freely available graphical user interface to empower a broad range of experimental biologists to employ complex evolutionary algorithms to optimize their experimental designs. Our approach exploits a Genetic Algorithm to discover the subspace containing the optimal combination of parameters, and Symbolic Regression to construct a model to evaluate the sensitivity of the experiment to each parameter under investigation. We demonstrate the utility of this method using an example in which the culture conditions for the microbial production of a bioactive human protein are optimized. CamOptimus is available through: (https://doi.org/10.17863/CAM.10257).
Experimenting with reproducibility in bioinformatics
Authors: Kim Yang-Min , Poline Jean-Baptiste , Dumas Guillaume
Published: June 2017

Reproducibility has been shown to be limited in many scientific fields. This question is a fundamental tenet of the scientific activity, but the related issues of reusability of scientific data are poorly documented. Here, we present a case study of our attempt to reproduce a promising bioinformatics method [1] and illustrate the challenges to use a published method for which code and data were available. First, we tried to re-run the analysis with the code and data provided by the authors. Second, we reimplemented the method in Python to avoid dependency on a MATLAB licence and ease the execution of the code on HPCC (High-Performance Computing Cluster). Third, we assessed reusability of our reimplementation and the quality of our documentation. Then, we experimented with our own software and tested how easy it would be to start from our implementation to reproduce the results, hence attempting to estimate the robustness of the reproducibility. Finally, in a second part, we propose solutions from this case study and other observations to improve reproducibility and research efficiency at the individual and collective level.

Availability

last version of StratiPy (Python) with two examples of reproducibility are available at GitHub [2].

Contact

yang-min.kim@pasteur.fr
Inferotemporal cortex multiplexes behaviorally-relevant target match signals and visual representations in a manner that minimizes their interference
Authors: Roth Noam , Rust Nicole C.
Published: June 2017

Finding a sought visual target object requires combining visual information about a scene with a remembered representation of the target to create a “target match” signal that indicates when a target is in view. Target match signals have been reported to exist within high-level visual brain areas including inferotemporal cortex (IT), where they are mixed with representations of image and object identity. However, these signals are not well understood, particularly in the context of the real-world challenge that the objects we search for typically appear at different positions, sizes, and within different background contexts. To investigate these signals, we recorded neural responses in IT as two rhesus monkeys performed a delayed-match-to-sample object search task in which target objects could appear at a variety of identity-preserving transformations. Consistent with the existence of behaviorally-relevant target match signals in IT, we found that IT contained a linearly separable target match representation that reflected behavioral confusions on trials in which the monkeys made errors. Additionally, target match signals were highly distributed across the IT population, and while a small fraction of units reflected target match signals as target match suppression, most units reflected target match signals as target match enhancement. Finally, we found that the potentially detrimental impact of target match signals on visual representations was mitigated by target match modulation that was approximately (albeit imperfectly) multiplicative. Together, these results support the existence of a robust, behaviorally-relevant target match representation in IT that is configured to minimally interfere with IT visual representations.
Silver fluoride as a treatment for the disease dental caries
Authors: Horst Jeremy A , Seto Jong
Published: June 2017

The current paradigm of treatment for dental caries (tooth decay) in primary teeth is dangerous, fails to reach many children, and suffers high recurrence. Acceptance of the paradigm arises from a misperception that untreated caries in primary teeth is a threat to life. We show a linear relationship between age and deaths in the United States from 1999 through 2015 caused by dental caries, pulpal / periapical abscess, or facial cellulitis. The intercept of 6 years coincides with emergence of the first permanent tooth: it appears that caries in primary teeth is not a threat to life. Thus, treatment goals should be to avoid pain, which is not possible with operative dentistry, as it causes pain. Medical management of caries is a distinct treatment philosophy which employs topical minimally invasive therapies that treat the disease, and is not merely prevention. Silver diamine fluoride (SDF) is a central agent to enable effective non-invasive treatment. The announcement of FDA Breakthrough Therapy designation suggests that SDF will become the first FDA approved drug for treating the disease dental caries. Since our last review, 4 clinical trials have been completed, which inform an update to the application protocol and frequency regimen. Suggestions from these studies are to skip the rinsing step due to demonstration of safety and concern of diminished effectiveness by dilution, and to start patients with an intensive regimen of multiple applications over the first few weeks. Breakthroughs in elucidating the impact of SDF on tooth structure and the plaque microbiome inform potential opportunities for bioengineering and understanding caries arrest, respectively. Dentists have been surprised by preference of this treatment over traditional invasive approaches. Renewed interest in this old material has delivered progress to optimize the judicious use of SDF, and enable a revolution in caries management – particularly for primary teeth.

