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  • 1
    Publication Date: 2016-07-02
    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b04661
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
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  • 2
    Publication Date: 2014-09-27
    Description: microRNAs (miRNAs) regulate expression by promoting degradation or repressing translation of target transcripts. miRNA target sites have been catalogued in databases based on experimental validation and computational prediction using various algorithms. Several online resources provide collections of multiple databases but need to be imported into other software, such as R, for processing, tabulation, graphing and computation. Currently available miRNA target site packages in R are limited in the number of databases, types of databases and flexibility. We present multiMiR, a new miRNA–target interaction R package and database, which includes several novel features not available in existing R packages: (i) compilation of nearly 50 million records in human and mouse from 14 different databases, more than any other collection; (ii) expansion of databases to those based on disease annotation and drug microRNAresponse, in addition to many experimental and computational databases; and (iii) user-defined cutoffs for predicted binding strength to provide the most confident selection. Case studies are reported on various biomedical applications including mouse models of alcohol consumption, studies of chronic obstructive pulmonary disease in human subjects, and human cell line models of bladder cancer metastasis. We also demonstrate how multiMiR was used to generate testable hypotheses that were pursued experimentally.
    Keywords: RNA characterisation and manipulation, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2013-10-19
    Description: The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species--less diverse than the North American tree flora--accounts for half of the world's most diverse tree community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉ter Steege, Hans -- Pitman, Nigel C A -- Sabatier, Daniel -- Baraloto, Christopher -- Salomao, Rafael P -- Guevara, Juan Ernesto -- Phillips, Oliver L -- Castilho, Carolina V -- Magnusson, William E -- Molino, Jean-Francois -- Monteagudo, Abel -- Nunez Vargas, Percy -- Montero, Juan Carlos -- Feldpausch, Ted R -- Coronado, Euridice N Honorio -- Killeen, Tim J -- Mostacedo, Bonifacio -- Vasquez, Rodolfo -- Assis, Rafael L -- Terborgh, John -- Wittmann, Florian -- Andrade, Ana -- Laurance, William F -- Laurance, Susan G W -- Marimon, Beatriz S -- Marimon, Ben-Hur Jr -- Guimaraes Vieira, Ima Celia -- Amaral, Ieda Leao -- Brienen, Roel -- Castellanos, Hernan -- Cardenas Lopez, Dairon -- Duivenvoorden, Joost F -- Mogollon, Hugo F -- Matos, Francisca Dionizia de Almeida -- Davila, Nallarett -- Garcia-Villacorta, Roosevelt -- Stevenson Diaz, Pablo Roberto -- Costa, Flavia -- Emilio, Thaise -- Levis, Carolina -- Schietti, Juliana -- Souza, Priscila -- Alonso, Alfonso -- Dallmeier, Francisco -- Montoya, Alvaro Javier Duque -- Fernandez Piedade, Maria Teresa -- Araujo-Murakami, Alejandro -- Arroyo, Luzmila -- Gribel, Rogerio -- Fine, Paul V A -- Peres, Carlos A -- Toledo, Marisol -- Aymard C, Gerardo A -- Baker, Tim R -- Ceron, Carlos -- Engel, Julien -- Henkel, Terry W -- Maas, Paul -- Petronelli, Pascal -- Stropp, Juliana -- Zartman, Charles Eugene -- Daly, Doug -- Neill, David -- Silveira, Marcos -- Paredes, Marcos Rios -- Chave, Jerome -- Lima Filho, Diogenes de Andrade -- Jorgensen, Peter Moller -- Fuentes, Alfredo -- Schongart, Jochen -- Cornejo Valverde, Fernando -- Di Fiore, Anthony -- Jimenez, Eliana M -- Penuela Mora, Maria Cristina -- Phillips, Juan Fernando -- Rivas, Gonzalo -- van Andel, Tinde R -- von Hildebrand, Patricio -- Hoffman, Bruce -- Zent, Eglee L -- Malhi, Yadvinder -- Prieto, Adriana -- Rudas, Agustin -- Ruschell, Ademir R -- Silva, Natalino -- Vos, Vincent -- Zent, Stanford -- Oliveira, Alexandre A -- Schutz, Angela Cano -- Gonzales, Therany -- Trindade Nascimento, Marcelo -- Ramirez-Angulo, Hirma -- Sierra, Rodrigo -- Tirado, Milton -- Umana Medina, Maria Natalia -- van der Heijden, Geertje -- Vela, Cesar I A -- Vilanova Torre, Emilio -- Vriesendorp, Corine -- Wang, Ophelia -- Young, Kenneth R -- Baider, Claudia -- Balslev, Henrik -- Ferreira, Cid -- Mesones, Italo -- Torres-Lezama, Armando -- Urrego Giraldo, Ligia Estela -- Zagt, Roderick -- Alexiades, Miguel N -- Hernandez, Lionel -- Huamantupa-Chuquimaco, Isau -- Milliken, William -- Palacios Cuenca, Walter -- Pauletto, Daniela -- Valderrama Sandoval, Elvis -- Valenzuela Gamarra, Luis -- Dexter, Kyle G -- Feeley, Ken -- Lopez-Gonzalez, Gabriela -- Silman, Miles R -- New York, N.Y. -- Science. 2013 Oct 18;342(6156):1243092. doi: 10.1126/science.1243092.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Naturalis Biodiversity Center, Leiden, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24136971" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; Models, Biological ; Population ; *Rivers ; South America ; Trees/*classification/*physiology
