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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Adams, C.; Strong, K.; Batchelor, R. L.; Bernath, P. F.; +25 Authors

    The Optical Spectrograph and Infra-Red Imager System (OSIRIS) and the Atmospheric Chemistry Experiment (ACE) have been taking measurements from space since 2001 and 2003, respectively. This paper presents intercomparisons between ozone and NO2 measured by the ACE and OSIRIS satellite instruments and by ground-based instruments at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Canada (80° N, 86° W) and is operated by the Canadian Network for the Detection of Atmospheric Change (CANDAC). The ground-based instruments included in this study are four zenith-sky differential optical absorption spectroscopy (DOAS) instruments, one Bruker Fourier transform infrared spectrometer (FTIR) and four Brewer spectrophotometers. Ozone total columns measured by the DOAS instruments were retrieved using new Network for the Detection of Atmospheric Composition Change (NDACC) guidelines and agree to within 3.2%. The DOAS ozone columns agree with the Brewer spectrophotometers with mean relative differences that are smaller than 1.5%. This suggests that for these instruments the new NDACC data guidelines were successful in producing a homogenous and accurate ozone dataset at 80° N. Satellite 14–52 km ozone and 17–40 km NO2 partial columns within 500 km of PEARL were calculated for ACE-FTS Version 2.2 (v2.2) plus updates, ACE-FTS v3.0, ACE-MAESTRO (Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) v1.2 and OSIRIS SaskMART v5.0x ozone and Optimal Estimation v3.0 NO2 data products. The new ACE-FTS v3.0 and the validated ACE-FTS v2.2 partial columns are nearly identical, with mean relative differences of 0.0 ± 0.2% and −0.2 ± 0.1% for v2.2 minus v3.0 ozone and NO2, respectively. Ozone columns were constructed from 14–52 km satellite and 0–14 km ozonesonde partial columns and compared with the ground-based total column measurements. The satellite-plus-sonde measurements agree with the ground-based ozone total columns with mean relative differences of 0.1–7.3%. For NO2, partial columns from 17 km upward were scaled to noon using a photochemical model. Mean relative differences between OSIRIS, ACE-FTS and ground-based NO2 measurements do not exceed 20%. ACE-MAESTRO measures more NO2 than the other instruments, with mean relative differences of 25–52%. Seasonal variation in the differences between NO2 partial columns is observed, suggesting that there are systematic errors in the measurements and/or the photochemical model corrections. For ozone spring-time measurements, additional coincidence criteria based on stratospheric temperature and the location of the polar vortex were found to improve agreement between some of the instruments. For ACE-FTS v2.2 minus Bruker FTIR, the 2007–2009 spring-time mean relative difference improved from −5.0 ± 0.4% to −3.1 ± 0.8% with the dynamical selection criteria. This was the largest improvement, likely because both instruments measure direct sunlight and therefore have well-characterized lines-of-sight compared with scattered sunlight measurements. For NO2, the addition of a ±1° latitude coincidence criterion improved spring-time intercomparison results, likely due to the sharp latitudinal gradient of NO2 during polar sunrise. The differences between satellite and ground-based measurements do not show any obvious trends over the missions, indicating that both the ACE and OSIRIS instruments continue to perform well.

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Copernicus Publications
    Other ORP type . 2018
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Copernicus Publicati...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Copernicus Publications
      Other ORP type . 2018
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Fletcher, Tamara L.; Warden, Lisa; Sinninghe Damsté, Jaap S.; Brown, Kendrick J.; +3 Authors

