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  • 11
    Publication Date: 2015-03-20
    Description: Efficient identification and follow-up of astronomical transients is hindered by the need for humans to manually select promising candidates from data streams that contain many false positives. These artefacts arise in the difference images that are produced by most major ground-based time-domain surveys with large format CCD cameras. This dependence on humans to reject bogus detections is unsustainable for next generation all-sky surveys and significant effort is now being invested to solve the problem computationally. In this paper, we explore a simple machine learning approach to real–bogus classification by constructing a training set from the image data of ~32 000 real astrophysical transients and bogus detections from the Pan-STARRS1 Medium Deep Survey. We derive our feature representation from the pixel intensity values of a 20 x 20 pixel stamp around the centre of the candidates. This differs from previous work in that it works directly on the pixels rather than catalogued domain knowledge for feature design or selection. Three machine learning algorithms are trained (artificial neural networks, support vector machines and random forests) and their performances are tested on a held-out subset of 25 per cent of the training data. We find the best results from the random forest classifier and demonstrate that by accepting a false positive rate of 1 per cent, the classifier initially suggests a missed detection rate of around 10 per cent. However, we also find that a combination of bright star variability, nuclear transients and uncertainty in human labelling means that our best estimate of the missed detection rate is approximately 6 per cent.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 12
    Publication Date: 2019
    Description: Summary Bacterial genes for molybdenum‐containing and tungsten‐containing enzymes are often differentially regulated depending on the metal availability in the environment. Here, we describe a new family of transcription factors with an unusual DNA‐binding domain related to excisionases of bacteriophages. These transcription factors are associated with genes for various molybdate and tungstate‐specific transporting systems as well as molybdo/tungsto‐enzymes in a wide range of bacterial genomes. We used a combination of computational and experimental techniques to study a member of the TF family, named TaoR (for tungsten‐containing aldehyde oxidoreductase regulator). In Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, TaoR activates expression of aldehyde oxidoreductase aor and represses tungsten‐specific ABC‐type transporter tupABC genes under tungsten‐replete conditions. TaoR binding sites at aor promoter were identified by electrophoretic mobility shift assay and DNase I footprinting. We also reconstructed TaoR regulons in 45 Deltaproteobacteria by comparative genomics approach and predicted target genes for TaoR family members in other Proteobacteria and Firmicutes.
    Print ISSN: 1462-2912
    Electronic ISSN: 1462-2920
    Topics: Biology
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  • 13
    Publication Date: 2018-12-07
    Description: The selective pressures on the microbial community in a metal-contaminated aquifer The selective pressures on the microbial community in a metal-contaminated aquifer, Published online: 06 December 2018; doi:10.1038/s41396-018-0328-1 The selective pressures on the microbial community in a metal-contaminated aquifer
    Print ISSN: 1751-7362
    Electronic ISSN: 1751-7370
    Topics: Biology
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  • 14
    Publication Date: 2019
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 15
    Publication Date: 2011-06-10
