bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and distribution of hepatitis C virus genotypes in Spain during the 2000‐2015 period (the GEHEP 005 study)
Authors: Aguilera A. , Navarro D. , Rodríguez‐Frias F. , Viciana I. , Martínez‐Sapiña A. M. , Rodríguez M. J. , Martró E. , Lozano M. C. , Coletta E. , Cardeñoso L. , Suárez A. , Trigo M. , Rodríguez‐Granjer J. , Montiel N. , de la Iglesia A. , Alados J. C. , Vegas C. , Bernal S. , Fernández‐Cuenca F. , Pena M. J. , Reina G. , García‐Bujalance S. , Echevarria M. J. , Benítez L. , Pérez‐Castro S. , Ocete D. , García‐Arata I. , Guerrero C. , Rodríguez‐Iglesias M. , Casas P. , García F. 
Published: March 2017

SummaryWe report the largest study on the prevalence and distribution of HCV genotypes in Spain (2000‐2015), and we relate them with clinical, epidemiological and virological factors. Patients from 29 hospitals in 10 autonomous communities (Andalusia, Aragon, Castilla‐Leon, Catalonia, Galicia, Canary Islands, Madrid Community, Valencian Community, Murcia Region and Basque Country) have been studied. Annual distribution of HCV genotypes and subtypes, as well as gender, age, transmission route, HIV and/or HBV coinfection, and treatment details were recorded. We included 48595 chronically HCV‐infected patients with the following characteristics: median age 51 years (IQR, 44‐58), 67.9% male, 19.1% HIV‐coinfected, 23.5% HBV‐coinfected. Parenteral transmission route was the most frequent (58.7%). Genotype distribution was 66.9% GT1 (24.9% subtype 1a and 37.9% subtype 1b), 2.8% GT2, 17.3% GT3, 11.4% GT4 and 0.1% GT5 and 0.02% GT6. LiPA was the most widely HCV genotyping test used (52.4%). HCV subtype 1a and genotypes 3 and 4 were closely associated with male gender, parenteral route of infection and HIV and HBV coinfection; in contrast, subtype 1b and genotype 2 were associated with female gender, nonparenteral route and mono‐infection. Age was related to genotype distribution, and different patterns of distribution and biodiversity index were observed between different geographical areas. Finally, we describe how treatment and changes in transmission routes may have affected HCV genotype prevalence and distribution patterns. We present the most recent data on molecular epidemiology of hepatitis C virus in Spain. This study confirms that genotype distributions vary with age, sex, HIV and HBV coinfection and within geographical areas and epidemiological groups.
Clinical Features, Imaging Characteristics, and Long‐term Outcome of Dogs with Cranial Meningocele or Meningoencephalocele
Authors: Lazzerini K. , Gutierrez‐Quintana R. , José‐López R. , McConnell F. , Gonçalves R. , McMurrough J. , De Decker S. , Muir C. , Priestnall S.L. , Mari L. , Stabile F. , De Risio L. , Loeffler C. , Tauro A. , Rusbridge C. , Rodenas S. , Añor S. , de la Fuente C. , Fischer A. , Bruehschwein A. , Penderis J. , Guevar J. 
Published: March 2017

