bluuebunny/crossref_metadata_2025 huggingface dataset:
Merkel cell polyomavirus T antigens promote cell proliferation and inflammatory cytokine gene expression
Authors: Richards Kathleen F. , Guastafierro Anna , Shuda Masahiro , Toptan Tuna , Moore Patrick S. , Chang Yuan
Published: September 2015

Merkel cell polyomavirus (MCV) is clonally integrated in over 80 % of Merkel cell carcinomas and mediates tumour development through the expression of viral oncoproteins, the large T (LT) and small T antigens (sT). Viral integration is associated with signature mutations in the T-antigen locus that result in deletions of C-terminal replicative functions of the LT antigen. Despite these truncations, the LT LXCXE retinoblastoma (Rb) pocket protein family binding domain is retained, and the entire sT isoform is maintained intact. To investigate the ability of MCV oncoproteins to regulate host gene expression, we performed microarray analysis on cells stably expressing tumour-derived LT, tumour-derived LT along with sT, and tumour-derived LT with a mutated Rb interaction domain. Gene expression alterations in the presence of tumour-derived LT could be classified into three main groups: genes that are involved in the cell cycle (specifically the G1/S transition), genes involved in DNA replication and genes involved in cellular movement. The LXCXE mutant LT largely reversed gene expression alterations detected with the WT tumour-derived LT, while co-expression of sT did not significantly affect these patterns of gene expression. LXCXE-dependent upregulation of cyclin E and CDK2 correlated with increased proliferation in tumour-derived LT-expressing cells. Tumour-derived LT and tumour-derived LT plus sT increased expression of multiple cytokines and chemokines, which resulted in elevated levels of secreted IL-8. We concluded that, in human fibroblasts, the LXCXE motif of tumour-derived LT enhances cellular proliferation and upregulates cell cycle and immune signalling gene transcription.
A pathway-centric view of spatial proximity in the 3D nucleome across cell lines
Authors: Karathia Hiren , Kingsford Carl , Girvan Michelle , Hannenhalli Sridhar
Published: September 2015

Spatial organization of the genome is critical for condition-specific gene expression. Previous studies have shown that functionally related genes tend to be spatially proximal. However, these studies have not been extended to multiple human cell types, and the extent to which context-specific spatial proximity of a pathway is related to its context-specific activity is not known. We report the first pathway-centric analyses of spatial proximity in six human cell lines. We find that spatial proximity of genes in a pathway tends to be context-specific, in a manner consistent with the pathway’s context-specific expression and function; housekeeping genes are ubiquitously proximal to each other, and cancer-related pathways such as p53 signaling are uniquely proximal in hESC. Intriguingly, we find a correlation between the spatial proximity of genes and interactions of their protein products, even after accounting for the propensity of co-pathway proteins to interact. Related pathways are also often spatially proximal to one another, and housekeeping genes tend to be proximal to several other pathways suggesting their coordinating role. Further, the spatially proximal genes in a pathway tend to be the drivers of the pathway activity and are enriched for transcription, splicing and transport functions. Overall, our analyses reveal a pathway-centric organization of the 3D nucleome whereby functionally related and interacting genes, particularly the initial drivers of pathway activity, but also genes across multiple related pathways, are in spatial proximity in a context-specific way. Our results provide further insights into the role of differential spatial organization in cell type-specific pathway activity.
Diffraction analysis of strongly inhomogeneous residual stress depth distributions by modification of the stress scanning method. II. Experimental implementation
Authors: Meixner Matthias , Fuss Tillman , Klaus Manuela , Genzel Martin , Genzel Christoph
Published: September 2015

The modified stress scanning method [Meixner, Fuss, Klaus & Genzel (2015).J. Appl. Cryst.48, 1451–1461] is experimentally implemented for the analysis of near-surface residual stress depth distributions that are strongly inhomogeneous. The suggested procedure is validated by analyzing the very steep in-plane residual stress depth profile of a shot-peened Al2O3ceramic specimen and comparing the results with those that were obtained by well established X-ray diffraction-based gradient methods. In addition, the evaluation formalism is adapted to the depth-dependent determination of the residual stresses inside of multilayer thin-film systems. The applicability for this purpose is demonstrated by investigating the residual stress depth distribution within the individual sublayers of a multilayered coating that consists of alternating Al2O3and TiCN thin films. In this connection, the specific diffraction geometry that was used for the implementation of the stress scanning method at the energy-dispersive materials science beamline EDDI@BESSYII is presented, and experimental issues as well as limitations of the method are discussed.
Representational analysis of extended disorder in atomistic ensembles derived from total scattering data
Authors: Neilson James R. , McQueen Tyrel M.
Published: September 2015

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atoms in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. This method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.
SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques
Authors: De la Mora Eugenio , Flores-Hernández Edith , Jakoncic Jean , Stojanoff Vivian , Siliqi Dritan , Sánchez-Puig Nuria , Moreno Abel
Published: September 2015

SdsA, a sodium dodecyl sulfate hydrolase, fromPseudomonas aeruginosawas crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorph and increase its internal order to determine its structure by X-ray diffraction. The results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.
Racial-ethnic diversity in Canada: competitive edge or corporate encumbrance? Part two
Authors: Appelbaum Steven H. , Kryvenko Oleksandr , Rodriguez Parada Mauricio , Soochan Melina Rodica , Shapiro Barbara T.
Published: September 2015

Purpose

– The purpose of this paper is to explore the relationship between multiculturalism and performance, and attempt to reconcile some of the varying points of views, in order to suggest practical implications for managers in the workplace.