    Description: A significant bottleneck in cardiovascular regenerative medicine is the identification of a viable source of stem/progenitor cells that could contribute new muscle after ischaemic heart disease and acute myocardial infarction. A therapeutic ideal--relative to cell transplantation--would be to stimulate a resident source, thus avoiding the caveats of limited graft survival, restricted homing to the site of injury and host immune rejection. Here we demonstrate in mice that the adult heart contains a resident stem or progenitor cell population, which has the potential to contribute bona fide terminally differentiated cardiomyocytes after myocardial infarction. We reveal a novel genetic label of the activated adult progenitors via re-expression of a key embryonic epicardial gene, Wilm's tumour 1 (Wt1), through priming by thymosin beta4, a peptide previously shown to restore vascular potential to adult epicardium-derived progenitor cells with injury. Cumulative evidence indicates an epicardial origin of the progenitor population, and embryonic reprogramming results in the mobilization of this population and concomitant differentiation to give rise to de novo cardiomyocytes. Cell transplantation confirmed a progenitor source and chromosome painting of labelled donor cells revealed transdifferentiation to a myocyte fate in the absence of cell fusion. Derived cardiomyocytes are shown here to structurally and functionally integrate with resident muscle; as such, stimulation of this adult progenitor pool represents a significant step towards resident-cell-based therapy in human ischaemic heart disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696525/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696525/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smart, Nicola -- Bollini, Sveva -- Dube, Karina N -- Vieira, Joaquim M -- Zhou, Bin -- Davidson, Sean -- Yellon, Derek -- Riegler, Johannes -- Price, Anthony N -- Lythgoe, Mark F -- Pu, William T -- Riley, Paul R -- FS/08/004/23625/British Heart Foundation/United Kingdom -- G0700933/Medical Research Council/United Kingdom -- PG/10/005/28175/British Heart Foundation/United Kingdom -- RG/08/003/25264/British Heart Foundation/United Kingdom -- U01 HL100401/HL/NHLBI NIH HHS/ -- British Heart Foundation/United Kingdom -- England -- Nature. 2011 Jun 8;474(7353):640-4. doi: 10.1038/nature10188.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Medicine Unit, UCL Institute of Child Health, London WC1N 1EH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21654746" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/*cytology ; Animals ; *Cell Differentiation ; Cellular Reprogramming ; Gene Expression Regulation ; *Heart Injuries ; Mice ; Myocardial Infarction/pathology ; Myocytes, Cardiac/*cytology/metabolism ; Thymosin/metabolism ; WT1 Proteins/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 16
    Publication Date: 2015-06-19
    Description: There is an urgent need for new drugs to treat malaria, with broad therapeutic potential and novel modes of action, to widen the scope of treatment and to overcome emerging drug resistance. Here we describe the discovery of DDD107498, a compound with a potent and novel spectrum of antimalarial activity against multiple life-cycle stages of the Plasmodium parasite, with good pharmacokinetic properties and an acceptable safety profile. DDD107498 demonstrates potential to address a variety of clinical needs, including single-dose treatment, transmission blocking and chemoprotection. DDD107498 was developed from a screening programme against blood-stage malaria parasites; its molecular target has been identified as translation elongation factor 2 (eEF2), which is responsible for the GTP-dependent translocation of the ribosome along messenger RNA, and is essential for protein synthesis. This discovery of eEF2 as a viable antimalarial drug target opens up new possibilities for drug discovery.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700930/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700930/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baragana, Beatriz -- Hallyburton, Irene -- Lee, Marcus C S -- Norcross, Neil R -- Grimaldi, Raffaella -- Otto, Thomas D -- Proto, William R -- Blagborough, Andrew M -- Meister, Stephan -- Wirjanata, Grennady -- Ruecker, Andrea -- Upton, Leanna M -- Abraham, Tara S -- Almeida, Mariana J -- Pradhan, Anupam -- Porzelle, Achim -- Martinez, Maria Santos -- Bolscher, Judith M -- Woodland, Andrew -- Norval, Suzanne -- Zuccotto, Fabio -- Thomas, John -- Simeons, Frederick -- Stojanovski, Laste -- Osuna-Cabello, Maria -- Brock, Paddy M -- Churcher, Tom S -- Sala, Katarzyna A -- Zakutansky, Sara E -- Jimenez-Diaz, Maria Belen -- Sanz, Laura Maria -- Riley, Jennifer -- Basak, Rajshekhar -- Campbell, Michael -- Avery, Vicky M -- Sauerwein, Robert W -- Dechering, Koen J -- Noviyanti, Rintis -- Campo, Brice -- Frearson, Julie A -- Angulo-Barturen, Inigo -- Ferrer-Bazaga, Santiago -- Gamo, Francisco Javier -- Wyatt, Paul G -- Leroy, Didier -- Siegl, Peter -- Delves, Michael J -- Kyle, Dennis E -- Wittlin, Sergio -- Marfurt, Jutta -- Price, Ric N -- Sinden, Robert E -- Winzeler, Elizabeth A -- Charman, Susan A -- Bebrevska, Lidiya -- Gray, David W -- Campbell, Simon -- Fairlamb, Alan H -- Willis, Paul A -- Rayner, Julian C -- Fidock, David A -- Read, Kevin D -- Gilbert, Ian H -- 079838/Wellcome Trust/United Kingdom -- 091625/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- 100476/Wellcome Trust/United Kingdom -- R01 AI090141/AI/NIAID NIH HHS/ -- R01 AI103058/AI/NIAID NIH HHS/ -- England -- Nature. 