bluuebunny/crossref_metadata_2025 huggingface dataset:
DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts
Authors: Lee Donghyung , Bigdeli T. Bernard , Williamson Vernell S. , Vladimirov Vladimir I. , Riley Brien P. , Fanous Ayman H. , Bacanu Silviu-Alin
Published: June 2015

Motivation: To increase the signal resolution for large-scale meta-analyses of genome-wide association studies, genotypes at unmeasured single nucleotide polymorphisms (SNPs) are commonly imputed using large multi-ethnic reference panels. However, the ever increasing size and ethnic diversity of both reference panels and cohorts makes genotype imputation computationally challenging for moderately sized computer clusters. Moreover, genotype imputation requires subject-level genetic data, which unlike summary statistics provided by virtually all studies, is not publicly available. While there are much less demanding methods which avoid the genotype imputation step by directly imputing SNP statistics, e.g. Directly Imputing summary STatistics (DIST) proposed by our group, their implicit assumptions make them applicable only to ethnically homogeneous cohorts.

Results: To decrease computational and access requirements for the analysis of cosmopolitan cohorts, we propose DISTMIX, which extends DIST capabilities to the analysis of mixed ethnicity cohorts. The method uses a relevant reference panel to directly impute unmeasured SNP statistics based only on statistics at measured SNPs and estimated/user-specified ethnic proportions. Simulations show that the proposed method adequately controls the Type I error rates. The 1000 Genomes panel imputation of summary statistics from the ethnically diverse Psychiatric Genetic Consortium Schizophrenia Phase 2 suggests that, when compared to genotype imputation methods, DISTMIX offers comparable imputation accuracy for only a fraction of computational resources.

Availability and implementation: DISTMIX software, its reference population data, and usage examples are publicly available at http://code.google.com/p/distmix.

Contact:  dlee4@vcu.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
UniAlign: protein structure alignment meets evolution
Authors: Zhao Chunyu , Sacan Ahmet
Published: June 2015

Motivation: During the evolution, functional sites on the surface of the protein as well as the hydrophobic core maintaining the structural integrity are well-conserved. However, available protein structure alignment methods align protein structures based solely on the 3D geometric similarity, limiting their ability to detect functionally relevant correspondences between the residues of the proteins, especially for distantly related homologous proteins.

Results: In this article, we propose a new protein pairwise structure alignment algorithm (UniAlign) that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles and residue conservation. We define a per-residue score (UniScore) as a weighted sum of these and other features and develop an iterative optimization procedure to search for an alignment with the best overall UniScore. Our extensive experiments on CDD, HOMSTRAD and BAliBASE benchmark datasets show that UniAlign outperforms commonly used structure alignment methods. We further demonstrate UniAlign's ability to develop family-specific models to drastically improve the quality of the alignments.

Availability and implementation: UniAlign is available as a web service at: http://sacan.biomed.drexel.edu/unialign

Contact:  ahmet.sacan@drexel.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automated profiling of individual cell–cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING)
Authors: Merouane Amine , Rey-Villamizar Nicolas , Lu Yanbin , Liadi Ivan , Romain Gabrielle , Lu Jennifer , Singh Harjeet , Cooper Laurence J.N. , Varadarajan Navin , Roysam Badrinath
Published: June 2015

Motivation: There is a need for effective automated methods for profiling dynamic cell–cell interactions with single-cell resolution from high-throughput time-lapse imaging data, especially, the interactions between immune effector cells and tumor cells in adoptive immunotherapy.

Results: Fluorescently labeled human T cells, natural killer cells (NK), and various target cells (NALM6, K562, EL4) were co-incubated on polydimethylsiloxane arrays of sub-nanoliter wells (nanowells), and imaged using multi-channel time-lapse microscopy. The proposed cell segmentation and tracking algorithms account for cell variability and exploit the nanowell confinement property to increase the yield of correctly analyzed nanowells from 45% (existing algorithms) to 98% for wells containing one effector and a single target, enabling automated quantification of cell locations, morphologies, movements, interactions, and deaths without the need for manual proofreading. Automated analysis of recordings from 12 different experiments demonstrated automated nanowell delineation accuracy >99%, automated cell segmentation accuracy >95%, and automated cell tracking accuracy of 90%, with default parameters, despite variations in illumination, staining, imaging noise, cell morphology, and cell clustering. An example analysis revealed that NK cells efficiently discriminate between live and dead targets by altering the duration of conjugation. The data also demonstrated that cytotoxic cells display higher motility than non-killers, both before and during contact.

