bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethical dilemmas and reflexivity in qualitative research
Authors: Reid Anne-Marie , Brown Jeremy M. , Smith Julie M. , Cope Alexandra C. , Jamieson Susan 
Published: March 2018

Context For medical education researchers, a key concern may be the practicalities of gaining ethical approval where this is a national or local requirement. However, in qualitative studies, where the dynamics of human interaction pervade, ethical considerations are an ongoing process which continues long after approval has been granted. Responding to ethical dilemmas arising ‘in the moment’ requires a reflexive approach whereby the researcher questions his/her own motivations, assumptions and interests. Drawing on empirical studies and their experiences in academic and clinical research practice, the authors share their reflections on adhering to ethical principles throughout the research process to illustrate the complexities and nuances involved.
Objectives and findings These reflections offer critical insights into dilemmas arising in view of the ethical principles driving good conduct, and through domains which distinguish between procedural ethics, situational ethics, ethical relationships and ethical issues in exiting the study. The accounts consider integrity and altruism in research, gatekeeping and negotiating access, consent and confidentiality, power dynamics and role conflict, and challenges in dissemination of findings. The experiences are based on a range of examples of research in a UK context from managing difficult conversations in the classroom to video-ethnography in the operating theatre.
Discussion and conclusions These critical reflections make visible the challenges encountered and decisions that must be taken in the moment and on reflection after the event. Through sharing our experiences and debating the decisions we made, we offer insights into reflexivity in qualitative research which will be of value to others.
MARKET SHOCKS IN SALMON AQUACULTURE: THE IMPACT OF THE CHILEAN DISEASE CRISIS
Authors: ASCHE F. , COJOCARU A.L. , SIKVELAND M. 
Published: March 2018

AbstractSeveral studies indicate an integrated global market for salmon. However, there is increasing evidence of market segmentation for various seafood species. A disease crisis in Chile that reduced production by two-thirds provides a strong market shock that can shed light on how strongly integrated the salmon market is. Our results indicate that Chilean producers changed the product mix and export markets as a result of the disease shock. Yet, the relative prices remained constant, indicating a high degree of market integration. Moreover, Chilean prices are endogenous to the Norwegian price, indicating that prices are determined at the global market.
Garden of Eden and specification
Authors: LI HANFENG 
Published: March 2018

We establish a Garden of Eden theorem for expansive algebraic actions of amenable groups with the weak specification property, i.e. for any continuous equivariant map
$T$
from the underlying space to itself,
$T$
is pre-injective if and only if it is surjective. In particular, this applies to all expansive principal algebraic actions of amenable groups and expansive algebraic actions of
$\mathbb{Z}^{d}$
with completely positive entropy.
Assessing the effectiveness of a protected area network: a case study of Bhutan
Authors: Lham Dechen , Wangchuk Sonam , Stolton Sue , Dudley Nigel 
Published: March 2018

AbstractAn assessment of management effectiveness was carried out for all the protected areas in the Kingdom of Bhutan. During 2014–2016 the Royal Government of Bhutan developed a custom-made tool for assessing management effectiveness: the Bhutan Management Effectiveness Tracking Tool Plus (Bhutan METT +). This was implemented in Bhutan's 10 protected areas and one botanical park, and the results were verified through field trips and expert reviews. The assessment indicates that protected areas in Bhutan are well managed and there are generally good relationships with local communities, despite an increase in livestock predation and crop damage. However, effectiveness is limited by a low level of resources (both financial and appropriate technical resources) and by gaps in monitoring and research data, which limits the ability to understand the impact of conservation, react to changing conditions and undertake adaptive management to improve efficiency and effectiveness. Bhutan is in the midst of mobilizing considerable conservation funding. The Government is working in partnership with WWF to create an innovative funding mechanism for the protected area system: the Bhutan for Life initiative. The Bhutan METT + study provides an example of how to develop a baseline against which to measure the effectiveness of protected areas over time and assess the impact of conservation inputs.
Overlap of heritable influences between cannabis use disorder, frequency of use and opportunity to use cannabis: trivariate twin modelling and implications for genetic design
Authors: Hines Lindsey A. , Morley Katherine I. , Rijsdijk Fruhling , Strang John , Agrawal Arpana , Nelson Elliot C. , Statham Dixie , Martin Nicholas G. , Lynskey Michael T. 
Published: March 2018