2015 Jun 18;522(7556):315-20. doi: 10.1038/nature14451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK. ; Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA. ; Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK. ; Department of Life Sciences, Imperial College, London SW7 2AZ, UK. ; University of California, San Diego, School of Medicine, 9500 Gilman Drive 0760, La Jolla, California 92093, USA. ; Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, Northern Territory 0811, Australia. ; Department of Global Health, College of Public Health University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, Florida 33612, USA. ; GlaxoSmithKline, Tres Cantos Medicines Development Campus-Diseases of the Developing World, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain. ; TropIQ Health Sciences, Geert Grooteplein 28, Huispost 268, 6525 GA Nijmegen, The Netherlands. ; Centre for Drug Candidate Optimisation, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia. ; Eskitis Institute, Brisbane Innovation Park, Nathan Campus, Griffith University, Queensland 4111, Australia. ; Malaria Pathogenesis Laboratory, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, 10430 Jakarta, Indonesia. ; Medicines for Malaria Venture, PO Box 1826, 20 route de Pre-Bois, 1215 Geneva 15, Switzerland. ; Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland. ; 1] Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, Northern Territory 0811, Australia [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK. ; 1] Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA [2] Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26085270" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antimalarials/administration & dosage/adverse ; effects/pharmacokinetics/*pharmacology ; Drug Discovery ; Female ; Gene Expression Regulation/*drug effects ; Life Cycle Stages/drug effects ; Liver/drug effects/parasitology ; Malaria/drug therapy/*parasitology ; Male ; Models, Molecular ; Peptide Elongation Factor 2/antagonists & inhibitors/metabolism ; Plasmodium/*drug effects/genetics/growth & development/*metabolism ; Plasmodium berghei/drug effects/physiology ; Plasmodium falciparum/drug effects/metabolism ; Plasmodium vivax/drug effects/metabolism ; Protein Biosynthesis/*drug effects ; Quinolines/administration & dosage/chemistry/pharmacokinetics/*pharmacology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 17
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Price, W Nicholson 2nd -- Rai, Arti K -- New York, N.Y. -- Science. 2015 Apr 10;348(6231):188-9. doi: 10.1126/science.aab1684. Epub 2015 Apr 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of New Hampshire School of Law, Concord, NH 03301, USA. nicholson.price@law.unh.edu rai@law.duke.edu. ; Duke Law School, Durham, NC 27705, USA. nicholson.price@law.unh.edu rai@law.duke.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25859034" target="_blank"〉PubMed〈/a〉
    Keywords: *Biosimilar Pharmaceuticals/economics ; Confidentiality ; *Drug Approval ; Drug Costs ; *Drug Discovery ; *Drug Industry ; United States ; United States Food and Drug Administration
    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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  • 18
    Publication Date: 2013-07-12