Design/methodology/approach

– A review of the literature regarding both diversity and performance was performed. Next, the focus was on the relationship specifically between racial-ethnic diversity and performance. To show the relevance of the paper, materials dedicated to Canadian population and immigration was included.

Findings

– It is still somewhat inconclusive whether diversity can have a definite positive or negative impact on organizational performance. The literature reviewed shows that authors have differing opinions. One element appears to be clear: diversity of itself does not necessarily bring benefit. For a diverse group to perform well, it must be well managed. Diversity remains an underused tool that managers have yet to learn to utilize.

Research limitations/implications

– At the time of writing, there was not a significant amount of published material on the direct relationship between multiculturalism and performance. This paper attempts to gather and make sense of the various views formalized thus far and puts forth a new question of how to turn multiculturalism in the workplace into an asset for organizations.

Practical implications

– Managers still do not agree on how to take full advantage of diversity. As the Canadian workforce becomes more and more diverse, so increases the importance of addressing and answering this question in practical terms. Especially facing the increased globalization of corporations, taking advantage of the untapped potential that resides in a culturally diverse work team should be at the top of every international company’s goals.

Social implications

– The importance of studying the relationship between multiculturalism and performance is crucial because in developed countries like Canada organizations are becoming increasingly culturally diverse. Much has been written about the effect of group diversity on conflict and creativity, on the performance of heterogeneous groups vs homogeneous groups, on organizational commitment among ethnic minorities, and on self-fulfilling performance expectations.

Originality/value

– This paper is a useful source for managers interested in understanding the real value of diversity in the workplace, as well as for researchers studying the relationship between corporate diversity and corporate performance.
The purchasing – and practical benefits – of a learning management system
Authors: Little Bob
Published: September 2015

Purpose

– An exploration of the corporate market for learning management systems (LMSs), looking at key issues in the buying process, LMS features and characteristics. It illustrates this with two case studies of global organisations’ LMS usage. The paper aims to discuss these issues.

Design/methodology/approach

– Discussion paper making use of analyst and buyer interviews.

Findings

– Having taken time and trouble to find the right LMS for your organisation can bring tangible benefits – for the organisation (via improving efficiency and achieving business goals), learning and development professionals (in charge of the whole process) and individual workers/ learners. From the case studies, this is true for companies in two widely diverse industries.

Research limitations/implications

– The value of understanding the differences between the 800 or so LMSs currently on the market – and going through a thorough and professional system to acquire the appropriate one for the organisation.

Practical implications

– Implemented successfully, an LMS enhances the user’s knowledge and skills; enables the learning and development professional to be more efficient and effective while reducing time pressures, and enables the organisation to achieve its business targets band goals.

Social implications

– Individual workers find learning – and performance support – simpler and easier to achieve as and when they require it.

Originality/value

– An attempt to discern some current trends and explore them through two recent cases.
The mediating effects of organizational conflict on the relationships between workplace ostracism with in-role behavior and organizational citizenship behavior
Authors: Chung Yang Woon
Published: September 2015

Purpose

– This study aims to examine the mediating effects of organizational conflict on the relationships between workplace ostracism with in-role behavior and organizational citizenship behaviors. The workplace is a social context where many individuals spend a great amount of their time. Frequently being excluded or ignored is a common experience within all social contexts, and the study emphasizes how those feelings can affect organizational members. The current study extends research, as prior empirical studies have focused mainly on the direct consequences of workplace ostracism.

Design/methodology/approach

– The study was longitudinally designed, as data were collected using a two-wave self-reported survey. Confirmatory factor analysis and structural equation modeling were conducted to test the study’s hypotheses.

Findings

– The study found workplace ostracism to be positively related to coworker conflict, supervisor conflict and task conflict. Coworker conflict was found to fully mediate the relationships between workplace ostracism with in-role behavior and organizational citizenship behaviors.

Research limitations/implications

– As the study was conducted in Korea, the results cannot be generalizable and should be tested in Western cultures. Although the study was longitudinally designed, the first-wave survey measured the independent variable, while the second-wave survey measured the mediating and dependent variables. Also, self-reported surveys are always of concern; thus, multiple sources should be considered to strengthen the research model’s relationships.