Contact: broysam@central.uh.edu or nvaradar@central.uh.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A NuSTAR observation of disc reflection from close to the neutron star in 4U 1608–52
Authors: Degenaar N. , Miller J. M. , Chakrabarty D. , Harrison F. A. , Kara E. , Fabian A. C.
Published: June 2015

Studying the reflection of X-rays off the inner edge of the accretion disc in a neutron star low-mass X-ray binary allows us to investigate the accretion geometry and to constrain the radius of the neutron star. We report on a NuSTAR observation of 4U 1608–52 obtained during a faint outburst in 2014 when the neutron star, which has a known spin frequency of ν = 620 Hz, was accreting at ≃1–2 per cent of the Eddington limit. The 3–79 keV continuum emission was dominated by a Γ ≃ 2 power law, with an ≃1–2 per cent contribution from a kTbb ≃ 0.3–0.6 keV blackbody component. The high-quality NuSTAR spectrum reveals the hallmarks of disc reflection; a broad iron-line peaking near 7 keV and a Compton back-scattering hump around ≃20–30 keV. Modelling the disc reflection spectrum points to a binary inclination of i ≃30°–40° and a small ‘coronal’ height of h ≲8.5GM/c2. Furthermore, our spectral analysis suggests that the inner disc radius extended to Rin ≃ 7–10GM/c2, close to the innermost stable circular orbit. This constrains the neutron star radius to R ≲21 km and the redshift from the stellar surface to z ≳0.12, for a mass of M = 1.5 M⊙ and a spin parameter of a = 0.29.
Female Intrasexual Competition in Primates
Authors: Scott Nicole M.
Published: June 2015

Males and females compete with each other and amongst their own sex, but often for different reasons. This chapter enriches current understanding of female-female competition in humans by examining competition in other primates; it explores why females compete and discusses when affiliation and cooperation may lead to better outcomes. Socioecological constraints on a species—such as social organization, food competition, and dispersal preference—play a major role in the structure of female-female relationships; notable attention is given to factors that affect social relationships: food competition, reproduction, dispersal, and dominance. Bond maintenance behaviors and communication strategies are also discussed relative to female-female relationships. Three nonhuman primate societies are examined, and potential lessons from these structures are gleaned where possible. The chapter reviews human progress in overcoming phylogenetic and ecological constraints in favor of women’s societal liberties.
Emerging Adulthood Theory and Social Class
Authors: du Bois-Reymond Manuela
Published: June 2015

Emerging adulthood theory (EAT) has gained wide support in the social sciences over the past 15 years despite critical comments also being voiced. This contribution positions EAT within the main European traditions of theories about change in the lives of young people. It shows that EAT has antecedents in many of these theories, but without taking social class as thoroughly into account as it should. This is demonstrated by reanalyzing a US survey and by, albeit indirectly, referring to a European project that established a typology on educational disadvantage based on a multilayered methodology. The chapter encourages increasing cooperation between scholars in the field of youth studies in order to both overcome disciplinary rigidity and discourage a naïve reliance on interdisciplinarity as remedy for all problems.
Luminosity and spin-period evolution of GX 304−1 during outbursts from 2009 to 2013 observed with the MAXI/GSC, RXTE/PCA, and Fermi/GBM
Authors: Sugizaki Mutsumi , Yamamoto Takayuki , Mihara Tatehiro , Nakajima Motoki , Makishima Kazuo
Published: June 2015

A report is made on the luminosity and pulse period evolution of the Be binary X-ray pulsar GX 304−1 during a series of outbursts from 2009 to 2013 observed by MAXI/GSC, RXTE/PCA, and Fermi/GBM. In total, 12 outbursts repeated by ∼ 132.2 d were observed, which is consistent with the X-ray periodicity of this object observed in the 1970s. These 12 outbursts, together with those in the 1970s, were all found to recur with a well-defined period of 132.189 ± 0.02 d, which can be identified with the orbital period. The pulse period of ∼ 275 s, obtained from the RXTE/PCA and Fermi/GBM data, apparently exhibited a periodic modulation synchronized with the outburst period, suggesting the pulsar orbital motion, which is superposed on a secular spin-up trend throughout the entire active phase. The observed pulse period changes were successfully represented by a model composed of the binary orbital modulation and pulsar spin up caused by mass accretion through an accretion disk. The orbital elements obtained from the best-fit model, including the projected orbital semi-major axis ax sin i ≃ 500–600 light-s and an eccentricity e ≃ 0.5, are typical of Be binary X-ray pulsars.
Characteristic Formation of Hyaluronan-Cartilage Link Protein-Proteoglycan Complex in Salivary Gland Tumors
Authors: Kuwabara Hiroko , Nishikado Akira , Hayasaki Hana , Isogai Zenzo , Yoneda Masahiko , Kawata Ryo , Hirose Yoshinobu
Published: June 2015

Hyaluronan (HA) and its binding molecules, cartilage link protein (LP) and proteoglycan (PG), are structural components of the hydrated extracellular matrix. Because these molecules play important roles in the tumor microenvironment, we examined the distribution of HA, LP, versican, and aggrecan in salivary gland tumors using histochemical and immunohistochemical methods, including double staining. LP was present in pleomorphic adenoma (PA) and adenoid cystic carcinoma (ACC) tissues, and aggrecan was absent in the malignant tumors that we investigated. LP colocalized with both HA and aggrecan in the chondromyxoid matrix of PA, suggesting the presence of a HA-LP-aggrecan complex. Furthermore, the HA-LP-versican complex could be observed in the pseudocystic space of the cribriform structures in ACC. The characteristic HA-LP-PG complex in PA and ACC might play a role in the behavior of tumors, and immunohistochemical analysis of these molecules could represent a diagnostic adjunct for salivary gland tumors.
Benzodiazepine Use and Cognitive Decline in Elderly With Normal Cognition
Authors: Zhang Yuhai , Zhou Xiao-hua , Meranus Dana H. , Wang Linbo , Kukull Walter A.
Published: June 2015

