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  • Oxford University Press  (156,963)
  • American Association for the Advancement of Science (AAAS)
  • American Association of Petroleum Geologists (AAPG)
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  • 1
    Publication Date: 2019-12-13
    Description: Deep-towed geophysical surveys require precise knowledge of navigational parameters such as instrument position and orientation because navigational uncertainties reflect in the data and therefore in the inferred geophysical properties of the subseafloor. We address this issue for the case of electrical conductivity inferred from controlled source electromagnetic data. We show that the data error is laterally variable due to irregular motion during deep towing, but also due to lateral variations in conductivity, including those resulting from topography. To address this variability and quantify the data error prior to inversion, we propose a 2-D perturbation study. Our workflow enables stable and geologically reliable results for multicomponent and multifrequency inversions. An error estimation workflow is presented, which comprises the assessment of navigational uncertainties, perturbation of navigational parameters, and forward modelling of electric field amplitudes for a homogeneous and then a heterogeneous subseafloor conductivity model. Some navigational uncertainties are estimated from variations of direct measurements. Other navigational parameters required for inversion are derived from the measured quantities and their error is calculated by means of error propagation. Some navigational parameters show direct correlation with the measured electric fields. For example, the antenna dip correlates with the vertical electric field and the depth correlates with the horizontal electric field. For the perturbation study each standard deviation is added to the navigational parameters. Forward models are run for each perturbation. Amplitude deviations are summed in quadrature with the stacking error for a total, laterally varying, data error. The error estimation is repeated for a heterogeneous subseafloor model due to the large conductivity range (several orders of magnitude), which affects the forward model. The approach enables us to utilize data from several components (multiple electric fields, frequencies and receivers) in the inversion to constrain the final model and reduce ambiguity. The final model is geologically reasonable, in this case enabling the identification of conductive metal sulphide deposits on the seafloor.
    Type: Article , PeerReviewed
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  • 2
    Publication Date: 2019-04-04
    Description: We quantify the oceanic sink for anthropogenic carbon dioxide (CO 2 ) over the period 1994 to 2007 by using observations from the global repeat hydrography program and contrasting them to observations from the 1990s. Using a linear regression–based method, we find a global increase in the anthropogenic CO 2 inventory of 34 ± 4 petagrams of carbon (Pg C) between 1994 and 2007. This is equivalent to an average uptake rate of 2.6 ± 0.3 Pg C year −1 and represents 31 ± 4% of the global anthropogenic CO 2 emissions over this period. Although this global ocean sink estimate is consistent with the expectation of the ocean uptake having increased in proportion to the rise in atmospheric CO 2 , substantial regional differences in storage rate are found, likely owing to climate variability–driven changes in ocean circulation.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 3
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    Oxford University Press
    In:  Climate Justice: Integrating Economics and Philosophy
    Publication Date: 2019-02-13
    Type: inbook
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  • 4
    Publication Date: 2019-04-03
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aslan, C., Beckman, N. G., Rogers, H. S., Bronstein, J., Zurell, D., Hartig, F., Shea, K., Pejchar, L., Neubert, M., Poulsen, J., HilleRisLambers, J., Miriti, M., Loiselle, B., Effiom, E., Zambrano, J., Schupp, G., Pufal, G., Johnson, J., Bullock, J. M., Brodie, J., Bruna, E., Cantrell, R. S., Decker, R., Fricke, E., Gurski, K., Hastings, A., Kogan, O., Razafindratsima, O., Sandor, M., Schreiber, S., Snell, R., Strickland, C., & Zhou, Y. Employing plant functional groups to advance seed dispersal ecology and conservation. AoB Plants, 11(2), (2019):plz006, doi:10.1093/aobpla/plz006.
    Description: Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequently develop into a reproductive plant is daunting. Quantifying all factors that may influence seed dispersal effectiveness for any potential seed-vector relationship would require an unrealistically large amount of time, materials and financial resources. On the other hand, being able to make dispersal predictions is critical for predicting whether single species and entire ecosystems will be resilient to global change. Building on current frameworks, we here posit that seed dispersal ecology should adopt plant functional groups as analytical units to reduce this complexity to manageable levels. Functional groups can be used to distinguish, for their constituent species, whether it matters (i) if seeds are dispersed, (ii) into what context they are dispersed and (iii) what vectors disperse them. To avoid overgeneralization, we propose that the utility of these functional groups may be assessed by generating predictions based on the groups and then testing those predictions against species-specific data. We suggest that data collection and analysis can then be guided by robust functional group definitions. Generalizing across similar species in this way could help us to better understand the population and community dynamics of plants and tackle the complexity of seed dispersal as well as its disruption.
    Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio‐Environmental Synthesis Center under the US National Science Foundation Grant DBI‐1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1- 1). Contributions by the authors C.A. led the development of the concepts, writing, and revising of the manuscript with input from N.G.B. and H.S.R. All authors contributed to the development of concepts and are listed in order of contribution and alphabetical order within each level of contribution.
