bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tidally Modulated Internal Hydraulic Flow and Energetics in the Central Canadian Arctic Archipelago
Authors: Hughes Kenneth G. , Klymak Jody M. , Williams William J. , Melling Humfrey 
Published: June 2018

AbstractThe Canadian Arctic Archipelago is a key conduit for comparatively fresh Arctic waters flowing to the Atlantic. Model estimates of the freshwater outflow, which is strongly correlated with the volume flux, contain major uncertainties because most existing models exclude tides, marginally resolve the internal Rossby radius, or both. At the same time, barotropic tidal models preclude stratified flow effects. Here we assess the relative importance of barotropic and baroclinic processes to water mass transformation, friction, and energy losses motivated by processes observed in a fine‐scale survey in the central Archipelago. A sharp separation of warmed Canada Basin water and locally formed water is observed over a long sill in a narrow channel and coincides with an internal hydraulic jump caused by the mean flow. Tidal currents, however, modulate the jump, as demonstrated by both scale analysis and a two‐dimensional simulation. The jump, together with internal tides propagating as Kelvin waves, leads to isopycnal displacements up to 50 m. The generation of these internal Kelvin waves has a leading‐order role in a regional energy budget. It is small, however, relative to bottom boundary layer dissipation, which accounts for an estimated 50% of the total tidal energy losses. Consequently, adding tides needs to be a priority for regional models.
A Numerical Study of Sheet Flow Under Monochromatic Nonbreaking Waves Using a Free Surface Resolving Eulerian Two‐Phase Flow Model
Authors: Kim Yeulwoo , Cheng Zhen , Hsu Tian‐Jian , Chauchat Julien 
Published: June 2018

AbstractWe present a new methodology that is able to concurrently resolve free surface wavefield, bottom boundary layer, and sediment transport processes throughout the entire water column. The new model, called SedWaveFoam, is developed by integrating an Eulerian two‐phase model for sediment transport, SedFoam, and a surface wave solver, InterFoam/waves2Foam, in the OpenFOAM framework. SedWaveFoam is validated with a large wave flume data for sheet flow driven by monochromatic nonbreaking waves. To isolate the effect of free surface, SedWaveFoam results are contrasted with one‐dimensional‐vertical SedFoam results, where the latter represents the oscillating water tunnel condition. Results demonstrate that wave‐averaged total sediment fluxes in both models are onshore‐directed; however, this onshore transport is significantly enhanced under surface waves. Onshore‐directed near‐bed sediment flux is driven by a small mean current mainly associated with velocity skewness. More importantly, progressive wave streaming drives onshore transport mostly in suspended load region due to an intrawave sediment flux. Further analysis suggests that the enhanced onshore transport in suspended load is due to a “wave‐stirring” mechanism, which signifies a nonlinear interaction between waves, streaming currents, and sediment suspension. We present some preliminary efforts to parameterize the wave‐stirring mechanism in intrawave sediment transport formulations.
The Assimilation of Phytoplankton Functional Types for Operational Forecasting in the Northwest European Shelf
Authors: Skákala Jozef , Ford David , Brewin Robert J.W. , McEwan Robert , Kay Susan , Taylor Benjamin , de Mora Lee , Ciavatta Stefano 
Published: June 2018

AbstractThis paper proposes the use of assimilation of phytoplankton functional types (PFTs) surface chlorophyll for operational forecasting of biogeochemistry on the North‐West European (NWE) Shelf. We explicitly compare the 5‐day forecasting skill of three runs of a physical‐biogeochemical model: (a) a free reference run, (b) a run with daily data assimilation (DA) of total surface chlorophyll (ChlTot), and (c) a run with daily PFTs DA. We show that small total chlorophyll model bias hides comparatively large biases in PFTs chlorophyll, which ChlTot DA fails to correct. This is because the ChlTot DA splits the assimilated total chlorophyll into PFTs by preserving their simulated ratios, rather than taking account of the observed PFT concentrations. Unlike ChlTot DA, PFTs DA substantially improves model representation of PFTs chlorophyll. During forecasting the DA reanalysis skill in representing PFTs chlorophyll degrades toward the free run skill; however, PFTs DA outperforms free run within the whole 5‐day forecasting period. We validated our results with in situ data, and we demonstrated that (in both DA cases) the DA substantially improves the model representation of CO2 fugacity (PFTs DA more than ChlTot DA). ChlTot DA has a positive impact on the representation of silicate, while the PFTs DA seems to have a negative impact. The impact of DA on nitrate and phosphate is not significant. The implications of using a univariate assimilation method, which preserves the phytoplankton stochiometry, and the impact of model biases on the nonassimilated variables are discussed.
Top‐Down Estimates of NOx and CO Emissions From Washington, D.C.‐Baltimore During the WINTER Campaign
Authors: Salmon O. E. , Shepson P. B. , Ren X. , He H. , Hall D. L. , Dickerson R. R. , Stirm B. H. , Brown S. S. , Fibiger D. L. , McDuffie E. E. , Campos T. L. , Gurney K. R. , Thornton J. A. 
Published: June 2018

