bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid expansion of immune-related gene families in the house fly,Musca domestica
Authors: Sackton Timothy B. , Lazzaro Brian P. , Clark Andrew G.
Published: August 2016

The house fly,Musca domestica, occupies an unusual diversity of potentially septic niches among sequenced Dipteran insects and is a vector of numerous diseases of humans and livestock. In the present study, we apply whole-transcriptome sequencing to identify genes whose expression is regulated in adult flies by bacterial infection. We then combine the transcriptomic data with analysis of rates of gene duplication and loss to provide insight into the evolutionary dynamics of immune-related genes. Genes up-regulated after bacterial infection are biased toward being evolutionarily recent innovations, suggesting the recruitment of novel immune components in theM. domesticaor ancestral Dipteran lineages. In addition, using new models of gene family evolution, we show that several different classes of immune-related genes, particularly those involved in either pathogen recognition or pathogen killing, are duplicating at a significantly accelerated rate on theM. domesticalineage relative to other Dipterans. Taken together, these results suggest that theM. domesticaimmune response includes an unusual diversity of genes, perhaps as a consequence of its lifestyle in septic environments.
Genomic insights into adaptive divergence and speciation among malaria vectors of theAnopheles niligroup
Authors: Fouet Caroline , Kamdem Colince , Gamez Stephanie , White Bradley J.
Published: August 2016

Ongoing speciation in most African malaria vectors gives rise to cryptic populations, which differ remarkably in their behaviour, ecology and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is critical for effective disease control because heterogeneity within species contribute to variability in malaria cases and allow fractions of vector populations to escape control efforts. To examine the population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to theAnopheles niligroup, a large taxonomic group that diverged ∼3-Myr ago. Using 4343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by highFSTvalues between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within theAnopheles niligroup is challenging due to incongruence between morphology, ribosomal DNA and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST= 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.
Extensive genetic diversity among populations of the malaria mosquito Anopheles moucheti revealed by population genomics
Authors: Fouet Caroline , Kamdem Colince , Gamez Stephanie , White Bradley J.
Published: August 2016

Malaria vectors are exposed to intense selective pressures due to large-scale intervention programs that are underway in most African countries. One of the current priorities is therefore to clearly assess the adaptive potential of Anopheline populations, which is critical to understand and anticipate the response mosquitoes can elicit against such adaptive challenges. The development of genomic resources that will empower robust examinations of evolutionary changes in all vectors including currently understudied species is an inevitable step toward this goal. Here we constructed double-digest Restriction Associated DNA (ddRAD) libraries and generated 6461 Single Nucleotide Polymorphisms (SNPs) that we used to explore the population structure and demographic history of wild-caught Anopheles moucheti from Cameroon. The genome-wide distribution of allelic frequencies among samples best fitted that of an old population at equilibrium, characterized by a weak genetic structure and extensive genetic diversity, presumably due to a large long term effective population size. Estimates of FST and Linkage Disequilibrium (LD) across SNPs reveal a very low genetic differentiation throughout the genome and the absence of segregating LD blocks among populations, suggesting an overall lack of local adaptation. Our study provides the first investigation of the genetic structure and diversity in An. moucheti at the genomic scale. We conclude that, despite a weak genetic structure, this species has the potential to challenge current vector control measures and other rapid anthropogenic and environmental changes thanks to its great genetic diversity.
Cytoarchitectonic similarity is a wiring principle of the human connectome
Authors: Goulas Alexandros , Werner René , Beul Sarah F , Säring Dennis , Heuvel Martijn van den , Triarhou Lazaros C , Hilgetag Claus C
Published: August 2016

Understanding the wiring diagram of the human cerebral cortex is a fundamental challenge in neuroscience. Elemental aspects of its organization remain elusive. Here we examine which structural traits of cortical regions, particularly their cytoarchitecture and thickness, relate to the existence and strength of inter-regional connections. We use the architecture data from the classic work of von Economo and Koskinas and state-of-the-art diffusion-based connectivity data from the Human Connectome Project. Our results reveal a prominent role of the cytoarchitectonic similarity of supragranular layers for predicting the existence and strength of connections. In contrast, cortical thickness similarity was not related to the existence or strength of connections. These results are in line with findings for non-human mammalian cerebral cortices, suggesting overarching wiring principles of the mammalian cerebral cortex. The results invite hypotheses about evolutionary conserved neurobiological mechanisms that give rise to the relation of cytoarchitecture and connectivity in the human cerebral cortex.
A complete tool set for molecular QTL discovery and analysis
Authors: Delaneau Olivier , Ongen Halit , Brown Andrew , Fort Alexandre , Panousis Nikolaos , Dermitzakis Emmanouil
Published: August 2016