ONE SENTENCE SUMMARY

Anesthesia is inappropriate for first-line treatment of early childhood caries now that safe topical treatments such as silver diamine fluoride are available.
A rapid and accurate approach for Prediction of interactomes from co-elution data (PrInCE)
Authors: Stacey R. Greg , Skinnider Michael A. , Scott Nichollas E. , Foster Leonard J.
Published: June 2017

Background

An organism’s protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to assess protein interactions. However, given the vast number of protein complexes, more scalable methods are necessary to accelerate interaction discovery and to construct whole interactomes. We recently developed a complementary technique based on the use of protein correlation profiling (PCP) and stable isotope labeling in amino acids in cell culture (SILAC) to assess chromatographic co-elution as evidence of interacting proteins. Importantly, PCP-SILAC is also capable of measuring protein interactions simultaneously under multiple biological conditions, allowing the detection of treatment-specific changes to an interactome. Given the uniqueness and high dimensionality of co-elution data, new tools are needed to compare protein elution profiles, control false discovery rates, and construct an accurate interactome.

Results

Here we describe a freely available bioinformatics pipeline, PrInCE, for the analysis of co-elution data. PrInCE is a modular, open-source library that is computationally inexpensive, able to use label and label-free data, and capable of detecting tens of thousands of protein-protein interactions. Using a machine learning approach, PrInCE offers greatly reduced run time, better performance, prediction of protein complexes, and greater ease of use over previous bioinformatics tools for co-elution data. PrInCE is implemented in Matlab (version R2015b). Source code and standalone executable programs for Windows and Mac OSX are available athttps://github.com/fosterlab/PrInCE,where usage instructions can be found. An example dataset and output are also provided for testing purposes.

Conclusions

PrInCE is the first fast and easy-to-use data analysis pipeline that predicts interactomes and protein complexes from co-elution data. PrInCE allows researchers without bioinformatics proficiency to analyze high-throughput co-elution datasets.
Normal CA1 place fields but discoordinated network discharge in a Fmr1-null mouse model of fragile X syndrome
Authors: Sparks Fraser Todd , Talbot Zoe Nicole , Dvorak Dino , Curran Bridget Mary , Alarcon Juan Marcos , Fenton André Antonio
Published: June 2017

Silence of FMR1 causes loss of fragile X mental retardation protein (FMRP) and dysregulated translation at synapses, resulting in the intellectual disability and autistic symptoms of Fragile X Syndrome (FXS). Synaptic dysfunction hypotheses for how intellectual disabilities like cognitive inflexibility arise in FXS, predict impaired neural coding in the absence of FMRP. We tested the prediction by comparing hippocampus place cells in wild-type and FXS-model mice. Experience-driven CA1 synaptic function and synaptic plasticity changes are excessive in Fmr1-null mice, but CA1 place fields are normal. However, Fmr1-null discharge relationships to local field potential oscillations are abnormally weak, stereotyped, and homogeneous; also discharge coordination within Fmr1-null place cell networks is weaker and less reliable than wild-type. Rather than disruption of single-cell neural codes, these findings point to invariant tuning of single-cell responses and inadequate discharge coordination within neural ensembles as a pathophysiological basis of cognitive inflexibility in FXS.
Control of recollection by slow gamma dominating mid-frequency gamma in hippocampus CA1
Authors: Dvorak Dino , Radwan Basma , Sparks Fraser T. , Talbot Zoe Nicole , Fenton André A.
Published: June 2017

Behavior is used to assess memory and cognitive deficits in animals like Fmrl-null mice that model Fragile X Syndrome, but behavior is a proxy for unknown neural events that define cognitive variables like recollection. We identified an electrophysiological signature of recollection in mouse dorsal CA1 hippocampus. During a shocked-place avoidance task, slow gamma (SG: 30-50 Hz) dominates mid-frequency gamma (MG: 70-90 Hz) oscillations 2-3 seconds before successful avoidance, but not failures. Wild-type but not Fmrl-null mice rapidly adapt to relocating the shock; concurrently, SG/MG maxima (SGdominance) decrease in wild-type but not in cognitively inflexible Fmrl-null mice. During SGdominance, putative pyramidal cell ensembles represent distant locations; during place avoidance, these are avoided places. During shock relocation, wild-type ensembles represent distant locations near the currently-correct shock zone but Fmrl-null ensembles represent the formerly-correct zone. These findings indicate that recollection occurs when CA1 slow gamma dominates mid-frequency gamma, and that accurate recollection of inappropriate memories explains Fmrl-null cognitive inflexibility.
Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells
Authors: Ghahramani Arsham , Donati Giacomo , Luscombe Nicholas M. , Watt Fiona M.
Published: June 2017