AbstractAirborne mass balance experiments were conducted around the Washington, D.C.‐Baltimore area using research aircraft from Purdue University and the University of Maryland to quantify emissions of nitrogen oxides (NOx = NO + NO2) and carbon monoxide (CO). The airborne mass balance experiments supported the Wintertime INvestigation of Transport, Emissions, and Reactivity (WINTER) campaign, an intensive airborne study of anthropogenic emissions along the Northeastern United States in February–March 2015, and the Fluxes of Atmospheric Greenhouse Gases in Maryland project which seeks to provide best estimates of anthropogenic emissions from the Washington, D.C.‐Baltimore area. Top‐down emission rates of NOx and CO estimated from the mass balance flights are compared with the Environmental Protection Agency's 2011 and 2014 National Emissions Inventory (NEI‐11 and NEI‐14). Inventory and observation‐derived NOx emission rates are consistent within the measurement uncertainty. Observed CO emission rates are a factor of 2 lower than reported by the NEI. The NEI's accuracy has been evaluated for decades by studies of anthropogenic emissions, yet despite continuous inventory updates, observation‐inventory discrepancies persist. WINTER NOx/CO2 enhancement ratios are consistent with inventories, but WINTER CO/NOx and CO/CO2 enhancement ratios are lower than those reported by other urban summertime studies, suggesting a strong influence of CO seasonal trends and/or nationwide CO reductions. There is a need for reliable observation‐based criterion pollutant emission rate measurements independent of the NEI. Such determinations could be supplied by the community's reporting of sector‐specific criteria pollutant/CO2 enhancement ratios and subsequent multiplication with currently available and forthcoming high‐resolution CO2 inventories.
Downregulation of the neuronal opioid gene expression concomitantly with neuronal decline in dorsolateral prefrontal cortex of human alcoholics
Authors: Bazov Igor , Sarkisyan Daniil , Kononenko Olga , Watanabe Hiroyuki , Karpyak Victor M. , Yakovleva Tatiana , Bakalkin Georgy 
Published: June 2018

AbstractMolecular changes in cortical areas of addicted brain may underlie cognitive impairment and loss of control over intake of addictive substances and alcohol. Prodynorphin (PDYN) gives rise to dynorphin (DYNs) opioid peptides which target kappa-opioid receptor (KOR). DYNs mediate alcohol-induced impairment of learning and memory, while KOR antagonists block excessive, compulsive-like drug and alcohol self-administration in animal models. In human brain, the DYN/KOR system may undergo adaptive changes, which along with neuronal loss, may contribute to alcohol-associated cognitive deficit. We addressed this hypothesis by comparing the expression levels and co-expression (transcriptionally coordinated) patterns of PDYN and KOR (OPRK1) genes in dorsolateral prefrontal cortex (dlPFC) between human alcoholics and controls. Postmortem brain specimens of 53 alcoholics and 55 controls were analyzed. PDYN was found to be downregulated in dlPFC of alcoholics, while OPRK1 transcription was not altered. PDYN downregulation was confined to subgroup of subjects carrying C, a high-risk allele of PDYN promoter SNP rs1997794 associated with alcoholism. Changes in PDYN expression did not depend on the decline in neuronal proportion in alcoholics, and thereby may be attributed to transcriptional adaptations in alcoholic brain. Absolute expression levels of PDYN were lower compared to those of OPRK1, suggesting that PDYN expression is a limiting factor in the DYN/KOR signaling, and that the PDYN downregulation diminishes efficacy of DYN/KOR signaling in dlPFC of human alcoholics. The overall outcome of the DYN/KOR downregulation may be disinhibition of neurotransmission, which when overactivated could contribute to formation of alcohol-related behavior.
An effect of serotonergic stimulation on learning rates for rewards apparent after long intertrial intervals
Authors: Iigaya Kiyohito , Fonseca Madalena S. , Murakami Masayoshi , Mainen Zachary F. , Dayan Peter 
Published: June 2018