    The mid-Pliocene is a valuable time interval for investigating equilibrium climate at current atmospheric CO2 concentrations because atmospheric CO2 concentrations are thought to have been comparable to the current day and yet the climate and distribution of ecosystems were quite different. One intriguing, but not fully understood, feature of the early to mid-Pliocene climate is the amplified Arctic temperature response and its impact on Arctic ecosystems. Only the most recent models appear to correctly estimate the degree of warming in the Pliocene Arctic and validation of the currently proposed feedbacks is limited by scarce terrestrial records of climate and environment. Here we reconstruct the summer temperature and fire regime from a subfossil fen-peat deposit on west–central Ellesmere Island, Canada, that has been chronologically constrained using cosmogenic nuclide burial dating to 3.9+1.5/-0.5 Ma. The estimate for average mean summer temperature is 15.4±0.8 ∘C using specific bacterial membrane lipids, i.e., branched glycerol dialkyl glycerol tetraethers. This is above the proposed threshold that predicts a substantial increase in wildfire in the modern high latitudes. Macro-charcoal was present in all samples from this Pliocene section with notably higher charcoal concentration in the upper part of the sequence. This change in charcoal was synchronous with a change in vegetation that included an increase in abundance of fire-promoting Pinus and Picea. Paleo-vegetation reconstructions are consistent with warm summer temperatures, relatively low summer precipitation and an incidence of fire comparable to fire-adapted boreal forests of North America and central Siberia. To our knowledge, this site provides the northernmost evidence of fire during the Pliocene. It suggests that ecosystem productivity was greater than in the present day, providing fuel for wildfires, and that the climate was conducive to the ignition of fire during this period. The results reveal that interactions between paleo-vegetation and paleoclimate were mediated by fire in the High Arctic during the Pliocene, even though CO2 concentrations were similar to modern values.

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    Copernicus Publications
    Other ORP type . 2019
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Copernicus Publications
      Other ORP type . 2019
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    Authors: Pérez-Vargas, Jimena; Worrall, Liam J.; Olmstead, Andrea D.; Ton, Anh-Tien; +26 Authors

    Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30 – 50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.

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    figshare
    Other ORP type . 2023
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      figshare
      Other ORP type . 2023
      License: CC BY
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Langowski, Martin P.; Savigny, Christian; Burrows, John P.; Fussen, Didier; +4 Authors

    During the last decade, several limb sounding satellites have measured the global sodium (Na) number densities in the mesosphere and lower thermosphere (MLT). Datasets are now available from Global Ozone Monitoring by Occultation of Stars (GOMOS), the SCanning Imaging Absorption spectroMeter for Atmospheric CHartography (SCIAMACHY) (both on Envisat) and the Optical Spectrograph and InfraRed Imager System (OSIRIS) (on Odin). Furthermore, global model simulations of the Na layer in the MLT simulated by the Whole Atmosphere Community Climate Model, including the Na species (WACCM-Na), are available. In this paper, we compare these global datasets.The observed and simulated monthly averages of Na vertical column densities agree reasonably well with each other. They show a clear seasonal cycle with a summer minimum most pronounced at the poles. They also show signs of a semi-annual oscillation in the equatorial region. The vertical column densities vary from 0. 5 × 109 to 7 × 109 cm−2 near the poles and from 3 × 109 to 4 × 109 cm−2 at the Equator. The phase of the seasonal cycle and semi-annual oscillation shows small differences between the Na amounts retrieved from different instruments. The full width at half maximum of the profiles is 10 to 16 km for most latitudes, but significantly smaller in the polar summer. The centroid altitudes of the measured sodium profiles range from 89 to 95 km, whereas the model shows on average 2 to 4 km lower centroid altitudes. This may be explained by the mesopause being 3 km lower in the WACCM simulations than in measurements. Despite this global 2–4 km shift, the model captures well the latitudinal and temporal variations. The variation of the WACCM dataset during the year at different latitudes is similar to the one of the measurements. Furthermore, the differences between the measured profiles with different instruments and therefore different local times (LTs) are also present in the model-simulated profiles. This capturing of latitudinal and temporal variations is also found for the vertical column densities and profile widths.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Copernicus Publicati...arrow_drop_down
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    Copernicus Publications
    Other ORP type . 2018
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Copernicus Publications
      Other ORP type . 2018
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    Authors: Jorgensen, Salvador J.; Micheli, Fiorenza; White, Timothy D.; Van Houtan, Kyle S.; +43 Authors