Practical implications

– Organizations and managers need to continuously address the quality of interpersonal relationships among all organizational members. As studies reveal that being “out of the loop” is quite a common phenomenon, individual and organizational performance can be greatly affected, as work is becoming more interdependent and team work is frequently implemented within organizations.

Social implications

– Individuals interact in numerous social contexts and as the workplace is an important context where many individuals spend a lot of their time and interact with other organizational members, the quality of the relationships at work can have spillover effects that can affect interpersonal relationships outside of the workplace.

Originality/value

– The study explores and empirically tests the mediating effects of organizational conflict on the relationships between workplace ostracism with in-role behavior and organizational citizenship behaviors. The study extends research on the consequences of workplace ostracism and helps further understand how workplace ostracism can affect workplace attitudes and behaviors.
Third party conflict management of transboundary river disputes
Authors: Bobekova Elvira
Published: September 2015

Purpose

– This paper aims to fill the gaps by conducting the first large n study examining the role of third parties in the emergence of river agreements in Asia and Africa during the time period 1948-2007. There is a growing literature on what explains agreements in river disputes. However, beyond individual case analysis, little systematic study has been done on the role of third parties in settling river disputes through agreement, in particular on the regions that are mostly affected by the global climate change.

Design/methodology/approach

– Through utilising new data on the role of third parties in river disputes, this study shows that third party involvement in the conflict management of river disputes increases the likelihood of reaching river agreements.

Findings

– The findings suggest that third parties use both diplomatic and economic means to increase the likelihood of emergence of river agreements, and both strategies are equally important to induce formalised cooperation.

Research limitations/implications

– Yet the present study covers only two regions, and it does not delve into a discussion of the conditions under which third party interventions are successful. Rather, these are aspects that need to be explored in the future.

Practical implications

– Given the current uncertainty around security challenges resulting from climate change, and with predictions of future water wars, this research contributes to the understanding how to peacefully manage current and potential conflicts around transboundary waters.

Originality/value

– This study is the first large n study examining the role of third parties in the emergence of river agreements in Asia and Africa.
A keyword-based organizing framework for ERP intellectual contributions
Authors: Fadlalla Adam , Amani Farzaneh
Published: September 2015

Purpose

– The purpose of this paper is to develop a keyword-based organizing framework for enterprise resource planning (ERP) intellectual contributions, and use the proposed framework to derive major areas of emphasis in ERP research.

Design/methodology/approach

– Using keyword persistence, a time-based measure, and keyword dominance, a frequency-based measure, the authors constructed an empirical framework to classify ERP intellectual contributions.

Findings

– Four major ERP themes were identified using the proposed framework; namely, emerging/phantom, intermittent, trendy, and core. Further examination of the keywords in each of these themes revealed that whereas the business aspects of ERP systems are discussed in an intermittent manner, its technical aspects are discussed in a trendy fashion.

Research limitations/implications

– The main limitation of this research is that it only used keywords from papers published in scholarly journals, and did not include conference proceedings, books, and other outlets. In this paper, the authors developed an objective keyword-based organizing framework. The proposed framework is simple, flexible, and is based on dimensions that are research domain independent, and thus can be used as an organizing framework for any research domain.

Practical implications

– The proposed framework may help managers to better focus consulting engagements on ERP implementations through identifying areas that are not well covered by researchers to ensure that such areas they are well covered by consulting services.

Originality/value

– The main contribution of this paper is the development of an objective keyword-based framework that can be used as an organizing tool for intellectual contributions. The framework can be used to derive insights in the macro characterizations of the research in a given domain, and is thus valuable to researchers – both academic and practitioner. To the best of the authors’ knowledge, this is the first such keyword-based research organizing framework.
Completing a PhD in business and management
Authors: Dwivedi Yogesh K , Ravishankar M. N. , Simintiras Antonis Constantinou
Published: September 2015

Purpose

– Despite the ever-growing number of PhD students all over the world, there remain significant doubts about whether entering students in business and management disciplines fully understand the process of producing a PhD thesis, defending it and developing a coherent publication strategy. Hence, the purpose of this paper is to offer some guidance on what it takes to successfully complete a doctoral research thesis.

Design/methodology/approach

– The arguments and guidance presented in this viewpoint paper are drawn on the authors’ collective supervision and doctoral examination experiences.

Findings

– The paper presents guidelines on three key issues related with the doctoral completion: choosing a research problem; demonstrating rigour and quality; developing a publication strategy.

Originality/value

– The content presented in this paper would be valuable aide to those pursuing doctoral research.
How leading organizations use big data and analytics to innovate
Authors: Marshall Anthony , Mueck Stefan , Shockley Rebecca
Published: September 2015

Purpose

– To understand how the most successful organizations use big data and analytics innovate, researchers studied 341 respondents’ usage of big data and analytics tools for innovation.

