bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential In HLA-Matched and Mismatched Donor-Recipient Pairs
Authors: Abdul Razzaq B , Scalora A , Koparde VN , Meier J , Mahmood M , Salman S , Jameson-Lee M , Serrano M , Sheth N , Voelkner M , Kobulnicky DJ , Roberts CH , Ferreira-Gonzalez A , Manjili MH , Buck GA , Neale MC , Toor AA 
Published: August 2015

Abstract.Immune reconstitution kinetics and subsequent clinical outcomes in HLA matched recipients of allogeneic stem cell transplantation (SCT) are variable and difficult to predict. Considering SCT as a dynamical system, may allow sequence differences across the exomes of the transplant donors and recipients to be used tosimulatean alloreactive T cell response, which may allow better clinical outcome prediction. To accomplish this, whole exome sequencing was performed on 34 HLA matched SCT donor-recipient pairs (DRP), and the nucleotide sequence differences translated to peptides. The binding affinity of the peptides to the relevant HLA in each DRP was determined. The resulting array of peptide-HLA binding affinity values in each patient was considered as anoperatormodifying a hypothetical T cell repertoirevector, in which each T cell clone proliferates in accordance to the logistic equation of growth. Using an iterating system of matrices, each simulated T cell clone’s growth was calculated with the steady state population being proportional to the magnitude of the binding affinity of the driving HLA-peptide complex. Incorporating competition between T cell clones responding to different HLA-peptide complexes reproduces a number of features of clinically observed T cell clonal repertoire in the simulated repertoire. These include, sigmoidal growth kinetics of individual T cell clones and overall repertoire, Power Law clonal frequency distribution, increase in repertoire complexity over time with increasing clonal diversity and finally, alteration of clonal dominance when a different antigen array is encountered, such as in stem cell transplantation. The simulated, alloreactive T cell repertoire was markedly different in HLA matched DRP. The patterns were differentiated by rate of growth, and steady state magnitude of the simulated T cell repertoire and demonstrate a possible correlation with survival. In conclusion, exome wide sequence differences in DRP may allow simulation of donor alloreactive T cell response to recipient antigens and may provide a quantitative basis for refining donor selection and titration of immunosuppression following SCT.
CG methylation covaries with differential gene expression between leaf and floral bud tissues ofBrachypodium distachyon
Authors: Roessler Kyria , Takuno Shohei , Gaut Brandon S. 
Published: August 2015

AbstractDNA methylation has the potential to influence plant growth and development through its influence on gene expression. To date, however, the evidence from plant systems is mixed as to whether patterns of DNA methylation vary significantly among tissues and, if so, whether these differences affect tissue-specific gene expression. To address these questions, we analyzed both bisulfite sequence (BSseq) and transcriptomic sequence data from three biological replicates of two tissues (leaf and floral bud) from the model grass speciesBrachypodium distachyon.Our first goal was to determine whether tissues were more differentiated in DNA methylation than explained by variation among biological replicates. Tissues were more differentiated than biological replicates, but the analysis of replicated data revealed high (>50%) false positive rates for the inference of differentially methylated sites (DMSs) and differentially methylated regions (DMRs). Comparing methylation to gene expression, we found that differential CG methylation consistently covaried negatively with gene expression, regardless as to whether methylation was within genes, within their promoters or even within their closest transposable element. The relationship between gene expression and either CHG or CHH methylation was less consistent. In total, CG methylation in promoters explained 9% of the variation in tissue-specific expression across genes, suggesting that CG methylation is a minor but appreciable factor in tissue differentiation.
Service provider barriers to treatment and care for people with mental health and alcohol and other drug comorbidity in a metropolitan region of South Australia
Authors: de Crespigny Charlotte , Grønkjær Mette , Liu Dennis , Moss John , Cairney Imelda , Procter Nicholas , Posselt Miriam , Francis Jebaraj Hepsibah Sharmil , Schultz Tim , Banders Andris , King Rosie , Lee Deb , Galletly Cherrie 
Published: August 2015

Purpose
– The purpose of this paper is to elicit clinicians’ and workers’ knowledge, experiences and opinions of key issues pertaining to comorbidity service needs of people aged 12 years and over in a metropolitan region of South Australia.

Design/methodology/approach
– As one component of a participatory action research project, this qualitative study used semi-structured interviews with mental health (MH) and alcohol and other drug (AOD) clinicians and workers (n=20).

Findings
– The participants expressed concerns involving stigma towards their clients. They highlighted lack of adequate MH and AOD comorbidity service accessibility and models, regularly available clinical comorbidity workforce development, and practice supervision and skills training. These factors influenced participants’ and their colleagues’ capacity and ability to access and provide appropriate help for people needing integrated treatment and care of their co-existing comorbid conditions.