    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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  • 4
    Publication Date: 2016-03-23
    Description: In contrast to other III-nitride semiconductors GaN and AlN, the intrinsic (or free) exciton transition in hexagonal boron nitride ( h- BN) consists of rather complex fine spectral features (resolved into six sharp emission peaks) and the origin of which is still unclear. Here, the free exciton transition (FX) in h- BN bulk crystals synthesized by a solution method at atmospheric pressure has been probed by deep UV time-resolved photoluminescence (PL) spectroscopy. Based on the separations between the energy peak positions of the FX emission lines, the identical PL decay kinetics among different FX emission lines, and the known phonon modes in h- BN, we suggest that there is only one principal emission line corresponding to the direct intrinsic FX transition in h- BN, whereas all other fine features are a result of phonon-assisted transitions. The identified phonon modes are all associated with the center of the Brillouin zone. Our results offer a simple picture for the understanding of the fundamental exciton transitions in h -BN.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 5
    Publication Date: 2018-10-30
    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.8b07900
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
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  • 6
    Publication Date: 2014-09-16
    Description: The Ras-like GTPases RalA and RalB are important drivers of tumour growth and metastasis. Chemicals that block Ral function would be valuable as research tools and for cancer therapeutics. Here we used protein structure analysis and virtual screening to identify drug-like molecules that bind to a site on the GDP-bound form of Ral. The compounds RBC6, RBC8 and RBC10 inhibited the binding of Ral to its effector RALBP1, as well as inhibiting Ral-mediated cell spreading of murine embryonic fibroblasts and anchorage-independent growth of human cancer cell lines. The binding of the RBC8 derivative BQU57 to RalB was confirmed by isothermal titration calorimetry, surface plasmon resonance and (1)H-(15)N transverse relaxation-optimized spectroscopy (TROSY) NMR spectroscopy. RBC8 and BQU57 show selectivity for Ral relative to the GTPases Ras and RhoA and inhibit tumour xenograft growth to a similar extent to the depletion of Ral using RNA interference. Our results show the utility of structure-based discovery for the development of therapeutics for Ral-dependent cancers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351747/" 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/PMC4351747/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, Chao -- Liu, Degang -- Li, Liwei -- Wempe, Michael F -- Guin, Sunny -- Khanna, May -- Meier, Jeremy -- Hoffman, Brenton -- Owens, Charles -- Wysoczynski, Christina L -- Nitz, Matthew D -- Knabe, William E -- Ahmed, Mansoor -- Brautigan, David L -- Paschal, Bryce M -- Schwartz, Martin A -- Jones, David N M -- Ross, David -- Meroueh, Samy O -- Theodorescu, Dan -- CA075115/CA/NCI NIH HHS/ -- CA091846/CA/NCI NIH HHS/ -- CA104106/CA/NCI NIH HHS/ -- GM47214/GM/NIGMS NIH HHS/ -- P01 CA104106/CA/NCI NIH HHS/ -- P30 CA044579/CA/NCI NIH HHS/ -- P30 CA046934/CA/NCI NIH HHS/ -- P50 CA091846/CA/NCI NIH HHS/ -- R01 CA075115/CA/NCI NIH HHS/ -- R01 CA143971/CA/NCI NIH HHS/ -- T32 GM007635/GM/NIGMS NIH HHS/ -- UL1 TR001082/TR/NCATS NIH HHS/ -- UL1TR001082/TR/NCATS NIH HHS/ -- England -- Nature. 