Design/methodology/approach

– Researchers asked about innovation goals, barriers to innovation, metrics used to measure innovation outcomes, treatment and types of innovation projects and the role of big data and analytics in innovation processes.

Findings

– Three distinct groups emerged: Leaders, Strivers and Strugglers. Leaders are markedly different as a group: they innovate using big data and analytics within a structured approach, and they focus in particular on collaboration.

Research limitations/implications

– Respondents were from the 2014 IBM Innovation Survey. We conducted cluster analysis with 81 variables. The three cluster solution was determined deploying latent class analysis (LCA), a family of techniques based around clustering and data reduction for segmentation projects. It uses a number of underlying statistical models to capture differences between observed data or stimuli in the form of discrete (unordered) population segments; group segments; ordered factors (segments with an underlying numeric order); continuous factors; or mixtures of the above.

Practical implications

– Leaders don’t just embrace analytics and actionable insights; they take them to the next level, integrating analytics and insights with innovation. Leaders follow three basic strategies that center on data, skills and tools and culture: promote excellent data quality and accessibility; make analytics and innovation a part of every role; build a quantitative innovation culture.

Originality/value

– The research found that leaders leverage big data and analytics more effectively over a wider range of organizational processes and functions. They are significantly better at leveraging big data and analytics throughout the innovation process – from conceiving new ideas to creating new business models and developing new products and services.
Evolution of the DEAD box helicase family in chicken: chickens have no DHX9 ortholog
Authors: Sato Haruko , Oshiumi Hiroyuki , Takaki Hiromi , Hikono Hirokazu , Seya Tsukasa
Published: September 2015

Viral RNA represents a pattern molecule that can be recognized by RNA sensors in innate immunity. Humans and mice possess cytoplasmic DNA/RNA sensors for detecting viral replication. There are a number of DEAD (Asp‐Glu‐Ala‐Asp; DExD/H) box‐type helicases in mammals, among which retinoic acid‐inducible gene 1 (RIG‐I) and melanoma differentiation‐associated protein 5 (MDA50) are indispensable for RNA sensing; however, they are functionally supported by a number of sensors that directly bind viral RNA or replicative RNA intermediates to convey signals to RIG‐I and MDA5. Some DEAD box helicase members recognize DNA irrespective of the origin. These sensors transmit IFN‐inducing signals through adaptors, including mitochondrial antiviral signaling. Viral double‐stranded RNAs are reportedly sensed by the helicases DDX1, DDX21, DHX36, DHX9, DDX3, DDX41, LGP2 and DDX60, in addition to RIG‐I and MDA5, and induce type I IFNs, thereby blocking viral replication. Humans and mice have all nucleic acid sensors listed here. In the RNA sensing system in chicken, it was found in the present study that most DEAD box helicases are conserved; however, DHX9 is genetically deficient in addition to reported RIG‐I. Based on the current genome databases, similar DHX9 deficiency was observed in ducks and several other bird species. Because chicken, but not duck, was found to be deficient in RIG‐I, the RNA‐sensing system of chicken lacks RIG‐I and DHX9 and is thus more fragile than that of duck or mammal. DHX9 may generally compensate for the function of RIG‐I and deficiency of DHX9 possibly participates in exacerbations of viral infection such as influenza in chickens.
Whole genome analysis of Vietnamese G2P[4] rotavirus strains possessing the NSP2 gene sharing an ancestral sequence with Chinese sheep and goat rotavirus strains
Authors: Do Loan Phuong , Doan Yen Hai , Nakagomi Toyoko , Gauchan Punita , Kaneko Miho , Agbemabiese Chantal , Dang Anh Duc , Nakagomi Osamu
Published: September 2015

Because imminent introduction into Vietnam of a vaccine against Rotavirus A is anticipated, baseline information on the whole genome of representative strains is needed to understand changes in circulating strains that may occur after vaccine introduction. In this study, the whole genomes of two G2P[4] strains detected in Nha Trang, Vietnam in 2008 were sequenced, this being the last period during which virtually no rotavirus vaccine was used in this country. The two strains were found to be >99.9% identical in sequence and had a typical DS‐1 like G2‐P[4]‐I2‐R2‐C2‐M2‐A2‐N2‐T2‐E2‐H2 genotype constellation. Analysis of the Vietnamese strains with >184 G2P[4] strains retrieved from GenBank/EMBL/DDBJ DNA databases placed the Vietnamese strains in one of the lineages commonly found among contemporary strains, with the exception of the NSP2 and NSP4 genes. The NSP2 genes were found to belong to a previously undescribed lineage that diverged from Chinese sheep and goat rotavirus strains, including a Chinese rotavirus vaccine strain LLR with 95% nucleotide identity; the time of their most recent common ancestor was 1975. The NSP4 genes were found to belong, together with Thai and USA strains, to an emergent lineage (VIII), adding further diversity to ever diversifying NSP4 lineages. Thus, there is a need to enhance surveillance of locally‐circulating strains from both children and animals at the whole genome level to address the effect of rotavirus vaccines on changing strain distribution.
Quantifying turnover in biodiversity of British breeding birds
Authors: Harrison Philip J. , Yuan Yuan , Buckland Stephen T. , Oedekoven Cornelia S. , Elston David A. , Brewer Mark J. , Johnston Alison , Pearce‐Higgins James W.
Published: September 2015