    Keywords: dependency ; directed dispersal ; dispersal vectors ; generalization ; mutualism ; seed dispersal effectiveness
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    Oxford University Press
    In:  Journal of travel medicine
    Publication Date: 2019-06-05
    Description: Humans have a long history of mobility on a spectrum from voluntary migration to forced displacement in response to social, political and environmental change. While many migration drivers exist, climate change is likely to amplify the environmental drivers of migration. At least 1.5?C of warming above pre-industrial levels between 2030 and 2052 are projected if global warming continues to increase at the current rate. The associated impacts are diverse and include temperature and precipitation extremes in most inhabited regions and increased probability of drought and flood. Migration can be an important and useful adaptive response to climate impacts when it increases household resilience and reduces socio-economic vulnerabilities, and yet can also have negative health consequences. The climate?migration?health nexus entails complex interactions including the following: first, climate-related risks to health faced by migrants at all stages of the migration journey. Second, the impacts of migration itself on health with possible specific health implications of climate-related migration. This article provides a brief overview of climate-related migration, identifies climate hotspots where substantial migration and displacement are anticipated and explores the health implications of climate-related migration.
    Language: English
    Type: http://purl.org/escidoc/metadata/ves/publication-types/article
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  • 6
    Publication Date: 2019-06-21
    Description: The Tibetan Plateau and its surroundings are known as the Third Pole (TP). This region is noted for its high rates of glacier melt and the associated hydrological shifts that affect water supplies in Asia. Atmospheric pollutants contribute to climatic and cryospheric changes through their effects on solar radiation and the albedos of snow and ice surfaces; moreover, the behavior and fates within the cryosphere and environmental impacts of environmental pollutants are topics of increasing concern. In this review, we introduce a coordinated monitoring and research framework and network to link atmospheric pollution and cryospheric changes (APCC) within the TP region. We then provide an up-to-date summary of progress and achievements related to the APCC research framework, including aspects of atmospheric pollution's composition and concentration, spatial and temporal variations, trans-boundary transport pathways and mechanisms, and effects on the warming of atmosphere and changing in Indian monsoon, as well as melting of glacier and snow cover. We highlight that exogenous air pollutants can enter into the TP?s environments and cause great impacts on regional climatic and environmental changes. At last, we propose future research priorities and map out an extended program at the global scale. The ongoing monitoring activities and research facilitate comprehensive studies of atmosphere?cryosphere interactions, represent one of China's key research expeditions to the TP and the polar regions and contribute to the global perspective of earth system science.
    Language: English
    Type: http://purl.org/escidoc/metadata/ves/publication-types/article
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  • 7
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    Oxford University Press
    In:  FEMS Microbiology Letters, 366 (11).
    Publication Date: 2019-07-10
    Description: Metabolites give us a window into the chemistry of microbes and are split into two subclasses: primary and secondary. Primary metabolites are required for life whereas secondary metabolites have historically been classified as those appearing after exponential growth and are not necessarily needed for survival. Many microbial species are estimated to produce hundreds of metabolites and can be affected by differing nutrients. Using various analytical techniques, metabolites can be directly detected in order to elucidate their biological significance. Currently, a single experiment can produce anywhere from megabytes to terabytes of data. This big data has motivated scientists to develop informatics tools to help target specific metabolites or sets of metabolites. Broadly, it is imperative to identify clear biological questions before embarking on a study of metabolites (metabolomics). For instance, studying the effect of a transposon insertion on phenazine biosynthesis in Pseudomonas is a very different from asking what molecules are present in a specific banana-derived strain of Pseudomonas. This review is meant to serve as a primer for a ‘choose your own adventure’ approach for microbiologists with limited mass spectrometry expertise, with a strong focus on liquid chromatography mass spectrometry based workflows developed or optimized within the past five years.
    Type: Article , PeerReviewed
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  • 8
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    Oxford University Press
    In:  Zoological Journal of the Linnean Society, 185 (3). pp. 555-635.
    Publication Date: 2019-08-06
    Description: Polynoidae contains ~900 species within 18 subfamilies, some of them restricted to the deep sea. Macellicephalinae is the most diverse among these deep-sea subfamilies. In the abyssal Equatorial Pacific Ocean, the biodiversity of benthic communities is at stake in the Clarion-Clipperton Fracture Zone (CCFZ) owing to increased industrial interest in polymetallic nodules. The records of polychaetes in this region are scarce. Data gathered during the JPI Oceans cruise SO239 made a significant contribution to fill this gap, with five different localities sampled between 4000 and 5000 m depth. Benthic samples collected using an epibenthic sledge or a remotely operated vehicle resulted in a large collection of polynoids. The aims of this study are as follows: (1) to describe new species of deep-sea polynoids using morphology and molecular data (COI, 16S and 18S); and (2) to evaluate the monophyly of Macellicephalinae. Based on molecular and morphological phylogenetic analyses, ten subfamilies are synonymized with Macellicephalinae in order to create a homogeneous clade determined by the absence of lateral antennae. Within this clade, the Anantennata clade was well supported, being determined by the absence of a median antenna. Furthermore, 17 new species and four new genera are described, highlighting the high diversity hidden in the deep. A taxonomic key for the 37 valid genera of the subfamily Macellicephalinae is provided.
    Type: Article , PeerReviewed
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  • 9
    Publication Date: 2019-09-05
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Alexander, H., Johnson, L. K., & Brown, C. T.. Keeping it light: (re)analyzing community-wide datasets without major infrastructure. Gigascience, 8(2),(2019): giy159, doi:10.1093/gigascience/giy159.
