bluuebunny/crossref_metadata_2025 huggingface dataset:
Are GMO Policies “Trade Related”? Empirical Analysis of Latin America
Authors: Smith Pamela J. , Katovich Erik S.
Published: November 2016

This paper empirically examines whether GMO policies are “trade related” for countries in Latin America (LA). First, we use the Balassa index to assess the “revealed comparative advantage” of LA countries. We find that LA countries have a revealed comparative advantage in GMO industries relative to the world, and that intra‐regional trade in these industries is modest relative to external trade. Second, we estimate the Gravity model to examine the effects of importers’ GMO policies on Argentina and Brazil’s bilateral exports of soybeans and maize. We find that strong GMO policies in importers have a negative effect on Argentina’s bilateral exports of soybeans (an industry and country with historically high GMO content). Further, we find that past GMO policies are a strong determinant of Argentina’s future bilateral exports, and that the negative trade effects of strong GMO policies are increasing over time. In contrast, we find a weaker relationship between the GMO policies of importers and Brazil’s bilateral exports (consistent with Brazil’s more recent increases in GMO content). These findings for Argentina and Brazil provide a benchmark for other developing countries that are looking for guidance on servicing trading partners with diverse GMO policies.
Tree invasions and biosecurity: eco-evolutionary dynamics of hitchhiking fungi
Authors: Burgess Treena I. , Crous Casparus J. , Slippers Bernard , Hantula Jarkko , Wingfield Michael J.
Published: November 2016

When non-native plants reach novel environments, they typically arrive with hidden microbiomes. In general, most of these hitchhikers remain on their co-evolved hosts, some contribute to the invasiveness of their hosts, and a small number can undergo host shifts and move onto native hosts. Invasion success can vary depending upon the different categories of fungal associates. When an invader tree relies on a fungal mutualism to survive in the new environment, there is a fundamentally lower likelihood of either the tree, or the fungus, establishing novel associations. In contrast, parasitic hitchhikers could merely use their host plants to move through the landscape and to become established on new hosts (host shifts). Evidence suggests the frequency of these host shifts is low and depends upon the fungal functional group. However, epidemics caused by invasive pathogens in native ecosystems have occurred globally. Thus, elucidating the potential for hidden non-native fungi to form novel host associations in a new environment is important for biodiversity conservation.
Cis-Compound Mutations are Prevalent in Triple Negative Breast Cancer and Can Drive Tumor Progression
Authors: Hiranuma Nao , Liu Jie , Song Chaozhong , Goldsmith Jacob , Dorschner Michael O. , Pritchard Colin C. , Burton Kimberly A. , Mahen Elisabeth M. , Blau Sibel , Senecal Francis M. , Monsky Wayne L. , Parker Stephanie , Schmechel Stephen C. , Allison Stephen K. , Gadi Vijayakrishna K. , Salama Sophie R. , Radenbaugh Amie J. , Goldman Mary , Johnsen Jill M. , Heimfeld Shelly , Komashko Vitalina , LaMadrid-Hermannsfeldt Marissa , Duan Zhijun , Benz Steven C. , Soon-Shiong Patrick , Haussler David , Zhu Jingchun , Ruzzo Walter L. , Noble William S. , Blau C. Anthony
Published: November 2016

About 16% of breast cancers fall into a clinically aggressive category designated triple negative (TNBC) due to a lack of ERBB2, estrogen receptor and progesterone receptor expression1-3. The mutational spectrum of TNBC has been characterized as part of The Cancer Genome Atlas (TCGA)4; however, snapshots of primary tumors cannot reveal the mechanisms by which TNBCs progress and spread. To address this limitation we initiated the Intensive Trial of OMics in Cancer (ITOMIC)-001, in which patients with metastatic TNBC undergo multiple biopsies over space and time5. Whole exome sequencing (WES) of 67 samples from 11 patients identified 426 genes containing multiple distinct single nucleotide variants (SNVs) within the same sample, instances we term Multiple SNVs affecting the Same Gene and Sample (MSSGS). We find that >90% of MSSGS result from cis-compound mutations (in which both SNVs affect the same allele), that MSSGS comprised of SNVs affecting adjacent nucleotides arise from single mutational events, and that most other MSSGS result from the sequential acquisition of SNVs. Some MSSGS drive cancer progression, as exemplified by a TNBC driven by FGFR2(S252W;Y375C). MSSGS are more prevalent in TNBC than other breast cancer subtypes and occur at higher-than-expected frequencies across TNBC samples within TCGA. MSSGS may denote genes that play as yet unrecognized roles in cancer progression.
The Utility of Red Cell Distribution Width as a Parameter for Calculating Indices of Allostatic Load
Authors: Bello Ghalib A , Dumancas Gerard G
Published: November 2016

Background

Allostatic Load is a construct used to quantify the cumulative burden of exposure to stressors that, over the course of an individual’s life, exert a toll on the body’s physiological functions, increasing risks of various chronic ailments and conditions. Studies attempting to quantify allostatic load have used a variety of clinical biomarkers representing primary and secondary mediators. In this study, we demonstrate the value of including red blood cell distribution width (RDW) among the panel of clinical parameters used to calculate allostatic load.