Population scale studies combining genetic information with molecular phenotypes (e.g. gene expression) become a standard to dissect the effects of genetic variants onto organismal. This kind of datasets requires powerful, fast and versatile methods able to discover molecular Quantitative Trait Loci (molQTL). Here we propose such a solution, QTLtools, a modular framework that contains multiple methods to prepare the data, to discover proximal and distal molQTLs and to finally integrate them with GWAS variants and functional annotations of the genome. We demonstrate its utility by performing a complete expression QTL study in a few and easy-to-perform steps. QTLtools is open source and available athttps://gtltools.github.io/gtltools/
Corporate social responsibility reporting in the mining sector of Tanzania
Authors: Lauwo Sarah George , Otusanya Olatunde Julius , Bakre Owolabi
Published: August 2016

Purpose

– The purpose of this paper is to contribute to the ongoing debate on governance, accountability, transparency and corporate social responsibility (CSR) in the mining sector of a developing country context. It examines the reporting practices of the two largest transnational gold-mining companies in Tanzania in order to draw attention to the role played by local government regulations and advocacy and campaigning by nationally organised non-governmental organisations (NGOs) with respect to promoting corporate social reporting practices.

Design/methodology/approach

– The paper takes a political economy perspective to consider the serious implications of the neo-liberal ideologies of the global capitalist economy, as manifested in Tanzania’s regulatory framework and in NGO activism, for the corporate disclosure, accountability and responsibility of transnational companies (TNCs). A qualitative field case study methodology is adopted to locate the largely unfamiliar issues of CSR in the Tanzanian mining sector within a more familiar literature on social accounting. Data for the case study were obtained from interviews and from analysis of documents such as annual reports, social responsibility reports, newspapers, NGO reports and other publicly available documents.

Findings

– Analysis of interviews, press clips and NGO reports draws attention to social and environmental problems in the Tanzanian mining sector, which are arguably linked to the manifestation of the broader crisis of neo-liberal agendas. While these issues have serious impacts on local populations in the mining areas, they often remain invisible in mining companies’ social disclosures. Increasing evidence of social and environmental ills raises serious questions about the effectiveness of the regulatory frameworks, as well as the roles played by NGOs and other pressure groups in Tanzania.

Practical implications

– By empowering local NGOs through educational, capacity building, technological and other support, NGOs’ advocacy, campaigning and networking with other civil society groups can play a pivotal role in encouraging corporations, especially TNCs, to adopt more socially and environmentally responsible business practices and to adhere to international and local standards, which in turn may help to improve the lives of many poor people living in developing countries in general, and Tanzania in particular.

Originality/value

– This paper contributes insights from gold-mining activities in Tanzania to the existing literature on CSR in the mining sector. It also contributes to political economy theory by locating CSR reporting within the socio-political and regulatory context in which mining operations take place in Tanzania. It is argued that, for CSR reporting to be effective, robust regulations and enforcement and stronger political pressure must be put in place.
Stock price synchronicity and stock price crash risk
Authors: Jin Yonghong , Yan Mengya , Xi Yuqin , Liu Chunmei
Published: August 2016

Purpose

– The purpose of this paper is to empirically analyze the effects of stock price synchronicity and herding behavior of qualified foreign institutional investors (QFII) on stock price crash risk, especially the mediating effect of herding behavior of QFII on the relation of stock price synchronicity and stock price crash risk.

Design/methodology/approach

– Taking China’s A-share listed companies from 2005 to 2014 and QFII holding shares data as the research sample, this study calculates herding effect index, sock price synchronicity index and stock price crash risk index, and perform linear regression.

Findings

– This study concludes that, either herding behavior of QFII or the stock price synchronicity can increase the stock price crash risk. Further study reveals that, the herding behavior of QFII also improves the effect of stock price synchronicity on stock price crash risk. Namely, herding behavior of QFII acts as the mediating role between stock price synchronicity and stock price crash risk.

Originality/value

– This study empirically analyzes and verifies the mediating roles of herding behavior of QFII in affecting the relation of sock price synchronicity and stock price crash risk for the first time. The findings of this study contribute to the study of the role of QFII in stabilizing Chinese security market.
An empirical study on the correlation structure of credit spreads based on the dynamic and pair copula functions
Authors: Luo Changqing , Li Mengzhen , Ouyang Zisheng
Published: August 2016

Purpose

– The purpose of this paper is to study the correlation structure of the credit spreads.

Design/methodology/approach

– The minimal spanning tree is used to find the risk center node and the basic correlation structure of the credit spreads. The dynamic copula and pair copula models are applied to capture the dynamic and non-linear correlation structure.