    Description: DNA sequencing technology has revolutionized the field of biology, shifting biology from a data-limited to data-rich state. Central to the interpretation of sequencing data are the computational tools and approaches that convert raw data into biologically meaningful information. Both the tools and the generation of data are actively evolving, yet the practice of re-analysis of previously generated data with new tools is not commonplace. Re-analysis of existing data provides an affordable means of generating new information and will likely become more routine within biology, yet necessitates a new set of considerations for best practices and resource development. Here, we discuss several practices that we believe to be broadly applicable when re-analyzing data, especially when done by small research groups.
    Description: Funding was provided by the Gordon and Betty Moore Foundation (award GBMF4551 to C.T.B.).
    Keywords: reproducibility ; data reuse ; open data
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2019-09-05
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, L. K., Alexander, H., & Brown, C. T. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience, 8(4), (2019): giy158, doi: 10.1093/gigascience/giy158.
    Description: Background: De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or “pipelines,” on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. Results: New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. Conclusions: Given current bioinformatics approaches, there is no single “best” reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
    Description: Funding was provided by the Gordon and Betty Moore Foundation under award number GBMF4551 to C.T.B. Jetstream cloud platform was used with XSEDE allocation TG-BIO160028 [66, 67].
    Keywords: marine microbial eukaryote ; transcriptome assembly ; automated pipeline ; re-analysis
    Repository Name: Woods Hole Open Access Server
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  • 11
    Publication Date: 2019-09-23
    Description: To provide an observational basis for the Intergovernmental Panel on Climate Change projections of a slowing Atlantic meridional overturning circulation (MOC) in the 21st century, the Overturning in the Subpolar North Atlantic Program (OSNAP) observing system was launched in the summer of 2014. The first 21-month record reveals a highly variable overturning circulation responsible for the majority of the heat and freshwater transport across the OSNAP line. In a departure from the prevailing view that changes in deep water formation in the Labrador Sea dominate MOC variability, these results suggest that the conversion of warm, salty, shallow Atlantic waters into colder, fresher, deep waters that move southward in the Irminger and Iceland basins is largely responsible for overturning and its variability in the subpolar basin.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 12
    Publication Date: 2019-10-01
    Description: Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.
    Type: Article , PeerReviewed
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  • 13
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    Oxford University Press
    In:  Geophysical Journal International, 219 (3). pp. 1876-1884.
    Publication Date: 2019-10-23
    Description: Standard seismic acquisition and processing require appropriate source-receiver offsets. P-cable technology represents the opposite, namely, very short source-receiver offsets at the price of increased spatial and lateral resolution with a high-frequency source. To use this advantage, a processing flow excluding offset information is required. This aim can be achieved with a processing tuned to diffractions because point diffractions scatter the same information in offset and midpoint direction. Usually, diffractions are small amplitude events and a careful diffraction separation is required as a first step. We suggest the strategy to use a multiparameter stacking operator, e.g, common-reflection surface, and stack along the midpoint direction. The obtained kinematic wavefront attributes are used to calculate time-migration velocities. A diffractivity map serves as filter to refine the velocities. This strategy is applied to a 3D P-cable data set to obtain a time-migrated image.
    Type: Article , PeerReviewed
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  • 14
    Publication Date: 2019-11-19
    Description: Cichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.
    Type: Article , PeerReviewed
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  • 15
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 16
    Publication Date: 2019
    Description: 〈p〉Environmentally transformative human use of land accelerated with the emergence of agriculture, but the extent, trajectory, and implications of these early changes are not well understood. An empirical global assessment of land use from 10,000 years before the present (yr B.P.) to 1850 CE reveals a planet largely transformed by hunter-gatherers, farmers, and pastoralists by 3000 years ago, considerably earlier than the dates in the land-use reconstructions commonly used by Earth scientists. Synthesis of knowledge contributed by more than 250 archaeologists highlighted gaps in archaeological expertise and data quality, which peaked for 2000 yr B.P. and in traditionally studied and wealthier regions. Archaeological reconstruction of global land-use history illuminates the deep roots of Earth’s transformation and challenges the emerging Anthropocene paradigm that large-scale anthropogenic global environmental change is mostly a recent phenomenon.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 17
    Publication Date: 2019
    Description: 〈p〉The requirement for next-generation antimalarials to be both curative and transmission-blocking necessitates the identification of previously undiscovered druggable molecular pathways. We identified a selective inhibitor of the 〈i〉Plasmodium falciparum〈/i〉 protein kinase 〈i〉Pf〈/i〉CLK3, which we used in combination with chemogenetics to validate 〈i〉Pf〈/i〉CLK3 as a drug target acting at multiple parasite life stages. Consistent with a role for 〈i〉Pf〈/i〉CLK3 in RNA splicing, inhibition resulted in the down-regulation of more than 400 essential parasite genes. Inhibition of 〈i〉Pf〈/i〉CLK3 mediated rapid killing of asexual liver- and blood-stage 〈i〉P. falciparum〈/i〉 and blockade of gametocyte development, thereby preventing transmission, and also showed parasiticidal activity against 〈i〉P. berghei〈/i〉 and 〈i〉P. knowlesi〈/i〉. Hence, our data establish 〈i〉Pf〈/i〉CLK3 as a target for drugs, with the potential to offer a cure—to be prophylactic and transmission blocking in malaria.〈/p〉
