bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of Advanced Neoplasia Using the National Cancer Institute’s Colorectal
Cancer Risk Assessment Tool
Authors: Imperiale Thomas F , Yu Menggang , Monahan Patrick O , Stump Timothy E , Tabbey Rebeka , Glowinski Elizabeth , Ransohoff David F 
Published: September 2016

Background: There is no validated, discriminating, and easy-to-apply tool for estimating risk of colorectal neoplasia. We studied whether the National Cancer Institute’s (NCI’s) Colorectal Cancer (CRC) Risk Assessment Tool, which estimates future CRC risk, could estimate current risk for advanced colorectal neoplasia among average-risk persons.
Methods: This cross-sectional study involved individuals age 50 to 80 years undergoing first-time screening colonoscopy. We measured medical and family history, lifestyle information, and physical measures and calculated each person’s future CRC risk using the NCI tool’s logistic regression equation. We related quintiles of future CRC risk to the current risk of advanced neoplasia (sessile serrated polyp or tubular adenoma ≥ 1 cm, a polyp with villous histology or high-grade dysplasia, or CRC). All statistical tests were two-sided.
Results: For 4457 (98.5%) with complete data (mean age = 57.2 years, SD = 6.6 years, 51.7% women), advanced neoplasia prevalence was 8.26%. Based on quintiles of five-year estimated absolute CRC risk, current risks of advanced neoplasia were 2.1% (95% confidence interval [CI] = 1.3% to 3.3%), 4.8% (95% CI = 3.5% to 6.4%), 6.4% (95% CI = 4.9% to 8.2%), 10.0% (95% CI = 8.1% to 12.1%), and 17.6% (95% CI = 15.5% to 20.6%; P &lt; .001). For quintiles of estimated 10-year CRC risk, corresponding current risks for advanced neoplasia were 2.2% (95% CI = 1.4% to 3.5%), 4.8% (95% CI = 3.5% to 6.4%), 6.5% (95% CI = 5.0% to 8.3%), 9.3% (95% CI = 7.5% to 11.4%), and 18.4% (95% CI = 15.9% to 21.1%; P &lt; .001). Among persons with an estimated five-year CRC risk above the median, current risk for advanced neoplasia was 12.8%, compared with 3.7% among those below the median (relative risk = 3.4, 95 CI = 2.7 to 4.4).
Conclusions: The NCI’s Risk Assessment Tool, which estimates future CRC risk, may be used to estimate current risk for advanced neoplasia, making it potentially useful for tailoring and improving CRC screening efficiency among average-risk persons.
Surveying for Virus-vectoring Nematodes in Container-grown Blueberry Plants in Oregon
Authors: Sharma-Poudyal D. , Fraley C. , Osterbauer N. K. 
Published: September 2016

The goal of this study was to determine the risk of finding virus-vectoring nematodes in containerized blueberry plants placed on gravel. To detect dagger nematode, soil, and potting media samples were collected from blueberry nurseries growing plants in containers using soilless potting media, with the containers placed on a gravel bed or, for one nursery, on a plastic sheet placed on the soil surface. Potting media samples were collected from containers holding plants and soil samples were collected from beneath the gravel or plastic barrier. Nematodes were extracted from all of the samples using sucrose centrifugation. No dagger or other plant parasitic nematodes were detected in any of the samples tested. These results suggest no treatment of soilless potting media is necessary before planting blueberries into containers. Similarly, the gravel layer seems to be an effective barrier for suppressing dagger and other plant parasitic nematodes. Accepted for publication 25 July 2016. Published 8 August 2016.
An immuno-suppressive aphid saliva protein is delivered into the cytosol of plant mesophyll cells during feeding
Authors: Mugford Sam T. , Barclay Elaine , Drurey Claire , Findlay Kim C. , Hogenhout Saskia A. 
Published: September 2016

