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  • 1
    Publication Date: 2013-12-29
    Description: MycoCosm is a fungal genomics portal ( http://jgi.doe.gov/fungi ), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other ‘omics’ data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2015-01-25
    Description: Genetic risk loci have been identified for a wide range of diseases through genome-wide association studies (GWAS), but the relevant functional mechanisms have been identified for only a small proportion of these GWAS-identified loci. By integrating results from the largest current GWAS of chronic obstructive disease (COPD) with expression quantitative trait locus (eQTL) analysis in whole blood and sputum from 121 subjects with COPD from the ECLIPSE Study, this analysis identifies loci that are simultaneously associated with COPD and the expression of nearby genes (COPD eQTLs). After integrative analysis, 19 COPD eQTLs were identified, including all four previously identified genome-wide significant loci near HHIP , FAM13A , and the 15q25 and 19q13 loci. For each COPD eQTL, fine mapping and colocalization analysis to identify causal shared eQTL and GWAS variants identified a subset of sites with moderate-to-strong evidence of harboring at least one shared variant responsible for both the eQTL and GWAS signals. Transcription factor binding site (TFBS) analysis confirms that multiple COPD eQTL lead SNPs disrupt TFBS, and enhancer enrichment analysis for loci with the strongest colocalization signals showed enrichment for blood-related cell types (CD3 and CD4+ T cells, lymphoblastoid cell lines). In summary, integrative eQTL and GWAS analysis confirms that genetic control of gene expression plays a key role in the genetic architecture of COPD and identifies specific blood-related cell types as likely participants in the functional pathway from GWAS-associated variant to disease phenotype.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 3
    Publication Date: 2015-07-15
    Description: Atom probe tomography (APT) is used to characterize the influence of hydrogen dosing during GaN barrier growth on the indium distribution of In x Ga 1−x N quantum wells, and correlated micro-photoluminescence is used to measure changes in the emission spectrum and efficiency. Relative to the control growth, hydrogen dosing leads to a 50% increase in emission intensity arising from discontinuous quantum wells that are narrower, of lower indium content, and with more abrupt interfaces. Simulations of carrier distributions based on APT composition profiles indicate that the greater carrier confinement leads to an increased radiative recombination rate. Furthermore, APT analysis of quantum well profiles enables refinement of x-ray diffraction analysis for more accurate nondestructive measurements of composition.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 4
    Publication Date: 2014-11-01
    Description: November 2014 GSA Today Featured Article SCIENCE ARTICLE p. 4 Preexisting fractures and the formation of an iconic American landscape: Tuolumne Meadows, Yosemite National Park, USA Richard A. Becker, Basil Tikoff, Paul R. Riley, Neal R. Iverson Abstract | Full Text | PDF (4MB) ABSTRACT Tuolumne Meadows, in Yosemite National Park (USA), is a large sub-alpine meadow in the Sierra Nevada Mountains. Immediately adjacent to Tuolumne Meadows—and underlain by the same bedrock lithology (Cathedral Peak Granodiorite)—are vertical rock faces that provide exceptional opportunities to climbers. While the presence of a broad meadow suggests bedrock erodibility, the vertical rock walls indicate bedrock durability. We propose that the Tuolumne Meadows’s landscape is the result of variable glacial erosion due to the presence or absence of pre-existing bedrock fractures. The meadows and valleys formed because of concentrated tabular fracture clusters—a distinctive and locally pervasive type of fracturing—that were particularly susceptible to glacial erosion. In contrast, the vertical rock walls consist of sparsely fractured bedrock that was originally bounded by zones of pervasive tabular fracture clusters. Glacial erosion preferentially removed the highly fractured rock, forming prominent ridges in the upland surrounding Tuolumne Meadows. The orientation and spacing of the tabular fracture clusters, relative to ice flow, has exerted a fundamental control on the geomorphology of the area. The erosional variability exhibited by a single lithology indicates that the degree of fracturing can be more important than the host lithology in controlling landscape evolution.