Methods

We develop a novel formulation of allostatic load using RDW and other standard biomarkers. This index is computed using clinical laboratory data from the NHANES study. The predictive validity of the new index for tertiary outcomes (all-cause mortality and physician-assessed health status) is compared to that of the current formulation using Harrell’s C index, ROC analysis and regression-based goodness-of-fit measures.

Results

Inclusion of RDW as an allostatic load biomarker yields a significantly improved index. It demonstrates a superior ability to predict mortality, health status and biological age than the standard formulation currently in use.

Conclusion

RDW has shown strong correlations with mortality and a broad spectrum of diseases. A review of the existing literature on allostatic load reveals its underutilization in this area, despite being a standard component of blood count panels. This study is the first to demonstrate its usefulness as a potential allostatic load biomarker.
A mathematical approach to correlating objective spectro-temporal features of environmental sounds with their subjective perceptions
Authors: Burns Thomas F , Rajan Ramesh
Published: November 2016

Many studies on the subjective perception of non-linguistic sounds have focused on only a single percept, e.g. pleasantness. In the present study, we have examined three different perception-related factors to also allow us to look at any inter-relationships between them that could be related to objective features. Objective features of the NLSs in this database were calculated and subjective perceptions were recorded from participants. These two elements - objective features and subjective perceptions - were then mapped together using various statistical and mathematical techniques. So as to ground our results in a meaningful context, we chose to map a set of objective features to human percepts which had been used in previous studies of NLS perception, but which had not yet been related back to objective features or combinations thereof.
Quark enables semi-reference-based compression of RNA-seq data
Authors: Sarkar Hirak , Patro Rob
Published: November 2016

Motivation

The past decade has seen an exponential increase in biological sequencing capacity, and there has been a simultaneous effort to help organize and archive some of the vast quantities of sequencing data that are being generated. While these developments are tremendous from the perspective of maximizing the scientific utility of available data, they come with heavy costs. The storage and transmission of such vast amounts of sequencing data is expensive.

Results

We presentQuark, a semi-reference-based compression tool designed for RNA-seq data.Quarkmakes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. This allowsQuarkto achieve markedly better compression rates than existing reference-free schemes, while still relieving the burden of assuming a specific, shared reference sequence between the encoder and decoder. We demonstrate thatQuarkachieves state-of-the-art compression rates, and that, typically, only a small fraction of the reference sequence must be encoded along with the reads to allow reference-free decompression.

Availability

Quarkis implemented inC++11, and is available under a GPLv3 license atwww.github.com/COMBINE-lab/quark.

Contact

rob.patro@cs.stonybrook.edu
Verticillium dahliaeLysM effectors differentially contribute to virulence on plant hosts
Authors: Kombrink Anja , Rovenich Hanna , Shi-Kunne Xiaoqian , Rojas-Padilla Eduardo , van den Berg Grardy C.M. , Domazakis Emmanouil , de Jonge Ronnie , Valkenburg Dirk-Jan , Sánchez-Vallet Andrea , Seidl Michael F. , Thomma Bart P.H.J.
Published: November 2016

Chitin-binding LysM effectors contribute to virulence of various plant pathogenic fungi that are causal agents of foliar diseases. Here, we report on LysM effectors of the soil-borne fungal vascular wilt pathogenVerticillium dahliae. Comparative genomics revealed three core LysM effectors that are conserved in a collection ofV. dahliaestrains. Remarkably, and in contrast to the previously studied LysM effectors of other plant pathogens, no expression of core LysM effectors was monitoredin plantain a taxonomically diverse panel of host plants. Moreover, targeted deletion of the individual LysM effector genes inV. dahliaestrain JR2 did not compromise virulence in infections on Arabidopsis, tomato orNicotiana benthamiana. Interestingly, an additional lineage-specific LysM effector is encoded in the genome ofV. dahliaestrain VdLs17 but not in any otherV. dahliaestrain sequenced to date. Remarkably, this lineage-specific effector is expressedin plantaand contributes to virulence ofV. dahliaestrain VdLs17 on tomato, but not on Arabidopsis or onN. benthamiana. Functional analysis revealed that this LysM effector binds chitin, is able to suppress chitin-induced immune responses, and protects fungal hyphae against hydrolysis by plant hydrolytic enzymes. Thus, in contrast to the core LysM effectors ofV. dahliae, this lineage-specific LysM effector of strain VdLs17 contributes to virulencein planta.
Harnessing the lymphocyte meta-phenotype to optimize adoptive cell therapy
Authors: Mullinax John , O’Farrelly Cliona , Scott Jacob G. , Buttenschön Andreas , Elkenawi Asmaa E. , Moustaid Fadoua El , Fletcher Alexander G. , Grassberger Clemens , Kim Eunjung , Marusyk Andriy , McClelland Harry L.O. , Miroshnychenko Daria , Nichol Daniel
Published: November 2016