BackgroundThe term meningoencephalocele (MEC) describes a herniation of cerebral tissue and meninges through a defect in the cranium, whereas a meningocele (MC) is a herniation of the meninges alone.Hypothesis/ObjectivesTo describe the clinical features, magnetic resonance imaging (MRI) characteristics, and outcomes of dogs with cranial MC and MEC.AnimalsTwenty‐two client‐owned dogs diagnosed with cranial MC or MEC.MethodsMulticentric retrospective descriptive study. Clinical records of 13 institutions were reviewed. Signalment, clinical history, neurologic findings and MRI characteristics as well as treatment and outcome were recorded and evaluated.ResultsMost affected dogs were presented at a young age (median, 6.5 months; range, 1 month – 8 years). The most common presenting complaints were seizures and behavioral abnormalities. Intranasal MEC was more common than parietal MC. Magnetic resonance imaging identified meningeal enhancement of the protruded tissue in 77% of the cases. Porencephaly was seen in all cases with parietal MC. Cerebrospinal fluid (CSF) analysis identified mild abnormalities in 4 of 11 cases. Surgery was not performed in any affected dog. Seventeen patients were treated medically, and seizures were adequately controlled with anti‐epileptic drugs in 10 dogs. Dogs with intranasal MEC and mild neurologic signs had a fair prognosis with medical treatment.Conclusion and clinical importanceAlthough uncommon, MC and MEC should be considered as a differential diagnosis in young dogs presenting with seizures or alterations in behavior. Medical treatment is a valid option with a fair prognosis when the neurologic signs are mild.
Sexual selection and sex ratios in Anolis lizards
Authors: Muralidhar P. , Johnson M. A. 
Published: March 2017

AbstractBiased sex ratios, or unequal numbers of males and females in a population, can alter the intensity of sexual selection by enhancing competition for mates, and thus may affect the evolution of reproductive strategies. Studies of sex ratio variation across a clade provide an opportunity to examine the morphological or behavioral consequences of different levels of sexual selection. We examined sex ratio variation, using phylogenetic comparative methods, across a diverse clade of terrestrial vertebrates, the Anolis lizards. Across a sample of 14 species in 21 localities, we found remarkable bidirectional variation in sex ratios across the Anolis clade: males are more common in some populations and females in others. However, we find no evidence that sex ratio bias is associated with sexual size dimorphism, a proxy for sexual selection. Nor do we find an association of sex ratio bias with ecological niches (i.e. ecomorphs), which vary in sexual selection pressures and mating systems. The observed inter‐specific variation in sex ratio suggests that a balance of different, possibly opposing, factors, including sex‐specific dispersal and mortality rates, may play a role in determining population sex ratio.
quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage
Authors: Franchini Paolo , Monné Parera Daniel , Kautt Andreas F. , Meyer Axel 
Published: March 2017

AbstractThe identification of thousands of variants across the genomes and their accurate genotyping are crucial for estimating the genetic parameters needed to address a host of molecular ecological and evolutionary questions. With rapid advances of massively parallel high‐throughput sequencing technologies, several methods have recently been developed to access genomewide data on population variation. One of the most successful and widely used techniques relies on the combination of restriction enzymes and sequencing‐by‐synthesis: restriction‐site‐associated DNA sequencing (RADSeq). We developed a new, more time‐ and cost‐efficient double‐digest RAD paired‐end protocol (quaddRAD) that simplifies and speeds up the identification of PCR duplicates and permits large‐scale multiplexing. Assessing its performance on a technical data set, we also applied the quaddRAD method on population samples of a Neotropical cichlid fish lineage (Archocentrus centrarchus) to assess its genetic structure and demographic history. While we identified allopatric interlake genetic divergence, most likely driven by drift, no signature of sympatric divergence was detected. This differs from what has been observed in the clade of Midas cichlids (Amphilophus citrinellus spp.), another cichlid lineage that inhabits the same lakes and shares a similar demographic history, but has evolved into small‐scale adaptive radiations via sympatric speciation. We demonstrate that quaddRAD is a robust and efficient method for genotyping a massive number and widely overlapping set of loci with high accuracy. Furthermore, the results on A. centrarchus open new research avenues providing an ideal system to investigate genome‐level mechanisms that could alter the speciation potential of different but closely related cichlid lineages.
Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction
Authors: Harrison Ellie , Hall James P. J. , Paterson Steve , Spiers Andrew J. , Brockhurst Michael A. 
Published: March 2017

AbstractBacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities, bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here, we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage, SBW25φ2, and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions.
The zinc efflux activator SczA protects Streptococcus pneumoniae serotype 2 D39 from intracellular zinc toxicity
Authors: Martin Julia E. , Edmonds Katherine A. , Bruce Kevin E. , Campanello Gregory C. , Eijkelkamp Bart A. , Brazel Erin B. , McDevitt Christopher A. , Winkler Malcolm E. , Giedroc David P. 
Published: March 2017

SummaryZinc is an essential trace element that serves as a catalytic cofactor in metalloenzymes and a structural element in proteins involved in general metabolism and cellular defenses of pathogenic bacteria. Despite its importance, high zinc levels can impair cellular processes, inhibiting growth of many pathogenic bacteria, including the major respiratory pathogen Streptococcus pneumoniae. Zinc intoxication is prevented in S. pneumoniae by expression of the zinc exporter CzcD, whose expression is activated by the novel TetR‐family transcriptional zinc‐sensing regulator SczA. How zinc bioavailability triggers activation of SczA is unknown. It is shown here through functional studies in S. pneumoniae that an unannotated homodimeric TetR from S. agalactiae (PDB 3KKC) is the bona fide zinc efflux regulator SczA, and binds two zinc ions per protomer. Mutagenesis analysis reveals two metal binding sites, termed A and B, located on opposite sides of the SczA C‐terminal regulatory domain. In vivo, the A‐ and B‐site SczA mutant variants impact S. pneumoniae resistance to zinc toxicity and survival in infected macrophages. A model is proposed for S. pneumoniae SczA function in which both A‐ and B‐sites were required for transcriptional activation of czcD expression, with the A‐site serving as the evolutionarily conserved intracellular sensing site in SczAs.
A common developmental program can produce diverse leaf shapes
Authors: Runions Adam , Tsiantis Miltos , Prusinkiewicz Przemyslaw 
Published: March 2017

Summary

Eudicot leaves have astoundingly diverse shapes. The central problem addressed in this paper is the developmental origin of this diversity.

To investigate this problem, we propose a computational model of leaf development that generalizes the largely conserved molecular program for the reference plants Arabidopsis thaliana, Cardamine hirsuta and Solanum lycopersicum. The model characterizes leaf development as a product of three interwoven processes: the patterning of serrations, lobes and/or leaflets on the leaf margin; the patterning of the vascular system; and the growth of the leaf blade spanning the main veins. The veins play a significant morphogenetic role as a local determinant of growth directions.

We show that small variations of this model can produce diverse leaf shapes, from simple to lobed to compound.

It is thus plausible that diverse shapes of eudicot leaves result from small variations of a common developmental program.
TSV, a putative plastidic oxidoreductase, protects rice chloroplasts from cold stress during development by interacting with plastidic thioredoxin Z
Authors: Sun Juan , Zheng Tianhui , Yu Jun , Wu Tingting , Wang Xinhua , Chen Gaoming , Tian Yunlu , Zhang Huan , Wang Yihua , Terzaghi William , Wang Chunming , Wan Jianmin 
Published: March 2017

Summary

Rice is vulnerable to cold stress. Seedlings are very sensitive to cold stress and this harms global rice production. The effects of cold on chloroplast development are well known, but little is known about the underlying molecular mechanisms.

Here, we isolated a temperature‐sensitive virescent (tsv) mutant that is extremely sensitive to cold stress. It displayed defective chloroplasts, decreased chlorophyll and zero survivorship under cold stress. We isolated and identified TSV by map‐based cloning and rescue experiments, combined with genetic, cytological and molecular biological analyses.

We found that TSV, a putative plastidic oxidoreductase, is a new type of virescent protein. A mutation in tsv causes premature termination of the gene product. The activity of plastid‐encoded RNA polymerase (PEP) and the expression of genes participating in chlorophyll synthesis were severely reduced in the tsv mutant under cold stress, but not at normal temperatures. TSV expression was induced by low temperatures. Strikingly, TSV interacted with OsTrxZ (a subunit of PEP in chloroplasts) and enhanced OsTrxZ stability under low temperatures. We demonstrated that TSV protects rice chloroplasts from cold stress by interacting with OsTrxZ.