Findings

– The authors take the enterprise bond with trading data from January 2013 to December 2013 as the research sample. The empirical study of minimum spanning tree shows that the credit risk of corporate bonds forms a network structure with a center node. Meanwhile, the correlation between credit spreads shows dynamic characteristics. Under the framework of dynamic copula, the lower tail dependence is less than the upper tail dependence, thus, in economic boom period, the dynamic correlation is more significant than in recession period. The authors also find that the centrality of credit risk network is not significant according to the pair copula and Granger causality test. The empirical study shows that the goodness-of-fit of D vine is superior to Canonical vine, and the Granger causality test additionally proves that the center node has influence on few other nodes in the risk network, thus the center node captured by the minimum spanning tree is a weak center node, and this characteristic of credit risk network indicates that the risk network of credit spreads is generated mostly by the external shocks rather than the internal risk contagion.

Originality/value

– This paper provides new ideas for investors and researchers to analyze the credit risk correlation or contagion.
On data-driven systems and system-driven data
Authors: Van Daele Koen , Meganck Leen , Mortier Sophie
Published: August 2016

Purpose

– Over the past 20 years, heritage inventories in Flanders (Belgium) have evolved from printed books to digital inventories. The purpose of this paper is to look at this evolution and highlight the interaction between the system and its users.

Design/methodology/approach

– After a short introduction about the history of inventories in Flanders, this paper mainly concerns itself with the last decade. Discrete topics will be highlighted to show the effects of the interaction that has taken place.

Findings

– It is obvious that a system that publishes a digital inventory needs to adapt to the user requirements. But, after years of working with a digital inventory system, it has become apparent that not only has the system been developed to the users’ needs, but also that user practice and the resulting data have been shaped by the system. Seeing data projected on a common basemap has led researchers to realise how intertwined and interdependent different types of heritage can be and how much their respective methodologies can benefit from more interaction. It has become apparent that data quality is of the utmost importance, something that can only be guaranteed by data entry standards, validation tools, and a strict editing workflow. The systems that are being developed are not expected to live on forever, but the data in them is.

Originality/value

– This paper presents real-life use cases and practical applications of building and maintaining a large digital inventory system over the years and through changes in organisational structure and focus. It provides insights that are hard to ascertain from smaller projects due to the volumes of data that are handled.
Concurrent and sustainable development of a local-scale digital heritage inventory through action research at Bat, Oman
Authors: Kondo Yasuhisa , Miki Takehiro , Kuronuma Taichi , Hayakawa Yuichi S. , Kataoka Kyoko , Oguchi Takashi
Published: August 2016

Purpose

– The purpose of this paper is to present a concurrent implementation of sustainable inventory for the UNESCO World Heritage sites of Bat, Al-Khutm and Al-Ayn in the interior of Oman.

Design/methodology/approach

– A digital heritage inventory (DHI) was developed through an action research to realize demands of the local agent and to co-design the solution. The Ministry of Heritage and Culture of Oman, the local agent, demanded to have archaeological information of the sites shared with foreign expeditions, which had worked at the sites for decades, for efficient heritage management, scientific research, outreach, and education. To this end, the Bat Digital Heritage Inventory (BatDHI) was implemented by a combination of network-access-ready database application, open source geographical information systems, and a web-based map service to incorporate and visualize previous works, which were concurrently cross-checked and updated by ground-truth surveys.

Findings

– The online inventory made it possible to update information during archaeological fieldwork in real time and accelerated the decision-making process in heritage management by prompt data updates and visualization.

Research limitations/implications

– The DHI is extendable for other sites or regions. It should also be considered to install Arches, an open-source suite of digital heritage inventories.

Practical implications

– The BatDHI was implemented through the action research mentioned in the design/methodology/approach section and yielded the implications mentioned in the findings section.

Originality/value

– This paper is a challenging application of transdisciplinary approach to the sustainable heritage management, in which researchers and societal stakeholders collaborate for co-design of research agendas, co-production of knowledge, and co-dissemination of outcomes.
The Arches heritage inventory and management system: a platform for the heritage field
Authors: Myers David , Dalgity Alison , Avramides Ioannis
Published: August 2016

Purpose

– The purpose of this paper is to describe the Arches heritage inventory and management system for the benefit of practitioners working with heritage inventories. Arches is a modern software platform purpose-built for the creation and management of inventories to support effective heritage place management. The system was developed as open source software jointly by the Getty Conservation Institute (GCI) and World Monuments Fund (WMF).

Design/methodology/approach

– The paper discusses the needs and challenges addressed by the GCI and WMF in developing Arches, explains the system’s design and functionality, reports on software releases and ongoing enhancements, describes current software implementations, and concludes by discussing the role and growth of the open source community and the Arches project’s aspirations.

Findings

– The needs and challenges in the heritage field that the GCI and WMF originally identified have been confirmed through interactions between the Arches project and a range of practitioners. The suitability of Arches to address these needs is demonstrated through steady growth of the open source community and an increasing number of implementations of the Arches platform.

Practical implications

– Arches provides a purpose-built system that is freely available and ready for use. It offers a system that requires a marginal investment by organizations compared to building digital inventories from scratch. The Arches project has created an international community of information technology and heritage practitioners to share experience, knowledge, and skills to address their common challenges in dealing with digital inventories.