There is an urgent need for reliable effective therapy for patients with metastatic sarcoma. Approaches that manipulate the immune system have shown promise for patients with advanced, widely disseminated malignancies. One of these approaches is adoptive cell therapy (ACT), where tumor-infiltrating lymphocytes (TIL) are isolated from the tumor, expandedex vivo, and then transferred back to the patient. This approach has shown great promise in melanoma, leading to an objective response in approximately half of treated patients [14]. Standard protocols involve characterization of TIL populations with respect to adaptive CD4+ and CD8+ T-lymphocytes, but neglect the possible role of the innate lymphoid repertoire. Due to toxicity and the high cost associated with ACT, the IFN-γ release assay is currently used as a proxy to identify suitable TIL isolates for ACT. Efforts in TIL-ACT for sarcoma, which are pre-clinical and pioneered at Moffitt Cancer Center, have shown that only a minority of the TIL cultures show tumor specific activity in ex vivo IFN-γ assays. Surprisingly, internal melanoma trial data reveal a lack of correlation between IFN-γ assay and clinical outcomes, highlighting the need for a more reliable proxy. We hypothesize the existence of a predictable TIL meta-phenotype that leads to optimal tumor response. Here, we describe preliminary efforts to integrate prospective and existing patient data with mathematical models to optimize the TIL meta-phenotype prior to re-injection.
Stable multi-level social structure is maintained by habitat geometry in a wild bird population
Authors: Farine Damien R. , Sheldon Ben C.
Published: November 2016

Social structure can have profound evolutionary and ecological implications for animal populations. Structure can arise and be maintained via social preferences or be indirectly shaped by habitat structure. Understanding how social structure emerges is important for understanding the potential links between social structure and evolutionary and ecological processes. Here, we study a large community of wild birds fitted with uniquely-coded passive integrated transponder (PIT) tags and recorded on a grid of automated feeders fitted with radio frequency identification (RFID) antennae. We show that both large-scale and fine-scale network communities are consistent across years in this population, despite high generational turn-over. Studying the process that generates community structure, here the movement of individual birds across the woodland, suggests an important role of habitat geometry in shaping population-level social community structure. Our study highlights how relatively simple factors can produce apparent emergent social structure at the population scale, which has widespread implications for understanding eco-evolutionary dynamics.
A network-based approach to eQTL interpretation and SNP functional characterization
Authors: Fagny M. , Paulson J.N. , Kuijjer M.L. , Sonawane A.R. , Chen C.-Y. , Lopes-Ramos C.M. , Glass K. , Quackenbush J. , Platig J.
Published: November 2016

Expression quantitative trait locus (eQTL) analysis associates genotype with gene expression, but most eQTL studies only includecis-acting variants and generally examine a single tissue. We used data from 13 tissues obtained by the Genotype-Tissue Expression (GTEx) project v6.0 and, in each tissue, identified bothcis- andtrans-eQTLs. For each tissue, we represented significant associations between single nucleotide polymorphisms (SNPs) and genes as edges in a bipartite network. These networks are organized into dense, highly modular communities often representing coherent biological processes. Global network hubs are enriched in distal gene regulatory regions such as enhancers, but are devoid of disease-associated SNPs from genome wide association studies. In contrast, local, community-specific network hubs (core SNPs) are preferentially located in regulatory regions such as promoters and enhancers and highly enriched for trait and disease associations. These results provide help explain how many weak-effect SNPs might together influence cellular function and phenotype.
Complete mapping of viral escape from neutralizing antibodies
Authors: Doud Michael B. , Hensley Scott E. , Bloom Jesse D.
Published: November 2016

Identifying viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. Here we quantify how every amino-acid mutation to influenza hemagglutinin affects neutralization by monoclonal antibodies targeting several antigenic regions. Our approach involves creating all replication-competent protein variants of the virus, selecting these variants with antibody, and using deep sequencing to identify enriched mutations. These high-throughput measurements are predictive of the effects of individual mutations in traditional neutralization assays. At many residues, only some of the possible mutations escape from an antibody. For instance, at a single residue targeted by two different antibodies, we identify some mutations that escape both antibodies and other mutations that escape only one or the other. Therefore, our approach maps how viruses can escape antibodies with mutation-level sensitivity, and shows that only some mutations at antigenic residues actually alter antigenicity.
Balance of microtubule stiffness and cortical tension determines the size of blood cells with marginal band across species
Authors: Dmitrieff Serge , Alsina Adolfo , Mathur Aastha , Nedéléc François
Published: November 2016

The fast blood stream of animals is associated with large shear stresses. Consequently, blood cells have evolved a special morphology and a specific internal architecture allowing them to maintain their integrity over several weeks. For instance, non-mammalian red blood cells, mammalian erythroblasts and platelets have a peripheral ring of microtubules, called the marginal band, that flattens the overall cell morphology by pushing on the cell cortex. In this article, we model how the shape of these cells stems from the balance between marginal band elasticity and cortical tension. We predict that the diameter of the cell scales with the total microtubule polymer, and verify the predicted law across a wide range of species. Our analysis also shows that the combination of the marginal band rigidity and cortical tension increases the ability of the cell to withstand forces without deformation. Finally, we model the marginal band coiling that occurs during the disc-to-sphere transition observed for instance at the onset of blood platelet activation. We show that when cortical tension increases faster than crosslinkers can unbind, the marginal band will coil, whereas if the tension increases slower, the marginal band may shorten as microtubules slide relative to each other.