AbstractBackgroundThe genetic component of Cannabis Use Disorder may overlap with influences acting more generally on early stages of cannabis use. This paper aims to determine the extent to which genetic influences on the development of cannabis abuse/dependence are correlated with those acting on the opportunity to use cannabis and frequency of use.MethodsA cross-sectional study of 3303 Australian twins, measuring age of onset of cannabis use opportunity, lifetime frequency of cannabis use, and lifetime DSM-IV cannabis abuse/dependence. A trivariate Cholesky decomposition estimated additive genetic (A), shared environment (C) and unique environment (E) contributions to the opportunity to use cannabis, the frequency of cannabis use, cannabis abuse/dependence, and the extent of overlap between genetic and environmental factors associated with each phenotype.ResultsVariance components estimates were A = 0.64 [95% confidence interval (CI) 0.58–0.70] and E = 0.36 (95% CI 0.29–0.42) for age of opportunity to use cannabis, A = 0.74 (95% CI 0.66–0.80) and E = 0.26 (95% CI 0.20–0.34) for cannabis use frequency, and A = 0.78 (95% CI 0.65–0.88) and E = 0.22 (95% CI 0.12–0.35) for cannabis abuse/dependence. Opportunity shares 45% of genetic influences with the frequency of use, and only 17% of additive genetic influences are unique to abuse/dependence from those acting on opportunity and frequency.ConclusionsThere are significant genetic contributions to lifetime cannabis abuse/dependence, but a large proportion of this overlaps with influences acting on opportunity and frequency of use. Individuals without drug use opportunity are uninformative, and studies of drug use disorders must incorporate individual exposure to accurately identify aetiology.
Meridional heat transport variability induced by mesoscale processes in the subpolar North Atlantic
Authors: Zhao Jian , Bower Amy , Yang Jiayan , Lin Xiaopei , Penny Holliday N. 
Published: March 2018

AbstractThe ocean’s role in global climate change largely depends on its heat transport. Therefore, understanding the oceanic meridional heat transport (MHT) variability is a fundamental issue. Prevailing observational and modeling evidence suggests that MHT variability is primarily determined by the large-scale ocean circulation. Here, using new in situ observations in the eastern subpolar North Atlantic Ocean and an eddy-resolving numerical model, we show that energetic mesoscale eddies with horizontal scales of about 10–100 km profoundly modulate MHT variability on time scales from intra-seasonal to interannual. Our results reveal that the velocity changes due to mesoscale processes produce substantial variability for the MHT regionally (within sub-basins) and the subpolar North Atlantic as a whole. The findings have important implications for understanding the mechanisms for poleward heat transport variability in the subpolar North Atlantic Ocean, a key region for heat and carbon sequestration, ice–ocean interaction, and biological productivity.
CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair
Authors: Charpentier M. , Khedher A. H. Y. , Menoret S. , Brion A. , Lamribet K. , Dardillac E. , Boix C. , Perrouault L. , Tesson L. , Geny S. , De Cian A. , Itier J. M. , Anegon I. , Lopez B. , Giovannangeli C. , Concordet J. P. 
Published: March 2018

AbstractIn genome editing with CRISPR–Cas9, transgene integration often remains challenging. Here, we present an approach for increasing the efficiency of transgene integration by homology-dependent repair (HDR). CtIP, a key protein in early steps of homologous recombination, is fused to Cas9 and stimulates transgene integration by HDR at the human AAVS1 safe harbor locus. A minimal N-terminal fragment of CtIP, designated HE for HDR enhancer, is sufficient to stimulate HDR and this depends on CDK phosphorylation sites and the multimerization domain essential for CtIP activity in homologous recombination. HDR stimulation by Cas9–HE, however, depends on the guide RNA used, a limitation that may be overcome by testing multiple guides to the locus of interest. The Cas9–HE fusion is simple to use and allows obtaining twofold or more efficient transgene integration than that with Cas9 in several experimental systems, including human cell lines, iPS cells, and rat zygotes.
An evolutionary hotspot defines functional differences between CRYPTOCHROMES
Authors: Rosensweig Clark , Reynolds Kimberly A. , Gao Peng , Laothamatas Isara , Shan Yongli , Ranganathan Rama , Takahashi Joseph S. , Green Carla B. 
Published: March 2018