Canonical Wnt/beta-catenin signalling regulates self-renewal and lineage selection within the mouse epidermis. Although the transcriptional response of keratinocytes that receive a Wnt signal is well characterised, little is known about the mechanism by which keratinocytes in proximity to the Wntreceiving cell are co-opted to undergo a change in cell fate. To address this, we performed single-cell mRNA-Seq on mouse keratinocytes co-cultured with and without the presence of beta-catenin activated neighbouring cells. We identified seven distinct cell states in cultures that had not been exposed to the beta-catenin stimulus and show that the stimulus redistributes wild type subpopulation proportions. Using temporal single-cell analysis we reconstruct the cell fate changes induced by neighbour Wnt activation. Gene expression heterogeneity was reduced in neighbouring cells and this effect was most dramatic for protein synthesis associated genes. The changes in gene expression were accompanied by a shift from a quiescent to a more proliferative stem cell state. By integrating imaging and reconstructed sequential gene expression changes during the state transition we identified transcription factors, including Smad4 and Bcl3, that were responsible for effecting the transition in a contact-dependent manner. Our data indicate that non cell-autonomous Wnt/beta-catenin signalling decreases transcriptional heterogeneity and further our understanding of how epidermal Wnt signalling orchestrates regeneration and self-renewal.
Opposing spatial gradients of inhibition and neural activity in mouse olfactory cortex
Authors: Large Adam M. , Vogler Nathan W. , Canto-Bustos Martha , Schick Paul , Oswald Anne-Marie M.
Published: June 2017

The spatial representation of stimuli in primary sensory cortices is a convenient scaffold for elucidating the circuit mechanisms underlying sensory processing. In contrast, the anterior piriform cortex (APC) lacks topology for odor identity and appears homogenous in terms of afferent and intracortical excitatory circuitry. Here, we show that an increasing rostral-caudal (RC) gradient of inhibition onto pyramidal cells is commensurate with a decrease in active neurons along the RC axis following exploration of a novel odor environment. This inhibitory gradient is supported by somatostatin interneurons that provide an opposing, rostrally-biased, gradient of inhibition to interneurons. Optogenetic or chemogenetic modulation of somatostatin cells neutralizes the inhibitory gradient onto pyramidal cells. This suggests a novel circuit mechanism whereby opposing spatial gradients of inhibition and disinhibition regulate neural activity along the RC-axis. These findings challenge our current understanding of the spatial profiles of neural circuits and odor processing within APC.
Weighted area/angle distortion minimization for Mesh Parameterization
Authors: Mejia Daniel , Acosta Diego A. , Ruiz-Salguero Oscar
Published: June 2017

Purpose

Mesh Parameterization is central to reverse engineering, tool path planning, etc. This work synthesizes parameterizations with un-constrained borders, overall minimum angle plus area distortion. This study aims to present an assessment of the sensitivity of the minimized distortion with respect to weighed area and angle distortions.

Design/methodology/approach

A Mesh Parameterization which does not constrain borders is implemented by performing: isometry maps for each triangle to the plane Z = 0; an affine transform within the plane Z = 0 to glue the triangles back together; and a Levenberg–Marquardt minimization algorithm of a nonlinear F penalty function that modifies the parameters of the first two transformations to discourage triangle flips, angle or area distortions. F is a convex weighed combination of area distortion (weight: α with 0 ≤ α ≤ 1) and angle distortion (weight: 1 − α).

Findings

The present study parameterization algorithm has linear complexity [𝒪(n), n = number of mesh vertices]. The sensitivity analysis permits a fine-tuning of the weight parameter which achieves overall bijective parameterizations in the studied cases. No theoretical guarantee is given in this manuscript for the bijectivity. This algorithm has equal or superior performance compared with the ABF, LSCM and ARAP algorithms for the Ball, Cow and Gargoyle data sets. Additional correct results of this algorithm alone are presented for the Foot, Fandisk and Sliced-Glove data sets.