Significance Statement

Many blood cells have a discoidal shape, which is essential for them to function properly within the organism. For some cells, such as blood platelets, this shape is due to the interplay between the elasticity of the marginal band, which is a closed ring of stiff filaments called microtubules, and the tension of the cell cortex, a polymer scaffold associated with the plasma membrane. Dmitrieff et al. examined how cell size is determined by the mechanical balance between these two components. Remarkably, the theory is confirmed over nearly three orders of magnitudes, by data collected from 25 species. The theory also shows how the composite structure is adapted to resist transient mechanical challenges, as encountered in the blood stream.
Connecting genetic risk to disease endpoints through the human blood plasma proteome
Authors: Suhre Karsten , Arnold Matthias , Bhagwat Aditya , Cotton Richard J. , Engelke Rudolf , Laser Annika , Raffler Johannes , Sarwath Hina , Thareja Gaurav , DeLisle Robert Kirk , Gold Larry , Pezer Marija , Lauc Gordan , Selim Mohammed A. El-Din , Mook-Kanamori Dennis O. , Al-Dous Eman K. , Mohamoud Yasmin A. , Malek Joel , Strauch Konstantin , Grallert Harald , Peters Annette , Kastenmuller Gabi , Gieger Christian , Graumann Johannes
Published: November 2016

Genome-wide association studies (GWAS) with intermediate phenotypes, like changes in metabolite and protein levels, provide functional evidence for mapping disease associations and translating them into clinical applications. However, although hundreds of genetic risk variants have been associated with complex disorders, the underlying molecular pathways often remain elusive. Associations with intermediate traits across multiple chromosome locations are key in establishing functional links between GWAS-identified risk-variants and disease endpoints. Here, we describe a GWAS performed with a highly multiplexed aptamer-based affinity proteomics platform. We quantified associations between protein level changes and gene variants in a German cohort and replicated this GWAS in an Arab/Asian cohort. We identified many independent, SNP-protein associations, which represent novel, inter-chromosomal links, related to autoimmune disorders, Alzheimer's disease, cardiovascular disease, cancer, and many other disease endpoints. We integrated this information into a genome-proteome network, and created an interactive web-tool for interrogations. Our results provide a basis for new approaches to pharmaceutical and diagnostic applications.
Low toxic polymeric surfactant as a corrosion inhibitor for mild steel in hydrochloric acid medium
Authors: de Souza Paulo Renato , Ferrari Jean Vicente , Guedes Isabel Correia
Published: November 2016

Purpose

Surfactants have been reported to have high inhibition efficiencies for corrosion of steel. This paper aims to study the performance of a low toxic copolymer of polydimethylsiloxane and polyoxyalkylene (POA) surfactant named as POPS, as a corrosion inhibitor for mild steel (ASTM 1005) in hydrochloric acid (HCl) solution at 25°C.

Design/methodology/approach

To evaluate POPS efficiency as a corrosion inhibitor, the following techniques were used: surface tension measurements, weight loss measurements, open circuit potential monitoring, potentiodynamic polarization curves, electrochemical impedance spectroscopy (EIS), scanning electron microscopy and contact angle measurements.

Findings

Results indicated that POPS acted as a mixed corrosion inhibitor and led to a hydrophobic protector film on the metal surface. The adsorption process obeyed the Langmuir adsorption isotherm by chemisorption. The maximum efficiency of the surfactant studied was achieved in a concentration around the critical micelle concentration.

Originality/value

Surfactant (POPS) of low level of toxicity acts as a mixed corrosion inhibitor in HCl medium. Inhibitor film formation was characterized by EIS results. A mechanism for corrosion inhibition is proposed.
Price promotions and products with low consumer ratings
Authors: Kuo Hsiao-Ching , Nakhata Chinintorn
Published: November 2016

Purpose

Previous research indicates the aversive effect of low consumer ratings on consumers’ purchasing decisions. This paper aims to apply decision justifiability theory to investigate how price promotions – price discount and price bundling – can reduce this effect.

Design/methodology/approach

Two scenario-based experiments were administered among college students (Experiment 1) and online consumer panels (Experiment 2) to test the research hypotheses.