AbstractSerotonin has widespread, but computationally obscure, modulatory effects on learning and cognition. Here, we studied the impact of optogenetic stimulation of dorsal raphe serotonin neurons in mice performing a non-stationary, reward-driven decision-making task. Animals showed two distinct choice strategies. Choices after short inter-trial-intervals (ITIs) depended only on the last trial outcome and followed a win-stay-lose-switch pattern. In contrast, choices after long ITIs reflected outcome history over multiple trials, as described by reinforcement learning models. We found that optogenetic stimulation during a trial significantly boosted the rate of learning that occurred due to the outcome of that trial, but these effects were only exhibited on choices after long ITIs. This suggests that serotonin neurons modulate reinforcement learning rates, and that this influence is masked by alternate, unaffected, decision mechanisms. These results provide insight into the role of serotonin in treating psychiatric disorders, particularly its modulation of neural plasticity and learning.
Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1
Authors: Kooshapur Hamed , Choudhury Nila Roy , Simon Bernd , Mühlbauer Max , Jussupow Alexander , Fernandez Noemi , Jones Alisha N. , Dallmann Andre , Gabel Frank , Camilloni Carlo , Michlewski Gracjan , Caceres Javier F. , Sattler Michael 
Published: June 2018

AbstractPost-transcriptional mechanisms play a predominant role in the control of microRNA (miRNA) production. Recognition of the terminal loop of precursor miRNAs by RNA-binding proteins (RBPs) influences their processing; however, the mechanistic basis for how levels of individual or subsets of miRNAs are regulated is mostly unexplored. We previously showed that hnRNP A1, an RBP implicated in many aspects of RNA processing, acts as an auxiliary factor that promotes the Microprocessor-mediated processing of pri-mir-18a. Here, by using an integrative structural biology approach, we show that hnRNP A1 forms a 1:1 complex with pri-mir-18a where both RNA recognition motifs (RRMs) bind to cognate RNA sequence motifs in the terminal loop of pri-mir-18a. Terminal loop binding induces an allosteric destabilization of base-pairing in the pri-mir-18a stem that promotes its downstream processing. Our results highlight terminal loop RNA recognition by RBPs as a potential general principle of miRNA biogenesis and regulation.
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance
Authors: Wang Tianmin , Guan Changge , Guo Jiahui , Liu Bing , Wu Yinan , Xie Zhen , Zhang Chong , Xing Xin-Hui 
Published: June 2018

AbstractTo fully exploit the microbial genome resources, a high-throughput experimental platform is needed to associate genes with phenotypes at the genome level. We present here a novel method that enables investigation of the cellular consequences of repressing individual transcripts based on the CRISPR interference (CRISPRi) pooled screening in bacteria. We identify rules for guide RNA library design to handle the unique structure of prokaryotic genomes by tiling screening and construct an E. coli genome-scale guide RNA library (~60,000 members) accordingly. We show that CRISPRi outperforms transposon sequencing, the benchmark method in the microbial functional genomics field, when similar library sizes are used or gene length is short. This tool is also effective for mapping phenotypes to non-coding RNAs (ncRNAs), as elucidated by a comprehensive tRNA-fitness map constructed here. Our results establish CRISPRi pooled screening as a powerful tool for mapping complex prokaryotic genetic networks in a precise and high-throughput manner.
Ab initio description of highly correlated states in defects for realizing quantum bits
Authors: Bockstedte Michel , Schütz Felix , Garratt Thomas , Ivády Viktor , Gali Adam 
Published: June 2018

AbstractCoupled localized electron spins hosted by defects in semiconductors implement quantum bits with the potential to revolutionize nanoscale sensors and quantum information processing. The present understanding of optical means of spin state manipulation and read-out calls for quantitative theoretical description of the active states, built-up from correlated electrons in a bath of extended electron states. Hitherto we propose a first-principles scheme based on many body perturbation theory and configuration interaction and address two room temperature point defect qubits, the nitrogen vacancy in diamond and the divacancy in silicon carbide. We provide a complete quantitative description of the electronic structure and analyze the crossings and local minima of the energy surface of triplet and singlet states. Our numerical results not only extend the knowledge of the spin-dependent optical cycle of these defects, but also demonstrate the potential of our method for quantitative theoretical studies of point defect qubits.
Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract
Authors: Graspeuntner Simon , Loeper Nathalie , Künzel Sven , Baines John F. , Rupp Jan 
Published: June 2018