Benzodiazepine (BZD) use may be associated with dementia. However, differing opinions exist regarding the effect of BZDs on long-term changes in cognition. We evaluated the association between BZD use and cognitive decline in the elderly with normal cognition from the National Alzheimer’s Disease Coordinating Center’s Uniform Data Set. The study exposure, BZD use, was classified 2 ways: any-use [reported BZD use at a minimum of 1 Alzheimer's disease center (ADC) visit] and always-use (reported BZD use at all ADC visits). The reference group included participants without any declared BZD use at any Alzheimer's Disease Center (ADC) visit. The main outcome measures were Clinical Dementia Rating Sum of Boxes score and Mini-Mental State Examination score. We observed a decline in cognitive status over time in the 2 comparison groups. All participants who reported taking BZDs had poorer cognitive performance at all visits than nonusers. However, cognitive decline was statistically similar among all participants. We found no evidence of an association between BZD use and cognitive decline. The poor cognitive performance in BZD users may be due to prodromal symptoms caused by preclinical dementia processes.
Discrete Distributional Differential Expression (D3E) - A Tool for Gene Expression Analysis of Single-cell RNA-seq Data
Authors: Delmans Mihails , Hemberg Martin
Published: June 2015

The advent of high throughput RNA-seq at the single-cell level has opened up new opportunities to elucidate the heterogeneity of gene expression. One of the most widespread applications of RNA-seq is to identify genes which are differentially expressed between two experimental conditions. Here, we present a discrete, distributional method for differential gene expression (D3E), a novel algorithm specifically designed for single-cell RNA-seq data. We use synthetic data to evaluate D3E, demonstrating that it can detect changes in expression, even when the mean level remains unchanged. Since D3E is based on an analytically tractable stochastic model, it provides additional biological insights by quantifying biologically meaningful properties, such as the average burst size and frequency. We use D3E to investigate experimental data, and with the help of the underlying model, we directly test hypotheses about the driving mechanism behind changes in gene expression.
A cell cycle-controlled redox switch regulates the topoisomerase IV activity
Authors: Narayanan Sharath , Janakiraman Balaganesh , Kumar Lokesh , Radhakrishnan Sunish Kumar
Published: June 2015

Topoisomerase IV (topo IV), an essential factor during chromosome segregation, resolves the catenated chromosomes at the end of each replication cycle. How the decatenating activity of the topo IV is regulated during the early stages of the chromosome cycle despite being in continuous association with the chromosome remains poorly understood. Here we report a novel cell cycle-regulated protein in Caulobacter crescentus, NstA (negative switch for topo IV decatenation activity), that inhibits the decatenation activity of the topo IV during early stages of the cell cycle. We demonstrate that in C. crescentus, NstA acts by binding to the ParC DNA-binding subunit of topo IV. Most importantly, we uncover a dynamic oscillation of the intracellular redox state during the cell cycle, which correlates with and controls NstA activity. Thus, we propose that predetermined dynamic intracellular redox fluctuations may act as a global regulatory switch to control cellular development and cell cycle progression and may help retain pathogens in a suitable cell cycle state when encountering redox stress from the host immune response.
Sequence determinants of improved CRISPR sgRNA design
Authors: Xu Han , Xiao Tengfei , Chen Chen-Hao , Li Wei , Meyer Clifford A. , Wu Qiu , Wu Di , Cong Le , Zhang Feng , Liu Jun S. , Brown Myles , Liu X. Shirley
Published: June 2015

The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques for discovering phenotype-associated gene function. We systematically assessed the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens. Leveraging the information from multiple designs, we derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments. Our model confirmed known features and suggested new features including a preference for cytosine at the cleavage site. The model was experimentally validated for sgRNA-mediated mutation rate and protein knockout efficiency. Tested on independent data sets, the model achieved significant results in both positive and negative selection conditions and outperformed existing models. We also found that the sequence preference for CRISPRi/a is substantially different from that for CRISPR/Cas9 knockout and propose a new model for predicting sgRNA efficiency in CRISPRi/a experiments. These results facilitate the genome-wide design of improved sgRNA for both knockout and CRISPRi/a studies.
Testing the effect of marketing strategy alignment and triple-A supply chain on performance in Egypt
Authors: Attia Ahmed
Published: June 2015

Purpose

– The purpose of this paper is to examine the effect of triple-A supply chain and marketing strategy alignment on the performance by collecting and analyzing data from the textile industry in Egypt.