These results provide novel insights into ways in which rice chloroplast development and chlorophyll synthesis are protected by TSV under cold stress.
Survey of the Bru1 gene for brown rust resistance in Brazilian local and basic sugarcane germplasm
Authors: Neuber Ana Caroline , Camilo dos Santos Fernanda Raquel , da Costa Juliana Borges , Volpin Maicon , Xavier Mauro Alexandre , Perecin Dilermando , Villavicencio Burbano Roberto Carlos , Landell Marcos Guimarães de Andrade , Pinto Luciana Rossini 
Published: March 2017

AbstractBru1 is currently the major gene conferring brown rust resistance in sugarcane, and diagnostic markers are available. A survey for the presence of this gene was conducted on 391 genotypes including Brazilian cultivars, clones and basic germplasm. The efficiency of these markers for identifying resistant cultivars and artificially inoculated basic germplasm was also evaluated. The Bru1 frequency among cultivars (73.5%) suggests this gene is the prevalent source of brown rust resistance in Brazilian sugarcane breeding programmes. Most of the cultivars known to be resistant were positive for Bru1, although other genes for resistance could be present in lines not having Bru1. Only 17.8% of the basic germplasm accessions were positive for the Bru1 gene, and a low correlation between Bru1 diagnostic markers and brown rust severity was observed for basic germplasm accessions. Overall, Bru1 diagnostic markers proved to be efficient identifying resistant cultivars and clones and have potential to be in screening brown rust resistance in Brazilian breeding programmes.
The rapid A–Ci response: photosynthesis in the phenomic era
Authors: Stinziano Joseph R. , Morgan Patrick B. , Lynch Douglas J. , Saathoff Aaron J. , McDermitt Dayle K. , Hanson David T. 
Published: March 2017

AbstractPhenotyping for photosynthetic gas exchange parameters is limiting our ability to select plants for enhanced photosynthetic carbon gain and to assess plant function in current and future natural environments. This is due, in part, to the time required to generate estimates of the maximum rate of ribulose‐1,5‐bisphosphate carboxylase oxygenase (Rubisco) carboxylation (Vc,max) and the maximal rate of electron transport (Jmax) from the response of photosynthesis (A) to the CO2 concentration inside leaf air spaces (Ci). To relieve this bottleneck, we developed a method for rapid photosynthetic carbon assimilation CO2 responses [rapid A–Ci response (RACiR)] utilizing non‐steady‐state measurements of gas exchange. Using high temporal resolution measurements under rapidly changing CO2 concentrations, we show that RACiR techniques can obtain measures of Vc,max and Jmax in ~5 min, and possibly even faster. This is a small fraction of the time required for even the most advanced gas exchange instrumentation. The RACiR technique, owing to its increased throughput, will allow for more rapid screening of crops, mutants and populations of plants in natural environments, bringing gas exchange into the phenomic era.
Questioning Kaufman: How Cross‐Level Political Coalitions Interact with Organizational Structure
Authors: Fleischman Forrest 
Published: March 2017

AbstractHerbert Kaufman's The Forest Ranger is considered a landmark study of how organizations can be structured to elicit compliance from field officials, yet there have been few attempts to validate Kaufman's claims. The author argues that the outcomes observed by Kaufman resulted from interplay between organizational structure and political context—a variable that Kaufman ignored. This argument is supported by case studies of two agencies with structures similar to Kaufman's U.S. Forest Service but poorer outcomes: the same agency today and India's forest departments. Both differences in organizational structure and poorer outcomes are found to be the result of political context. Specifically, coalitions assembled around agencies use the implementation process to shape outcomes in ways that could not be accomplished solely through changing laws or formal administrative structure. This points to the importance of building supportive field‐level coalitions to complement administrative reforms.
Time, space, place, and the Bonn Challenge global forest restoration target
Authors: Verdone Michael , Seidl Andrew 
Published: March 2017