    Over the past 4 decades there has been a growing concern for the conservation status of elasmobranchs (sharks and rays). In 2002, the first elasmobranch species were added to Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Less than 20 yr later, there were 39 species on Appendix II and 5 on Appendix I. Despite growing concern, effective conservation and management remain challenged by a lack of data on population status for many species, human−wildlife interactions, threats to population viability, and the efficacy of conservation approaches. We surveyed 100 of the most frequently published and cited experts on elasmobranchs and, based on ranked responses, prioritized 20 research questions on elasmobranch conservation. To address these questions, we then convened a group of 47 experts from 35 institutions and 12 countries. The 20 questions were organized into the following broad categories: (1) status and threats, (2) population and ecology, and (3) conservation and management. For each section, we sought to synthesize existing knowledge, describe consensus or diverging views, identify gaps, and suggest promising future directions and research priorities. The resulting synthesis aggregates an array of perspectives on emergent research and priority directions for elasmobranch conservation. S.J.J. and K.S.V. acknowledge the generous contributions of members, visitors and donors to the Monterey Bay Aquarium. F.M., F.F., B.D.S., and S.A. acknowledge the support of the Bertarelli Foundation. J.K.B. and N.K.D. acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC). G.L.B. acknowledges funding from the Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology. D.W.S. was supported by the Natural Environment Research Council (NE/R00997X/1) and the European Research Council (ERC- 2019-AdG 883583). N.Q. was funded by Fundação para a Ciência e a Tecnologia (FCT, Portugal) under CEECIND/ 02857/2018 and PTDC/BIA/28855/2017. We acknowledge the Virginia Tech's Open Access Subvention Fund for paying the publication costs of this paper. Published version

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    VTechWorks
    Other ORP type . 2022
    License: CC BY
    Data sources: VTechWorks
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    Authors: González, Angélica L.; Dézerald, Olivier; Marquet, Pablo A.; Romero, Gustavo Q.; +1 Authors

    The niche concept is essential to understanding how biotic and abiotic factors regulate the abundance and distribution of living entities, and how these organisms utilize, affect and compete for resources in the environment. However, it has been challenging to determine the number and types of important niche dimensions. By contrast, there is strong mechanistic theory and empirical evidence showing that the elemental composition of living organisms shapes ecological systems, from organismal physiology to food web structure. We propose an approach based on a multidimensional elemental view of the ecological niche. Visualizing the stoichiometric composition of individuals in multivariate space permits quantification of niche dimensions within and across species. This approach expands on previous elemental characterizations of plant niches, and adapts metrics of niche volume, overlap and nestedness previously used to quantify isotopic niches. We demonstrate the applicability of the multidimensional stoichiometric niche using data on carbon, nitrogen, and phosphorus of terrestrial and freshwater communities composed by multiple trophic groups. First, we calculated the stoichiometric niche volumes occupied by terrestrial and freshwater food webs, by trophic groups, by individual species, and by individuals within species, which together give a measure of the extent of stoichiometric diversity within and across levels of organization. Then we evaluated complementarity between these stoichiometric niches, through metrics of overlap and nestedness. Our case study showed that vertebrates, invertebrates, and primary producers do not overlap in their stoichiometric niches, and that large areas of stoichiometric space are unoccupied by organisms. Within invertebrates, niche differences emerged between freshwater and terrestrial food webs, and between herbivores and non-herbivores (detritivores and predators). These niche differences were accompanied by changes in the covariance structure of the three elements, suggesting fundamental shifts in organismal physiology and/or structure. We also demonstrate the sensitivity of results to sample size, and suggest that representative sampling is better than rarefaction in characterizing the stoichiometric niche occupied by food webs. Overall, our approach demonstrates that stoichiometric traits provide a common currency to estimate the dimensionality of stoichiometric niches, and help reduce and rationalize the number of axis required to characterize communities.