Design/methodology/approach

– A research model is proposed which describes the impact marketing strategy alignment, triple-A supply chain on supply chain performance and organizational performance. The proposed research model and hypotheses were tested using correlation analysis and structural equation modeling based on data collected from 153 companies working in the Egyptian textile industry.

Findings

– The results of the study support that organizational performance is positively associated supply chain performance. Also supply chain performance is directly affected by triple-A supply chain and marketing strategy alignment.

Research limitations/implications

– The data used in this study were collected from 153 companies working in the Egyptian textile industry. The generalization of the study results may be limited by the size of the sample.

Originality/value

– This study provides a useful working model in the textile industry. The results suggest successful implementation of triple-A supply chain and marketing strategy alignment will help in improving the supply chain performance, which in turn improves organizational performance.
Managing diversity and social divisions in nurses’ work teams
Authors: Desivilya Helena , Raz Michal
Published: June 2015

Purpose

– The purpose of this paper is to discern the legacies of social divisions, notably protracted social conflict on team members’ relations, collaborative interactions and ways of coping with such work-life reality.

Design/methodology/approach

– This study constitutes a pilot phase of a research on nationally and ethnically diverse nurses’ teams operating in medical centers. It used qualitative methodology: a semi-structured individual interviews with 12 nurses.

Findings

– The findings underscore the challenge of engaging diversity in mixed work teams operating in the shadow of protracted conflict. The results indicated inter-group biases, implicit discrimination and tensions due to the salience of social categorization and the faultline phenomenon. These tensions mount in crisis situations, such as violent incidents associated with the national conflict. The major coping pattern was directing the disagreements to a hidden sphere. The findings showed paucity of organizational level efforts to engage diversity and social divisions-related issues. In spite of the complexities associated with diverse workplaces, the nurses revealed high capability of maintaining cooperative interactions and effectively performing their healthcare tasks.

Research limitations/implications

– The current study represents a pilot phase of a larger research project. Subsequent stages will extend the sample size and use additional research instruments for data collection.

Practical implications

– Human resources managers need to address the organizational issues related to diversity and social divisions, including policy and training activities.

Social implications

– Engaging “otherness” remains a considerable challenge in diverse work setting, especially when team work constitutes the main work pattern. It should be faced by work organizations and social institutions.

Originality/value

– The study involves an innovative element as it attempts to elucidate the ramifications of diversity and inter-group tensions in “real-life” circumstances; namely, work setting in the context of a divided society. Most of the previous research examined such phenomena in the laboratory and/or on ad hoc groups.
Thermophoresis and Brownian effects on natural convection of nanofluids in a square enclosure with two pairs of heat source/sink
Authors: Noghrehabadi Aminreza , Samimi Behbahan Amin , Pop I.
Published: June 2015

Purpose

– The purpose of this paper is to study natural convection heat transfer and fluid flow in a square cavity filled with CuO-water nanofluid.

Design/methodology/approach

– The entire length of the bottom wall of the cavity is covered by two pairs of heat source-sink, whereas the other walls are insulated. The governing equations of fluid flow are discretized using a finite volume method with a collocated grid arrangement. The coupling between velocity and pressure is solved using the SIMPLEC and the Rhie and Chow interpolation is used to avoid the checker-board solutions for the pressure.

Findings

– The numerical results are reported for the effect of Rayleigh number, solid volume fraction and both presence and absence of thermophoresis and Brownian motion effects. The numerical results show an improvement in heat transfer rate for the whole range of Rayleigh numbers when Brownian and thermophoresis effects are considered. Furthermore, an increase in the Rayleigh number and nanoparticle volume fraction in both cases – when Brownian and thermophoresis effects are neglected or considered – has an excellent influence on heat transfer of nanofluids.

Originality/value

– The area of nanofluids is very original.
Exploring the meanings and experiences of health among Filipino female household service workers in Hong Kong
Authors: Bernadas Jan Michael Alexandre Cortez
Published: June 2015

Purpose

– The purpose of this paper is to explore the meanings and experiences of health of Filipino female household service workers (FHSWs) in Hong Kong (HK).

Design/methodology/approach

– It draws theoretic insights from culture-centered approach to health communication and uses in-depth interviews and field notes.

Findings

– For FHSWs, meanings of health are contingent on work. Health is valued not just because it allows FHSWs to fulfill the daily demands of employers but also it provides assurance for sustained employment contracts. Relative to formal labor and migration policies, informal rules and regulations of employers put unreasonable demand for FHSWs to be healthy. Furthermore, FHSWs experience health along the themes of periphery and center, physical and non-physical, internal and external, and right and privilege.

Research limitations/implications

– The experiences and meanings of health reported in this paper are limited to FHSWs in HK and may differ from other countries. Employers, non-government organizations, and private and public health care personnel need to be included to generate a more nuanced discussion of migration health in HK.

Practical implications

– In designing health promotion for FHSWs, employers as target audience should also be considered.