    Description: The sea slug Elysia chlorotica offers a unique opportunity to study the evolution of a novel function (photosynthesis) in a complex multicellular host. Elysia chlorotica harvests plastids (absent of nuclei) from its heterokont algal prey, Vaucheria litorea . The "stolen" plastids are maintained for several months in cells of the digestive tract and are essential for animal development. The basis of long-term maintenance of photosynthesis in this sea slug was thought to be explained by extensive horizontal gene transfer (HGT) from the nucleus of the alga to the animal nucleus, followed by expression of algal genes in the gut to provide essential plastid-destined proteins. Early studies of target genes and proteins supported the HGT hypothesis, but more recent genome-wide data provide conflicting results. Here, we generated significant genome data from the E. chlorotica germ line (egg DNA) and from V. litorea to test the HGT hypothesis. Our comprehensive analyses fail to provide evidence for alga-derived HGT into the germ line of the sea slug. Polymerase chain reaction analyses of genomic DNA and cDNA from different individual E. chlorotica suggest, however, that algal nuclear genes (or gene fragments) are present in the adult slug. We suggest that these nucleic acids may derive from and/or reside in extrachromosomal DNAs that are made available to the animal through contact with the alga. These data resolve a long-standing issue and suggest that HGT is not the primary reason underlying long-term maintenance of photosynthesis in E. chlorotica. Therefore, sea slug photosynthesis is sustained in as yet unexplained ways that do not appear to endanger the animal germ line through the introduction of dozens of foreign genes.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 19
    Publication Date: 2013-05-21
    Description: We present the results of a pilot study for the extended Massive Cluster Survey (eMACS), a comprehensive search for distant, X-ray luminous galaxy clusters at z 〉 0.5. Our pilot study applies the eMACS concept to the 71 deg 2 area extended by the 10 fields of the Pan-STARRS1 (PS1) Medium Deep Survey (MDS). Candidate clusters are identified by visual inspection of PS1 images in the g , r , i and z bands in a 5  x 5 arcmin 2 region around X-ray sources detected in the ROSAT All-Sky Survey (RASS). To test and optimize the eMACS X-ray selection criteria, our pilot study uses the largest possible RASS data base, i.e. all RASS sources listed in the Bright and Faint Source Catalogues (BSC and FSC) that fall within the MDS footprint. We apply no additional constraints regarding X-ray flux, spectral hardness ratio or photon statistics and lower the redshift threshold to z 〉 0.3 to extend the probed luminosity range to poorer systems. Scrutiny of PS1/MDS images for 41 BSC and 200 FSC sources combined with dedicated spectroscopic follow-up observations results in a sample of 11 clusters with estimated or spectroscopic redshifts of z 〉 0.3. In order to assess and quantify the degree of point source contamination of the observed RASS fluxes, we examine archival Chandra data obtained in targeted and serendipitous observations of six of the 11 clusters found. As expected, the diffuse emission from all six systems is contaminated by point sources to some degree, and for half of them active galactic nucleus emission dominates. X-ray follow-up observations will thus be crucial in order to establish robust cluster luminosities for eMACS clusters. Although the small number of distant X-ray luminous clusters in the MDS does not allow us to make firm predictions for the over 20 000 deg 2 of extragalactic sky covered by eMACS, the identification of two extremely promising eMACS cluster candidates at z 0.6 (both yet to be observed with Chandra ) in such a small solid angle is encouraging. Representing a tremendous gain over the presently known two dozen such systems from X-ray, optical and Sunyaev–Zel’dovich cluster surveys combined, the sample of over 100 extremely massive clusters at z 〉 0.5 expected from eMACS would be invaluable for the identification of the most powerful gravitational lenses in the Universe, as well as for in-depth and statistical studies of the physical properties of the most massive galaxy clusters out to z  ~ 1.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 20
    Publication Date: 2013-07-04
    Description: Article Hydrogen peroxide attracts immune cells and induces wound inflammation. Evans et al . show that hydrogen peroxide also leads to the production of thymosin β4–sulfoxide in zebrafish wounds and in mouse hearts after myocardial infarction, where it acts as an anti-inflammatory factor that promotes wound healing. Nature Communications doi: 10.1038/ncomms3081 Authors: Mark A. Evans, Nicola Smart, Karina N. Dubé, Sveva Bollini, James E. Clark, Hayley G. Evans, Leonie S. Taams, Rebecca Richardson, Mathieu Lévesque, Paul Martin, Kevin Mills, Johannes Riegler, Anthony N. Price, Mark F. Lythgoe, Paul R. Riley
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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