A key aspect of monitoring regional changes in biodiversity is to quantify the temporal turnover in communities. Turnover has traditionally been assessed by observing range change. However, we are often interested in trends in biodiversity of large regions as opposed to single sites, as with Convention for Biological Diversity targets. Extinctions and colonizations tend to be rare events at the regional level; changes in species proportions estimated from spatio‐temporal models of species abundance are then more sensitive measures of community change.

We investigated three measures for quantifying turnover based on species proportions, and estimated how each varies across Great Britain using data from the British Trust for Ornithology's Breeding Bird Survey.

All three measures identify high turnover associated with loss of biodiversity in the south‐east of England. This seems to be driven by changes in the farmland bird community, and by turnover in the scarcer species of the woodland bird community. The measures also show evidence of high turnover in the west of Scotland; these changes may be linked to climate change, although precision in our measures for this region is relatively poor due to low survey effort.

Policy implications. Turnover in ecological communities may be quantified by modelling species abundance, and measuring how resulting species proportions change over time. When used alongside estimated temporal trends in biodiversity, these can identify areas and communities showing greatest evidence for change. How, and indeed even whether, society should respond to such changes depends on further investigation into the causes of the changes, and the extent to which these are seen as undesirable and avoidable. For those communities with adequate survey data, we recommend that these methods augment the suite of measures used for routine assessment of change, hence acting as a more sensitive trigger to set in motion exploration of causes and consideration of adaptive actions to be taken by land managers and policymakers.
When Conflict Strikes: Contesting Neoliberal Urbanism outside Participatory Structures in Inner‐city Dublin
Authors: Attuyer Katia
Published: September 2015

This article examines how community representatives from a disadvantaged neighbourhood engage with neoliberal urban governance structures and assess the power afforded to them. It seeks to understand how community groups manage the challenges they face in times of neoliberal urbanism. This study follows calls to pay greater attention to the existence of imaginaries other than neoliberal ones, examining community actions and discourses surrounding the Historic Area Rejuvenation Project (HARP) area in Dublin, a project aimed at stimulating private property development and investment. The case highlights tensions between the pursuit of community‐based and collaborative urban regeneration and the increased legitimacy of neoliberalism as a guiding principle of public policy. It confirms the existence of resistance movements and the importance of local and national contexts in explaining the outcomes of contestation. Despite participative structures established by the local authority, the views and interests of local community activists were ignored and excluded. Furthermore, in contrast to trends towards co‐option within participative structures, the community actively resisted the imposition of neoliberal plans. Overall, while they had little success in influencing the plans or mindsets of the local authority, they did succeed in delaying the process until the project became unviable as a result of the economic crisis.
The contours of employee voice in SMEs: the importance of context
Authors: Gilman Mark , Raby Simon , Pyman Amanda
Published: September 2015

This article develops a context‐sensitive approach to analyse how and why voice operates in small‐ to medium‐sized enterprises (SMEs), an area that remains under‐theorised and under‐researched. By building on a priori frameworks with proven ability to unpack complexity and take account of the wider context of SMEs, this article explores how resources (human and social capital) and constraints (product market, labour market and strategic orientation) interact to shape voice practices. The article finds significant differences between ‘reported’ compared with ‘actual’ practices in situ, and identifies different types of firms (‘strategic market regulation’, ‘strategic market‐led’ and ‘non‐strategic market‐led’) along with the factors that influence the form and practice of voice. Overall, the article argues that researchers should further pursue research that appreciates the layered nature of ontology and the role played by firm context to explain complex organisational phenomena, if we are to advance our understanding of voice practices in SMEs and beyond.
Spatio‐Temporal Patterns of Open Surface Water in the Central Valley of California 2000‐2011: Drought, Land Cover, and Waterbirds
Authors: Reiter Matthew E. , Elliott Nathan , Veloz Sam , Jongsomjit Dennis , Hickey Catherine M. , Merrifield Matt , Reynolds Mark D.
Published: September 2015