Originality/value

– Despite growing evidence, the consequences of international and temporary labor migration on women’s health largely remain under-theorized. To date, this paper is one of the few to engage health communication theory in rethinking migration health scholarship.
Colorectal cancer screening behaviors among South Asian immigrants in Canada: a qualitative study
Authors: Crawford Joanne , Ahmad Farah , Beaton Dorcas E. , Bierman Arlene S.
Published: June 2015

Purpose

– The purpose of this paper is to gain an in-depth understanding of beliefs, attitudes, and reasons for decision making about colorectal cancer (CRC) screening among South Asian (SA) immigrants.

Design/methodology/approach

– Six focus groups conducted in English, Punjabi, and Urdu were held with 42 SA immigrants, 50-74 years old and at average risk for CRC, from November 2012 to May 2013. All focus group discussions were audio-taped and transcribed verbatim. Data analysis used an inductive and systematic approach employing constant comparison techniques.

Findings

– Three dominant themes emerged. Beliefs and attitudes towards cancer and screening represented SA immigrant’s perceptions that early detection was beneficial; screening was not necessary in the absence of symptoms; cancer was scary; and the loss of previously established bowel practices upon immigration as potential risks for CRC. Knowledge and awareness focused on unscreened participants’ cancer stories; screened participants’ knowledge of CRC, risk factors, and screening; experiential learning from focus groups; and screened participants’ strategies to promote screening. Support and accessibility concentrated on physician support and responsibility to provide information, explanation, and recommend screening to facilitate access.

Originality/value

– Findings provide novel insights on socio-cultural context, beliefs, and barriers to CRC screening among SA immigrants. Culturally appropriate community-based strategies included story-telling, the use of social networks, and greater physician engagement. Enhancing collaborative partnerships with physicians and public health may minimize structural barriers and reduce health disparities. Future research could explore effectiveness of outreach strategies including these collaborations.
Expert views of peer-based interventions for prisoner health
Authors: Woodall James , South Jane , Dixey Rachael , de Viggiani Nick , Penson William
Published: June 2015

Purpose

– Formalised support services for prisoners that rely on peer methods of delivery show promising health and social outcomes but there is also conjecture that negative effects, both at an individual and organisational level, can occur. The paper aims to discuss these issues.

Design/methodology/approach

– Individuals with recognised professional expertise from various sectors (including ex-prisoners) were invited to contribute to an expert symposium to share their perceptions of the positive and negative effects of peer interventions in prison. Discussions and debate were audio recorded with the consent of all delegates and verbatim transcripts were analysed using framework analysis.

Findings

– According to the participants, peer interventions in the prison setting created both positive and negative impacts. It was clear from the evidence gathered that peer interventions in prisons can impact positively on health outcomes, but these effects were perceived to be more well-defined for peer deliverers. The notion that peer deliverers can be subjected to “burnout” suggests that supervisory processes for peer workers need to be considered carefully in order to avoid the intervention from being counter-productive. Organisationally, one of the salient issues was the adverse effects that peer interventions cause to the security of the prison.

Originality/value

– To the authors’ knowledge, this is the first time an expert symposium has been conducted to specifically examine peer interventions in prison and to consider the effects, both positive and negative, of such schemes.
Initial Impacts of the Patient Care Networks of Alabama Initiative
Authors: Bronstein Janet M. , Morrisey Michael A. , Sen Bisakha , Engler Sally , Smith Wilson K.
Published: June 2015

Objectives

To estimate the effects of medical home support on the use of clinical services and Medicaid expenditures.

Data Source

Medicaid claims.

Study Design

A difference‐in‐differences model where changes in utilization and expenditures of the intervention group are compared to changes in the nonintervention group.

Extraction Methods

Using Medicaid claims from October 2010 through September 2013, service use and expenditures are measured for 12 months before and 21 months after implementation. Changes for four health status groups are examined separately.

Principal Findings

The introduction of community‐based support was associated with a small reduction in use and no statistically significant overall effect on expenditures. However, among those with chronic and/or mental health conditions, there were modest, statistically significant increases in use of and expenditures for a range of ambulatory and inpatient health care services, while service use for those without these conditions declined. Emergency department use increased for all groups.

Conclusions

Community‐based support for medical home practices is associated with a shift in the service mix provided to higher cost, more vulnerable subgroups in Medicaid. Such systems are unlikely to be associated with significant overall cost savings, at least in the short term, but may have other benefits.
Immune alterations in acute bipolar depression
Authors: Dickerson F. , Katsafanas E. , Schweinfurth L. A. B. , Savage C. L. G. , Stallings C. , Origoni A. , Khushalani S. , Lillehoj E. , Yolken R.
Published: June 2015

Objective

Immunologic abnormalities have been found in bipolar disorder and acute mania. However, there have been fewer studies of patients with acute bipolar depression.

Method

Blood samples were obtained from individuals with acute bipolar depression, acute mania, and controls. These samples were evaluated for antibodies to human herpesviruses, gliadin, Toxoplasma gondii, and endogenous retroviruses as well as for C‐reactive protein (CRP) and pentraxin‐3 using immunoassay methods. Linear regression models were used to compare the levels of the markers controlling for demographic and clinical variables. A subset of the bipolar depressed group was evaluated at a 6‐month follow‐up.