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    Frontiers in Ecology and Evolution
    2017 . Peer-reviewed
    Data sources: Frontiers
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      Frontiers in Ecology and Evolution
      2017 . Peer-reviewed
      Data sources: Frontiers
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    Authors: Rivera-Casas, Ciro; Gonzalez-Romero, Rodrigo; Garduño, Rafael A.; Cheema, Manjinder S.; +2 Authors

    Bivalve molluscs constitute a ubiquitous taxonomic group playing key functions in virtually all ecosystems, and encompassing critical commercial relevance. Along with a sessile and filter-feeding lifestyle in most cases, these characteristics make bivalves model sentinel organisms routinely used for environmental monitoring studies in aquatic habitats. The study of epigenetic mechanisms linking environmental exposure and specific physiological responses (i.e., environmental epigenetics) stands out as a very innovative monitoring strategy, given the role of epigenetic modifications in acclimatization and adaptation. Furthermore, the heritable nature of many of those modifications constitutes a very promising avenue to explore the applicability of epigenetic conditioning and selection in management and restoration strategies. Chromatin provides a framework for the study of environmental epigenetic responses. Unfortunately, chromatin and epigenetic information are very limited in most non-traditional model organisms and even completely lacking in most environmentally and ecologically relevant organisms. The present work aims to provide a comprehensive and reproducible experimental workflow for the study of bivalve chromatin. First, a series of guidelines for the molecular isolation of genes encoding chromatin-associated proteins is provided, including information on primers suitable for conventional PCR, Rapid Amplification of cDNA Ends (RACE), genome walking and quantitative PCR (qPCR) experiments. This section is followed by the description of methods specifically developed for the analysis of histone and SNBP proteins in different bivalve tissues, including protein extraction, purification, separation and immunodetection. Lastly, information about available antibodies, their specificity and performance is also provided. The tools and protocols described here complement current epigenetic analyses (usually limited to DNA methylation) by incorporating the study of structural elements modulating chromatin dynamics.

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    Frontiers in Physiology
    2017 . Peer-reviewed
    Data sources: Frontiers
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      Frontiers in Physiology
      2017 . Peer-reviewed
      Data sources: Frontiers
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    Authors: Abe K.; others;

    The Tokai to Kamioka (T2K) long baseline neutrino experiment consists of a muon neutrino beam produced at the J PARC accelerator a near detector complex and a large 295km distant far detector. The present work utilizes the T2K event timing measurements at the near and far detectors to study neutrino time of flight as function of derived neutrino energy. Under the assumption of a relativistic relation between energy and time of flight constraints on the neutrino rest mass can be derived. The sub GeV neutrino beam in conjunction with timing precision of order tens of ns provide sensitivity to neutrino mass in the few MeV/c2 range. We study the distribution of relative arrival times of muon and electron neutrino candidate events at the T2K far detector as a function of neutrino energy. The 90 C.L. upper limit on the mixture of neutrino mass eigenstates represented in the data sample is found to be m2?<5.6MeV2/c4.

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    Authors: Shatil, Anwar S.; Matsuda, Kant M.; Figley, Chase R.;

    Magnetic resonance imaging (MRI) is a non-destructive technique that is capable of localizing pathologies and assessing other anatomical features (e.g., tissue volume, microstructure, and white matter connectivity) in postmortem, ex vivo human brains. However, when brains are removed from the skull and cerebrospinal fluid (i.e., their normal in vivo magnetic environment), air bubbles and air–tissue interfaces typically cause magnetic susceptibility artifacts that severely degrade the quality of ex vivo MRI data. In this report, we describe a relatively simple and cost-effective experimental setup for acquiring artifact-free ex vivo brain images using a clinical MRI system with standard hardware. In particular, we outline the necessary steps, from collecting an ex vivo human brain to the MRI scanner setup, and have also described changing the formalin (as might be necessary in longitudinal postmortem studies). Finally, we share some representative ex vivo MRI images that have been acquired using the proposed setup in order to demonstrate the efficacy of this approach. We hope that this protocol will provide both clinicians and researchers with a straight-forward and cost-effective solution for acquiring ex vivo MRI data from whole postmortem human brains.