We used Landsat satellite imagery to (1) quantify the distribution of open surface water across the Central Valley of California 2000‐2011, (2) summarize spatio‐temporal variation in open surface water during this time series, and (3) assess factors influencing open surface water, including drought and land cover type. We also applied the imagery to identify available habitat for waterbirds in agriculture. Our analyses indicated that between 2000 and 2011 open surface water has declined across the Central Valley during the months of July‐October. On average, drought had a significant negative effect on open surface water in July, September, and October, though the magnitude and timing of the effect varied spatially. The negative impact of a drought year on open water was experienced immediately in the southern Central Valley; however, there was a one year time‐lag effect in the northern Central Valley. The highest proportion of open surface water was on agricultural lands followed by lakes, rivers, and streams, yet the relative proportions varied spatially and across months. Our data were consistent with previous descriptions of waterbird habitat availability in post‐harvest rice in the northern Central Valley. Tracking water distribution using satellites enables empirically based assessments of the impacts of changing water policy, land‐use, drought, climate, and management on water resources.
Comparison of research experience and support needs of rural versus regional allied health professionals
Authors: Pain Tilley , Plummer David , Pighills Alison , Harvey Desley
Published: September 2015

Objective

We compared the research experience or support needs of allied health professionals in rural versus regional cities to identify if they were the same or different.

Design

Descriptive study using a cross sectional survey.

Setting

This study was carried within Queensland Health's northern six health services.

Participants

Queensland health staff classified as Health Practitioners.

Interventions

This survey was conducted as part of a research capacity building initiative within Queensland Health to increase AHPs’ participation in research in regional cities and rural areas of Queensland.

Main outcome measures

Questions in the survey identified demographics, research experience, need for research support, research knowledge and beliefs about research. Data were compared using Chi‐square and t‐tests.

Results

The total response rate was 54.5% with 18% of the HPs located in rural communities of less than 5000 people and the rest from the three major cities in northern Queensland. Rural HPs have less research experience in most research activities than regional city HPs and need more research support. Rural HPs have more qualitative research experience than regional city HPs and research is perceived positively by both. Barriers to conducting research were similar across both groups and included insufficient time, lack of staff and no statistical support.

Conclusion

Rural HPs are younger and have less research experience than their counterparts working in regional cities. Therefore, building rural HP research capacity initiatives may require more access to facilitators such as the Research Fellows.
Randomised clinical study: discrepancies between patient‐reported outcomes and endoscopic appearance in moderate to severe ulcerative colitis
Authors: Jharap B. , Sandborn W. J. , Reinisch W. , D'Haens G. , Robinson A. M. , Wang W. , Huang B. , Lazar A. , Thakkar R. B. , Colombel J.‐F.
Published: September 2015

Background

Associations between patient‐reported outcomes and mucosal healing have not been established in ulcerative colitis (UC).

Aim

To evaluate relationships of rectal bleeding and stool frequency with mucosal healing and quality of life (QoL) in patients with UC in two Phase 3 studies (ULTRA 1 and 2).

Methods

Associations of patient‐reported rectal bleeding and stool frequency subscores with mucosal healing (Mayo endoscopy subscore = 0 or 0/1) and QoL [inflammatory bowel disease questionnaire (IBDQ)] were assessed in adalimumab‐randomised patients (160/80 mg at Weeks 0/2 followed by 40 mg biweekly or weekly) at Weeks 8 (n = 433) and 52 (n = 299), and in patients with mucosal healing [endoscopy subscore = 0 (n = 17); 0/1 (n = 52)] at Weeks 8 and 52.

Results

At Week 8, the positive predictive values (PPVs) of rectal bleeding subscore = 0, stool frequency subscore = 0 or both scores = 0 for endoscopy subscore = 0/1 were 69%, 84% and 90% respectively; all proportions increased at Week 52. Equivalent PPVs for these subscores in patients with endoscopy subscore = 0 were 26%, 37% and 46% respectively. Among patients with endoscopy subscore = 0 at Week 8, 87% reported no rectal bleeding, while only 29% reported normal stool frequency; these proportions had increased to 94% and 41% respectively, at Week 52. Among patients with mucosal healing, IBDQ scores trended highest for patients with both rectal bleeding and stool frequency subscores = 0.

Conclusions

Absence of rectal bleeding and normal stool frequency are often predictive of mucosal healing and QoL, but complete normalisation of stool frequency is encountered rarely in patients with mucosal healing.
Can Social Capital Reduce Poverty? A Study of Rural Households in Eastern Bhutan
Authors: Tenzin Galey , Otsuka Kozo , Natsuda Kaoru
Published: September 2015

This study examines the impact of social capital on the poverty of rural households in eastern Bhutan, with a particular focus on households' participation in community groups, which can be a proxy for the structural aspect of social capital. Using a two‐stage probit least squares simultaneous equation model, the present study reveals that social capital positively contributes to poverty reduction in Bhutan. This study also finds that non‐farm income is important for poverty reduction in rural areas. Our results, however, indicate that poor households in remote areas are discouraged from participating in community groups.
Awareness of Child Maltreatment among Professionals in Shanghai
Authors: Shang Xiaoyuan , Katz Ilan
Published: September 2015