AbstractThe Bonn Challenge, a global effort to begin restoring 350 million hectares of degraded forest landscapes by 2030, was launched in 2011. To date countries have committed to restore more than 60 million hectares as part of the Bonn Challenge. As global decision‐makers, governments, and communities join the effort to restore degraded land, new questions about the economics of restoration have emerged. Critics argue that restoration takes too long, costs too much, and produces too few benefits to justify public or private expenditures. This paper addresses these concerns by presenting a methodology for valuing the net benefits of large‐scale ecosystem restoration initiatives by estimating the net benefit of achieving the Bonn Challenge. This paper also estimates the net benefit of achieving the Bonn Challenge restoration target under different social discounting regimes, different valuations of public goods, and different time horizons to see how they affect the argument for investing society's scarce resources in restoration. The results suggest that achieving the Bonn Challenge would generate a net benefit of between U.S.$0.7 and U.S.$9 trillion. The results show that restoration can create benefits that exceed its costs and that the value of these benefits might differ depending on the discount rate. The results show that lower social discount rates correspond to higher restoration rates. This suggests that the Bonn Challenge target is more likely to be met when a low social discount rate is used to discount the benefits and costs of restoration.
Old age rational suicide
Authors: Richards Naomi 
Published: March 2017

AbstractIn the societal debate surrounding voluntary euthanasia or physician‐assisted suicide, there is a concern that older people will be left exposed to any legislation, subject to either faint suggestion or outright coercion from familial or professional carers. Whilst it is critical to take account of older people's potential vulnerability to any current or proposed assisted suicide legislation, there is a parallel strand of research exploring another relationship which older people can have with this debate: one of activism. Sociological research has shown that older people make up the “rank and file” of those active within the right‐to‐die movement. One of the stated motivations of some older people requesting hastened death has been that, in spite of an absence of life‐threatening disease, they feel “tired of life” or that they have lived a “completed life” and feel ready to die. The notion of suicide for reasons of longevity and being tired of life are becoming increasingly significant given the fact of global ageing. This article brings together empirical and theoretical research on the phenomenon of old age rational suicide in order to develop an underexplored area in both the sociology of death and the sociology of ageing.
WikiLeaks: Between disclosure and whistle‐blowing in digital times
Authors: Brevini Benedetta 
Published: March 2017

AbstractThe 2010 WikiLeaks' disclosures of U.S. war logs were the first megaleaks to shake the world of international diplomacy and political elites. Since then, more leaks followed, from the Snowden to the Panama Papers. As this phenomenon continues to evolve, a significant body of scholarly work has analysed the emergence, the struggle, and the history of WikiLeaks .This article aims to provide a cross disciplinary overview of the research that has explored the rise and the legacy of the disclosure platform and whistle‐blowing website WikiLeaks. It identifies four scholarship approaches to research focusing on Julian Assange's platform in order to understand its impact on various aspects of the media and of public life.The approaches considered range from the effect WikiLeaks has had on traditional journalism to the platform's challenge to power in the realm of the balance between openness and secrecy in domestic and international politics; further scholarships use WikiLeaks as a case study to understand the relationship between media and social movements and to study the platform's ethics and the legal consequences of its operations.The impact of WikiLeaks's revelations still poses relevant questions the media, politics, and regulators must address in such a pivotal time that sees a change in news consumption and an increasingly bitter debate between online privacy and transparency.The conclusion reflects upon current development of what the author calls “new digital culture of disclosure.” Future research should explore questions about the opportunities, challenges, and obstacles for this emerging culture of disclosure. What are the socio‐political‐economic conditions that have enabled this new culture? Are these leaks becoming a renewed example of democratic accountability? Is this culture of disclosure replacing public interest journalism in times of crisis?