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    Frontiers in Neurology
    2016 . Peer-reviewed
    Data sources: Frontiers
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      Frontiers in Neurology
      2016 . Peer-reviewed
      Data sources: Frontiers
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    Authors: Sandell, Linnea; Sharp, Nathaniel;

    We used previously published datasets of growth rates of, and mutations in, mutation accumulation lines in Saccharomyces cerevisiae and Chlamydomonas reinhardtii. We computed the mutated proteins and ran the protein variant, as compared to the laboratory ancestor, through PROVEAN. We ran PROVEAN on the ComputeCanada cluster. As the program failed to run with the recent BLAST software (version 2.9.0), we configured PROVEAN to run with PSI-BLAST and BLASTDBCMD (Altschul et al. 1997)from BLAST version 2.4.0. We used version 4.8.1 of CD-HIT. We ran our variants with the NCBI nr database from 12/11/2019, which holds 142 GB of non-redundant sequences (229,636,095 sequences). We ran a subset of variants using the 2012 database, on which PROVEAN was developed (the first 5 GB), without radical changes to the PROVEAN scores of variants. The supporting sequence sets used to compute the alignment scores for all proteins were saved. Sc1 We used the mutations reported in Sharp et al. (2018; Dataset_S2.xlsx). There were 1474 genic mutations in the dataset, occurring in 1219 unique genes across 218 MA lines. We extracted the nucleotide and protein sequence of the genes affected using YeastMine (Balakrishnan et al. 2012). From the same database, we downloaded the location of introns in these genes. The reference nucleotide sequence was then mutated in silicoto represent the mutant sequence, which was then transcribed and translated, using the seqinr package (Charif and Lobry 2007)in R (R Core Team 2019). Additionally, we analyzed VCF files to obtain a table of mutations in the ancestral line as compared to the yeast reference genome (version R64-2-1). In cases where the ancestor and reference strain differed for a mutated gene (126 genes) we separately computed the ancestral protein and used it for comparison to the MA lines. We wrote a script to produce protein variants in the format PROVEAN requires. From 1474 genic mutations, 1126 protein variants were computed (in 961 unique proteins). Two samples (lines 113 and 206) had no nonsynonymous mutations. When an MA line had more than one nonsynonymous mutation in a particular gene both mutations were considered when altering the protein and the number of mutant proteins is reported once. Out of 961 altered proteins, 126 already differed between the S288C reference genome and the laboratory ancestor, in which case the latter was used as the query sequence. Sc2 We used the mutations reported in Liu and Zhang (2019; Data_S1.xlsx). Additionally, the authors supplied us with a table of mutations in their ancestral line relative to the S288C reference genome. We used the same method as described above for dataset Sc1. There were 1147 genic mutations, occurring in 968 unique genes, across 165 MA lines. From 1147 genic mutations, 877 protein variants were computed (in 754 unique proteins). Out of 754 altered proteins, 16 already differed between the S288C reference genome and the laboratory ancestor, in which case the latter was used as the query sequence. Cr We received an annotated table of the mutations reported in Ness et al. (2015)as well as VCF files containing the mutations in their six ancestral lines compared to the reference genome. We downloaded an annotated table for all transcripts in the Chlamydomonasreference genome from Dicots PLAZA 4.0 (version 5.5, Van Bel et al., 2018)to identify mutations in coding sequences. Out of the original 6843 mutations, 3889 affected protein sequence, representing 1439 mutated proteins after combining mutations. We found that the majority of transcripts that were mutated during mutation accumulation already had existing variants in the ancestral strain, relative to the reference (table 1). 1397 out of the originally predicted 1439 protein variants remained once ancestral variation had been considered (table 1). As in the other datasets, we use the ancestral protein as the query protein. We found 2 cases in the C. reinhardtiidataset where the reported reference nucleotide deviated from that found in the Dicots PLAZA 4.0 sequence; in each case, the differences between the two reference sequences were synonymous. This discrepancy was likely due to the two different reference genomes used (Ness et al. used v5.3; Van Bel et al. used v5.5). To test the accuracy of our sequence-mutating code, we mutated the coding sequence to the reference nucleotide given by the C. reinhardtiidataset and verified that this produced the reference transcript. We converted the protein variants into the format PROVEAN requires. In cases with alternative transcripts, we treat these as separate proteins in PROVEAN and then report the minimum score given to any protein variant of a gene. This occurred in 42 unique cases, involving all genetic backgrounds. While the difference in scores between transcripts in general was small, we found two cases where the score for one affected transcript was below the default threshold of –2.5 while the other was above it, and six cases where the scores fell above and below zero. Six out of the total 1397 protein variants failed to receive a score from PROVEAN, likely because the changes to the protein were too large to compute alignment scores between the clusters gathered and the mutant protein and were ignored in the analysis (these occurred in six different samples across five ancestral backgrounds). Predicting fitness in natural populations is a major challenge in biology. It may be possible to leverage fast-accumulating genomic datasets to infer the fitness effects of mutant alleles, allowing evolutionary questions to be addressed in any organism. In this paper, we investigate the utility of one such tool, called PROVEAN. This program compares a query sequence with existing data to provide an alignment-based score for any protein variant, with scores categorized as neutral or deleterious based on a preset threshold. PROVEAN has been used widely in evolutionary studies, e.g., to estimate mutation load in natural populations, but has not been formally tested as a predictor of aggregate mutational effects on fitness. Using three large, published datasets on the genome sequences of laboratory mutation accumulation lines, we assessed how well PROVEAN predicted the actual fitness patterns observed, relative to other metrics. In most cases, we find that a simple count of the total number of mutant proteins is a better predictor of fitness than the number of variants scored as deleterious by PROVEAN. We also find that the sum of all mutant protein scores explains variation in fitness better than the number of mutant proteins in one of the datasets. We discuss the implications of these results for studies of populations in the wild. Details and usage notes can be found in Sandell_provean_project_README.txt.