Findings

When time-to-purchase is long (vs short), a large discount is more effective in alleviating consumers’ negative responses toward products with low consumer ratings. However, when a price discount is presented as a bundle rather than a separate deal, a small discount size becomes as attractive as a large discount size for consumers with a longer time-to-purchase.

Practical implications

This paper identifies two controllable factors, price discounts and price bundling, that could help to alleviate the negative impact of low consumer ratings. Marketing managers can apply the findings of this paper as guidelines to deal with the aversive effect of low consumer ratings.

Originality/value

This paper makes an initial attempt to examine situations where consumers would be less averse to products with low consumer ratings. It identifies the roles of two price promotions (i.e. price discount size and price bundling) and an important contextual factor (i.e. time-to-purchase) that influence consumers’ decision justifiability and, subsequently, alter consumers’ online purchase decisions for such products.
The Suburb as a Space of Capital Accumulation: The Development of New Towns in Shanghai, China
Authors: Shen Jie , Wu Fulong
Published: November 2016

Drawing attention to the governing role of capital accumulation and its interaction with the state, this study examines the dynamics of the new wave of suburbanization in China, which is characterized by the development of new towns. New towns essentially function as a spatial fix in China's contemporary accumulation regime. Rather than resulting from capital switching from the primary to the secondary circuits, new towns help to collect funds for the leverage of industrial capital and thus simultaneously sustain both circuits. Meanwhile, the development of new towns is also a process of territorial development, in which municipal governments expand the space of accumulation under strengthened fiscal and land controls and develop a metropolitan structure. Underlying the specific form and dynamics, however, is the worldwide trend of capital switching from declining manufacturing industries in developed countries to the new investment frontier in developing countries.
Influence of topography on long‐term successional trajectories in canyon grasslands
Authors: Bernards Samantha J. , Morris Lesley R.
Published: November 2016

Question

Some of the last remaining grassland communities of the Pacific Northwest Bunchgrass Region (PNWBR) in North America are found in canyon grasslands, primarily because the rugged topography has left many of these associations untouched by agricultural development. However, there have been no prior examinations into how canyon grassland communities change over the long term or how topography relates to these changes. In this study, we examined how successional stages changed over a 33‐yr time period and which topographical variables were most related to these long‐term outcomes (elevation, aspect or slope). We predicted that areas with more gentle slopes (<20%) would have changed the most because they have seen a higher concentration of historical land uses (e.g. livestock grazing, wildlife herbivory, and cultivation).

Location

Canyon grasslands of Hells Canyon National Recreation Area, northwest USA.

Methods

We looked at how the canyon grasslands have changed over the long term by repeating a vegetation survey of plant species cover and frequency that was completed in 1981 and comparing the results after a 33‐yr time period.

Results

We found that 58% of our plots stayed in the same seral stage or transitioned into later ones. As predicted, the plots that remained in early seral condition or transitioned from later to early seral stages were found on more shallow slopes. In addition, drier aspects within all plant associations appeared to be less resistant and resilient to change, particularly invasion by exotic species.

Conclusions

The results of this resurvey suggest that topographic patterns may not only be related to the distribution of plant associations across the canyon grasslands, but may also influence which sites change most over time. Our findings are consistent with other studies of the relationships between topography and land uses through time in other grasslands, and are highly relevant to conservation management where unique vegetation communities develop within heterogeneous topographic areas.
Infants’ Social Experiences in Three African Sociocultural Contexts
Authors: Otto Hiltrud W. R. , Schuitmaker Nicole , Lamm Bettina , Abels Monika , Serdtse Yan , Yovsi Relindis , Tomlinson Mark
Published: November 2016

This study introduces a peri‐urban context of poverty to the study of child development in Africa in contrast to the more typical assessments in middle‐class and rural contexts. Spot observations were used to assess universal caregiving behaviors toward seventy‐six 3‐month‐old infants. Results show that middle‐class infants experienced distal parenting behaviors instantiated by mothers, whereas rural children experienced proximal parenting practices in interactions with others. Infants growing up in poverty had mothers and other caretakers involved at mostly low levels. They experienced low levels of body contact, body stimulation, and object stimulation, and high levels of face‐to‐face positions. The study indicates that caregiving in the context of poverty does not necessarily follow familiar pathways and needs to be contextualized accordingly.
Physical and cognitive fitness in young adulthood and risk of amyotrophic lateral sclerosis at an early age
Authors: Longinetti E. , Mariosa D. , Larsson H. , Almqvist C. , Lichtenstein P. , Ye W. , Fang F.
Published: November 2016

Background and purpose

There is a clinical impression that patients with amyotrophic lateral sclerosis (ALS) have a higher level of physical fitness and lower body mass index (BMI) than average. However, there is a lack of literature examining the relationship between cognitive fitness and ALS risk. In this study we explored the associations of both physical and cognitive fitness with future risk of ALS.