Originality/value

The devised free boundary nonlinear Mesh Parameterization method does not require a valid initial parameterization and produces locally bijective parameterizations in all of our tests. A formal sensitivity analysis shows that the resulting parameterization is more stable, i.e. the UV mapping changes very little when the algorithm tries to preserve angles than when it tries to preserve areas. The algorithm presented in this study belongs to the class that parameterizes meshes with holes. This study presents the results of a complexity analysis comparing the present study algorithm with 12 competing ones.
Practical expressions to calculate the main vertical actions on load-bearing columns/walls to Eurocode
Authors: Hassan Osama A.B.
Published: June 2017

Purpose

The aim of this review study is to present useful and practical expressions to compute the design vertical actions on load-bearing columns/walls of typical building structures on the basis of EN 1991: Eurocode 1.

Design/methodology/approach

It is derived by a typical case in which wind actions, snow actions and permanents actions are loading a roof construction. The results are finally used to calculate the loading on columns/walls. Both ultimate limit state and serviceability limit state are considered.

Findings

From an instructive point of view, the advantage of this method is that it is simplified, general, not time-consuming, and it can be standardised to typical building structures.

Research limitations/implications

A number of example applications are introduced to illustrate the calculation procedure.

Practical implications

From an educational point of view, this problem is of interest to civil engineering students because the reviewed method is not cumbersome or time-consuming.

Social implications

From an engineering educational point of view, this problem is of interest to civil engineering students because the reviewed method is not cumbersome or time-consuming.

Originality/value

New formulated expressions to calculate the loadings on structural membranes based on Eurocode are presented.
Relative influence of authentic and transformational leadership of local union representatives on the adoption of union citizenship behaviors
Authors: Fortin-Bergeron Chloé , Doucet Olivier , Hennebert Marc-Antonin
Published: June 2017

Purpose

The purpose of this paper is to analyze the different mediating processes by which authentic leadership and transformational leadership on the part of local union representatives influence members’ union citizenship behaviors (UCB) (i.e. UCBO and UCBI). Drawing from the social learning perspective, the authors suggest that authentic and transformational forms of leadership are associated with UCB through specific mechanisms i.e. member-representative value congruence and members’ collectivist orientation, respectively.

Design/methodology/approach

This research adopts a cross-sectional design. Structural equation modeling and bootstrap analysis were used to test the hypotheses among 343 members of a Canadian union federation representing professionals in the education sector.

Findings

The results show that the influence of authentic leadership on UCB is explained through value congruence and the influence of transformational leadership is principally exerted through members’ collectivist orientation.

Practical implications

By enhancing the understanding of the behavioral manifestations of local union leadership and its influential mechanisms, this research offers interesting avenues for union organizations that wish to develop and implement leadership training programs at the local level.

Originality/value

Only a handful of studies have investigated the relational antecedents of UCB, such as leadership. This research thus contributes to the UCB literature by extending the spectrum of examined local union leaders’ behaviors.
Role of the tumour necrosis factor‐like weak inducer of apoptosis (TWEAK)/fibroblast growth factor‐inducible 14 (Fn14) axis in autoimmune thyroid disease
Authors: Peng Shiqiao , Yu Xiaohui , Zhao Xuemin , Wang Xinyi , Sun Xuren , Han Cheng , Shan Zhongyan , Li Chenyan , Teng Weiping
Published: June 2017

Background

TNF‐like weak inducer of apoptosis (TWEAK), its receptor fibroblast growth factor‐inducible 14 (Fn14) and its scavenger receptor CD163 (sCD163) have known associations with many autoimmune diseases. However, the role of the TWEAK axis in autoimmune thyroid disease (AITD) remains unclear. Therefore, the aim of this study was to investigate the role of the TWEAK‐Fn14 axis in the pathogenesis of AITD.

Methods

Serum levels of soluble TWEAK (sTWEAK) and sCD163 were measured in 38 patients with Graves’ disease (GD), 40 patients with Hashimoto's thyroiditis (HT) and 40 healthy controls (HCs). Additionally, the mRNA expression of TWEAK and Fn14 in peripheral blood mononuclear cells (PBMCs) was explored, and the protein expression of TWEAK and Fn14 in thyroid glands surgically removed from 10 patients with GD, 10 patients with HT and 10 HCs was studied by immunohistochemical staining.