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    ZENODO
    Other ORP type . 2022
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    ZENODO
    Other ORP type . 2022
    License: CC BY
    Data sources: Datacite
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      ZENODO
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      ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Adams, C.; Strong, K.; Batchelor, R. L.; Bernath, P. F.; +25 Authors

    The Optical Spectrograph and Infra-Red Imager System (OSIRIS) and the Atmospheric Chemistry Experiment (ACE) have been taking measurements from space since 2001 and 2003, respectively. This paper presents intercomparisons between ozone and NO2 measured by the ACE and OSIRIS satellite instruments and by ground-based instruments at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Canada (80° N, 86° W) and is operated by the Canadian Network for the Detection of Atmospheric Change (CANDAC). The ground-based instruments included in this study are four zenith-sky differential optical absorption spectroscopy (DOAS) instruments, one Bruker Fourier transform infrared spectrometer (FTIR) and four Brewer spectrophotometers. Ozone total columns measured by the DOAS instruments were retrieved using new Network for the Detection of Atmospheric Composition Change (NDACC) guidelines and agree to within 3.2%. The DOAS ozone columns agree with the Brewer spectrophotometers with mean relative differences that are smaller than 1.5%. This suggests that for these instruments the new NDACC data guidelines were successful in producing a homogenous and accurate ozone dataset at 80° N. Satellite 14–52 km ozone and 17–40 km NO2 partial columns within 500 km of PEARL were calculated for ACE-FTS Version 2.2 (v2.2) plus updates, ACE-FTS v3.0, ACE-MAESTRO (Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) v1.2 and OSIRIS SaskMART v5.0x ozone and Optimal Estimation v3.0 NO2 data products. The new ACE-FTS v3.0 and the validated ACE-FTS v2.2 partial columns are nearly identical, with mean relative differences of 0.0 ± 0.2% and −0.2 ± 0.1% for v2.2 minus v3.0 ozone and NO2, respectively. Ozone columns were constructed from 14–52 km satellite and 0–14 km ozonesonde partial columns and compared with the ground-based total column measurements. The satellite-plus-sonde measurements agree with the ground-based ozone total columns with mean relative differences of 0.1–7.3%. For NO2, partial columns from 17 km upward were scaled to noon using a photochemical model. Mean relative differences between OSIRIS, ACE-FTS and ground-based NO2 measurements do not exceed 20%. ACE-MAESTRO measures more NO2 than the other instruments, with mean relative differences of 25–52%. Seasonal variation in the differences between NO2 partial columns is observed, suggesting that there are systematic errors in the measurements and/or the photochemical model corrections. For ozone spring-time measurements, additional coincidence criteria based on stratospheric temperature and the location of the polar vortex were found to improve agreement between some of the instruments. For ACE-FTS v2.2 minus Bruker FTIR, the 2007–2009 spring-time mean relative difference improved from −5.0 ± 0.4% to −3.1 ± 0.8% with the dynamical selection criteria. This was the largest improvement, likely because both instruments measure direct sunlight and therefore have well-characterized lines-of-sight compared with scattered sunlight measurements. For NO2, the addition of a ±1° latitude coincidence criterion improved spring-time intercomparison results, likely due to the sharp latitudinal gradient of NO2 during polar sunrise. The differences between satellite and ground-based measurements do not show any obvious trends over the missions, indicating that both the ACE and OSIRIS instruments continue to perform well.

