69 research outputs found

    Circumstellar habitable zones for deep terrestrial biospheres

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    SM and JOJ are grateful to the UK Science and Technology Facilities Council (STFC) for Aurora Studentships. We thank Dr. Stephen Clifford (LPI), Dr. Ravi Kopparapu (Penn State), and Claire Davis (St. Andrews) for generous technical advice. We thank Norm Sleep and two anonymous reviewers for constructive reviews of the manuscriptPeer reviewedPostprin

    CTD electromechanical termination users manual

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    This report desribes a new, easy to install, reliable electromechanical cable termination to mechanically attach and electrically connect cable lowered instrument packages to their lowering cable.Funding was provided by the National Science Foundation through Grant No. OCE 8821977

    Plagiarism on the rise? Combating contract cheating in science courses

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    This paper describes a relatively new, but rapidly expanding, cause for concern for academics and administrators, that of students plagiarizing by using online auctions, a practice also known as “contract cheating”. The prevention and detection of such plagiarism in the context of science education presents particular difficulties. The paper suggests several innovative and possibly controversial methods to minimize the number of occurrences, ensuring that as few students cheat as possible, and describes various techniques to aid in the detection of those that do

    Towards a Semantic Perceptual Image Metric

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    We present a full reference, perceptual image metric based on VGG-16, an artificial neural network trained on object classification. We fit the metric to a new database based on 140k unique images annotated with ground truth by human raters who received minimal instruction. The resulting metric shows competitive performance on TID 2013, a database widely used to assess image quality assessments methods. More interestingly, it shows strong responses to objects potentially carrying semantic relevance such as faces and text, which we demonstrate using a visualization technique and ablation experiments. In effect, the metric appears to model a higher influence of semantic context on judgments, which we observe particularly in untrained raters. As the vast majority of users of image processing systems are unfamiliar with Image Quality Assessment (IQA) tasks, these findings may have significant impact on real-world applications of perceptual metrics

    6-OHDA generated ROS induces DNA damage and p53- and PUMA-dependent cell death

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    <p>Abstract</p> <p>Background</p> <p>Parkinson's disease (PD) is characterized by the selective loss of dopaminergic neurons in the substantia nigra (SN), resulting in tremor, rigidity, and bradykinesia. Although the etiology is unknown, insight into the disease process comes from the dopamine (DA) derivative, 6-hydroxydopamine (6-OHDA), which produces PD-like symptoms. Studies show that 6-OHDA activates stress pathways, such as the unfolded protein response (UPR), triggers mitochondrial release of cytochrome-c, and activates caspases, such as caspase-3. Because the BH3-only protein, Puma (p53-upregulated mediator of apoptosis), is activated in response to UPR, it is thought to be a link between cell stress and apoptosis.</p> <p>Results</p> <p>To test the hypothesis that Puma serves such a role in 6-OHDA-mediated cell death, we compared the response of dopaminergic neurons from wild-type and <it>Puma</it>-null mice to 6-OHDA. Results indicate that Puma is required for 6-OHDA-induced cell death, in primary dissociated midbrain cultures as well as <it>in vivo</it>. In these cultures, 6-OHDA-induced DNA damage and p53 were required for 6-OHDA-induced cell death. In contrast, while 6-OHDA led to upregulation of UPR markers, loss of ATF3 did not protect against 6-OHDA.</p> <p>Conclusions</p> <p>Together, our results indicate that 6-OHDA-induced upregulation of <it>Puma </it>and cell death are independent of UPR. Instead, p53 and DNA damage repair pathways mediate 6-OHDA-induced toxicity.</p

    The deep history of Earth's biomass

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    This paper was improved by the comments and suggestions of Graham Shields-Zhou and two anonymous reviewers. We thank E. Buitenhuis for sharing insights into aquatic biomass. S.M. acknowledges support from the European Union’s Horizon 2020 Research and Innovation Programme under Marie SkƂodowska-Curie grant agreement 747877.Peer reviewedPostprin

    Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

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    available in PMC 2016 November 07The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, untreated plant biomass and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite-repressed and are further regulated by a rich landscape of noncoding regulatory RNAs. Additionally, we identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.United States. Dept. of Energy. Office of Science (Biological and Environmental Research (BER) program)United States. Department of Energy (DOE Grant DE-SC0010352)United States. Department of Agriculture (Award 2011-67017-20459)Institute for Collaborative Biotechnologies (grant W911NF-09-0001

    PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi:Insights, Challenges, and Opportunities

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    Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit
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