Results

The results showed that the serum levels of sTWEAK were significantly reduced in patients with HT and inversely correlated with antithyroid peroxidase antibody (TPOAb) levels. Additionally, high levels of sCD163 and a high sCD163/sTWEAK ratio were positively associated with the TPOAb levels in patients with HT and the thyrotropin receptor antibody (TRAb) levels in patients with GD. TWEAK mRNA expression and protein expression were upregulated in thyroid glands and PBMCs from patients with HT.

Conclusion

Expression of the TWEAK‐Fn14 axis was upregulated in patients with AITD and might play a role in the pathogenesis of AITD.
Women's expectations and experiences of rupture of membranes and views of the potential use of reagent pads for detecting amniotic fluid
Authors: Spiby Helen , Borrelli Sara , Hughes Anita J
Published: June 2017

Aims

To explore first‐time mothers’ expectations and experiences regarding rupture of membranes at term and their views on the potential use of reagent pads that detect amniotic fluid.

Background

There is little information available on women's experiences of spontaneous rupture of membranes, or interest in using methods to confirm rupture of membranes (e.g. reagent pads).

Design

Descriptive qualitative study, using focus groups and telephone interviews with women during pregnancy and after the birth of their first baby. Thematic analysis was undertaken to analyse women's responses.

Methods

Ethics committee approval was obtained. Twenty‐five women participated in the study of whom 13 contributed both during pregnancy and postpartum between October 2015–March 2016.

Findings

Three overarching themes were identified from the data from women's expectations and experiences: uncertainty in how, when and where membranes may rupture; information which was felt to be limited and confirmation of rupture of membranes. The potential use of reagent pads met with varied responses.

Conclusion

Women were interested in having facts and figures regarding rupture of membranes, such as characteristics of liquor; volume and probability of membranes rupturing spontaneously at term. Use of a pad as a means of confirmation was viewed as helpful, although the potential for increasing anxiety was raised.
Uncovering the decision‐making work of transferring dying patients home from critical care units: An integrative review
Authors: Lin Yanxia , Myall Michelle , Jarrett Nikki
Published: June 2017

Aims

To understand how decisions are made to transfer dying patients home from critical care units.

Background

Many people prefer a home death, but a high proportion die in critical care units. Transferring dying patients home is recognized to be complex but transfer decision‐making itself remains unclear.

Design

Integrative review.

Data sources

Seven bibliographic databases (origin–2015), grey literature and reference lists were searched.

Review methods

An integrative review method was used to synthesize data from diverse sources. Papers were selected through title and abstract screening and full‐text reviewing, using inclusion and exclusion criteria derived from review questions. Following quality appraisal, data were extracted and synthesized using normalization process theory as a framework.

Results

The number of patients transferred home ranged from 1–346, with most papers reporting on the transfer of one or two patients. Four themes regarding transfer decision‐making work were generated: divergent views and practice, multiple stakeholders’ involvement in decision‐making, collective work and limited understanding of individuals’ experiences.

Conclusion

The practice of transferring patients home to die and its decision‐making varies internationally and is usually influenced by the care system, culture or religion. It is less common to transfer patients home to die from critical care units in western societies. A better understanding of the decision‐making work was obtained but mainly from the perspective of hospital‐based healthcare professionals. Further research is needed to develop decision‐making practice guidance to facilitate patients’ wishes to die at home.
Concentration‐ and flux‐based dose–responses of isoprene emission from poplar leaves and plants exposed to an ozone concentration gradient
Authors: Yuan Xiangyang , Feng Zhaozhong , Liu Shuo , Shang Bo , Li Pin , Xu Yansen , Paoletti Elena
Published: June 2017

Concentration‐ and flux‐based O3 dose–responses of isoprene emission from single leaves and whole plants were developed. Two poplar clones differing in O3 sensitivity were exposed to five O3 levels in open‐top chambers for 97 d: charcoal‐filtered ambient air (CF), non‐filtered ambient air (NF) and NF plus 20 ppb (NF + 20), 40 ppb (NF + 40) and 60 ppb (NF + 60). At both leaf and plant level, isoprene emission was significantly decreased by NF + 40 and NF + 60 for both clones. Although intra‐specific variability was found when the emissions were up‐scaled to the whole plant, both leaf‐ and plant‐level emissions decreased linearly with increasing concentration‐based (AOT40, cumulative exposure to hourly O3 concentrations >40 ppb) and flux‐based indices (PODY, cumulative stomatal uptake of O3 > Y nmol O3 m−2 PLA s−1). AOT40‐ and POD7‐based dose–responses performed equally well. The two clones responded differently to AOT40 and similarly to PODY (with a slightly higher R2 for POD7) when the emission was expressed as change relative to clean air. We thus recommend POD7 as a large‐scale risk assessment metric to estimate isoprene emission responses to O3 in poplar.
Food culture of faith communities and potential impact on childhood obesity
Authors: Opalinski Andra S. , Dyess Susan M. , Gropper Sareen S.
Published: June 2017

Objective

To explore the food culture within faith communities (FC) in order to examine the consumption of away‐from‐home foods, and to provide an evidence base for the future development of healthy away‐from‐home meal initiatives though FCs.