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  • 18
    Publication Date: 2019
    Description: 〈p〉Charge density modulations have been observed in all families of high–critical temperature (〈i〉T〈/i〉〈sub〉c〈/sub〉) superconducting cuprates. Although they are consistently found in the underdoped region of the phase diagram and at relatively low temperatures, it is still unclear to what extent they influence the unusual properties of these systems. Using resonant x-ray scattering, we carefully determined the temperature dependence of charge density modulations in YBa〈sub〉2〈/sub〉Cu〈sub〉3〈/sub〉O〈sub〉7–〈/sub〉 and Nd〈sub〉1+〈/sub〉〈i〉〈sub〉x〈/sub〉〈/i〉Ba〈sub〉2–〈/sub〉〈i〉〈sub〉x〈/sub〉〈/i〉Cu〈sub〉3〈/sub〉O〈sub〉7–〈/sub〉 for several doping levels. We isolated short-range dynamical charge density fluctuations in addition to the previously known quasi-critical charge density waves. They persist up to well above the pseudogap temperature 〈i〉T*〈/i〉, are characterized by energies of a few milli–electron volts, and pervade a large area of the phase diagram.〈/p〉
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  • 19
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 20
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Description: 〈p〉Astronomical calculations reveal the Solar System’s dynamical evolution, including its chaoticity, and represent the backbone of cyclostratigraphy and astrochronology. An absolute, fully calibrated astronomical time scale has hitherto been hampered beyond ~50 million years before the present (Ma) because orbital calculations disagree before that age. Here, we present geologic data and a new astronomical solution (ZB18a) showing exceptional agreement from ~58 to 53 Ma. We provide a new absolute astrochronology up to 58 Ma and a new Paleocene–Eocene boundary age (56.01 ± 0.05 Ma). We show that the Paleocene–Eocene Thermal Maximum (PETM) onset occurred near a 405-thousand-year (kyr) eccentricity maximum, suggesting an orbital trigger. We also provide an independent PETM duration (170 ± 30 kyr) from onset to recovery inflection. Our astronomical solution requires a chaotic resonance transition at ~50 Ma in the Solar System’s fundamental frequencies.〈/p〉
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  • 21
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Description: 〈p〉The central and peripheral nervous system (CNS and PNS, respectively) are composed of distinct neuronal and glial cell types with specialized functional properties. However, a small number of select cells traverse the CNS-PNS boundary and connect these two major subdivisions of the nervous system. This pattern of segregation and selective connectivity is established during embryonic development, when neurons and glia migrate to their destinations and axons project to their targets. Here, we provide an overview of the cellular and molecular mechanisms that control cell migration and axon guidance at the vertebrate CNS-PNS border. We highlight recent advances on how cell bodies and axons are instructed to either cross or respect this boundary, and present open questions concerning the development and plasticity of the CNS-PNS interface.〈/p〉
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  • 22
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 23
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 24
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 25
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Description: 〈p〉Actin, spectrin, and related molecules form a membrane-associated periodic skeleton (MPS) in neurons. The function of the MPS, however, remains poorly understood. Using super-resolution imaging, we observed that G protein–coupled receptors (GPCRs), cell adhesion molecules (CAMs), receptor tyrosine kinases (RTKs), and related signaling molecules were recruited to the MPS in response to extracellular stimuli, resulting in colocalization of these molecules and RTK transactivation by GPCRs and CAMs, giving rise to extracellular signal–regulated kinase (ERK) signaling. Disruption of the MPS prevented such molecular colocalizations and downstream ERK signaling. ERK signaling in turn caused calpain-dependent MPS degradation, providing a negative feedback that modulates signaling strength. These results reveal an important functional role of the MPS and establish it as a dynamically regulated platform for GPCR- and CAM-mediated RTK signaling.〈/p〉
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  • 26
    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Uncertainty estimation and quality control are critically missing in most geophysical tomographic applications. The few solutions to cope with that issue are often left out in practical applications when these ones grow in scale and involve complex modeling. We present a joint full waveform inversion and ensemble data assimilation scheme, allowing local Bayesian estimation of the solution that brings uncertainty estimation to the tomographic problem. This original methodology relies on a deterministic square root ensemble Kalman filter commonly used in the data assimilation community: the ensemble transform Kalman filter. Combined with a 2D visco-acoustic frequency domain full waveform inversion scheme, the resulting method allows to access a low-rank approximation of the posterior covariance matrix of the solution. It yields uncertainty information through an ensemble-representation, that can conveniently be mapped across the physical domain for visualization and interpretation. The combination of ensemble transform Kalman filter with full waveform inversion is discussed along with the scheme design and algorithmic details that lead to our mixed application. Both synthetic and field-data results are presented, along with the biases that are associated with the limited rank ensemble representation. Finally, we review the open questions and developments perspectives linked with data assimilation applications to the tomographic problem.〈/span〉
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    Topics: Geosciences
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  • 27