Originality/value

– The paper offers heritage practitioners details on a new tool for overcoming their challenges in building and managing digital heritage inventories.
Conceptualizing and measuring resistance to change in brand relationships
Authors: Ramaswami Sridhar N. , Raju Sekar , Page Dana C.
Published: August 2016

Purpose

This research aims to examine two constructs that define loyal brand relationships – greater resistance to changing their brand beliefs and attitudes (resistance to change) and greater willingness to shun competitor brands (determinism). The paper develops and tests psychometrically sound scales to measure these two constructs and proposes and tests a model that identifies antecedent and outcome linkages between resistance and determinism and other brand relationship measures across two studies.

Design/methodology/approach

Scale development was done following the guidelines recommended by Nunnally and Bernstein (1994) and Churchill (1979). Factor analysis was used to test scale item fit. Discriminant validity, scale reliability tests, nomological and predictive validity tests were conducted.

Findings

This study adds to the literature by identifying the specific dimensions that compose the resistance concept. It finds that strong resistance leads to determinism at the high end. It also finds that brand engagement is an outcome of resistance. In addition, three sub-components of the resistance dimension – resistance to new products that offer higher value, resistance to value improvements of competing offerings and resistance to quality deterioration for the focal or object brand – are also identified and scale items developed to measure them.

Research limitations/implications

Resistance to change and determinism are less understood and researched concepts in the context of brand relationships. Further, these two dimensions are of particular importance in emerging markets such as India because of the changes taking place in these markets with the introduction of many global brands competing with traditional strong brands. For new brands, a key question is how to reduce the resistance that consumers exhibit toward trying out new brands. For existing brands, the key question is how to leverage the resistance that consumers have in trying out a new brand so that greater determinism is built and defections are minimized. This research helps answer some of these questions.

Originality/value

The primary purpose of the study was to identify the specific dimensions that compose the resistance concept. An important aspect of brand relationships is the ability to foster greater strength in the relationship. While the important of resistance has been known, a good scale to measure it has been lacking.
Constraints of cold and shade on the phenology of spring ephemeral herb species
Authors: Augspurger Carol K. , Salk Carl F.
Published: August 2016

Spring ephemeral herb species in temperate deciduous forests are active above‐ground only briefly each year. This study tested experimentally how two countervailing constraints – cold and darkness – influence the phenology of six spring herb species.

Dormancy of underground structures, maintained by cold temperatures in a growth chamber, was broken at six 25‐day intervals from January or February to June in two consecutive years. Upon emergence, survival and flowering were measured on cohorts grown outdoors. Shade cloth was added at the time of normal canopy closure.

Cardamine concatenata,Dicentra cucullaria,Erythronium albidumandTrillium recurvatumhad no or low 2‐year survival in the two or three earliest cohorts and no or low survival in the latest cohort, relative to their natural cohort.Allium canadenseandClaytonia virginicahad survival in all cohorts. Flowering never occurred in the first two or three cohorts for three species and never occurred or declined in later cohorts in all species.

Despite widely differing emergence dates, senescence was completed within a 40‐day period soon after shade was imposed for all cohorts for all species. Consequently, leaf life span became shorter as date of emergence was delayed among cohorts.

In general, the brief growth period of spring herb species is an adaptation to avoid winter cold and late‐spring canopy shade. These constraints are species‐specific and differ for survival and flowering for some species.Claytonia virginicais the most tolerant among the species to a wider range of conditions.

Synthesis. Knowing that cold and shade constrain a plant's non‐dormant period is important because of the significant role plant phenology plays in responses to climate change.
Landscape spatial configuration is a key driver of wild bee demographics
Authors: Neokosmidis Lazaros , Tscheulin Thomas , Devalez Jelle , Petanidou Theodora
Published: August 2016

The majority of studies investigating the effects of landscape composition and configuration on bee populations have been conducted in regions of intensive agricultural production, ignoring regions which are dominated by seminatural habitats, such as the islands of the Aegean Archipelago. In addition, research so far has focused on the landscape impacts on bees sampled in cropped fields while the landscape effects on bees inhabiting seminatural habitats are understudied. Here, we investigate the impact of the landscape on wild bee assemblages in 66 phryganic (low scrubland) communities on 8 Aegean islands. We computed landscape metrics (total area and total perimeter–area ratio) in 4 concentric circles (250, 500, 750, and 1000 m) around the center of each bee sampling site including 3 habitat groups (namely phrygana, cultivated land, and natural forests). We further measured the local flower cover in 25 quadrats distributed randomly at the center of each sampling site. We found that the landscape scale is more important than the local scale in shaping abundance and species richness of bees. Furthermore, habitat configuration was more important than the total area of habitats, probably because it affects bees’ movement across the landscape. Phrygana and natural forests had a positive effect on bee demographics, while cultivated land had a negative effect. This demonstrates that phryganic specialists drive bee assemblages in these seminatural landscapes. This finding, together with the shown importance of landscape scale, should be considered for the management of wild bees with special emphasis placed on the spatial configuration of seminatural habitats.
A review of the ecosystem functions in oil palm plantations, using forests as a reference system
Authors: Dislich Claudia , Keyel Alexander C. , Salecker Jan , Kisel Yael , Meyer Katrin M. , Auliya Mark , Barnes Andrew D. , Corre Marife D. , Darras Kevin , Faust Heiko , Hess Bastian , Klasen Stephan , Knohl Alexander , Kreft Holger , Meijide Ana , Nurdiansyah Fuad , Otten Fenna , Pe'er Guy , Steinebach Stefanie , Tarigan Suria , Tölle Merja H. , Tscharntke Teja , Wiegand Kerstin
Published: August 2016