Design and Sample

A qualitative descriptive design informed by an ethnographic method of free listing was utilized. A purposive sample of 34 FC leaders from seven distinct FCs participated in this study.

Results

The top five salience scores for five research questions are considered in detail. Of note, food is provided at multiple FC events including at worship time and Bible or group study, but also as part of school, youth programming, and special events. The purposes of serving food were reported to be not only for modes of entertainment and fellowship but also for promoting attendance and providing basic nutrition needs.

Conclusions

Professionals practicing in public health, faith community nursing, or in community health nursing are apt to engage in focused dialogues regarding the multidimensional health problem of childhood obesity. This research study directs nurses to consider food culture as a dimension of importance, especially within FCs. Appreciating FC food culture is important because many families engage in the settings for years, decades, and possibly a life span.
Morphology agrees with molecular data: phylogenetic affinities of Euptychiina butterflies (Nymphalidae: Satyrinae)
Authors: MARÍN MARIO A. , PEÑA CARLOS , URIBE SANDRA I. , FREITAS ANDRÉ V. L.
Published: June 2017

Euptychiina is the most species‐rich subtribe of Neotropical Satyrinae, with over 450 known species in 47 genera (14 monotypic). Here, we use morphological characters to examine the phylogenetic relationships within Euptychiina. Taxonomic sampling included 105 species representing the majority of the genera, as well as five outgroups. A total of 103 characters were obtained: 45 from wing pattern, 48 from genitalia and 10 from wing venation. The data matrix was analysed using maximum parsimony under both equal and extended implied weights. Euptychiina was recovered as monophyletic with ten monophyletic genera, contrasting previous DNA sequence‐based phylogenies that did not recover the monophyly of the group. In agreement with sequence‐based hypotheses, however, three main clades were recognized: the ‘Megisto clade’ with six monophyletic and three polyphyletic genera, the ‘Taygetis clade’ with nine genera of which three were monophyletic, and the ‘Pareuptyhia clade’ with four monophyletic and two polyphyletic genera. This is the first morphology‐based phylogenetic hypothesis for Euptychiina and the results will be used to complement molecular data in a combined analysis and to provide critical synapomorphies for clades and genera in this taxonomically confused group.
New Space–Time Metaphors Foster New Nonlinguistic Representations
Authors: Hendricks Rose K. , Boroditsky Lera
Published: June 2017

What is the role of language in constructing knowledge? In this article, we ask whether learning new relational language can create new ways of thinking. In Experiment 1, we taught English speakers to talk about time using new vertical linguistic metaphors, saying things like “breakfast is above dinner” or “breakfast is below dinner” (depending on condition). In Experiment 2, rather than teaching people new metaphors, we relied on the left–right representations of time that our American college student participants have already internalized through a lifetime of visuospatial experience reading and writing text from left to right. In both experiments, we asked whether the representations (whether newly acquired from metaphor or acquired over many years of visuospatial experience) are susceptible to verbal interference. We found that (a) learning new metaphors created new space–time associations that could be detected in a nonlinguistic implicit association task; (b) these newly learned representations were not susceptible to verbal interference; and (c) with respect to both verbal and visual interference, representations newly learned from linguistic metaphor behaved just like those on the left–right axis that our participants had acquired through years of visuospatial experience. Taken together, these results suggest that learning new relational language can be a powerful tool in constructing new representations and expanding our cognitive repertoire.
NUMERICAL MODELING OF PHASE TRANSFORMATION DURING GRINDING PROCESS
Authors: Ahmed Shah Syed Mushtaq , Khattak M. A. , Asad Muhammad , Iqbal Javed , Badshah Saeed , Khan M. S.
Published: June 2017