    Print ISSN: 1052-5173
    Topics: Geosciences
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  • 5
    Publication Date: 2018-06-16
    Description: IJERPH, Vol. 15, Pages 1271: The Impact of Road Construction on Subjective Well-Being in Communities in Madre de Dios, Peru International Journal of Environmental Research and Public Health doi: 10.3390/ijerph15061271 Authors: Amy R. Riley-Powell Gwenyth O. Lee Nehal S. Naik Kelly E. Jensen Christina O’Neal Gabriela Salmón-Mulanovich Stella M. Hartinger Daniel G. Bausch Valerie A. Paz-Soldan The interoceanic highway (IOH) in Madre de Dios, Peru has driven dramatic change in the Peruvian Amazon basin. We conducted a mixed methods study to examine the impact of these changes on the subjective well-being (SWB) of four communities on the IOH. Themes that emerged qualitatively included changing health threats, environmental degradation, and the impact of increased migration. To achieve a higher level of SWB, respondents emphasized the need for higher incomes, opportunities to learn new skills, and a better education for their children. Potential threats to SWB included marital problems and poorer health. Quantitative analyses suggested that social support and a sense of security impacted reported SWB scores based on life satisfaction, and the impact of income on life satisfaction was mediated by food security. Although long-term residents felt that specific determinants of SWB had both increased (food variety, transport and access to work) and decreased (access to natural resources and hunting), the majority reported that their lives had improved overall. Health had been affected by the IOH in both negative ways (increased dengue and road accidents) and positive ways (improved access to health services). Our results suggest that the rapidly-changing communities near the IOH link well-being to health, income, community, and the environment.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by MDPI Publishing
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  • 6
    Publication Date: 2015-05-21
    Description: The lymphatic vasculature is a blind-ended network crucial for tissue-fluid homeostasis, immune surveillance and lipid absorption from the gut. Recent evidence has proposed an entirely venous-derived mammalian lymphatic system. By contrast, here we show that cardiac lymphatic vessels in mice have a heterogeneous cellular origin, whereby formation of at least part of the cardiac lymphatic network is independent of sprouting from veins. Multiple Cre-lox-based lineage tracing revealed a potential contribution from the putative haemogenic endothelium during development, and discrete lymphatic endothelial progenitor populations were confirmed by conditional knockout of Prox1 in Tie2+ and Vav1+ compartments. In the adult heart, myocardial infarction promoted a significant lymphangiogenic response, which was augmented by treatment with VEGF-C, resulting in improved cardiac function. These data prompt the re-evaluation of a century-long debate on the origin of lymphatic vessels and suggest that lymphangiogenesis may represent a therapeutic target to promote cardiac repair following injury.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458138/" 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/PMC4458138/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klotz, Linda -- Norman, Sophie -- Vieira, Joaquim Miguel -- Masters, Megan -- Rohling, Mala -- Dube, Karina N -- Bollini, Sveva -- Matsuzaki, Fumio -- Carr, Carolyn A -- Riley, Paul R -- CH/11/1/28798/British Heart Foundation/United Kingdom -- PG/13/34/30216/British Heart Foundation/United Kingdom -- RG/08/003/25264/British Heart Foundation/United Kingdom -- RM/13/3/30159/British Heart Foundation/United Kingdom -- British Heart Foundation/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2015 Jun 4;522(7554):62-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25992544" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Lineage ; Endothelial Cells/cytology/metabolism ; Female ; Heart/physiology/physiopathology ; Homeodomain Proteins/metabolism ; *Lymphangiogenesis ; Lymphatic Vessels/*cytology/*injuries/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Myocardial Infarction/metabolism/physiopathology ; Myocardium/*cytology/metabolism ; Proto-Oncogene Proteins c-vav/metabolism ; Receptor, Macrophage Colony-Stimulating Factor/metabolism ; Receptor, Platelet-Derived Growth Factor beta/metabolism ; Receptor, TIE-2/metabolism ; Spatio-Temporal Analysis ; Tumor Suppressor Proteins/deficiency/metabolism ; Vascular Endothelial Growth Factor C/metabolism ; Veins/cytology ; Yolk Sac/cytology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2012-06-30
    Description: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Floudas, Dimitrios -- Binder, Manfred -- Riley, Robert -- Barry, Kerrie -- Blanchette, Robert A -- Henrissat, Bernard -- Martinez, Angel T -- Otillar, Robert -- Spatafora, Joseph W -- Yadav, Jagjit S -- Aerts, Andrea -- Benoit, Isabelle -- Boyd, Alex -- Carlson, Alexis -- Copeland, Alex -- Coutinho, Pedro M -- de Vries, Ronald P -- Ferreira, Patricia -- Findley, Keisha -- Foster, Brian -- Gaskell, Jill -- Glotzer, Dylan -- Gorecki, Pawel -- Heitman, Joseph -- Hesse, Cedar -- Hori, Chiaki -- Igarashi, Kiyohiko -- Jurgens, Joel A -- Kallen, Nathan -- Kersten, Phil -- Kohler, Annegret -- Kues, Ursula -- Kumar, T K Arun -- Kuo, Alan -- LaButti, Kurt -- Larrondo, Luis F -- Lindquist, Erika -- Ling, Albee -- Lombard, Vincent -- Lucas, Susan -- Lundell, Taina -- Martin, Rachael -- McLaughlin, David J -- Morgenstern, Ingo -- Morin, Emanuelle -- Murat, Claude -- Nagy, Laszlo G -- Nolan, Matt -- Ohm, Robin A -- Patyshakuliyeva, Aleksandrina -- Rokas, Antonis -- Ruiz-Duenas, Francisco J -- Sabat, Grzegorz -- Salamov, Asaf -- Samejima, Masahiro -- Schmutz, Jeremy -- Slot, Jason C -- St John, Franz -- Stenlid, Jan -- Sun, Hui -- Sun, Sheng -- Syed, Khajamohiddin -- Tsang, Adrian -- Wiebenga, Ad -- Young, Darcy -- Pisabarro, Antonio -- Eastwood, Daniel C -- Martin, Francis -- Cullen, Dan -- Grigoriev, Igor V -- Hibbett, David S -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1715-9. doi: 10.1126/science.1221748.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Clark University, Worcester, MA 01610, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745431" target="_blank"〉PubMed〈/a〉