AbstractHerbivore selection of plant hosts and plant responses to insect colonization have been subjects of intense investigations. A growing body of evidence suggests that for successful colonization to occur, (effector/virulence) proteins in insect saliva must modulate plant defense responses to the benefit of the insect. A range of insect saliva proteins that modulate plant defense responses have been identified, but there is no direct evidence that these proteins are delivered into specific plant tissues and enter plant cells. Aphids and other sap-sucking insects of the order Hemiptera use their specialized mouthparts (stylets) to probe plant mesophyll cells, until they reach the phloem cells for long-term feeding. Here we show by immunogold-labeling of ultrathin sections of aphid feeding sites that an immuno-suppressive aphid effector localizes in the cytoplasm of mesophyll cells near aphid stylets, but not in cells further away from aphid feeding sites. In contrast, another aphid effector protein localizes in the sheaths composed of gelling saliva that surround the aphid stylets. Thus, insects deliver effectors directly into plant tissue. Moreover, different aphid effectors locate extracellularly in the sheath saliva or are introduced into the cytoplasm of plant cells.
Disentangling the Relative Strength of Niche Competition from Grazing-Induced Phytoplankton Mortality
Authors: Beckett Stephen J. , Weitz Joshua S. 
Published: September 2016

AbstractThe dilution method is the principal tool used to inferin situmicrozooplankton grazing rates. However, grazing is the only mortality process considered in the theoretical model underlying the interpretation of dilution method experiments. Here we evaluate the robustness of mortality estimates inferred from dilution experiments when there is concurrent niche competition amongst phytoplankton. Using a combination of mathematical analysis and numerical simulations, we find that grazing rates may be overestimated – the degree of overestimation is related to the importance of niche competition relative to microzooplankton grazing. In response, we propose a conceptual method to disentangle the effects of niche competition and grazing by diluting out microzooplankton, but not phytoplankton. Our theoretical results suggest this revised “Z-dilution” method can robustly infer grazing mortality, regardless of the dominant phytoplankton mortality driver in our system. Further, we show it is possible to independently estimate both grazing mortality and niche competition if the classical and Z-dilution methods can be used in tandem. We discuss the significance of these results for quantifying phytoplankton mortality rates; and the feasibility of using the Z-dilution method in practice.
A Neural Oscillatory Signature of Reference
Authors: Nieuwland Mante S. , Martin Andrea E. 
Published: September 2016

ABSTRACTThe ability to use words to refer to the world is vital to the communicative power of human language. In particular, the anaphoric use of words to refer to previously mentioned concepts (antecedents) allows dialogue to be coherent and meaningful. Psycholinguistic theory posits that anaphor comprehension involves reactivating a memory representation of the antecedent. Whereas this implies the involvement of recognition memory, the neural processes for reference resolution are largely unknown. Here, we report time-frequency analysis of four EEG experiments to reveal the increased coupling of functional neural systems associated with referentially coherent expressions compared to referentially ambiguous expressions. Despite varying in modality, language, and type of referential expression, all experiments showed larger gamma-band power for coherence compared to ambiguity. Beamformer analysis in high-density Experiment 4 localised this increase to posterior parietal cortex around 400-600 ms after anaphor-onset and to frontal-temporal cortex around 500-1000 ms. We argue that the observed gamma-band power increases reflect successful referential binding and resolution, which links incoming information to antecedents through an interaction between the brain’s recognition memory networks and frontal-temporal language network. We integrate these findings with previous results from patient and neuroimaging studies, and outline a nascent cortico-hippocampal theory of reference.
GAVIN - Gene-Aware Variant INterpretation for medical sequencing
Authors: van der Velde K. Joeri , de Boer Eddy N. , van Diemen Cleo C. , Sikkema-Raddatz Birgit , Abbott Kristin M. , Knopperts Alain , Franke Lude , Sijmons Rolf H. , de Koning Tom J. , Wijmenga Cisca , Sinke Richard J. , Swertz Morris A. 
Published: September 2016