Oil palm plantations have expanded rapidly in recent decades. This large‐scale land‐use change has had great ecological, economic, and social impacts on both the areas converted to oil palm and their surroundings. However, research on the impacts of oil palm cultivation is scattered and patchy, and no clear overview exists. We address this gap through a systematic and comprehensive literature review of all ecosystem functions in oil palm plantations, including several (genetic, medicinal and ornamental resources, information functions) not included in previous systematic reviews. We compare ecosystem functions in oil palm plantations to those in forests, as the conversion of forest to oil palm is prevalent in the tropics. We find that oil palm plantations generally have reduced ecosystem functioning compared to forests: 11 out of 14 ecosystem functions show a net decrease in level of function. Some functions show decreases with potentially irreversible global impacts (e.g. reductions in gas and climate regulation, habitat and nursery functions, genetic resources, medicinal resources, and information functions). The most serious impacts occur when forest is cleared to establish new plantations, and immediately afterwards, especially on peat soils. To variable degrees, specific plantation management measures can prevent or reduce losses of some ecosystem functions (e.g. avoid illegal land clearing via fire, avoid draining of peat, use of integrated pest management, use of cover crops, mulch, and compost) and we highlight synergistic mitigation measures that can improve multiple ecosystem functions simultaneously. The only ecosystem function which increases in oil palm plantations is, unsurprisingly, the production of marketable goods. Our review highlights numerous research gaps. In particular, there are significant gaps with respect to socio‐cultural information functions. Further, there is a need for more empirical data on the importance of spatial and temporal scales, such as differences among plantations in different environments, of different sizes, and of different ages, as our review has identified examples where ecosystem functions vary spatially and temporally. Finally, more research is needed on developing management practices that can offset the losses of ecosystem functions. Our findings should stimulate research to address the identified gaps, and provide a foundation for more systematic research and discussion on ways to minimize the negative impacts and maximize the positive impacts of oil palm cultivation.
CD10 down expression in follicular lymphoma correlates with gastrointestinal lesion involving the stomach and large intestine
Authors: Ohnishi Nobuhiko , Takata Katsuyoshi , Miyata‐Takata Tomoko , Sato Yasuharu , Tari Akira , Gion Yuka , Noujima‐Harada Mai , Taniguchi Kohei , Tabata Tetsuya , Nagakita Keina , Omote Shizuma , Takahata Hiroyuki , Iwamuro Masaya , Okada Hiroyuki , Maeda Yoshinobu , Yanai Hiroyuki , Yoshino Tadashi
Published: August 2016

Follicular lymphoma (FL) shows co‐expression of B‐cell lymphoma 2 (BCL2) and CD10, whereas downexpression of CD10 is occasionally experienced in gastrointestinal (GI) FL with unknown significance. Gastrointestinal FL is a rare variant of FL, and its similarity with mucosa‐associated lymphoid tissue lymphoma was reported. We investigated the clinicopathological and genetic features of CD10 downexpressed (CD10down) GI‐FL. The diagnosis of CD10down FL was carried out with a combination of pathological and molecular analyses. The incidence of CD10down GI‐FL was shown in 35/172 (20.3%) cases, which was more frequent than nodal FL (3.5%, P < 0.001). The difference was additionally significant between GI‐FL and nodal FL when the analysis was confined to primary GI‐FL (55.2% vs 3.5%, P < 0.001). Compared to CD10+ GI‐FL, CD10down GI‐FL significantly involved the stomach or large intestine (P = 0.015), and additionally showed the downexpression of BCL6 (P < 0.001). The follicular dendritic cell meshwork often showed a duodenal pattern in the CD10down group (P = 0.12). Furthermore, a lymphoepithelial lesion was observed in 5/12 (40%) gastric FL cases, which indicated caution in the differentiation of mucosa‐associated lymphoid tissue lymphoma. Molecular analyses were undertaken in seven cases of CD10down GI‐FL, and an identical clone was found between CD10down follicles and CD10+BCL2+ neoplastic follicles. In the diagnosis of cases with CD10down BCL2+ follicles, careful examination with molecular studies should be carried out.
Fhit loss‐associated initiation and progression of neoplasia in vitro
Authors: Karras Jenna R. , Schrock Morgan S. , Batar Bahadir , Zhang Jie , La Perle Krista , Druck Teresa , Huebner Kay
Published: August 2016