    Keywords: Basidiomycota/classification/*enzymology/*genetics ; Bayes Theorem ; *Evolution, Molecular ; *Genome, Fungal ; Indoles ; Lignin/*metabolism ; Peroxidases/*genetics/metabolism ; Wood/metabolism
    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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  • 8
    Publication Date: 2011-01-14
    Description: Brain changes in response to nerve damage or cochlear trauma can generate pathological neural activity that is believed to be responsible for many types of chronic pain and tinnitus. Several studies have reported that the severity of chronic pain and tinnitus is correlated with the degree of map reorganization in somatosensory and auditory cortex, respectively. Direct electrical or transcranial magnetic stimulation of sensory cortex can temporarily disrupt these phantom sensations. However, there is as yet no direct evidence for a causal role of plasticity in the generation of pain or tinnitus. Here we report evidence that reversing the brain changes responsible can eliminate the perceptual impairment in an animal model of noise-induced tinnitus. Exposure to intense noise degrades the frequency tuning of auditory cortex neurons and increases cortical synchronization. Repeatedly pairing tones with brief pulses of vagus nerve stimulation completely eliminated the physiological and behavioural correlates of tinnitus in noise-exposed rats. These improvements persisted for weeks after the end of therapy. This method for restoring neural activity to normal may be applicable to a variety of neurological disorders.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295231/" 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/PMC3295231/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Engineer, Navzer D -- Riley, Jonathan R -- Seale, Jonathan D -- Vrana, Will A -- Shetake, Jai A -- Sudanagunta, Sindhu P -- Borland, Michael S -- Kilgard, Michael P -- R43 DC010084-01/DC/NIDCD NIH HHS/ -- R44 DC010084-03/DC/NIDCD NIH HHS/ -- England -- Nature. 2011 Feb 3;470(7332):101-4. doi: 10.1038/nature09656. Epub 2011 Jan 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cortical Plasticity Laboratory, Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA. navzer@utdallas.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21228773" target="_blank"〉PubMed〈/a〉
    Keywords: Acoustic Stimulation ; Animals ; Auditory Perception/physiology ; Behavior, Animal/physiology ; Disease Models, Animal ; Electric Stimulation ; Female ; Models, Neurological ; Neuronal Plasticity/*physiology ; Noise/adverse effects ; Rats ; Rats, Sprague-Dawley ; Tinnitus/etiology/pathology/*physiopathology/*therapy ; Vagus Nerve/physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    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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  • 10
    Publication Date: 2011-07-19
    Description: Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eastwood, Daniel C -- Floudas, Dimitrios -- Binder, Manfred -- Majcherczyk, Andrzej -- Schneider, Patrick -- Aerts, Andrea -- Asiegbu, Fred O -- Baker, Scott E -- Barry, Kerrie -- Bendiksby, Mika -- Blumentritt, Melanie -- Coutinho, Pedro M -- Cullen, Dan -- de Vries, Ronald P -- Gathman, Allen -- Goodell, Barry -- Henrissat, Bernard -- Ihrmark, Katarina -- Kauserud, Havard -- Kohler, Annegret -- LaButti, Kurt -- Lapidus, Alla -- Lavin, Jose L -- Lee, Yong-Hwan -- Lindquist, Erika -- Lilly, Walt -- Lucas, Susan -- Morin, Emmanuelle -- Murat, Claude -- Oguiza, Jose A -- Park, Jongsun -- Pisabarro, Antonio G -- Riley, Robert -- Rosling, Anna -- Salamov, Asaf -- Schmidt, Olaf -- Schmutz, Jeremy -- Skrede, Inger -- Stenlid, Jan -- Wiebenga, Ad -- Xie, Xinfeng -- Kues, Ursula -- Hibbett, David S -- Hoffmeister, Dirk -- Hogberg, Nils -- Martin, Francis -- Grigoriev, Igor V -- Watkinson, Sarah C -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):762-5. doi: 10.1126/science.1205411. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College of Science, University of Swansea, Singleton Park, Swansea SA2 8PP, UK. d.c.eastwood@swansea.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764756" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/microbiology ; Basidiomycota/classification/enzymology/*genetics/physiology ; *Biodiversity ; Biological Evolution ; Biota ; Cell Wall/*metabolism ; Coniferophyta/microbiology ; Coriolaceae/enzymology/genetics/physiology ; Gene Expression Profiling ; Genes, Fungal ; Genomics ; Lignin/metabolism ; Mycorrhizae/enzymology/*genetics/physiology ; Oxidoreductases/genetics/metabolism ; Peroxidases/genetics/metabolism ; Phylogeny ; Proteome ; Symbiosis ; Trees/*microbiology ; Wood/metabolism/*microbiology
    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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