The rapid heating and cooling in a grinding process may cause phase transformations. This will introduce thermal strains and plastic strains simultaneously in a workpiece with substantial residual stresses. The properties of the workpiece material will change when phase transformation occurs. The extent of such change depends on the temperature history experienced and the instantaneous thermal stresses developed. To carry out a reliable residual stress analysis, a comprehensive modelling technique and a sophisticated computational procedure that can accommodate the property change with the metallurgical change of material need to be developed. The objective of this work is to propose a simplified model to predict phase evolution during given temperature history for heating and cooling as encountered during grinding process. The numerical implementation of the proposed model is carried out through the developed FORTRAN subroutine called PHASE using the FEM commercial software Abaqus®/standard. Micro-structural constituents are defined as state variables. They are computed and updated inside the subroutine PHASE. The heating temperature is assumed to be uniform while the cooling characteristics in relation to phase transformations are obtained from the continuous cooling transformation (CCT) diagram of the given material (here AISI 52100 steel). Four metallurgical phases are assumed for the simulations: austenite, pearlite, bainite, and martensite. It was shown that at low cooling rates high percentage of pearlite phase is obtained when the material is heated and cooled to ambient temperature. Bainite is formed usually at medium cooling rates. Similarly at high cooling rates maximum content of martensite may be observed. It is also shown that the continuous cooling transformation kinetics may be described by plotting the transformation temperature, directly against the cooling rate as an alternative to the continuous cooling transformation diagram. The simulated results are also compared with experimental results of Wever [20] and Hunkle [21] and are found to be in a very good agreement. The model may be used for further thermo-mechanical analysis coupled with phase transformation during grinding process.
FIREFLYCLUST: AN AUTOMATED HIERARCHICAL TEXT CLUSTERING APPROACH
Authors: Mohammed Athraa Jasim , Yusof Yuhanis , Husni Husniza
Published: June 2017

Text clustering is one of the text mining tasks that is employed in search engines. Discovering the optimal number of clusters for a dataset or repository is a challenging problem. Various clustering algorithms have been reported in the literature but most of them rely on a pre-defined value of the k clusters. In this study, a variant of Firefly algorithm, termed as FireflyClust, is proposed to automatically cluster text documents in a hierarchical manner. The proposed clustering method operates based on five phases: data pre-processing, clustering, item re-location, cluster selection and cluster refinement. Experiments are undertaken based on different selections of threshold value. Results on the TREC collection named TR11, TR12, TR23 and TR45, showed that the FireflyClust is a better approach than the Bisect K-means, hybrid Bisect K-means and Practical General Stochastic Clustering Method. Such a result would enlighten the directions in developing a better information retrieval engine for this dynamic and fast growing big data era.
Menelusuri Daya Tahan Wanita Islam Generasi Awal Bagi Mencapai Keunggulan Melalui Analisis Wacana Hadis Nabawi
Authors: Abdullah Ariza , Abdul Jabar Mohd Azidan , Mustapha Nik Farhan , Toklubok@Hajimaming Pabiyah
Published: June 2017

Women are the main driving force of society along side men. High personality of women will  bring into the world strong generation and community in facing challenges of life. If they are weak, the community also will become strengthless. Muslims, regardless being  majorities in Moslem countries or minorities in non Moslem countries should revive excellency as early generations of Islam that bring forth advanced world civilization for several centuries. The stories of the early generations had been written by many authors such as Mohammad Rashid Rida’s writing about the wives of the Prophet, as well as contained in history books known as “sirah”, autobiographies as well as other forms of writings, translations of thousands of titles in the subject but not studied analytically. Thus analyzing the social processes that apply at that time through the content of Prophetic hadith and discourse analysis texts as proposed by social language analysts, prevail to expose the excellency and sustainability of  women implied in the events as had been narrated by themselves and others. Methodology of this study is based on analysis of the content of hadith and Fairclough (2003, 1992, 1989)’s concept of discourse analysis through the dimension of intertextuality. Several prophetic Hadith are selected, analyzed and being related to social practice to formulate the principles that should serve as a model to modern  women especially by Moslim women. This is because the development of human capital especially female identity is the backbone of the nation’s development.
Kompetensi Pembimbing dalam Sistem Latihan Kemahiran Dua Hala: Satu Sorotan Literatur
Authors: Nasir Nasyitah , Adam Siti Balkhis , Rosli Nur Najihah , Abdullah Mai Shihah , Azman Mohamed Nor Azhari
Published: June 2017