Methods

Data on physical fitness, BMI, intelligence quotient (IQ) and stress resilience were collected from 1 838 376 Swedish men aged 17–20 years at conscription during 1968–2010. Their subsequent ALS diagnoses were identified through the Swedish Patient Register. Hazard ratios (HRs) and 95% CIs from flexible parametric models were used to assess age‐specific associations of physical fitness, BMI, IQ and stress resilience with ALS.

Results

We identified 439 incident ALS cases during follow‐up (mean age at diagnosis: 48 years). Individuals with physical fitness above the highest tertile tended to have a higher risk of ALS before the age of 45 years (range of HRs: 1.42–1.75; statistically significant associations at age 41–43 years) compared with others. Individuals with BMI ≥ 25 tended to have a lower risk of ALS at all ages (range of HRs: 0.42–0.80; statistically significant associations at age 42–48 years) compared with those with BMI < 25. Individuals with IQ above the highest tertile had a statistically significantly increased risk of ALS at an age of 56 years and above (range of HRs: 1.33–1.81), whereas individuals with stress resilience above the highest tertile had a lower risk of ALS at an age of 55 years and below (range of HRs: 0.47–0.73).

Conclusions

Physical fitness, BMI, IQ and stress resilience in young adulthood might be associated with the development of ALS at an early age.
Merging pedigree databases to describe and compare mating practices and gene flow between pedigree dogs in France, Sweden and the UK
Authors: Wang S. , Leroy G. , Malm S. , Lewis T. , Strandberg E. , Fikse W.F.
Published: November 2016

Merging pedigree databases across countries may improve the ability of kennel organizations to monitor genetic variability and health‐related issues of pedigree dogs. We used data provided by the Société Centrale Canine (France), Svenska Kennelklubben (Sweden) and the Kennel Club (UK) to study the feasibility of merging pedigree databases across countries and describe breeding practices and international gene flow within the following four breeds: Bullmastiff (BMA), English setter (ESE), Bernese mountain dog (BMD) and Labrador retriever (LBR). After merging the databases, genealogical parameters and founder contributions were calculated according to the birth period, breed and registration country of the dogs. Throughout the investigated period, mating between close relatives, measured as the proportion of inbred individuals (considering only two generations of pedigree), decreased or remained stable, with the exception of LBR in France. Gene flow between countries became more frequent, and the origins of populations within countries became more diverse over time. In conclusion, the potential to reduce inbreeding within purebred dog populations through exchanging breeding animals across countries was confirmed by an improved effective population size when merging populations from different countries.
Interconnections between meiotic recombination and sequence polymorphism in plant genomes
Authors: Ziolkowski Piotr A. , Henderson Ian R.
Published: November 2016

Meiosis is fundamental to sexual reproduction and creates genetic variation in progeny. During meiosis paired homologous chromosomes undergo recombination, which can result in reciprocal crossovers. This process can recombine independently arising mutations onto the same chromosome. Recombination locations are highly variable between meioses, although total crossover numbers are tightly regulated. In addition to the effect of meiosis on genetic variation, sequence polymorphisms between homologous chromosomes can feedback onto the recombination pathways. Here we review the major crossover pathways in plants and some of the known homeostatic mechanisms that act during meiotic recombination. We then examine how sequence polymorphisms between homologous chromosomes, that is, heterozygosity, can influence meiotic recombination pathways in cis and trans. Finally, we provide a brief perspective on the relevance of these interconnections for natural selection and adaptation in plants.

Contents

Summary
1022

I.
Introduction
1022

II.
Initiation and resolution of meiotic recombination
1023

III.
Interference between meiotic recombination locations
1023

IV.
Feedback of genetic variation onto meiotic recombination
1025

V.
Perspectives
1026

Acknowledgements
1027

References
1027
Methods matter: a meta‐regression on the determinants of willingness‐to‐pay studies on biofortified foods
Authors: De Steur Hans , Wesana Joshua , Blancquaert Dieter , Van Der Straeten Dominique , Gellynck Xavier
Published: November 2016

Following the growing evidence on biofortification as a cost‐effective micronutrient strategy, various researchers have elicited consumers’ willingness to pay (WTP) for biofortified crops in an effort to justify and determine their adoption. This review presents a meta‐analysis of WTP studies on biofortified foods, either developed through conventional breeding or using genetic modification technology. On the basis of 122 estimates from 23 studies (9507 respondents), consumers are generally willing to pay 21.3% more for biofortified crops. Because WTP estimates are often determined through different valuation methods and procedures, a meta‐regression was carried out to examine the role of potential determinants. Aside from contextual factors, such as type of food crop, target nutrient, and region (but not breeding technique), various methodological factors significantly influence premiums, including the type of respondent, nature of the study, study environment, participation fee, and provided information. The findings allow researchers to better anticipate potential methodological biases when examining WTP for (biofortified) foods, while it gives policy makers a broad understanding of the potential demand for different biofortified crops in various settings.
Locating Animals in Political Philosophy
Authors: Kymlicka Will , Donaldson Sue
Published: November 2016