ABSTRACTHere, we present GAVIN, a new method that delivers accurate classification of variants for next-generation sequencing molecular diagnostics. It is based on gene-specific calibrations of allele frequencies (from the ExAC database), effect impact (using SnpEff) and estimated deleteriousness (CADD scores) for >3,000 genes. In a benchmark on 18 clinical gene sets, we achieved a sensitivity of 91.6%, with a specificity of 78.2%. This accuracy was unmatched by 12 other tools we tested. We provide GAVIN as an online MOLGENIS service to annotate VCF files, and as open source executable for use in bioinformatic pipelines. It can be found athttp://molgenis.org/gavin.
Evolution of cell-to-cell variability in stochastic, controlled, heteroplasmic mtDNA populations
Authors: Johnston Iain G. , Jones Nick S. 
Published: September 2016

AbstractPopulations of physiologically vital mitochondrial DNA (mtDNA) molecules evolve in cells under control from the nucleus. The evolution of populations of mixed mtDNA types is complicated and poorly understood, and variability of these controlled admixtures plays a central role in the inheritance and onset of genetic disease. Here, we develop a mathematical theory describing the evolution and variability in these stochastic populations for any type of cellular control, showing that cell-to-cell variability in mtDNA, and mutant load, inevitably increases with time, according to rates which we derive and which are notably independent of the mechanistic details of feedback signalling. We show with a set of experimental case studies that this theory explains disparate quantitative results from classical and modern experimental and computational studies on heteroplasmy variance in different species. We demonstrate that our general model provides a host of specific insights, including a modification of the often-used but hard-to-interpret Wright formula to correspond directly to biological observables, the ability to quantify selective and mutational pressure in mtDNA populations, and the pronounced variability inevitably arising from the action of possible mtDNA quality-control mechanisms. Our general theoretical framework, supported by existing experimental results, thus helps understand and predict the evolution of stochastic mtDNA populations in cell biology.
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways
Authors: Yi Lynn , Pimentel Harold , Pachter Lior 
Published: September 2016

AbstractBackgroundA recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and identified cell-cycle-related pathways that are affected by infection. However deeper exploration of the information present in the RNA-Seq data can be used to further elucidate the manner in which Zika infection of hNPCs affects the transcriptome, refining pathway predictions and revealing isoform-specific dynamics.Methodology/Principal FindingsWe analyzed data published by Tanget al.using state-of-the-art tools for transcriptome analysis. By accounting for the experimental design and estimation of technical and inferential variance we were able to pinpoint Zika infection affected pathways that highlight Zika’s neural tropism. The examination of differential genes reveals cases of isoform divergence.Conclusions/SignificanceTranscriptome analysis of Zika infected hNPCs has the potential to identify the molecular signatures of Zika infected neural cells. These signatures may be useful for diagnostics and for the resolution of infection pathways that can be used to harvest specific targets for further study.
Content analysis of comparative claims in drug advertisements
Authors: Boudewyns Vanessa , Williams Pamela A. 
Published: September 2016

Purpose
The purpose of this study is to describe the trends and practices of comparative prescription drug advertising by examining the types of comparative claims made in direct-to-consumer (DTC) and direct-to-physician (DTP) print advertisements.

Design/methodology/approach
The authors conducted a content analysis of 54 DTC and DTP print prescription drug advertisements (published between 1997 and 2014) with comparative claims.

Findings
Efficacy-based comparisons appeared in 64 per cent of advertisements, and attribute-based comparisons appeared in 37 per cent of advertisements. Most advertisements made direct (vs indirect) references to competitors (85 per cent), compared the advertised drug to a single (vs multiple) competitor (78 per cent), focused exclusively on one type of comparison claim (i.e. efficacy-, risk- or attribute-based) (70 per cent) and did not contain data-driven visual aids (82 per cent). Some differences between DTC and DTP advertisements emerged. More DTP than DTC advertisements included data-driven visual aids (82 per cent vs 0 per cent, respectively), included numerical data (88 per cent vs 53 per cent) and conveyed statistical significance (52 per cent vs 12 per cent).

Research limitations/implications
The study used a convenience sample rather than a random sample of advertisements; thus, the findings might not be generalizable to all pharmaceutical DTC and DTP advertisements. Examining the tactics that advertisers use to educate and influence consumers and physicians sets the foundation for future studies that examine the effects of their exposure to comparative claims. Suggestions for future research are discussed.