    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉Full Green’s functions between image points and the recording surface is crucial to constructing accurate subsurface wavefields and images beyond the single scattering assumption. A direct approach to do so is offered by utilizing the recorded data combined with a background imaging velocity. The process includes extrapolating the recorded data back in time followed by a simple interferometric crosscorrelation of the back propagated wavefield with the recorded data. This interferometric step offers the opportunity to extract subsurface Green’s functions with first order scattering forming the transmission component, and the second-order scattering becoming the leading scattering term. A crosscorrelation of the resulting, assumed upgoing, wavefield with a forward modeled down going wavefield highlights the double scattered reflectivity in a process referred to as the generalized internal multiple imaging (GIMI). The resulting image is vulnerable to crosstalk between different order multiples interacting with each other. Thus, we develop the adjoint GIMI operation that takes us from the image to the data, and use it to formulate a least square optimization problem to fit the image to the data. The result is reduced crosstalk and cleaner higher resolution multiple scattered images. We also extract space extensions of the image, which offers the opportunity to evaluate the focussing capability of the velocity model, and formulate updates for that model based on double scattering. We show the features of this approach on the modified Marmousi model.〈/span〉
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  • 28
    Publication Date: 2019
    Description: 〈p〉Host cell metabolism can be modulated by viral infection, affecting viral survival or clearance. The cellular metabolism rewiring mediated by 〈i〉N〈/i〉〈sup〉6〈/sup〉-methyladenosine (m〈sup〉6〈/sup〉A) modification in virus-host interaction remains largely unknown. Here we report that in response to viral infection, host cells impair the enzymatic activity of RNA m〈sup〉6〈/sup〉A demethylase ALKBH5. This increases the m〈sup〉6〈/sup〉A methylation on α-ketoglutarate dehydrogenase (OGDH) mRNA to reduce its mRNA stability and protein expression. Reduced OGDH decreases the production of metabolite itaconate that is required for viral replication. With reduced OGDH and itaconate production in vivo, ALKBH5-deficient mice display an innate immune response-independent resistance to viral challenge. Our findings reveal that m〈sup〉6〈/sup〉A RNA modification-mediated down-regulation of OGDH-Itaconate pathway reprograms cellular metabolism to inhibit viral replication, proposing potential targets for controlling viral infection.〈/p〉
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  • 29
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  • 30
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  • 31
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  • 32
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  • 33
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  • 34
    Publication Date: 2019
    Description: 〈p〉Stimuli-responsive materials activated by biological signals play an increasingly important role in biotechnology applications. We exploit the programmability of CRISPR-associated nucleases to actuate hydrogels containing DNA as a structural element or as an anchor for pendant groups. After activation by guide RNA–defined inputs, Cas12a cleaves DNA in the gels, thereby converting biological information into changes in material properties. We report four applications: (i) branched poly(ethylene glycol) hydrogels releasing DNA-anchored compounds, (ii) degradable polyacrylamide-DNA hydrogels encapsulating nanoparticles and live cells, (iii) conductive carbon-black–DNA hydrogels acting as degradable electrical fuses, and (iv) a polyacrylamide-DNA hydrogel operating as a fluidic valve with an electrical readout for remote signaling. These materials allow for a range of in vitro applications in tissue engineering, bioelectronics, and diagnostics.〈/p〉
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  • 35
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  • 36
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  • 37
    Publication Date: 2019
    Description: 〈p〉Investigating slow earthquake activity in subduction zones provides insight into the slip behavior of megathrusts, which can provide important clues about the rupture extent of future great earthquakes. Using the S-net ocean-bottom seismograph network along the Japan Trench, we mapped a detailed distribution of tectonic tremors, which coincided with very-low-frequency earthquakes and a slow slip event. Compiling these and other related observations, including repeating earthquakes and earthquake swarms, we found that the slow earthquake distribution is complementary to the Tohoku-Oki earthquake rupture. We used our observations to divide the megathrust in the Japan Trench into three along-strike segments characterized by different slip behaviors. We found that the rupture of the Tohoku-Oki earthquake, which nucleated in the central segment, was terminated by the two adjacent segments.〈/p〉
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  • 38
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  • 39
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  • 40
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  • 41
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  • 42
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  • 43
    Publication Date: 2019
    Description: 〈p〉Understanding genomic variation and population structure of 〈i〉Plasmodium falciparum〈/i〉 across Africa is necessary to sustain progress toward malaria elimination. Genome clustering of 2263 〈i〉P. falciparum〈/i〉 isolates from 24 malaria-endemic settings in 15 African countries identified major western, central, and eastern ancestries, plus a highly divergent Ethiopian population. Ancestry aligned to these regional blocs, overlapping with both the parasite’s origin and with historical human migration. The parasite populations are interbred and shared genomic haplotypes, especially across drug resistance loci, which showed the strongest recent identity-by-descent between populations. A recent signature of selection on chromosome 12 with candidate resistance loci against artemisinin derivatives was evident in Ghana and Malawi. Such selection and the emerging substructure may affect treatment-based intervention strategies against 〈i〉P. falciparum〈/i〉 malaria.〈/p〉