The FHIT gene, encompassing an active common fragile site, FRA3B, is frequently silenced in preneoplasia and cancer, through gene rearrangement or methylation of regulatory sequences. Silencing of Fhit protein expression causes thymidine kinase 1 downregulation, resulting in dNTP imbalance, and spontaneous replication stress that leads to chromosomal aberrations, allele copy number variations, insertions/deletions, and single‐base substitutions. Thus, Fhit, which is reduced in expression in the majority of human cancers, is a genome “caretaker” whose loss initiates genome instability in preneoplastic lesions. To follow the early genetic alterations and functional changes induced by Fhit loss that may recapitulate the neoplastic process in vitro, we established epithelial cell lines from kidney tissues of Fhit−/− and +/+ mouse pups early after weaning, and subjected cell cultures to nutritional and carcinogen stress, which +/+ cells did not survive. Through transcriptome profiling and protein expression analysis, we observed changes in the Trp53/p21 and survivin apoptotic pathways in −/− cells, and in expression of proteins involved in epithelial–mesenchymal transition. Some Fhit‐deficient cell lines showed anchorage‐independent colony formation and increased invasive capacity in vitro. Furthermore, cells of stressed Fhit−/− cell lines formed s.c. and metastatic tumors in nude mice. Collectively, we show that Fhit loss and subsequent thymidine kinase 1 inactivation, combined with selective pressures, leads to neoplasia‐associated alterations in genes and gene expression patterns in vitro and in vivo.
A qualitative investigation of recovery after femoral fracture in Rett syndrome
Authors: Horne T. , Leonard H. , Stannage K. , Downs J.
Published: August 2016

Background

Children with severe disability often develop osteoporosis and have an increased risk of fracture. In Rett syndrome, the prevalence of fracture is four times greater than in the general population, and the femur is commonly affected. This study used qualitative methods to investigate the regaining of mobility within 12 months following femoral fracture in Rett syndrome and parent caregiver experiences.

Methods

Caregivers (n = 14) of cases registered with the Australian Rett Syndrome Database with a daughter with Rett syndrome were recruited if their daughter sustained a femoral fracture between 2009 and 2014. Median (interquartile range) age at fracture was 11 years and 4 months (8 years and 8 months to 22 years and 3 months). Qualitative methods were used to investigate parent/caregiver experiences and their daughter's recovery following fracture. Themes in the interview data were identified with thematic analysis.

Results

Operative management was chosen for those walking independently and non‐operative management for most of the remaining. All who walked independently and one of the four who required assistance recovered pre‐operative walking skills within 6 months. Themes identified by caregivers related to the complexities of pain recognition, the caregiver emotional journey and later rebuilding of relationships with service providers.

Conclusions

Those who walked with assistance were vulnerable to loss of this skill. Difficulties in pain recognition increased time to diagnose fracture, and the acute episode was associated with heightened caregiver stress. Service providers can use family‐centred practice models to support the strengthening of family functioning following this acute event that is surprisingly common in those with severe disability.
Investor Sentiment and Return Predictability of the Option to Stock Volume Ratio
Authors: Kim Jun Sik , Kim Da‐Hea , Seo Sung Won
Published: August 2016

We study the effect of investor sentiment on the relation between the option to stock volume ratio (O/S) and future stock returns. Relative option volume has return predictability under short sale constraints. For this reason, we expect and find a stronger O/S‐return relation during high sentiment periods than during low sentiment periods. We find that Baker and Wurgler's Investor Sentiment Index affects the O/S‐return relation after controlling for consumer sentiment indices and economic environment factors. While prior studies have used consumer sentiment indices as alternative measures of investor sentiment, our results suggest these effects are distinct.
A cautionary note on the use of hypervolume kernel density estimators in ecological niche modelling
Authors: Qiao Huijie , Escobar Luis E. , Saupe Erin E. , Ji Liqiang , Soberón Jorge
Published: August 2016

Blonder et al. (, Global Ecology and Biogeography, 23, 595–609) introduced a new multivariate kernel density estimation (KDE) method to infer Hutchinsonian hypervolumes in the modelling of ecological niches. The authors argued that their KDE method matches or outperforms several methods for estimating hypervolume geometries and for conducting species distribution modelling. Further clarification, however, is appropriate with respect to the assumptions and limitations of KDE as a method for species distribution modelling. Using virtual species and controlled environmental scenarios, we show that KDE both under‐ and overestimates niche volumes depending on the dimensionality of the dataset and the number of occurrence records considered. We suggest that KDE may be a viable approach when dealing with large sample sizes, limited sampling bias and only a few environmental dimensions.
Effect of Left Atrial Wall Thickness on Radiofrequency Ablation Success
Authors: INOUE JIRO , SKANES ALLAN C. , GULA LORNE J. , DRANGOVA MARIA
Published: August 2016