Practical implications
– Findings highlight the need for coordinated and integrated, individualised holistic comorbidity services, including treatment and care best suited to Aboriginal people and refugees.

Originality/value
– This study emphasises the importance of government and non-government MH and AOD services ensuring that comorbidity is responded to collaboratively and systemically. It also demonstrates the importance of professional development.
You never know what’s around the next corner: exploring practitioners ' hope inspiring practices
Authors: Sælør Knut Tore , Ness Ottar , Borg Marit , Biong Stian 
Published: August 2015

Purpose– Hope is regarded central to recovery in a broad range of health conditions including mental health and substance use problems. Still the phenomenon, along with its implications to research and practice, has gained limited attention. The purpose of this paper is to explore first-person accounts of how practitioners nurture and inspire hope.Design/methodology/approach– This qualitative study is part of a larger action research project. Data were collected using in-depth interviews with eight participants. The interviews were transcribed verbatim and analyzed applying thematic analysis.Findings– Hope was perceived as a central phenomenon to practitioners within mental health and substance use services. The following overarching themes were identified through thematic analysis: “Believing in oneself and others,” “Seeing and acknowledging opportunities” and “maneuvering towards hope.”Research limitations/implications– It seems that there is a need for extending knowledge in how practitioners may inspire hope. In addition there seems to be a need for developing more knowledge on how practitioners’ own hope may be nurtured within a system that is constantly undergoing change and new demands.Practical implications– Participants considered their own hope as a prerequisite in being able to hope on behalf of others and strategies for inspiring hope were presented on both an individual and system level. Working conditions and challenges within the service system in itself entailed challenges, which at times made nurturing hope difficult. Systems need to embrace flexibility and openness, allowing efforts aimed at inspiring hope to be made. In addition, practitioner’s own hope and the importance of nurturing it, needs to be acknowledged within services. Hope needs to be viewed as a joint venture, in context and in relation to others.Originality/value– The paper contributes to the knowledge base on hope inspiring practices within a field sometimes associated with challenges and despair. It points out some important preconditions in relation to the challenges practitioners might encounter, both on an individual level and in relation to the service systemper se.
Cannabis psychosis, gender matters
Authors: Hamilton Ian , Galdas Paul , Essex Holly 
Published: August 2015

Purpose
– The purpose of this paper is to draw together key literature and analyses of data on admissions for cannabis psychosis in National Health Service hospitals in England (extracted from Hospital Episode Statistics (HES)) to highlight what is known about gender differences in cannabis psychosis and point towards suggestions for improving gender-sensitive treatment and future research.

Design/methodology/approach
– Analysis of British Crime Survey data and HES data were used in combination with data from previously published epidemiological studies to compare gender differences.

Findings
– Male cannabis users outnumber female users by 2:1, a similar gender ratio is found for those admitted to hospital with a diagnosis of schizophrenia or psychosis. However this ratio increases significantly for those admitted to hospital with a diagnosis of cannabis psychosis, with males outnumbering females by 4:1.

Research limitations/implications
– Consistent patterns in gender ratios for people admitted to hospital with cannabis psychosis over a period of 11 years are reported, it is not clear why this gender difference persists but it warrants further investigation which would be aided by improved gender recording at a systemic level.

Practical implications
– This review brings into focus the marked gender differences in cannabis psychosis. Attending to gender is important for research and treatment with the aim of improving understanding and providing gender-sensitive services.

Originality/value
– This paper adds to the literature on gender differences in cannabis psychosis.
An efficient clustering algorithm for wireless sensor networks
Authors: Alnuaimi Mariam , Shuaib Khaled , Alnuaimi Klaithem , Abed-Hafez Mohammed 
Published: August 2015

Purpose
– This paper aims to propose a new node energy-efficient algorithm with energy threshold to replace cluster heads. The proposed algorithm uses node ranking to elect cluster heads based on energy levels and positions of the nodes in reference to the base station (BS) used as a sink for gathered information. Because the BS calculates the number of rounds a cluster head can remain for as a cluster head in advance, this reduces the amount of energy wasted on replacing cluster heads each round which is the case in most existing algorithms, thus prolonging the network lifetime. In addition, a hybrid redundant nodes duty cycle is used for nodes to take turn in covering the monitored area is shown to improve the performance further.

Design/methodology/approach
– Authors designed and implemented the proposed algorithm in MATLAB. The performance of the proposed algorithm was compared to other well-known algorithms using different evaluation metrics. The performance of the proposed algorithm was enhanced over existing ones by incorporating different mechanisms such as the use of an energy-based threshold value to replace CHs and the use of a hybrid duty-cycle on nodes.