AbstractMammalian circadian clocks are driven by a transcription/translation feedback loop composed of positive regulators (CLOCK/BMAL1) and repressors (CRYPTOCHROME 1/2 (CRY1/2) and PER1/2). To understand the structural principles of regulation, we used evolutionary sequence analysis to identify co-evolving residues within the CRY/PHL protein family. Here we report the identification of an ancestral secondary cofactor-binding pocket as an interface in repressive CRYs, mediating regulation through direct interaction with CLOCK and BMAL1. Mutations weakening binding between CLOCK/BMAL1 and CRY1 lead to acceleration of the clock, suggesting that subtle sequence divergences at this site can modulate clock function. Divergence between CRY1 and CRY2 at this site results in distinct periodic output. Weaker interactions between CRY2 and CLOCK/BMAL1 at this pocket are strengthened by co-expression of PER2, suggesting that PER expression limits the length of the repressive phase in CRY2-driven rhythms. Overall, this work provides a model for the mechanism and evolutionary variation of clock regulatory mechanisms.
Glycogen synthase kinase 3 controls migration of the neural crest lineage in mouse and Xenopus
Authors: Gonzalez Malagon Sandra G. , Lopez Muñoz Anna M. , Doro Daniel , Bolger Triòna G. , Poon Evon , Tucker Elizabeth R. , Adel Al-Lami Hadeel , Krause Matthias , Phiel Christopher J. , Chesler Louis , Liu Karen J. 
Published: March 2018

AbstractNeural crest migration is critical to its physiological function. Mechanisms controlling mammalian neural crest migration are comparatively unknown, due to difficulties accessing this cell population in vivo. Here we report requirements of glycogen synthase kinase 3 (GSK3) in regulating the neural crest inXenopusand mouse models. We demonstrate that GSK3 is tyrosine phosphorylated (pY) in mouse neural crest cells and that loss of GSK3 leads to increased pFAK and misregulation of Rac1 and lamellipodin, key regulators of cell migration. Genetic reduction of GSK3 results in failure of migration. We find that pY-GSK3 phosphorylation depends on anaplastic lymphoma kinase (ALK), a protein associated with neuroblastoma. Consistent with this, neuroblastoma cells with increased ALK activity express high levels of pY-GSK3, and blockade of GSK3 or ALK can affect migration of these cells. Altogether, this work identifies a role for GSK3 in cell migration during neural crest development and cancer.
Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots
Authors: Pärn Jaan , Verhoeven Jos T. A. , Butterbach-Bahl Klaus , Dise Nancy B. , Ullah Sami , Aasa Anto , Egorov Sergey , Espenberg Mikk , Järveoja Järvi , Jauhiainen Jyrki , Kasak Kuno , Klemedtsson Leif , Kull Ain , Laggoun-Défarge Fatima , Lapshina Elena D. , Lohila Annalea , Lõhmus Krista , Maddison Martin , Mitsch William J. , Müller Christoph , Niinemets Ülo , Osborne Bruce , Pae Taavi , Salm Jüri-Ott , Sgouridis Fotis , Sohar Kristina , Soosaar Kaido , Storey Kathryn , Teemusk Alar , Tenywa Moses M. , Tournebize Julien , Truu Jaak , Veber Gert , Villa Jorge A. , Zaw Seint Sann , Mander Ülo 
Published: March 2018

AbstractNitrous oxide (N2O) is a powerful greenhouse gas and the main driver of stratospheric ozone depletion. Since soils are the largest source of N2O, predicting soil response to changes in climate or land use is central to understanding and managing N2O. Here we find that N2O flux can be predicted by models incorporating soil nitrate concentration (NO3−), water content and temperature using a global field survey of N2O emissions and potential driving factors across a wide range of organic soils. N2O emissions increase with NO3− and follow a bell-shaped distribution with water content. Combining the two functions explains 72% of N2O emission from all organic soils. Above 5 mg NO3−-N kg−1, either draining wet soils or irrigating well-drained soils increases N2O emission by orders of magnitude. As soil temperature together with NO3− explains 69% of N2O emission, tropical wetlands should be a priority for N2O management.
The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development
Authors: Schumacher Maria A. , den Hengst Chris D. , Bush Matthew J. , Le T. B. K. , Tran Ngat T. , Chandra Govind , Zeng Wenjie , Travis Brady , Brennan Richard G. , Buttner Mark J. 
Published: March 2018