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    Copernicus Publications
    Other ORP type . 2018
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      Copernicus Publications
      Other ORP type . 2018
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    Authors: Fletcher, Tamara L.; Warden, Lisa; Sinninghe Damsté, Jaap S.; Brown, Kendrick J.; +3 Authors

    The mid-Pliocene is a valuable time interval for investigating equilibrium climate at current atmospheric CO2 concentrations because atmospheric CO2 concentrations are thought to have been comparable to the current day and yet the climate and distribution of ecosystems were quite different. One intriguing, but not fully understood, feature of the early to mid-Pliocene climate is the amplified Arctic temperature response and its impact on Arctic ecosystems. Only the most recent models appear to correctly estimate the degree of warming in the Pliocene Arctic and validation of the currently proposed feedbacks is limited by scarce terrestrial records of climate and environment. Here we reconstruct the summer temperature and fire regime from a subfossil fen-peat deposit on west–central Ellesmere Island, Canada, that has been chronologically constrained using cosmogenic nuclide burial dating to 3.9+1.5/-0.5 Ma. The estimate for average mean summer temperature is 15.4±0.8 ∘C using specific bacterial membrane lipids, i.e., branched glycerol dialkyl glycerol tetraethers. This is above the proposed threshold that predicts a substantial increase in wildfire in the modern high latitudes. Macro-charcoal was present in all samples from this Pliocene section with notably higher charcoal concentration in the upper part of the sequence. This change in charcoal was synchronous with a change in vegetation that included an increase in abundance of fire-promoting Pinus and Picea. Paleo-vegetation reconstructions are consistent with warm summer temperatures, relatively low summer precipitation and an incidence of fire comparable to fire-adapted boreal forests of North America and central Siberia. To our knowledge, this site provides the northernmost evidence of fire during the Pliocene. It suggests that ecosystem productivity was greater than in the present day, providing fuel for wildfires, and that the climate was conducive to the ignition of fire during this period. The results reveal that interactions between paleo-vegetation and paleoclimate were mediated by fire in the High Arctic during the Pliocene, even though CO2 concentrations were similar to modern values.

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    Copernicus Publications
    Other ORP type . 2019
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      Copernicus Publications
      Other ORP type . 2019
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    Authors: Pérez-Vargas, Jimena; Worrall, Liam J.; Olmstead, Andrea D.; Ton, Anh-Tien; +26 Authors

    Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30 – 50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.