Findings
– Through simulation, the authors showed how the proposed algorithm outperformed PEGASIS by 15 per cent and LEACH by almost 70 per cent for the network life-time criterion. They found that using a fixed pre-defined energy threshold to replace CHs improved the network lifetime by almost 15 per cent. They also found that the network lifetime can be further improved by almost 7 per cent when incorporating a variable energy threshold instead of a fixed value. In addition to that, using hybrid-redundant nodes duty-cycle has improved the network lifetime by an additional 8 per cent.

Originality/value
– The authors proposed an energy-efficient clustering algorithm for WSNs using node ranking in electing CHs and energy threshold to replace CHs instead of being replaced every round.
Managerial decision making under specific emotions
Authors: Bachkirov Alexandre A. 
Published: August 2015

Purpose– The purpose of this paper is to investigate decision-processing effects of incidental emotions in managerial decision-making situations.Design/methodology/approach– A complex multi-attribute, multi-alternative decision task related to international human resources management is used as a research vehicle. The data are obtained by means of an electronic information board.Findings– Happiness and anger cause the decision maker to process less decision-relevant information, whereas fear activates more detail-oriented processing. The results are explained within the valence model and cognitive-appraisal framework.Research limitations/implications– A boundary condition of the study is the level of induced emotions. Processing effects of extremely high levels of emotions are not examined, which necessarily limits the generalizability of the findings. Also, the experiment focusses on the decision-processing effects of single isolated emotions extracted by manipulations; future research needs to examine decision-making implications of an entire emotion episode, which is likely to contain emotion mixtures.Practical implications– For managers, this study demonstrates the importance of being mindful of how incidental emotional states can bias choice processing in complex managerial decisions.Originality/value– This study extends earlier organizational research by focussing on decision-making consequences of emotion, rather than those of mood or stress. It brings together research on incidental emotions and process-tracing methodologies, thereby allowing for more direct assessment of the observed effects. Decision-processing consequences of emotion are shown to persist throughout a content-rich managerial decision task without being neutralized by an intensive cognitive engagement.
eMaintenance ontologies for data quality support
Authors: Aljumaili Mustafa , Wandt Karina , Karim Ramin , Tretten Phillip 
Published: August 2015

Purpose– The purpose of this paper is to explore the main ontologies related to eMaintenance solutions and to study their application area. The advantages of using these ontologies to improve and control data quality will be investigated.Design/methodology/approach– A literature study has been done to explore the eMaintenance ontologies in the different areas. These ontologies are mainly related to content structure and communication interface. Then, ontologies will be linked to each step of the data production process in maintenance.Findings– The findings suggest that eMaintenance ontologies can help to produce a high-quality data in maintenance. The suggested maintenance data production process may help to control data quality. Using these ontologies in every step of the process may help to provide management tools to provide high-quality data.Research limitations/implications– Based on this study, it can be concluded that further research could broaden the investigation to identify more eMaintenance ontologies. Moreover, studying these ontologies in more technical details may help to increase the understandability and the use of these standards.Practical implications– It has been concluded in this study that applying eMaintenance ontologies by companies needs additional cost and time. Also the lack or the ineffective use of eMaintenance tools in many enterprises is one of the limitations for using these ontologies.Originality/value– Investigating eMaintenance ontologies and connecting them to maintenance data production is important to control and manage the data quality in maintenance.
Phase III clinical study of maxacalcitol ointment in patients with palmoplantar pustulosis: A randomized, double‐blind, placebo‐controlled trial
Authors: Umezawa Yoshinori , Nakagawa Hidemi , Tamaki Kunihiko 
Published: August 2015

AbstractPalmoplantar pustulosis (PPP) often shows resistance to treatment. Vitamin D3 analog (VitD3) has been widely used for the treatment of psoriasis, however, the efficacy and safety of topical VitD3 treatment of PPP are not fully confirmed. Maxacalcitol topical ointment (22‐oxacalcitriol [OCT]) was applied twice daily for 8 weeks. Evaluation of efficacy was based on scored skin findings for three main symptoms (erythema, pustules/vesicles and keratinization/scales). The primary and secondary end‐points were the total and symptom‐specific scores of skin findings, respectively. A total of 188 patients with moderate or severe PPP were enrolled in the study and were randomized into either the OCT group (n = 95) or placebo group (n = 93). The total scores (mean ± standard error) of skin findings at the last observation adjusting for those on day 1 were 5.0 ± 0.20 in the OCT group and 6.9 ± 0.20 in the placebo group. There was a significant decrease in the total score of skin findings in the OCT group compared with the placebo group (P < 0.0001). In particular, the score of pustules/vesicles drastically decreased in the OCT group. In terms of safety, the incidence of adverse reactions in the OCT and placebo groups were 11.6% and 9.7%, respectively. These results indicate that OCT is effective and highly safe in the management of PPP. Topical OCT treatment was found to show a potent action on pustules/vesicles thereby contributing to the cure of PPP.
Analysis of laboratory data on ultrasonic monitoring of permeability reduction due to biopolymer formation in unconsolidated granular media
Authors: Berryman J.G. , Kwon T.‐H. , Dou S. , Ajo‐Franklin J.B. , Hubbard S.S. 
Published: August 2015