Results

The sample consisted of 82 individuals with acute bipolar depression, 147 with acute mania, and 280 controls. The levels of CRP and IgG antibodies to an endogenous retrovirus, Mason‐Pfizer monkey virus (MPMV), were significantly elevated in the bipolar depressed group. Levels of pentraxin‐3 were reduced in both psychiatric groups. An evaluation of 32 individuals 6 months after hospitalization for bipolar depression showed a significant decrease in the levels of MPMV antibodies, but not a change in the other markers.

Conclusion

Individuals with acute bipolar depression show immune alterations. Some of the alterations are similar to those found in acute mania.
Austerity, Right Populism, and the Crisis of Labour in Canada
Authors: Thomas Mark P. , Tufts Steven
Published: June 2015

In the aftermath of the 2008 financial crisis, neoliberal governments embarked on austerity programs that include reducing public services, imposing public sector wage restraint, and reorganizing public sector working conditions and labour relations. In this context of economic crisis and austerity, populism has risen across North America and Europe on both the right and left of the political spectrum. The rise of right populism in particular confronts unions with key organizational and strategic challenges as neoliberal governments seek to mobilize right populist discourses in their efforts to restructure work and labour relations. Using a socio‐geographic framework, and based on an examination of post‐2008 legislative and policy measures undertaken at the federal, provincial, municipal levels in Canada, this paper explores the nexus between “uneven austerity”, rising populism, and union strategic capacities. We examine this intersection of austerity and populism at multiple scales to reveal the implications for organized labour.
Systematic review: cessation of long‐term nucleos(t)ide analogue therapy in patients with hepatitis B e antigen‐negative chronic hepatitis B
Authors: Chang M.‐L. , Liaw Y.‐F. , Hadziyannis S. J.
Published: June 2015

Background

It has been debated whether finite nucleos(t)ide analogue therapy is feasible in HBeAg‐negative chronic hepatitis B.

Aim

To review this issue systematically.

Methods

Using text terms HBsAg and various nucleos(t)ide analogues, PubMed was searched between 1995 and 2014 to find studies on therapy >6 months in adult HBeAg‐negative chronic hepatitis B patients with off‐therapy follow‐up >6 months.

Results

Twenty‐two studies with a total of 1732 patients were identified and included. The median duration of therapy, consolidation therapy and off‐therapy follow‐up ranged from 6 months to 8 years, 4 to 96 weeks and 6 to 80 months respectively. Patients were monitored with serum ALT and HBV DNA monthly in the first 1–3 months and every 3–6 months afterwards in most studies. The 1‐year off‐therapy ‘virological relapse’ (HBV DNA >2000 IU/mL) and ‘clinical relapse’ (HBV DNA > 2000 IU/mL + ALT elevation) occurred in <70% and <50% of the patients, respectively, and <40% of the patients received re‐treatment. These rates were higher in patients with shorter treatment, shorter consolidation therapy and those treated with less potent nucleos(t)ide analogues. Off‐therapy severe flares were rare and hepatic decompensation was reported in only one patient with cirrhosis. Biochemical relapse reflecting enhanced immune‐mediated hepatocyte killing may lead to a higher chance for off‐therapy HBsAg seroclearance and be possibly desirable.

Conclusion

With an appropriate stopping rule and a proper off‐therapy monitoring plan, cessation of long‐term nucleos(t)ide analogue therapy prior to HBsAg seroclearance in HBeAg‐negative chronic hepatitis B is a feasible alternative to indefinite treatment.
Step carefully, there is an elephant in the room: human trampling as threat or treat in conservation
Authors: Ejrnæs Rasmus
Published: June 2015

The impact from tourism, e.g. trampling, may be a real concern in nature reserves. Conradi et al. (2015, this issue) studied disturbance effects on grassland vegetation along paths in a nature reserve and found only small negative effects, in good accordance with the local history. Our understanding of disturbances has changed over history and I advocate an evolutionary perspective.
Emergence and early survival of early versus late seral species in Great Basin restoration in two different soil types
Authors: Uselman Shauna M. , Snyder Keirith A. , Leger Elizabeth A. , Duke Sara E.
Published: June 2015

Questions

How does performance of a native early seral seed mix during early life stages compare to that of a late seral mix when seeded with Bromus tectorum or Taeniatherum caput‐medusae? Does either mix reduce survival of exotic annual grasses during early life stages, and does this effect differ with soil type? Is exotic performance stronger in one soil type, and does native performance when growing with exotics differ between soil types as a result of exotic preference?

Location

University of Nevada Agricultural Research Station, Reno, NV, US.

Methods

We compared seedling emergence and early survival (Nov through May) of two native seed mixes, each composed of grass, forb and shrub functional groups, when growing with B. tectorum or T. caput‐medusae in soils of contrasting texture (sandy loam and clay loam). Natives were also seeded without exotics. Performance of an early seral mix was compared with that of a late seral mix representative of species commonly used in Great Basin restoration.