National Dual Training System (NDTS) implementation in Malaysia was designed to produce highly skilled and knowledgeable K-workers, equipped with the social skills and learning methodologies. Research used documentation as data collection methods and data was analysed using historical, inductive and deductive reasoning method. The Ninth Malaysia Plan has stated four challenges which  need to be addressed  in  developing  the Technical  and  Vocational  Education  Training (TVET)  sector.  One of  the issues  is competency gaps among instructors. Based on the issue, the research objective is to identify the competency levels among instructors of NDTS. There are three aspects need to be applied by instructors during their teaching and learning session which include (1) technical  skills, (2) knowledge,  and (3) behaviour. This research  is further  into  assessment  as  the platform to  measure competency quality among the instructors of NDTS. The result showed that, the assessment based competency is able to  improve the competency levels among the instructors of NDTS.
Kempen “Kepimpinan melalui Teladan”semasa Era Pemerintahan Tun Dr. Mahathir Mohamad di Malaysia
Authors: Abdul rohman Muniroh , Ahmad Sabri Ahmad Zaharuddin Sani
Published: June 2017

This study on leadership examines the purposes of the Leadership by Example Campaign during Tun Dr Mahathir Mohamad’s tenure as Prime Minister of Malaysia. Leadership studies are interested in people from all walks of life because the struggles of the brave and wise leaders have become the source of legends and myths.Therefore, the issue of leadership is an important agenda for both the private and public sectors ineither developed countries or developing countries. The issue becomes more acute due to a constantly changing environment.In fact, every change that happens in the environment becomes a constant challenge for leaders in all sectors.In the context of the political leadership in Malaysia, the position and interests of UMNO and Barisan Nasional led by Tun Dr Mahathir Mohamad was quite evident because it was the leadership that had led the country for a long period of time to the extent that it was considered as a bridge connecting two generations of UMNO. However, people who were born in the 1980s only recognised one Prime Minister and four Deputy Prime Ministers until the day of his retirement. Thus, the study found that the Leadership by Example Campaign introduced by Tun Dr Mahathir Mohamad that aimed for instilling and cultivating effective leadership was emulated, appreciated and practised by all levels of society.In general, this study used a qualitative approach. While, this data was gathered through document review and analysis of the content to obtain the results. The Leadership by Example Campaign was a noble effort from Tun Dr Mahathir Mohamad to foster a spirit of discipline and establish the identity of every Malaysian to be able to stand tall together with other nations.
The effect of sustained virological response on the risk of extrahepatic manifestations of hepatitis C virus infection
Authors: Mahale Parag , Engels Eric A , Li Ruosha , Torres Harrys A , Hwang Lu-Yu , Brown Eric L , Kramer Jennifer R
Published: June 2017

Background and aim

Chronic HCV infection is associated with several extrahepatic manifestations (EHMs). Data on the effect of sustained virological response (SVR) on the risk of EHMs are limited.

Methods

We conducted a retrospective cohort study using data of patients from the US Veterans Affairs HCV Clinical Case Registry who had a positive HCV RNA test (10/1999-08/2009). Patients receiving interferon-based antiviral therapy (AVT) were identified. SVR was defined as negative HCV RNA at least 12 weeks after end of AVT. Risks of eight incident EHMs were evaluated in Cox regression models.

Results

Of the 160 875 HCV-infected veterans, 31 143 (19.4%) received AVT, of whom 10 575 (33.9%) experienced SVR. EHM risk was reduced in the SVR group compared with untreated patients for mixed cryoglobulinaemia (adjusted HR (aHR)=0.61; 95% CI 0.39 to 0.94), glomerulonephritis (aHR=0.62; 95% CI 0.48 to 0.79), porphyria cutanea tarda (PCT) (aHR=0.41; 95% CI 0.20 to 0.83), non-Hodgkin’s lymphoma (NHL) (aHR=0.64; 95% CI 0.43 to 0.95), diabetes (aHR=0.82; 95% CI 0.76 to 0.88) and stroke (aHR=0.84; 95% CI 0.74 to 0.94), but not for lichen planus (aHR=1.11; 95% CI 0.78 to 1.56) or coronary heart disease (aHR=1.12; 95% CI 0.81 to 1.56). Risk reductions were also observed when patients with SVR were compared with treated patients without SVR for mixed cryoglobulinaemia, glomerulonephritis, PCT and diabetes. Significant reductions in the magnitude of aHRs towards the null with increasing time to initiation of AVT after HCV diagnosis were observed for glomerulonephritis, NHL and stroke.

Conclusions

Risks of several EHMs of HCV infection are reduced after AVT with SVR. However, early initiation of AVT may be required to reduce the risk of glomerulonephritis, NHL and stroke.