AbstractNext-generation sequencing-based methods are extensively applied in studies of the human microbiota using partial 16 S rRNA gene amplicons. However, they carry drawbacks that are critical to consider when interpreting results, including differences in outcome based on the hypervariable region(s) used. Here, we show that primers spanning the V3/V4 region identify a greater number of taxa in the vaginal microbiota than those spanning the V1/V2 region. In particular, taxa such as Gardnerella vaginalis, Bifidobacterium bifidum and Chlamydia trachomatis, all species that influence vaginal health and disease, are not represented in V1/V2-based community profiles. Accordingly, missing or underestimating the frequency of these species overestimates the abundance of other taxa and fails to correctly assess the bacterial diversity in the urogenital tract. We elaborate that covering these taxa using the V3/V4 region leads to profound changes in the assignment of community state types. Altogether, we show that the choice of primers used for studying the vaginal microbiota has deep implications on the biological evaluation of the results.
Recovery of coral assemblages despite acute and recurrent disturbances on a South Central Pacific reef
Authors: Adjeroud Mehdi , Kayal Mohsen , Iborra-Cantonnet Claudie , Vercelloni Julie , Bosserelle Pauline , Liao Vetea , Chancerelle Yannick , Claudet Joachim , Penin Lucie 
Published: June 2018

AbstractCoral reefs are increasingly threatened by various types of disturbances, and their recovery is challenged by accelerating, human-induced environmental changes. Recurrent disturbances reduce the pool of mature adult colonies of reef-building corals and undermine post-disturbance recovery from newly settled recruits. Using a long-term interannual data set, we show that coral assemblages on the reef slope of Moorea, French Polynesia, have maintained a high capacity to recover despite a unique frequency of large-scale disturbances which, since the 1990s, have caused catastrophic declines in coral cover and abundance. In 2014, only four years after one of the most extreme cases of coral decline documented, abundance of juvenile and adult colonies had regained or exceeded pre-disturbance levels, and no phase-shift to macroalgal dominance was recorded. This rapid recovery has been achieved despite constantly low coral recruitment rates, suggesting a high post-disturbance survivorship of recruits. However, taxonomic differences in coral susceptibility to disturbances and contrasting recovery trajectories have resulted in changes in the relative composition of species. In the present context of global coral reef decline, our study establishes a new benchmark for the capacity of certain benthic reef communities to sustain and recover their coral cover from repeated, intense disturbances.
Double Strand Break DNA Repair occurs via Non-Homologous End-Joining in Mouse MII Oocytes
Authors: Martin Jacinta H. , Bromfield Elizabeth G. , Aitken R. John , Lord Tessa , Nixon Brett 
Published: June 2018

AbstractThe unique biology of the oocyte means that accepted paradigms for DNA repair and protection are not of direct relevance to the female gamete. Instead, preservation of the integrity of the maternal genome depends on endogenous protein stores and/or mRNA transcripts accumulated during oogenesis. The aim of this study was to determine whether mature (MII) oocytes have the capacity to detect DNA damage and subsequently mount effective repair. For this purpose, DNA double strand breaks (DSB) were elicited using the topoisomerase II inhibitor, etoposide (ETP). ETP challenge led to a rapid and significant increase in DSB (P = 0.0002) and the consequential incidence of metaphase plate abnormalities (P = 0.0031). Despite this, ETP-treated MII oocytes retained their ability to participate in in vitro fertilisation, though displayed reduced developmental competence beyond the 2-cell stage (P = 0.02). To account for these findings, we analysed the efficacy of DSB resolution, revealing a significant reduction in DSB lesions 4 h post-ETP treatment. Notably, this response was completely abrogated by pharmacological inhibition of key elements (DNA-PKcs and DNA ligase IV) of the canonical non-homologous end joining DNA repair pathway, thus providing the first evidence implicating this reparative cascade in the protection of the maternal genome.
S-nitrosation of protein phosphatase 1 mediates alcohol-induced ciliary dysfunction
Authors: Price Michael E. , Case Adam J. , Pavlik Jacqueline A. , DeVasure Jane M. , Wyatt Todd A. , Zimmerman Matthew C. , Sisson Joseph H. 
Published: June 2018