This study reports on a series of qualitative interviews with professionals in Shanghai, China who work with children. The interviews explored the awareness of child protection issues amongst a range of people who work with children, how they differentiate corporal punishment from maltreatment and what they would do in response to cases of child abuse. Shanghai has one of the most well developed child welfare systems in China, and compared to similar professionals in other cities, those in Shanghai had higher awareness and more training, but were nevertheless reluctant to intervene and did not feel well prepared to deal with cases of child abuse should they be encountered. However there are some indications that practice is improving, and examples of recent developments are provided.
Bayesian networks with examples in R
Authors: Choi Taeryon
Published: September 2015

EDITOR: TAESUNG PARK

Bayesian Networks With Examples in R

(Marco Scutari and Jean‐Baptiste Denis)

Taeryon Choi

Applied Meta‐Analysis with R

(Ding‐Geng Chen and Karl E. Peace)

Mira Park
Social network structure and status competition
Authors: Alexeev Michael , Chih Yao‐Yu
Published: September 2015

In status competition studies, the utility of heterogeneous individuals typically depends on an economy‐wide average indicator of status. In our model, emulative and jealous agents are embedded in an exogenous network where agent‐specific reference group is determined by the direct link emanating from the agent. Similarly to Ghiglino and Goyal (2010) but in a somewhat different framework, we show that individual consumption is proportional to the agent's “outbound” Katz‐Bonacich network centrality measure and equilibrium is generally inefficient. More important, the negative externality associated with each agent depends on her “inbound” centrality measure—the conspicuousness index. A tax based on this index combined with a uniform lump‐sum transfer attains efficiency.
XRCC3 is a promising target to improve the radiotherapy effect of esophageal squamous cell carcinoma
Authors: Cheng Jingjing , Liu Weiran , Zeng Xianliang , Zhang Bin , Guo Yihang , Qiu Minghan , Jiang Chao , Wang Huanhuan , Wu Zhiqiang , Meng Maobin , Zhuang Hongqing , Zhao Lujun , Hao Jihui , Cai Qingqing , Xie Dan , Pang Qingsong , Wang Ping , Yuan Zhiyong , Qian Dong
Published: September 2015

Radiotherapy is widely applied for treatment of esophageal squamous cell carcinoma (ESCC). The Rad51‐related protein XRCC3 plays roles in the recombinational repair of DNA double‐strand breaks to maintain chromosome stability and repair DNA damage. The present study aimed to investigate the effect of XRCC3 on the radiotherapy response of ESCC and the underlying mechanisms of the roles of XRCC3 in ESCC radiosensitivity. XRCC3 expression in ESCC cells and tissues was higher than that in normal esophageal epithelial cells and corresponding adjacent noncancerous esophageal tissue. High XRCC3 expression was positively correlated with resistance to chemoradiotherapy in ESCC and an independent predictor for short disease‐specific survival of ESCC patients. Furthermore, the therapeutic efficacy of radiotherapy in vitro and in vivo was substantially increased by knockdown of XRCC3 in ESCC cells. Ectopic overexpression of XRCC3 in both XRCC3‐silenced ESCC cells dramatically enhanced ESCC cells' resistance to radiotherapy. Moreover, radiation resistance conferred by XRCC3 was attributed to enhancement of homologous recombination, maintenance of telomere stability, and a reduction of ESCC cell death by radiation‐induced apoptosis and mitotic catastrophe. Our data suggest that XRCC3 protects ESCC cells from ionizing radiation‐induced death by promoting DNA damage repair and/or enhancing telomere stability. XRCC3 may be a novel radiosensitivity predictor and promising therapeutic target for ESCC.
Nice–Nastiness and Other Raced Social Interactions on Public Transport Systems
Authors: Purifoye Gwendolyn Y.
Published: September 2015

Research on public transportation systems has often focused on racialized and institutionalized dynamics that result in poor and ethno–racial minority neighborhoods being underserved. Few scholars have studied raced social interactions on the buses and trains themselves. In this article, I explore how legacies of racism are reproduced through raced social interactions on public buses and trains in Chicago. Drawing on over 3 years of ethnographic field work and interviews, this article demonstrates how ethno–racial minorities, particularly Blacks, experience racial hostilities that are often masked as nice–nastiness. Nice–nastiness is a type of individual expression that combines expressions of politeness with disdain and distancing. Nice–nastiness can be expressed as (1) pretending the “other” does not exist; (2) whispering and lowering one's voice; (3) standing instead of taking a seat; (4) letting others have space for auditory expression; and (5) pseudo–swagger. I locate nice–nastiness on the racial microaggressions and color–blindness continuum and show that this expressive tool is shaped, at least in part, by the closeness, confinement and mobility of public transportation, where escape is not possible, unlike in wide–open spaces. I use public transportation as a space to examine how raced behaviors are enacted in everyday life, and shaped by confinement and motion.
Early immunosuppression treatment correlates with later de novo donor‐specific antibody development after kidney and pancreas transplantation
Authors: Pelletier Ronald P. , Rajab Amer A. , Diez Alejandro , DiPaola Nicholas R. , Bumgardner Ginny L. , Elkhammas Elmahdi A. , Henry Mitchell L.
Published: September 2015

Background

De novo donor‐specific antibodies (dnDSA) post‐transplant correlate with a higher risk of immunologic graft injury and loss following kidney and pancreas transplantation. Post‐transplant dnDSA can occur within the first post‐transplant year.