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  • 44
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  • 45
    Publication Date: 2019
    Description: 〈p〉Ballard 〈i〉et al〈/i〉. argue that our prediction of a 30-year or longer recovery time for Gulf of Mexico water quality is highly uncertain, and that much shorter time lags are equally likely. We demonstrate that their argument, based on the use of a two-component regression model, does not sufficiently consider fundamental watershed processes or multiple lines of evidence suggesting the existence of decadal-scale lags.〈/p〉
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  • 46
    Publication Date: 2019
    Description: 〈p〉The concept of topological phases is a powerful framework for characterizing ground states of quantum many-body systems that goes beyond the paradigm of symmetry breaking. Topological phases can appear in condensed-matter systems naturally, whereas the implementation and study of such quantum many-body ground states in artificial matter require careful engineering. Here, we report the experimental realization of a symmetry-protected topological phase of interacting bosons in a one-dimensional lattice and demonstrate a robust ground state degeneracy attributed to protected zero-energy edge states. The experimental setup is based on atoms trapped in an array of optical tweezers and excited into Rydberg levels, which gives rise to hard-core bosons with an effective hopping generated by dipolar exchange interaction.〈/p〉
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  • 47
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  • 48
    Publication Date: 2019
    Description: 〈p〉Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors activate cell death and confer disease resistance by unknown mechanisms. We demonstrate that plant Toll/interleukin-1 receptor (TIR) domains of NLRs are enzymes capable of degrading nicotinamide adenine dinucleotide in its oxidized form (NAD〈sup〉+〈/sup〉). Both cell death induction and NAD〈sup〉+〈/sup〉 cleavage activity of plant TIR domains require known self-association interfaces and a putative catalytic glutamic acid that is conserved in both bacterial TIR NAD〈sup〉+〈/sup〉-cleaving enzymes (NADases) and the mammalian SARM1 (sterile alpha and TIR motif containing 1) NADase. We identify a variant of cyclic adenosine diphosphate ribose as a biomarker of TIR enzymatic activity. TIR enzymatic activity is induced by pathogen recognition and functions upstream of the genes 〈i〉enhanced disease susceptibility 1〈/i〉 (〈i〉EDS1〈/i〉) and 〈i〉N requirement gene 1〈/i〉 (〈i〉NRG1〈/i〉), which encode regulators required for TIR immune function. Thus, plant TIR-NLR receptors require NADase function to transduce recognition of pathogens into a cell death response.〈/p〉
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  • 49
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  • 50
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  • 51
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  • 52
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  • 53
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  • 54
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  • 55
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  • 56
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  • 57
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    Description: 〈p〉How do neurons encode long-term memories? Bilateral imaging of neuronal activity in the mouse hippocampus reveals that, from one day to the next, ~40% of neurons change their responsiveness to cues, but thereafter only 1% of cells change per day. Despite these changes, neuronal responses are resilient to a lack of exposure to a previously completed task or to hippocampus lesions. Unlike individual neurons, the responses of which change after a few days, groups of neurons with inter- and intrahemispheric synchronous activity show stable responses for several weeks. The likelihood that a neuron maintains its responsiveness across days is proportional to the number of neurons with which its activity is synchronous. Information stored in individual neurons is relatively labile, but it can be reliably stored in networks of synchronously active neurons.〈/p〉
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  • 58
    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉We derive a theoretical relationship between the cross correlation of ambient Rayleigh waves (seismic ambient noise) and the attenuation parameter α associated with Rayleigh-wave propagation. In particular, we derive a mathematical expression for the multiplicative factor relating normalized cross correlation to the Rayleigh-wave Green’s function. Based on this expression, we formulate an inverse problem to determine α from cross correlations of recorded ambient signal. We conduct a preliminary application of our algorithm to a relatively small instrument array, conveniently deployed on an island. In our setup, the mentioned multiplicative factor has values of about 2.5 to 3, which, if neglected, could result in a significant underestimate of α. We find that our inferred values of α are reasonable, in comparison with independently obtained estimates found in the literature. Allowing α to vary with respect to frequency results in a reduction of misfit between observed and predicted cross correlations.〈/span〉
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  • 59
    Publication Date: 2019
    Description: 〈p〉Development of safe and efficient nanoscale vehicles that can deliver large molecular cargos into human cells could transform future human therapies and personalized medicine. Here, we design a hybrid viral vector composed of a prokaryotic virus (bacteriophage T4) and a eukaryotic virus [adeno-associated virus (AAV)]. The small 25-nm AAV is attached to the large 120 nm x 86 nm T4 head through avidin-biotin cross-bridges using the phage decoration proteins Soc and Hoc. AAV "piggy-backed" on T4 capsid, by virtue of its natural ability to enter human cells acted as an efficient "driver," delivering the largest payloads of foreign DNA (up to 170 kb) and protein (up to 1025 molecules) reported to date, and elicited robust immune responses in mice against flu and plague pathogens and conferred complete protection against lethal pneumonic plague challenge. The T4-AAV represents a unique platform for assembly of natural building blocks into potential therapeutics against genetic and infectious diseases.〈/p〉