AbstractStreptomycetes are notable for their complex life cycle and production of most clinically important antibiotics. A key factor that controls entry into development and the onset of antibiotic production is the 68-residue protein, BldC. BldC is a putative DNA-binding protein related to MerR regulators, but lacks coiled-coil dimerization and effector-binding domains characteristic of classical MerR proteins. Hence, the molecular function of the protein has been unclear. Here we show that BldC is indeed a DNA-binding protein and controls a regulon that includes other key developmental regulators. Intriguingly, BldC DNA-binding sites vary significantly in length. Our BldC-DNA structures explain this DNA-binding capability by revealing that BldC utilizes a DNA-binding mode distinct from MerR and other known regulators, involving asymmetric head-to-tail oligomerization on DNA direct repeats that results in dramatic DNA distortion. Notably, BldC-like proteins radiate throughout eubacteria, establishing BldC as the founding member of a new structural family of regulators.
Spatially heterogeneous dynamics in a metallic glass forming liquid imaged by electron correlation microscopy
Authors: Zhang Pei , Maldonis Jason J. , Liu Ze , Schroers Jan , Voyles Paul M. 
Published: March 2018

AbstractSupercooled liquids exhibit spatial heterogeneity in the dynamics of their fluctuating atomic arrangements. The length and time scales of the heterogeneous dynamics are central to the glass transition and influence nucleation and growth of crystals from the liquid. Here, we report direct experimental visualization of the spatially heterogeneous dynamics as a function of temperature in the supercooled liquid state of a Pt-based metallic glass, using electron correlation microscopy with sub-nanometer resolution. An experimental four-point space-time correlation function demonstrates a growing dynamic correlation length, ξ, upon cooling of the liquid toward the glass transition temperature. ξ as a function of the relaxation time τ are in good agreement with Adam-Gibbs theory, inhomogeneous mode-coupling theory and random first-order transition theory of the glass transition. The same experiments demonstrate the existence of a nanometer thickness near-surface layer with order of magnitude shorter relaxation time than inside the bulk.
Carbon dioxide sequestration through silicate degradation and carbon mineralisation: promises and uncertainties
Authors: Daval Damien 
Published: March 2018

AbstractTurning carbon dioxide (CO2) into rocks: controlling this process, which naturally operates at the Earth’s surface over geological timescales, is likely to represent a major technological challenge of this century. One of the recurring criticisms with the carbonation reactions is their sluggishness, as it is commonly admitted that converting silicates into carbonates within geologic reservoirs may take up to several thousands of years, i.e., a duration which is hardly compatible with the goal of achieving net zero emissions by mid-century. Last year, a study that generated substantial interest suggested that after 2 years, more than 95% of the CO2 injected over the course of a pilot project of CO2 injection in lava flows in Iceland might have been mineralised into carbonates. While such results could have been considered as a green light for industrial applications, a new high-profile study based on the same pilot experiment tempered this idea, as it revealed unexpected modifications of deep ecosystems in response to CO2 injection, evidencing a bloom of chemolithoautotrophic bacteria, which have the ability to promote autotrophic C-fixation. Stated in other words, part of the CO2 that was initially thought to be mineralised under the form of stable carbonates might instead have been converted into (much more labile) biomass. Assessing the respective contributions of carbonates and biomass to the C-sequestration should therefore represent a prerequisite prior to large-scale carbon capture and storage through mineral carbonation, to make sure that the cure is not worse than the disease.
Impact of directionality and correlation on contagion
Authors: Xu Xin-Jian , Li Jia-Yan , Fu Xinchu , Zhang Li-Jie 
Published: March 2018