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    Other ORP type . 2023
    License: CC BY
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      Other ORP type . 2023
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    Authors: Langowski, Martin P.; Savigny, Christian; Burrows, John P.; Fussen, Didier; +4 Authors

    During the last decade, several limb sounding satellites have measured the global sodium (Na) number densities in the mesosphere and lower thermosphere (MLT). Datasets are now available from Global Ozone Monitoring by Occultation of Stars (GOMOS), the SCanning Imaging Absorption spectroMeter for Atmospheric CHartography (SCIAMACHY) (both on Envisat) and the Optical Spectrograph and InfraRed Imager System (OSIRIS) (on Odin). Furthermore, global model simulations of the Na layer in the MLT simulated by the Whole Atmosphere Community Climate Model, including the Na species (WACCM-Na), are available. In this paper, we compare these global datasets.The observed and simulated monthly averages of Na vertical column densities agree reasonably well with each other. They show a clear seasonal cycle with a summer minimum most pronounced at the poles. They also show signs of a semi-annual oscillation in the equatorial region. The vertical column densities vary from 0. 5 × 109 to 7 × 109 cm−2 near the poles and from 3 × 109 to 4 × 109 cm−2 at the Equator. The phase of the seasonal cycle and semi-annual oscillation shows small differences between the Na amounts retrieved from different instruments. The full width at half maximum of the profiles is 10 to 16 km for most latitudes, but significantly smaller in the polar summer. The centroid altitudes of the measured sodium profiles range from 89 to 95 km, whereas the model shows on average 2 to 4 km lower centroid altitudes. This may be explained by the mesopause being 3 km lower in the WACCM simulations than in measurements. Despite this global 2–4 km shift, the model captures well the latitudinal and temporal variations. The variation of the WACCM dataset during the year at different latitudes is similar to the one of the measurements. Furthermore, the differences between the measured profiles with different instruments and therefore different local times (LTs) are also present in the model-simulated profiles. This capturing of latitudinal and temporal variations is also found for the vertical column densities and profile widths.

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    Copernicus Publications
    Other ORP type . 2018
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      Copernicus Publications
      Other ORP type . 2018
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    Authors: Jorgensen, Salvador J.; Micheli, Fiorenza; White, Timothy D.; Van Houtan, Kyle S.; +43 Authors

    Over the past 4 decades there has been a growing concern for the conservation status of elasmobranchs (sharks and rays). In 2002, the first elasmobranch species were added to Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Less than 20 yr later, there were 39 species on Appendix II and 5 on Appendix I. Despite growing concern, effective conservation and management remain challenged by a lack of data on population status for many species, human−wildlife interactions, threats to population viability, and the efficacy of conservation approaches. We surveyed 100 of the most frequently published and cited experts on elasmobranchs and, based on ranked responses, prioritized 20 research questions on elasmobranch conservation. To address these questions, we then convened a group of 47 experts from 35 institutions and 12 countries. The 20 questions were organized into the following broad categories: (1) status and threats, (2) population and ecology, and (3) conservation and management. For each section, we sought to synthesize existing knowledge, describe consensus or diverging views, identify gaps, and suggest promising future directions and research priorities. The resulting synthesis aggregates an array of perspectives on emergent research and priority directions for elasmobranch conservation. S.J.J. and K.S.V. acknowledge the generous contributions of members, visitors and donors to the Monterey Bay Aquarium. F.M., F.F., B.D.S., and S.A. acknowledge the support of the Bertarelli Foundation. J.K.B. and N.K.D. acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC). G.L.B. acknowledges funding from the Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology. D.W.S. was supported by the Natural Environment Research Council (NE/R00997X/1) and the European Research Council (ERC- 2019-AdG 883583). N.Q. was funded by Fundação para a Ciência e a Tecnologia (FCT, Portugal) under CEECIND/ 02857/2018 and PTDC/BIA/28855/2017. We acknowledge the Virginia Tech's Open Access Subvention Fund for paying the publication costs of this paper. Published version

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    VTechWorks
    Other ORP type . 2022
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