While animal rights have been a central topic within moral philosophy since the 1970s, it has remained virtually invisible within political philosophy. This article explores two key reasons for the difficulties in locating animals within political philosophy. First, even if animals are seen as having intrinsic moral status, they are often seen as ultimately distant others or strangers, beyond the bounds of human society. Insofar as political philosophy focuses on the governing of a shared social life, animals are seen as falling outside its remit. Second, even if animals are recognized as members of society, they are seen as lacking the capacities or competences said to be essential for politics, and for membership in the demos. We challenge both assumptions. Many animals live and work alongside us, within an interspecies society, and all members of society should have the right to shape decisions about how that society is governed. An interspecies society requires interspecies politics.
Cytocentrifuge preparation in veterinary cytology: a quick, simple, and affordable manual method to concentrate low cellularity fluids
Authors: Marcos Ricardo , Santos Marta , Marrinhas Carla , Correia‐Gomes Carla , Caniatti Mario
Published: November 2016

Background

Smears prepared by cytocentrifugation, the so‐called cytospins, are widely used in human and veterinary cytology. However, the high cost has hampered the availability of commercial cytospin centrifuges in some veterinary clinics and laboratories. Nevertheless, cytospins are important for evaluating fluids with very low cellularity such as cerebrospinal fluid (CSF) or bronchoalveolar lavage fluid (BALF).

Objectives

The aim of this study was to devise and test the use of a low‐cost, in‐house manual cytocentrifuge to obtain cytospin preparations.

Methods

Twenty‐two fluid samples (including CSF and BALF) were collected from dogs and cats. These were processed in a conventional cytocentrifuge and in an in‐house, manual centrifuge (salad spinner). The cytospins obtained by the 2 methods were compared by scoring cellularity, number of cells per field, hemodilution, cell preservation, and proportion of ruptured cells. Additionally, cell number and size were compared by morphometry. Differences between the automated and manual method were statistically assessed.

Results

The morphology and cellular detail of cytospin preparations produced by both methods were identical. There was an almost perfect agreement for cellularity, number of cells per HPF, hemodilution and cell preservation (kappa ≥ 0.85), and a moderate agreement for the amount of ruptured cells. Cell recovery was comparable (including in CSF and BALF).

Conclusions

The manual cytocentrifuge produced cytospins with similar cell yield as the automated cytocentrifuge. Considering the low cost and portability, this new method should be particularly useful for cytologic diagnosis in small clinics, developing countries, and in field studies.
Reinforcement of Planar Defects in Low-Frequency ERW Long Seams Using Composite Reinforcing Materials
Authors: Alexander Chris , Rizk Tony , Wang Henry , Clayton Rodney , Scrivner Ron
Published: November 2016

A comprehensive study was conducted to investigate the reinforcement of LF-ERW flaws located in a 16-inch × 0.312-inch (406-mm × 7.93-mm), w.t. Grade X52 ethylene pipeline. The study was prompted by an in-service leak that was discovered in an LF-ERW seam during routine maintenance activities. The investigation was subsequently expanded as a result of the discovery of several additional leaks. An initial failure analysis of the leak location was conducted followed by broader material testing, full-scale testing, and metallurgical analysis of the remaining pipe. The use of composite repair systems as a feasible method of LF-ERW seam reinforcement was also examined. As part of this study, testing was also conducted on 8.625-inch × 0.250-inch. (219-mm × 6.35-mm) pipe material having LF-ERW seams.

Test results documented the potential for composite repair systems to provide reinforcement to LF-ERW flaws and crack-like defects. Distinct contrasts were observed between the performance of samples with unreinforced and reinforced notches subjected to cyclic pressure and burst tests. Reinforced samples exhibited improvements in pressure cycle life and significantly increased burst pressure capacities as compared to unreinforced samples. The results of this program demonstrate that, when properly designed and installed, composite materials are an effective means for reinforcing LF-ERW long seam weld flaws and other planar defects. The composite repairs served to ensure that cracks neither form nor propagate during aggressive pressure cycling and burst testing. It should be noted that the testing program was specific to the operating and material conditions associated with a particular ethylene pipeline that is the subject of this paper.
Experimental and Numerical Investigation Into the Behavior of Buried Steel Pipelines Under Strike-Slip Fault Movement
Authors: van Es Sjors H. J. , Gresnigt Arnold M.
Published: November 2016

Buried steel pipelines for water and hydrocarbon transmission in seismic regions may be subjected to large imposed deformations. When a buried pipeline crosses an active strike-slip fault, the relative motion of the two soil bodies in which is it embedded can lead to significant deformation of the pipeline and possibly to loss of containment.

To be able to fully understand the effects of this movement and the interaction between pipe and soil on the strain demands in the pipeline, a novel full scale experimental setup has been developed. To allow accurate monitoring of the pipeline deformation, the pipe-surrounding soil has been replaced with appropriate nonlinear springs, leaving the pipe bare during the experiment.