Results

Comparing emergence and survival probabilities, early seral natives generally outperformed late seral natives when growing with exotics and had earlier emergence timing, although results differed among functional groups and soil types. In contrast, survival probabilities did not differ between the early and late seral mixes when growing without exotics. Within each seed mix, native grasses exhibited the highest emergence probabilities of the functional groups. Natives did not suppress exotics in early life stages. Performance of B. tectorum was higher on sandy loam, while T. caput‐medusae was highly successful in both soil types. Performance of native functional groups differed by soil type when growing with exotics but did not differ when growing without exotics. Survival of native grasses, in particular, was generally higher on sandy loam when growing with exotics.

Conclusions

Findings suggest that the use of early seral natives in areas invaded by exotic annual grasses may improve early seedling survival in the Great Basin, in comparison to the use of later seral species in traditional seed mixes. Variation in native performance in the two soil types may be helpful in tailoring seed mixes to different sites.
Co‐creation and New Media: The Entrepreneurial Work of Climbing Photographers in Digital Times
Authors: Dumont Guillaume
Published: June 2015

The term co‐creation refers to the emergence and rise of consumers’ participation in making and circulating media content, participation that has become a salient source of economic and symbolic value. The recuperation of this content for commercial purposes has been progressively acknowledged, but less is known about how these co‐creative practices shape the work of professional media producers. In this article, I investigate this issue by exploring the work of professional climbing photographers. Climbing magazines and brands now use consumers’ produced content and the latter circulates on the channels traditionally reserved for professional content. Professional photographers, therefore, have to develop different strategies to secure work opportunities, and their work is becoming increasingly multilayered. In addition, while the co‐creative practices may be pleasurable for consumers, their impacts on the work of professionals are not as they result in an increase of labor effort to sustain professionals’ livelihoods as media producers.
The development of bystander intentions and social–moral reasoning about intergroup verbal aggression
Authors: Palmer Sally B. , Rutland Adam , Cameron Lindsey
Published: June 2015

A developmental intergroup approach was taken to examine the development of prosocial bystander intentions among children and adolescents. Participants as bystanders (N = 260) aged 8–10 and 13–15 years were presented with scenarios of direct aggression between individuals from different social groups (i.e., intergroup verbal aggression). These situations involved either an ingroup aggressor and an outgroup victim or an outgroup aggressor and an ingroup victim. This study focussed on the role of intergroup factors (group membership, ingroup identification, group norms, and social–moral reasoning) in the development of prosocial bystander intentions. Findings showed that prosocial bystander intentions declined with age. This effect was partially mediated by the ingroup norm to intervene and perceived severity of the verbal aggression. However, a moderated mediation analysis showed that only when the victim was an ingroup member and the aggressor an outgroup member did participants become more likely with age to report prosocial bystander intentions due to increased ingroup identification. Results also showed that younger children focussed on moral concerns and adolescents focussed more on psychological concerns when reasoning about their bystander intention. These novel findings help explain the developmental decline in prosocial bystander intentions from middle childhood into early adolescence when observing direct intergroup aggression.
Making sense of varying standards of care: the experiences of staff working in residential care environments for adults with learning disabilities
Authors: Hutchison Andrew , Kroese Biza Stenfert
Published: June 2015

Accessible summary

To find out why standards of care might vary in residential homes for adults with learning disabilities, this study describes the experiences of six care workers currently working in residential homes.

Each care worker took part in an interview where they were asked to talk about their jobs in detail.

Three things were found to be important aspects of care workers experiences: the quality of their relationships with others; their levels of motivation for their work; and their feelings about the environments they worked in.

The study discusses how each of those things can lead to variations in care standards.

Research evidence reveals that adults with learning disabilities who live in residential care facilities are being exposed to considerable variation in the standards of care they receive. High profile cases of substandard care have also raised concerns regarding the appropriateness of existing care provisions and practices. While attempts have been made to understand variations in care standards, there remains a need for more research in this area. Additionally, little attention has been paid to understanding support staff experiences of working in residential services and to developing a more theoretical understanding of the role they fulfil. Using interpretive phenomenological analysis (IPA), this study aimed to examine front‐line staff members' experiences of working in residential care for people with learning disabilities. Six experienced front‐line care workers (four female, two male) took part in semi‐structured interviews. Data were analysed according to the principles of IPA, and three superordinate themes were identified as being central to participants' experiences of their work roles: Degree of Positive Relationship Reciprocity; Value Congruence and Intrinsic Motivation; and Experiences of Environmental and Organisational Constraints. Results are discussed in relation to the existing literature on care standards and the factors associated with abusive or neglectful practices, and in terms of their contribution to theory and applied practice.
Fracture resistance of weakened bovine teeth after long‐term use of calcium hydroxide
Authors: Valera Marcia Carneiro , Albuquerque Maria Tereza Pedrosa , Yamasaki Mayra Cristina , Vassallo Flávia Nicolle Stefani , da Silva Denise Almeida e Silva Alves , Nagata Juliana Yuri
Published: June 2015

Background/Aim

In some parts of the world, revascularization may not be the most feasible treatment option for necrotic immature teeth. Therefore, apexification remains the most widely utilized treatment option for these cases. This study aimed to evaluate the fracture resistance of weakened bovine tooth roots treated with various irrigant solutions as well as long‐term application of calcium hydroxide intracanal medication (ICM).