    Electronic ISSN: 2375-2548
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  • 60
    Publication Date: 2019
    Description: 〈p〉Age-associated changes in CD4 T-cell functionality have been linked to chronic inflammation and decreased immunity. However, a detailed characterization of CD4 T cell phenotypes that could explain these dysregulated functional properties is lacking. We used single-cell RNA sequencing and multidimensional protein analyses to profile thousands of CD4 T cells obtained from young and old mice. We found that the landscape of CD4 T cell subsets differs markedly between young and old mice, such that three cell subsets—exhausted, cytotoxic, and activated regulatory T cells (aT〈sub〉regs〈/sub〉)—appear rarely in young mice but gradually accumulate with age. Most unexpected were the extreme pro- and anti-inflammatory phenotypes of cytotoxic CD4 T cells and aT〈sub〉regs〈/sub〉, respectively. These findings provide a comprehensive view of the dynamic reorganization of the CD4 T cell milieu with age and illuminate dominant subsets associated with chronic inflammation and immunity decline, suggesting new therapeutic avenues for age-related diseases.〈/p〉
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  • 61
    Publication Date: 2019
    Description: 〈p〉Macrocyclic compounds are an attractive modality for drug development, but the limited availability of large, structurally diverse macrocyclic libraries hampers the discovery of leads. Here, we describe the discovery of efficient macrocyclization reactions based on thiol-to-amine ligations using bis-electrophiles, their application to synthesize and screen large libraries of macrocyclic compounds, and the identification of potent small macrocyclic ligands. The thiol-to-amine cyclization reactions showed unexpectedly high yields for a wide substrate range, which obviated product purification and enabled the generation and screening of an 8988 macrocycle library with a comparatively small effort. X-ray structure analysis of an identified thrombin inhibitor (〈i〉K〈/i〉〈sub〉i〈/sub〉 = 42 ± 5 nM) revealed a snug fit with the target, validating the strategy of screening large libraries with a high skeletal diversity. The approach provides a route for screening large sub-kilodalton macrocyclic libraries and may be applied to many challenging drug targets.〈/p〉
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  • 62
    Publication Date: 2019
    Description: 〈p〉Sea surface temperature variability in the equatorial eastern Atlantic, which is referred to as an Atlantic Niño (Niña) at its warm (cold) phase and peaks in boreal summer, dominates the interannual variability in the equatorial Atlantic. By strengthening of the Walker circulation, an Atlantic Niño favors a Pacific La Niña, which matures in boreal winter, providing a precursory memory for El Niño–Southern Oscillation (ENSO) predictability. How this Atlantic impact responds to greenhouse warming is unclear. Here, we show that greenhouse warming leads to a weakened influence from the Atlantic Niño/Niña on the Pacific ENSO. In response to anomalous equatorial Atlantic heating, ascending over the equatorial Atlantic is weaker due to an increased tropospheric stability in the mean climate, resulting in a weaker impact on the Pacific Ocean. Thus, as greenhouse warming continues, Pacific ENSO is projected to be less affected by the Atlantic Niño/Niña and more challenging to predict.〈/p〉
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  • 63
    Publication Date: 2019
    Description: 〈p〉We report a general strategy based on digital counting principle that enables an efficient acquisition of enzyme mutants with desired activities from just a few clones within a day. We prepared a high-density femtoliter droplet array, consisting of 1 million uniform droplets per 1 cm〈sup〉2〈/sup〉 to carry out high-throughput protein synthesis and screening. Single DNA molecules were randomly distributed into each droplet following a Poisson process to initiate the protein synthesis with coupled cell-free transcription and translation reactions and then recovered by a microcapillary. The protein yield in each droplet was proportional to the number of DNA molecules, meaning that droplets with apparent intensities higher than the Poisson distribution–predicted maximum can be readily identified as the exact hits exhibiting the desired increased activity. We improved the activity of an alkaline phosphatase up to near 20-fold by using less than 10 nl of reagents.〈/p〉
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  • 64
    Publication Date: 2019
    Description: 〈p〉Sickle cell disease is induced by a mutation that converts normal adult hemoglobin to sickle hemoglobin (HbS) and engenders intracellular polymerization of deoxy-HbS and erythrocyte sickling. Development of anti-sickling therapies requires quantitative understanding of HbS polymerization kinetics under organ-specific conditions, which are difficult to assess with existing experimental techniques. Thus, we developed a kinetic model based on the classical nucleation theory to examine the effectiveness of potential anti-sickling drug candidates. We validated this model by comparing its predictability against prior in vivo and in vitro experimental results. We used the model to quantify the efficacy of sickling inhibitors and obtain results consistent with recent screening assays. Global sensitivity analysis on the kinetic parameters in the model revealed that the solubility, nucleation rate prefactor, and oxygen affinity are quantities that dictate HbS polymerization. This finding provides quantitative guidelines for the discovery of intracellular processes to be targeted by sickling inhibitors.〈/p〉
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  • 65
    Publication Date: 2019
    Description: 〈p〉In eukaryotic membranes, P4-ATPases mediate the translocation of phospholipids from the outer to inner leaflet and maintain lipid asymmetry, which is critical for membrane trafficking and signaling pathways. Here we report the cryo-EM structures of six distinct intermediates of the human ATP8A1-CDC50a hetero-complex, at 2.6–3.3 Å resolutions, elucidating lipid translocation cycle of this P4-ATPase. ATP-dependent phosphorylation induces a large rotational movement of the actuator domain around the phosphorylation site in the phosphorylation domain, accompanied by lateral shifts of the first and second transmembrane helices, thereby allowing phosphatidylserine binding. The phospholipid head group passes through the hydrophilic cleft, while the acyl chain is exposed toward the lipid environment. These findings advance our understanding of the flippase mechanism and the disease-associated mutants of P4-ATPases.〈/p〉