2014 Nov 20;515(7527):443-7. doi: 10.1038/nature13713. Epub 2014 Sep 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Surgery, University of Colorado, Aurora, Colorado 80045, USA. ; Department of Biochemistry, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA. ; Department of Pharmaceutical Sciences, University of Colorado, Aurora, Colorado 80045, USA. ; Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia 22908, USA. ; Department of Pharmacology, University of Colorado, Aurora, Colorado 80045, USA. ; Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908, USA. ; 1] Department of Cardiology, Yale University, New Haven, Connecticut 06511, USA [2] Department of Cell Biology, Yale University, New Haven, Connecticut 06511, USA. ; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA. ; 1] Department of Biochemistry, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA [2] Department of Chemistry and Chemical Biology, Indiana University - Purdue University, Indianapolis, Indiana 46202, USA. ; 1] Department of Surgery, University of Colorado, Aurora, Colorado 80045, USA [2] Department of Pharmacology, University of Colorado, Aurora, Colorado 80045, USA [3] University of Colorado Comprehensive Cancer Center, Aurora, Colorado 80045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25219851" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/metabolism ; Animals ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Computer Simulation ; *Drug Screening Assays, Antitumor ; Female ; GTPase-Activating Proteins/metabolism ; Humans ; Mice ; Models, Molecular ; *Molecular Targeted Therapy ; Neoplasms/drug therapy/enzymology/metabolism/pathology ; Protein Binding/drug effects ; Signal Transduction/drug effects ; Small Molecule Libraries/*chemistry/*pharmacology ; Substrate Specificity ; Xenograft Model Antitumor Assays ; ral GTP-Binding Proteins/*antagonists & inhibitors/chemistry/metabolism ; ras Proteins/metabolism
    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: 2013-03-20
    Description: Journal of the American Chemical Society DOI: 10.1021/ja309782m
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
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  • 8
    Publication Date: 2016-11-24
    Description: We report the results of the combined experimental and theoretical studies of the low-lying exciton states in crystalline copper phthalocyanine. We derive the eigen energy spectrum for the two lowest intramolecular Frenkel excitons coupled to the intermolecular charge transfer exciton state and compare it with temperature dependent optical absorption spectra measured experimentally, to obtain the parameters of the Frenkel-charge-transfer exciton intermixing. The two Frenkel exciton states are spaced apart by 0.26 eV, and the charge transfer exciton state is 50 meV above the lowest Frenkel exciton. Both Frenkel excitons are strongly mixed with the charge transfer exciton, showing the coupling constant 0.17 eV which agrees with earlier experimental measurements. These results can be used for the proper interpretation of the physical properties of crystalline phthalocyanines.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 9
    Publication Date: 2015-01-10
    Description: : We have developed an integrated molecular network learning method, within a well-grounded mathematical framework, to construct differential dependency networks with significant rewiring. This knowledge-fused differential dependency networks (KDDN) method, implemented as a Java Cytoscape app, can be used to optimally integrate prior biological knowledge with measured data to simultaneously construct both common and differential networks, to quantitatively assign model parameters and significant rewiring p-values and to provide user-friendly graphical results. The KDDN algorithm is computationally efficient and provides users with parallel computing capability using ubiquitous multi-core machines. We demonstrate the performance of KDDN on various simulations and real gene expression datasets, and further compare the results with those obtained by the most relevant peer methods. The acquired biologically plausible results provide new insights into network rewiring as a mechanistic principle and illustrate KDDN’s ability to detect them efficiently and correctly. Although the principal application here involves microarray gene expressions, our methodology can be readily applied to other types of quantitative molecular profiling data. Availability: Source code and compiled package are freely available for download at http://apps.cytoscape.org/apps/kddn Contact: yuewang@vt.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
    Publication Date: 2024-01-12
    Description: The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species\xe2\x80\x94less diverse than the North American tree flora\xe2\x80\x94accounts for half of the world\xe2\x80\x99s most diverse tree community.
    Keywords: hyperdominance ; Amazonia ; Amazon Basin ; Guiana Shield ; trees ; commonness ; rarity ; richness ; tree species
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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