AbstractAlcohol use disorder (AUD) is a strong risk factor for development and mortality of pneumonia. Mucociliary clearance, a key innate defense against pneumonia, is perturbed by alcohol use. Specifically, ciliated airway cells lose the ability to increase ciliary beat frequency (CBF) to β-agonist stimulation after prolonged alcohol exposure. We previously found that alcohol activates protein phosphatase 1 (PP1) through a redox mechanism to cause ciliary dysfunction. Therefore, we hypothesized that PP1 activity is enhanced by alcohol exposure through an S-nitrosothiol-dependent mechanism resulting in desensitization of CBF stimulation. Bronchoalveolar S-nitrosothiol (SNO) content and tracheal PP1 activity was increased in wild-type (WT) mice drinking alcohol for 6-weeks compared to control mice. In contrast, alcohol drinking did not increase SNO content or PP1 activity in nitric oxide synthase 3-deficient mice. S-nitrosoglutathione induced PP1-dependent CBF desensitization in mouse tracheal rings, cultured cells and isolated cilia. In vitro expression of mutant PP1 (cysteine 155 to alanine) in primary human airway epithelial cells prevented CBF desensitization after prolonged alcohol exposure compared to cells expressing WT PP1. Thus, redox modulation in the airways by alcohol is an important ciliary regulatory mechanism. Pharmacologic strategies to reduce S-nitrosation may enhance mucociliary clearance and reduce pneumonia prevalence, mortality and morbidity with AUD.
Aquatic behaviour of polar bears (Ursus maritimus) in an increasingly ice-free Arctic
Authors: Lone Karen , Kovacs Kit M. , Lydersen Christian , Fedak Mike , Andersen Magnus , Lovell Philip , Aars Jon 
Published: June 2018

AbstractPolar bears are ice-associated marine mammals that are known to swim and dive, yet their aquatic behaviour is poorly documented. Reductions in Arctic sea ice are clearly a major threat to this species, but understanding polar bears’ potential behavioural plasticity with respect to the ongoing changes requires knowledge of their swimming and diving skills. This study quantified time spent in water by adult female polar bears (n = 57) via deployment of various instruments bearing saltwater switches, and in some case pressure sensors (79 deployments, 64.8 bear-years of data). There were marked seasonal patterns in aquatic behaviour, with more time spent in the water during summer, when 75% of the polar bears swam daily (May-July). Females with cubs-of-the-year spent less time in the water than other females from den emergence (April) until mid-summer, consistent with small cubs being vulnerable to hypothermia and drowning. Some bears undertook notable long-distance-swims. Dive depths up to 13.9 m were recorded, with dives ≥5 m being common. The considerable swimming and diving capacities of polar bears might provide them with tools to exploit aquatic environments previously not utilized. This is likely to be increasingly important to the species’ survival in an Arctic with little or no persistent sea ice.
Metformin add-on continuous subcutaneous insulin infusion on precise insulin doses in patients with type 2 diabetes
Authors: Li Feng-fei , Liu Bing-li , Yin Guo-ping , Yan Reng-na , Zhang Dan-feng , Wu Jin-dan , Ye Lei , Su Xiao-fei , Ma Jian-hua 
Published: June 2018

AbstractTo investigate whether metformin add-on to the continuous subcutaneous insulin infusion (Met + CSII) therapy leads to a significant reduction in insulin doses required by type 2 diabetes (T2D) patients to maintain glycemic control, and an improvement in glycemic variation (GV) compared to CSII only therapy. We analyzed data from our two randomized, controlled open-label trials. Newly diagnoses T2D patients were randomized assigned to receive either CSII therapy or Met + CSII therapy for 4 weeks. Subjects were subjected to a 4-day continuous glucose monitoring (CGM) at the endpoint. Insulin doses and GV profiles were analyzed. The primary endpoint was differences in insulin doses and GV between the two groups. A total of 188 subjects were admitted as inpatients. Subjects in metformin add-on therapy required significantly lower total, basal and bolus insulin doses than those of control group. CGM data showed that patients in Met + CSII group exhibited significant reduction in the 24-hr mean amplitude of glycemic excursions (MAGE), the standard deviation, and the coefficient of variation compared to those of control group. Our data suggest that metformin add-on to CSII therapy leads to a significant reduction in insulin doses required by T2D patients to control glycemic variations.