Effect of LA Wall Thickness on RF Ablation

Introduction

Radiofrequency (RF) ablation in thicker regions of the left atrium (LA) may require increased ablation energy in order to achieve effective transmural lesions. Consequently, many cases of recurrent atrial fibrillation (AF) postablation may be due to thicker‐than‐normal atrial tissue. The aim of this study was to test the hypotheses that patients with recurrent AF have thicker tissue overall and that electrical reconnection is more likely in regions of thicker tissue.

Methods and Results

Retrospective analysis was performed on 86 CT images acquired preoperatively from a cohort of 119 patients who had undergone RF ablation for AF. Of these, 33 patients experienced recurrence of AF within 1 year of initial treatment and 29 returned for a repeat ablation. For each patient, LA wall thickness (LAWT) was measured from the images in 12 anatomical regions using custom software. Patients with recurrent AF had larger LAWT compared to successfully treated patients (1.6 ± 0.6 mm vs. 1.5 ± 0.5 mm, P < 0.001) and reconnection was found to be at regions of thicker tissue (1.6 ± 0.6 mm, P = 0.038) compared to nonreconnected regions (1.5 ± 0.5 mm). The superior right posterior wall of the LA was significantly related to both recurrence (P = 0.048) and reconnection (P = 0.014).

Conclusion

Increased LAWT has a small but significant effect on postablation recurrence and reconnection. Measures of LAWT may facilitate appropriate dosing of RF energy, but other factors will be critical in transmural lesion formation and ablation success.
Effects of Obesity and Hypertension on Pulse Wave Velocity in Children
Authors: Kulsum‐Mecci Nazia , Goss Charles , Kozel Beth A. , Garbutt Jane M. , Schechtman Kenneth B. , Dharnidharka Vikas R.
Published: August 2016

Pulse wave velocity (PWV) is a biomarker of arterial stiffness. Findings from prior studies are conflicting regarding the impact of obesity on PWV in children. The authors measured carotid‐femoral PWV in 159 children aged 4 to 18 years, of whom 95 were healthy, 25 were obese, 15 had hypertension (HTN), and 24 were both obese and hypertensive. Mean PWV increased with age but did not differ by race or sex. In adjusted analyses in children 10 years and older (n=102), PWV was significantly higher in children with hypertension (PWV±standard deviation, 4.9±0.7 m/s), obesity (5.0±0.9 m/s), and combined obesity‐hypertension (5.2±0.6 m/s) vs healthy children (4.3±0.7 m/s) (each group, P<.001 vs control). In our study, obesity and HTN both significantly and independently increased PWV, while African American children did not have a higher PWV than Caucasian children.
Preferential binding of a stable G3BP ribonucleoprotein complex to intron‐retaining transcripts in mouse brain and modulation of their expression in the cerebellum
Authors: Martin Sophie , Bellora Nicolas , González‐Vallinas Juan , Irimia Manuel , Chebli Karim , de Toledo Marion , Raabe Monika , Eyras Eduardo , Urlaub Henning , Blencowe Ben J. , Tazi Jamal
Published: August 2016

Neuronal granules play an important role in the localization and transport of translationally silenced messenger ribonucleoproteins in neurons. Among the factors associated with these granules, the RNA‐binding protein G3BP1 (stress‐granules assembly factor) is involved in neuronal plasticity and is induced in Alzheimer's disease. We immunopurified a stable complex containing G3BP1 from mouse brain and performed high‐throughput sequencing and cross‐linking immunoprecipitation to identify the associated RNAs. The G3BP‐complex contained the deubiquitinating protease USP10, CtBP1 and the RNA‐binding proteins Caprin‐1, G3BP2a and splicing factor proline and glutamine rich, or PSF. The G3BP‐complex binds preferentially to transcripts that retain introns, and to non‐coding sequences like 3’‐untranslated region and long non‐coding RNAs. Specific transcripts with retained introns appear to be enriched in the cerebellum compared to the rest of the brain and G3BP1 depletion decreased this intron retention in the cerebellum of G3BP1 knockout mice. Among the enriched transcripts, we found an overrepresentation of genes involved in synaptic transmission, especially glutamate‐related neuronal transmission. Notably, G3BP1 seems to repress the expression of the mature Grm5 (metabotropic glutamate receptor 5) transcript, by promoting the retention of an intron in the immature transcript in the cerebellum. Our results suggest that G3BP is involved in a new functional mechanism to regulate non‐coding RNAs including intron‐retaining transcripts, and thus have broad implications for neuronal gene regulation, where intron retention is widespread.