ABSTRACTWe show how to estimate the fluid permeability changes due to accumulated biopolymer within the pore space of a granular material using laboratory measurements of overall permeability, together with various well‐known quantitative measures (e.g., porosity, specific surface area, and formation factor) of the granular medium microstructure. The main focus of the paper is on mutual validation of existing theory and a synthesis of new experimental results. We find that the theory and data are in good agreement within normal experimental uncertainties. We also establish quantitative empirical relationships between seismic and/or acoustic attenuation and overall permeability for these same systems.
Contrasting responses of male and female foraging effort to year‐round wind conditions
Authors: Lewis Sue , Phillips Richard A. , Burthe Sarah J. , Wanless Sarah , Daunt Francis 
Published: August 2015

Summary

There is growing interest in the effects of wind on wild animals, given evidence that wind speeds are increasing and becoming more variable in some regions, particularly at temperate latitudes. Wind may alter movement patterns or foraging ability, with consequences for energy budgets and, ultimately, demographic rates.

These effects are expected to vary among individuals due to intrinsic factors such as sex, age or feeding proficiency. Furthermore, this variation is predicted to become more marked as wind conditions deteriorate, which may have profound consequences for population dynamics as the climate changes. However, the interaction between wind and intrinsic effects has not been comprehensively tested.

In many species, in particular those showing sexual size dimorphism, males and females vary in foraging performance. Here, we undertook year‐round deployments of data loggers to test for interactions between sex and wind speed and direction on foraging effort in adult European shags Phalacrocorax aristotelis, a pursuit‐diving seabird in which males are c. 18% heavier.

We found that foraging time was lower at high wind speeds but higher during easterly (onshore) winds. Furthermore, there was an interaction between sex and wind conditions on foraging effort, such that females foraged for longer than males when winds were of greater strength (9% difference at high wind speeds vs. 1% at low wind speeds) and when winds were easterly compared with westerly (7% and 4% difference, respectively).

The results supported our prediction that sex‐specific differences in foraging effort would become more marked as wind conditions worsen. Since foraging time is linked to demographic rates in this species, our findings are likely to have important consequences for population dynamics by amplifying sex‐specific differences in survival rates.
Understanding snacking through a practice theory lens
Authors: Twine Richard 
Published: August 2015

AbstractThis article approaches snacking from a practice theory perspective in order to understand how this reframing may afford new insights. In doing so it also contributes to sociological thinking on eating practices and their reproduction as well as reflecting upon the ontological assertions of practice theory and its theory of social change. In particular this article argues that the re‐conceptualisation serves to clarify a sociological research agenda for eating practices associated with snacking. It is argued that setting snacking within routine temporalities and spatialities and as bound up in the recursivity between practices and relations is especially important for thinking about snacking sociologically. In common with applications of practice theory in the field of sustainability transitions the aim is to move beyond individualistic assumptions of behaviour change and instead situate snacking as an eating practice with health implications that has emerged within the social, temporal, economic and cultural organisation of everyday life.
Evaluating estimators of species richness: the importance of considering statistical error rates
Authors: Gwinn Daniel C. , Allen Michael S. , Bonvechio Kimberly I. , V. Hoyer Mark , Beesley Leah S. 
Published: August 2015

Summary

The performance of species richness estimators can be highly variable. Evaluating the accuracy and precision of different estimators for different assemblages is common in the ecological literature, but estimator performance is rarely measured in terms of research goals such as detecting patterns in diversity.

We evaluated the efficacy of nonparametric richness estimators to detect changes (i.e. type‐I and type‐II error rates) in species richness using two experimental designs: a block design and a trend analysis. We also evaluated estimator efficacy across a variety of species‐abundance distributions, species number and sample sizes. The evaluation was performed using simulated data that mimicked the qualities of real data to ensure real‐world relevance.

We found that the bias and precision of all estimators evaluated had high sensitivity to sample size and shifts in the species‐abundance distribution. Importantly, all estimators demonstrated elevated type‐I error rates when the species‐abundance distribution varied. These inflated type‐I error rates resulted in spurious conclusions about patterns in species richness.

Results suggest that caution should be taken when using nonparametric estimators to detect pattern in species richness. Furthermore, estimator evaluations should always include measures of type‐I and type‐II error rates. These quantities can reveal the inference consequences of the dependency of estimator bias and precision on community and sampling characteristics.