Methods

In this study, 817 of 1290 kidney and simultaneous kidney/pancreas recipients were tested for dnDSA post‐transplant. Recipient immunosuppressive treatment at one, three, six, and 12 months post‐transplant was correlated with dnDSA incidence by univariate and multivariate analyses.

Results

The overall incidence of dnDSA was 21.3% detected a median of 3.5 yr post‐transplant. By univariate analysis, the immunosuppressive treatment at all time points correlated with dnDSA (p < 0.01). Month 6 treatment correlated best in multivariable analysis (p = 0.004). At six months, recipients receiving rapamune/mycophenolic acid (Rapa/MPA) had the highest dnDSA incidence at five yr (25.3%) and last follow‐up (30.7%), those treated with cyclosporine/rapamune (CNI/Rapa) had the lowest incidence at five yr (10.8%) and last follow‐up (18.6%), and cyclosporine/mycophenolic acid (CNI/MPA) treatment had an intermediate incidence at five yr (16.7%) and last follow‐up (20.4%) (p < 0.01). Six‐month CNI/MPA and Rapa/MPA treatment significantly correlated with dnDSA (hazard ratios of 2.36 and 1.80, respectively) by Cox proportional hazards regression modeling.

Conclusion

The risk of post‐transplant dnDSA development correlates with early immunosuppressive management.
Impact of Number of Interactions, Different Interaction Patterns, and Human Inconsistencies on Some Hybrid Evolutionary Multiobjective Optimization Algorithms*
Authors: Marquis Jon , Gel Esma S. , Fowler John W. , Köksalan Murat , Korhonen Pekka , Wallenius Jyrki
Published: September 2015

We investigate the impact of the number of human–computer interactions, different interaction patterns, and human inconsistencies in decision maker responses on the convergence of an interactive, evolutionary multiobjective algorithm recently developed by the authors. In our context “an interaction” means choosing the best and worst solutions among a sample of six solutions. By interaction patterns we refer to whether preference questioning is more front‐, center‐, rear‐, or edge‐loaded. As test problems we use two‐ to four‐objective knapsack problems, multicriteria scheduling problems, and multiobjective facility location problems. In the tests, two different preference functions are used to represent actual decision maker preferences, linear and Chebyshev. The results indicate that it is possible to obtain solutions that are very good or even nearly optimal with a reasonable number of interactions. The results also indicate that the algorithm is robust to minor inconsistencies in decision maker responses. There is also surprising robustness toward different patterns of interaction with the decision maker. The results are of interest to the evolutionary multiobjective (EMO) community actively developing hybrid interactive EMO approaches.
Inhibition of the multidrug and toxin extrusion (MATE) transporter by pyrimethamine increases the plasma concentration of metformin but does not increase antihyperglycaemic activity in humans
Authors: Oh J. , Chung H. , Park S.‐I. , Yi S. J. , Jang K. , Kim A. H. , Yoon J. , Cho J.‐Y. , Yoon S. H. , Jang I.‐J. , Yu K.‐S. , Chung J.‐Y.
Published: September 2015

We hypothesized that the pharmacodynamic (PD) characteristics of metformin would change with inhibition of the multidrug and toxin extrusion (MATE) transporter, which mediates renal elimination of metformin. Twenty healthy male subjects received two doses (750/500 mg) of metformin, with and without 50 mg of pyrimethamine (a potent MATE inhibitor), with 1 week of washout in between each dose. The PD characteristics of metformin were assessed using oral glucose tolerance tests (OGTTs) before and after the metformin dose. Metformin concentrations in plasma and urine were determined using liquid chromatography‐electrospray ionization‐tandem mass spectrometry. When metformin was co‐administered with pyrimethamine, its area under the concentration–time curve from 0 to 12 h was 2.58‐fold greater (p < 0.05), whereas the antihyperglycaemic effects of metformin were decreased. The mean differences (90% confidence interval) in mean and maximum serum glucose concentrations and in 2‐h‐post‐OGTT serum glucose concentration were −0.6 (−1, −0.2), −0.9 (−1.6, −0.3) and −0.5 (−1.1, 0.1) mmol/l, respectively. These findings indicate that the response to metformin is not only related to the plasma exposure of metformin but is also related to other factors, such as inhibition of uptake transporters and the gastrointestinal‐based pharmacology of metformin.