In a total of ten tests, the strain demand in a pipeline as a result of these ground-induced deformations has been investigated. The testing program includes variations of pipeline geometry, steel grade and internal pressure. Furthermore, cohesive and non-cohesive soils have been simulated in the tests. Observed responses of the pipeline include local buckling, high tensile strains (up to 5%) and, in one case, cracking of the pipeline.

Based on experiences with these experiments, a numerical model has been developed that uses non-linear springs to model the pipe-soil interaction. By modelling the pipe and soil conditions that were simulated in the ten experiments, this model has been calibrated and validated. Comparisons between the model predictions and test results show that the numerical model is able to predict the deformational behavior of the pipeline accurately. Moreover, also the formation of local buckles is predicted with satisfying results. The results of the validation operation lead to the conclusion that the new model is performing well. By omitting the modelling of the full soil body, computation time is reduced, increasing practical use of the developed model.
Hydrotesting and In-Line Inspection: Now and in the Future
Authors: Rau Jerry , Kirkwood Mike
Published: November 2016

Pressure testing of pipelines has been around in some form or another since the 1950s1–14. In its earliest form, operators used inert gases such as Nitrogen or even air to test for pipeline integrity. However, with the significant increases in pipeline pressures and inherent safety issues with a pressurized gas, the switch to using water happened in the late 1960’s15–17. Hydrostatic tests (referred to as hydrotests) have been used since then to set and reset the Maximum Allowable Operating Pressure (MAOP) for pipelines but as other technologies develop and gain acceptance will hydrotesting still play a key role in pipeline integrity in the years ahead?

Currently, hydrotesting is a topic for the impending US Pipeline and Hazardous Materials Safety Administration’s (PHMSA) Proposed New Rule Making (PNRM)18. Under the NPRM, hydrotesting is required to verify MAOP on pre-1970s US “grandfathered” pipelines, as well as on pipelines of any age with incomplete or missing testing record and include a high level test with a “spike” in pressure. But hydrotesting may not be the only method. Alternative methods and new technologies — used alone or used in combination with hydrotesting — may help provide a more comprehensive way for operators to identify and address potential problems before they become a significant threat. This paper explores both sides of the argument.

Before In-Line Inspection (ILI) technology was even available, hydrotesting was the absolute means of the proof of integrity. However, hydrotesting is under scrutiny for many reasons that this paper explores. ILI was introduced in the 1960’s with the first commercially available Magnetic Flux Leakage (MFL) tools that presented the industry with an alternative. Currently there are a huge array of available technologies on an ILI tool and so is the role of the hydrotest over? The paper looks at the benefits of the hydrotest and these are presented and balanced against available ILI technology.

Furthermore, as pipelines are being developed in even more harsh environments such as deepwater developments, the actual logistics of performing a hydrotest become more challenging. The paper will also look at both applications onshore and offshore where regulators have accepted waivers to a hydrotest using alternative methods of proving integrity.

The paper concludes with the current use and needs for hydrotesting, the regulatory viewpoint, the alternatives and also what the future developments need to focus on and how technology may be improved to provide at least a supplement if not a replacement to this means of integrity assurance.
Robust Direct Hydrocarbon Sensor Based on Novel Carbon Nanotube Nanocomposites for Leakage Detection
Authors: Parmar Kaushik , Park Chaneel , Park Simon
Published: November 2016

Leakage in oil and gas infrastructure, often cause significant financial losses, severe damage to the environment and raises public concern. In order to minimize the impact of spills, quick detection of a leak and a rapid response are needed. The systems currently employed to detect pipeline leakage range from simple visual checking to complex hardware and software systems such as mass balance, pressure point analysis, flow deviation, acoustic emission systems, and fibre-optic-based sensing technologies. These methods are useful, but there are certain limitations. The main drawback of the majority of these leak detection technologies is that they detect leakage indirectly, often unable to detect the leakage until the major spill.

The preventive monitoring system and direct detection of hydrocarbon leakage are urgently needed to enable fast response and timely repairs with less deleterious effects. Research is being conducted for the development of a functional prototype and environmental testing of in-situ carbon nanotube (CNT) nanocomposite based sensors for hydrocarbon leakage detection. The CNT nanocomposite offers a unique approach to the direct hydrocarbon leakage detection in pipelines and aboveground storage tanks (ASTs).

Expanding the study from the previous report of sensor characteristics under the optimal ambient condition, it was further investigated to identify the sensor performance under harsh conditions such as the underground (exposed to the soil) with compost and moisture, high pressure, changing temperature and long-term exposure to the outdoor environment. Investigation of the sensor behavior is studied, and a performance matrix is developed that accounts for the change in sensor response to various environmental conditions. Results showed that the proposed CNT nanocomposite sensor was applicable under given conditions with immediate responses while maintaining high sensitivity to the hydrocarbon leakage.

Once a list of sensor detection specifications is defined, it is anticipated that the CNT sensor technology is applicable as part of a robust, reliable and accurate early detection system for the pipeline industry.