Originality/value
This study is the first to examine and statistically compare the comparative advertising tactics used in both consumer and physician prescription drug advertisements.
Causes and effects of wine tourism development in wineries
Authors: Lavandoski Joice , Pinto Patrícia , Silva João Albino , Vargas-Sánchez Alfonso 
Published: September 2016

PurposeThis study aims to propose that the institutional environment exerts pressure on the behavior of wineries toward wine tourism development (WTD) and the effect of this influence confers legitimacy to the business of wine tourism.Design/methodology/approachStructural equation modeling through partial least squares was applied to estimate and validate a model using data from a quantitative survey in the universe of 62 wineries with a wine tourism component along the Alentejo Wine Route in Portugal. The proposed model is based on institutional theory through an inter-organizational perspective of wineries.FindingsThe results show that WTD coexists with a highly institutionalized environment, exerting distinctive mechanisms of external pressure together with the search for social legitimacy through actions and practices on the part of the involved wineries. However, the relationship between legitimacy and organizational performance in wineries with wine tourism is not validated.Research limitations/implicationsThe specific sample of the Alentejo wine companies does not allow the results to be generalized. Future studies should replicate the proposed research model using other geographic areas.Practical implicationsThe results are particularly interesting for managers of wineries and should be considered in the decision-making and strategic processes regarding wine tourism.Originality/valueThe use of institutional theory in the wine tourism context is novel and original. This study fills a research gap by conducting an empirical investigation of wine tourism based on institutional theory, which allows the identification of exogenous factors that can influence and impose restrictions on the organizational behavior of winery companies toward wine tourism.
Mechanical compaction in heterogeneous clastic formations from plastic–poroelastic deformation principles: theory and applications
Authors: Bachrach Ran 
Published: September 2016

ABSTRACTMechanical compaction or loss of porosity due to increase in effective stress is a fundamental geological process that governs many of the rock elastic and transport parameters, all of great importance in exploring and developing subsurface reservoirs. The ability to model the compaction process enables us to improve our understanding of the seismic signature of the basin and better relate the geology of deposition to current porosity, velocity, pore pressure, and other mechanical parameters that depend on the state of compaction of the sediment. In this paper, a set of mathematical equations that can be used to model the plastic deformation associated with primary and secondary loading curves is presented. Compaction laws are posed in terms of natural strain increment formulation often used in plasticity theory to model large deformation. Laboratory and field estimates of constitutive plastic deformation relations for sand–shale mixtures are used in a numerical model that generates estimates of porosity under various pore pressures, shale content, and loading scenarios. These estimates can be used in a variety of settings to predict various basin and reservoir properties associated with different loading conditions and/or sedimentation processes.
Bone morphogenetic protein 6—a possible new player in pathophysiology of heart failure
Authors: Banach Joanna , Gilewski Wojciech , Słomka Artur , Buszko Katarzyna , Błażejewski Jan , Karasek Danuta , Rogowicz Daniel , Żekanowska Ewa , Sinkiewicz Wadyslaw 
Published: September 2016

SummaryDerangement of bone morphogenetic protein (BMP) signalling was observed in cardiovascular disorders. The present study assesses the diagnostic and prognostic value of BMP6 plasma concentration in chronic heart failure (CHF). 130 CHF patients and 32 controls participated in the study. BMP6 plasma level was measured at baseline. During 12‐month follow‐up death and hospitalisation with CHF exacerbation were recorded. BMP6 was significantly increased in CHF patients with highest concentration in most advanced disease. Individuals with pulmonary congestion or peripheral oedema had higher levels of BMP6 than isovolemic patients. BMP6 was not a predictor of all‐cause mortality or CHF hospitalisation. BMP6 may be involved in pathophysiology of systolic CHF. BMP6 plasma level is related to the disease severity and signs of exacerbation.
Fungal community composition in soils subjected to long‐term chemical fertilization is most influenced by the type of organic matter
Authors: Sun Ruibo , Dsouza Melissa , Gilbert Jack A. , Guo Xisheng , Wang Daozhong , Guo Zhibin , Ni Yingying , Chu Haiyan 
Published: September 2016