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  • 66
    Publication Date: 2019
    Description: 〈span〉〈div〉ABSTRACT〈/div〉The Paleogene shale of the Dongying depression, a continental basin in eastern China, is taken as the study subject to examine the microscopic features of lacustrine shale reservoirs in the oil window. This study shows that shale pores in this evolutionary stage are present at the micrometer to nanometer scale, but fractures commonly have extension distances at the millimeter scale. Pores and fractures can be divided into three types, namely, primary pores, secondary pores, and cracks. Primary pores commonly have good connectivity at shallow burial depth. With the increase of burial depth, primary porosity is reduced because of compaction and cementation. Secondary pores are important in shale, including dissolved pores inside grains and at grain edge, and dissolution pores inside the hybrid of organic matter (OM) and clay minerals, and evaporite minerals, including carbonates or sulfates. Types of cracks were observed: bedding fissures, dissolution fractures, and structural fractures. The development of bedding fissures is related to the deposition of shale laminae. The formation of dissolution fractures is related to acidic fluids, such as organic acids and hydrogen sulfide, whereas the formation of structural fractures is jointly controlled by fault development, fluid overpressure, and lithofacies. The pores and fractures in the oil window of lacustrine shale can store and channel oil and gas. The hybrid OM–clay–carbonate (sulfate) and the pores inside are important through the oil window. Moreover, the development of the pores depends not only on hydrocarbon generation but also on the interaction of hydrocarbons and organic acid dissolution. This finding has important significance in the accumulation of oil and gas in continental shales.〈/span〉
    Print ISSN: 0149-1423
    Electronic ISSN: 1943-2674
    Topics: Geosciences
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  • 67
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    American Association of Petroleum Geologists (AAPG)
    Publication Date: 2019
    Description: 〈span〉〈div〉ABSTRACT〈/div〉Oil API gravity predictions using published basin modeling source rock (SR) reaction kinetics have displayed poor matches between modeled output and field observations because these kinetic models do not predict increasing API gravities with increasing maturity. Ideally, an SR kinetic model should use at least two liquid components of different densities, which are generated and expelled from the SR such that the API gravities are a consequence of relative mixing. Very few available kinetic models predict APIs with reasonable trends, but those are either not adjustable to calibrate to field observations or do not consider sorption, which is a necessary process when evaluating unconventional resources. Five new kinetics data sets are presented in this paper, each representing a standard SR type, which provide geologically reasonable API gravity trends and ranges. Each kinetic model uses two liquid pseudocomponents and two vapor pseudocomponents. The relative ratios between the pseudocomponents at full kerogen transformation are average ratios available from public and proprietary kinetic data sets. The primary generation follows published activation energies, including minor shifts, which allow peak generation to occur at lower activation energies for the heavier liquid pseudocomponent and at higher energies for the lighter one. This systematic shift of activation energies thus results in a constant change in API gravity as primary generation progresses. Additional in-SR sorption and secondary cracking schemes support the primary generated API gravity trends. The default ranges of API gravity for the new five kinetic models represent observed averages but can be adjusted easily.〈/span〉
    Print ISSN: 0149-1423
    Electronic ISSN: 1943-2674
    Topics: Geosciences
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  • 68
    Publication Date: 2019
    Description: 〈span〉〈div〉ABSTRACT〈/div〉In the past, determination of rock properties using image analysis relied upon petrographic transmitted-light images, but with limited success because of a lack of resolution and restricted computer processing power. A new technique that employs confocal laser scanning microscopy (CLSM) can be considered complementary to laboratory measurements and applicable to several samples, saving time and money and requiring only a limited amount of rock sample for analysis. We have studied several types of rocks with CLSM and fluorescent dye–impregnated thin sections. The two-dimensional scans of each thin section images is an area of 12 mm〈sup〉2〈/sup〉, with a pixel size of 0.198 µm and were used to simulate capillary pressure curves for pore bodies and pore throats. The CLSM technique also enables three-dimensional (3-D) visualization of the rock porosity. The studied rock samples were taken from diverse oil and gas field reservoirs: case A, a conventional sandstone (15.1% porosity, 29.8 md permeability); case B, a tight sandstone (3.7%, 0.02 md); case C, an oolitic carbonate (9.6%, 0.1 md); case D, a rhodolithic algal carbonate (19.8%, 43.7 md); case E, dolomitized carbonate (17%, 21.7 md); and case F, a naturally fractured carbonate (2.4%, 0.6 md). Our results confirm that the CLSM technique can be applied to rocks of contrasting porosity and permeability to obtain computed synthetic capillary pressure curves faster than with conventional measurement methods. The technique quantifies different pore-body and pore-throat sizes and distributions, with the added ability to visualize 3-D porosity and to extract from thin section analysis petrologic properties.〈/span〉
    Print ISSN: 0149-1423
    Electronic ISSN: 1943-2674
    Topics: Geosciences
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  • 69
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 70
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2019
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 71
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    American Association for the Advancement of Science (AAAS)
    In: Science