Material and methods

One hundred seventy bovine teeth were randomly divided into three experimental groups (n = 50) and two control groups (n = 10). Group SS was irrigated with physiologic solution; group CHX was treated with 2% chlorhexidine gel and group NaOCl was irrigated with 1% sodium hypochlorite. After instrumentation, root canals were dressed with calcium hydroxide and evaluated at different periods (15, 60, 90, 180, and 360 days). The specimens were loaded at a 45° angle to measure fracture resistance through the use of an EMIC test machine.

Results

A decrease in fracture resistance was observed during the time of ICM dressing. The highest values of fracture resistance were observed in group SS with 15 days of ICM, not differing from the control group. Irrigation with NaOCl associated with ICM for 15 days presented the lowest fracture resistance; however, a statistically significant difference was not observed when compared with SS and CHX in the same time period. In longer periods of exposure to ICM (180 and 360 days), root canals irrigated with NaOCl and CHX showed significantly lower fracture resistance than SS (P < 0.05).

Conclusion

Apexification with periodic changes of calcium hydroxide medicament leads to weakness of the teeth independent of the irrigation solution used.
Mammals, freshwater reference states, and the mitigation of climate change
Authors: Moss Brian
Published: June 2015

Freshwater habitats have been severely altered by human activities, and legislation has variously been passed requiring assessment of the damage in preparation for its repair. The current condition is generally measured against a reference state, which may be ‘natural’, meaning pre‐Columbian, in the United States, pre‐European in Australia or, in Europe, a habitat with ‘no, or negligible human influence’. Such standards are mostly unachievable at present because of a current economic philosophy that promotes exploitation of nature, but they are also nebulous. Even pristine habitats naturally change, so that there can be no single immutable reference state. Nonetheless, in Europe at least, the concept of the reference state has been particularly compromised, compared with the aspirations of the legislation.

Apart from a very liberal approach to setting reference standards, there has been a major omission in contemplating the general nature of the reference state. The potential former roles of large herbivorous land mammals, such as horses, bovines, deer and, early in the Holocene, elephants and rhinoceri, and their predators, in nutrient transfers, have been ignored. The effects of such large mammals, particularly in influencing lakes, are assessed in the light of major losses of much of the Pleistocene fauna during the hunter‐gatherer phase of human colonisation, and then subsequent near‐complete attrition when agriculture, husbandry and forestry converted the majority of biomes to ‘anthromes’.

Animals, and particularly large herbivorous mammals, transfer nutrients across catchments. Large mammals are likely to have maintained a state of turbid water and algal blooms in pristine, poorly flushed, shallow floodplain lakes. In contrast, we currently perceive these to be in a reference state when dominated by submerged plant communities in clear water. Although of conceptual interest, this may seem to have little practical relevance because the reference state has become a pragmatic and political construct rather than an ecological one.

I counter such a view by arguing that mitigation of climate change must require replacement of substantial carbon sinks that have been lost, that ecological sinks within restored biomes are likely to be the most effective and that restoration of such systems must involve the important roles of large mammals, with the implications these have for our concepts of lake restoration.
Species composition of coastal dune vegetation in Scotland has proved resistant to climate change over a third of a century
Authors: Pakeman Robin J. , Alexander Jim , Beaton Joan , Brooker Rob , Cummins Roger , Eastwood Antonia , Fielding Debbie , Fisher Julia , Gore Sarah , Hewison Richard , Hooper Russell , Lennon Jack , Mitchell Ruth , Moore Emily , Nolan Andrew , Orford Katy , Pemberton Clare , Riach Dave , Sim Dave , Stockan Jenni , Trinder Clare , Lewis Rob
Published: June 2015

Climate change is expected to have an impact on plant communities as increased temperatures are expected to drive individual species' distributions polewards. The results of a revisitation study after c. 34 years of 89 coastal sites in Scotland, UK, were examined to assess the degree of shifts in species composition that could be accounted for by climate change. There was little evidence for either species retreat northwards or for plots to become more dominated by species with a more southern distribution. At a few sites where significant change occurred, the changes were accounted for by the invasion, or in one instance the removal, of woody species. Also, the vegetation types that showed the most sensitivity to change were all early successional types and changes were primarily the result of succession rather than climate‐driven changes. Dune vegetation appears resistant to climate change impacts on the vegetation, either as the vegetation is inherently resistant to change, management prevents increased dominance of more southerly species or because of dispersal limitation to geographically isolated sites.