SummaryOrganic matter application is a widely used practice to increase soil carbon content and maintain soil fertility. However, little is known about the effect of different types of organic matter, or the input of exogenous species from these materials, on soil fungal communities. In this study, fungal community composition was characterized from soils amended with three types of organic matter over a 30‐year fertilization experiment. Chemical fertilization significantly changed soil fungal community composition and structure, which was exacerbated by the addition of organic matter, with the direction of change influenced by the type of organic matter used. The addition of organic matter significantly increased soil fungal richness, with the greatest richness achieved in soils amended with pig manure. Importantly, following addition of cow and pig manure, fungal taxa associated with these materials could be found in the soil, suggesting that these exogenous species can augment soil fungal composition. Moreover, the addition of organic matter decreased the relative abundance of potential pathogenic fungi. Overall, these results indicate that organic matter addition influences the composition and structure of soil fungal communities in predictable ways.
Tax Compliance and Data: What Is Available and What Is Needed
Authors: Torgler Benno 
Published: September 2016

AbstractAfter first providing an overview of useful survey data sources and commonly studied variables in the area of tax compliance, this article outlines the major tools and exploratory methods used in the field, including laboratory and field experiments, simulations and surveys. It also discusses future possibilities and the data required to progress in this area. It is thus particularly useful as a guide for those planning or just beginning to work in the tax compliance field.
The Attrition Rate, Lifetime and Hoarding of Australian Decimal Coins
Authors: Frazer Eric J. , van der Touw John 
Published: September 2016

AbstractSamples of Australian decimal coinage were taken in 2008 and 2012 from a major currency processing centre in Melbourne. A generic model was developed to analyse the pooled data and give separate estimates of loss, hoarding and return rates, as well as the numbers of coins in circulation, hoarded and permanently lost. For standard design coins, no particular trend in attrition rate with denomination was observed and average lifetimes were generally more than 30 years. Higher attrition rates were observed for the commemorative 20 cent and 50 cent coins versus the standard design. Hoarding was quantified for the 5 cent and 50 cent coins.
Retirees, Creatives and Housing Market Complexity: Challenges for Policy‐Makers
Authors: de Silva Ashton , Sinclair Sarah , Angelopoulos Sveta 
Published: September 2016

AbstractRetirees and creatives, significant cohorts in the Australian economy, are used in this article to demonstrate the challenges faced by policy‐makers when addressing the housing environment. The housing market is characterised by many participants, often with competing needs and wants, all contributing to the complexity of housing policy. As a result, policy can be difficult to define with multi‐directional interdependencies. We identify five characteristics of complexity—uniqueness, layers of government, dynamism, actors and knowledge spheres—that if duly considered in the policy formation process could contribute to a more integrated approach that minimises negative and conflicting policy consequences.
The Power of Policy: Reinforcing the Paris Trajectory
Authors: Figueres Christiana 
Published: September 2016

AbstractThe Paris Agreement is a critical global response that enables a transition toward human and planetary wellbeing. It articulates a new trajectory toward a low‐carbon economic system. It encompasses all countries, in the global North and South, and engages public and private sectors at local and global levels. Every country has stepped up to contribute to addressing the challenge of climate change. Governments, civil society, businesses, investors, academics expressed commitment to tackling climate change not as an end in itself, but as a means to a resilient society, to sustainable development and to more fulfilling and enriching lifestyles and livelihoods.
Information linkages between emission allowance and energy markets
Authors: Schultz Emma , Swieringa John 
Published: September 2016

AbstractWe employ a rational expectations framework similar to that proposed by Fleming et al. (1998) to examine the source, and nature of, information linkages between the emission allowance and energy markets as gauged by the correlation of return volatilities. Estimating the model for bivariate pairings of securities suggests that market linkages arise from sensitivities to common information rather than from indirect spillovers, with emission allowances most strongly linked to the crude oil market.