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Gait in children and adolescents with Charcot‐Marie‐Tooth disease: a systematic review
Authors: Kennedy Rachel A. , Carroll Kate , McGinley Jennifer L.
Published: August 2016

Symptoms of Charcot‐Marie‐Tooth (CMT) disease typically arise in childhood or adolescence with gait difficulty most common. A systematic review was conducted to synthesise, review, and characterise gait in paediatric CMT. Health‐related electronic databases were reviewed with search terms related to CMT and gait. Of 454 articles, 10 articles describing seven studies met eligibility criteria; samples ranged from 1 to 81, included mixed CMT sub‐types and had a participant mean age of 13 years. Assessments included a variety of methods to examine only barefoot gait. Heterogeneity of gait patterns was noted. Children and adolescents with CMT walked slower, most likely due to shorter stride length. Common kinematic and kinetic abnormalities included significant foot drop during swing, reduced calf muscle power, and proximal compensatory mechanisms in the lower limb. Little data were found to inform typical functional gait characteristics or change over time. Of note, barefoot assessment does not reflect function in everyday life where footwear is commonly worn. With limited existing literature, future studies of gait in paediatric CMT need to evaluate the influence of diagnostic sub‐types and disease progression; the effect of factors such as footwear and the environment; and to explore changes in gait and function throughout childhood and adolescence.
Media Plurality: Private versus Mixed Duopolies
Authors: PIRES ARMANDO JOSÉ GARCIA
Published: August 2016

In this paper, we analyze the level of media plurality in a market with two private news firms (private duopoly) and in a market with a private news firm and a public news firm (mixed duopoly). In the private duopoly news firms maximize profits. In the mixed duopoly, the private news firm maximizes profits, while the public news firm maximizes social welfare. We show that, in spite of the public news firm maximizing social welfare, neither media plurality nor social welfare needs to be higher under the mixed duopoly compared with the private duopoly. This will depend on the relation between the costs of adapting news to readers' political preferences, the intensity of the readers' political preferences, and the size of the advertising market.
Melatonin prevents radiation‐induced oxidative stress and periodontal tissue breakdown in irradiated rats with experimental periodontitis
Authors: Köse O. , Arabaci T. , Kizildag A. , Erdemci B. , Özkal Eminoğlu D. , Gedikli S. , Özkanlar S. , Zihni M. , Albayrak M. , Kara A. , Kermen E.
Published: August 2016

Background and Objective

The aim of this study was to analyze the biochemical and histochemical effects of radiation therapy and protective melatonin administration on periodontal tissues in rats with experimental periodontitis.

Material and Methods

Sixty male Sprague Dawley rats were divided into six groups, as follows: control; experimental periodontitis (Ped); radiotherapy administration (Rt); experimental periodontitis and exposure to irradiation (Ped‐Rt); radiotherapy and protective melatonin administration (Rt‐Mel); and periodontitis, radiation therapy and protective melatonin administration (Ped‐Rt‐Mel). The rats were killed at the end of the experimental procedure, and the oxidative stress level and periodontal destruction were compared among the groups.

Results

The oxidative stress index and the levels of 8‐hydroxy‐2′‐deoxyguanosine, malondialdehyde and C‐terminal telopeptide of type I collagen were found to be significantly higher in the Ped‐Rt group compared with the Ped group (p < 0.05), and the levels were lower in the Ped‐Rt‐Mel group than in the Ped‐Rt group (p < 0.05). Alveolar bone destruction and attachment level were also significantly lower in the Ped‐Rt‐Mel group than in the Ped‐Rt group (p < 0.05).

Conclusion

It was found that radiotherapy increased oxidative stress, the periodontal attachment level and alveolar bone loss, and protective melatonin administration significantly reduced the oxidative parameters and prevented periodontal damage in irradiated rats with experimental periodontitis. Further research is needed regarding the use of systemic melatonin administration before radiation therapy.
What Religion Affords Grassroots NGOs: Frames, Networks, Modes of Action
Authors: Schnable Allison
Published: August 2016

The international relief and development sector has swelled in the last two decades thanks to American grassroots NGOs: groups that rely on volunteer labor and individual contributions, often on budgets of less than $25,000 a year. Most of these organizations reject the label of “faith‐based organization,” yet they find the symbolic and material resources of religion indispensable. Religion affords these NGOs three kinds of resources to meet their distinct organizational needs. First, it providesframes, or ways of thinking and speaking about relief and development work that imbue it with legitimacy. Next, religion offersnetworksthat provide money, volunteers, and entrée into aid‐receiving communities. Finally, religion affords familiarmodes of actionthat link the NGO, supporters, and local aid recipients. I support these claims with LDA topic modeling (a computerized method of text analysis), content analysis of websites, and in‐depth interviews with 43 informants.