AbstractThe threshold model has been widely adopted for modelling contagion processes on social networks, where individuals are assumed to be in one of two states: inactive or active. This paper studies the model on directed networks where nodal inand out-degrees may be correlated. To understand how directionality and correlation affect the breakdown of the system, a theoretical framework based on generating function technology is developed. First, the effects of degree and threshold heterogeneities are identified. It is found that both heterogeneities always decrease systematic robustness. Then, the impact of the correlation between nodal in- and out-degrees is investigated. It turns out that the positive correlation increases the systematic robustness in a wide range of the average in-degree, while the negative correlation has an opposite effect. Finally, a comparison between undirected and directed networks shows that the presence of directionality and correlation always make the system more vulnerable.
Longitudinal demographic study of wild populations of African annual killifish
Authors: Vrtílek Milan , Žák Jakub , Polačik Matej , Blažek Radim , Reichard Martin 
Published: March 2018

AbstractThe natural history of model organisms is often overlooked despite its importance to correctly interpret the outcome of laboratory studies. Ageing is particularly understudied in natural populations. To address this gap, we present lifetime demographic data from wild populations of an annual species, the turquoise killifish,Nothobranchius furzeri, a model species in ageing research, and two other species of coexisting annual killifishes. Annual killifish hatch synchronously, have non-overlapping generations, and reproduce daily after reaching sexual maturity. Data from 13 isolated savanna pools in southern Mozambique demonstrate that the pools supporting killifish populations desiccated 1–4 months after their filling, though some pools persisted longer. Declines in population size over the season were stronger than predicted, because they exceeded the effect of steady habitat shrinking on population density that, contrary to the prediction, decreased. Populations ofN. furzerialso became more female-biased with progressing season suggesting that males had lower survival.Nothobranchiuscommunity composition did not significantly vary across the season. Our data clearly demonstrate that natural populations ofN. furzeriand its congeners suffer strong mortality throughout their lives, with apparent selective disappearance (condition-dependent mortality) at the individual level. This represents selective force that can shape the evolution of lifespan, and its variation across populations, beyond the effects of the gradient in habitat persistence.
Successful knock-in of Hypertrophic Cardiomyopathy-mutation R723G into the MYH7 gene mimics HCM pathology in pigs
Authors: Montag J. , Petersen B. , Flögel A. K. , Becker E. , Lucas-Hahn A. , Cost G. J. , Mühlfeld C. , Kraft T. , Niemann H. , Brenner B. 
Published: March 2018

AbstractFamilial Hypertrophic Cardiomyopathy (HCM) is the most common inherited cardiac disease. About 30% of the patients are heterozygous for mutations in the MYH7 gene encoding the ß-myosin heavy chain (MyHC). Hallmarks of HCM are cardiomyocyte disarray and hypertrophy of the left ventricle, the symptoms range from slight arrhythmias to sudden cardiac death or heart failure. To gain insight into the underlying mechanisms of the diseases’ etiology we aimed to generate genome edited pigs with an HCM-mutation. We used TALEN-mediated genome editing and successfully introduced the HCM-point mutation R723G into the MYH7 gene of porcine fibroblasts and subsequently cloned pigs that were heterozygous for the HCM-mutation R723G. No off-target effects were determined in the R723G-pigs. Surprisingly, the animals died within 24 h post partem, probably due to heart failure as indicated by a shift in the a/ß-MyHC ratio in the left ventricle. Most interestingly, the neonatal pigs displayed features of HCM, including mild myocyte disarray, malformed nuclei, and MYH7-overexpression. The finding of HCM-specific pathology in neonatal R723G-piglets suggests a very early onset of the disease and highlights the importance of novel large animal models for studying causative mechanisms and long-term progression of human cardiac diseases.
Photoresponse of graphene field-effect-transistor with n-type Si depletion layer gate
Authors: Kobayashi Shiho , Anno Yuki , Takei Kuniharu , Arie Takayuki , Akita Seiji 
Published: March 2018

AbstractGraphene/semiconductor Schottky junctions are an emerging field for high-performance optoelectronic devices. This study investigates not only the steady state but also the transient photoresponse of graphene field-effect transistor (G-FET) of which gate bias is applied through the Schottky barrier formed at an n-type Si/graphene interface with a thin oxide layer, where the oxide thickness is sufficiently thin for tunneling of the charge carrier. To analyze the photoresponse, we formulate the charge accumulation process at the n-Si/graphene interface, where the tunneling process through the SiOx layer to graphene occurs along with recombination of the accumulated holes and the electrons in the graphene at the surface states on the SiOx layer. Numerical calculations show good qualitative agreement with the experimentally obtained results for the photoresponse of G-FET.