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  • 1
    Publication Date: 2001-07-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alverson, K -- Bradley, R -- Briffa, K -- Cole, J -- Hughes, M -- Larocque, I -- Pedersen, T -- Thompson, L -- Tudhope, S -- New York, N.Y. -- Science. 2001 Jul 6;293(5527):47-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11444288" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carbon Dioxide/metabolism ; *Climate ; Cnidaria/physiology ; Conservation of Natural Resources ; Greenhouse Effect ; Humans ; Ice ; Oceans and Seas ; Rain ; Seawater/analysis/chemistry ; Specimen Handling/*methods ; Temperature ; Time Factors ; Trees/growth & development/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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  • 2
    Publication Date: 2001-07-28
    Description: Ecological extinction caused by overfishing precedes all other pervasive human disturbance to coastal ecosystems, including pollution, degradation of water quality, and anthropogenic climate change. Historical abundances of large consumer species were fantastically large in comparison with recent observations. Paleoecological, archaeological, and historical data show that time lags of decades to centuries occurred between the onset of overfishing and consequent changes in ecological communities, because unfished species of similar trophic level assumed the ecological roles of overfished species until they too were overfished or died of epidemic diseases related to overcrowding. Retrospective data not only help to clarify underlying causes and rates of ecological change, but they also demonstrate achievable goals for restoration and management of coastal ecosystems that could not even be contemplated based on the limited perspective of recent observations alone.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jackson, J B -- Kirby, M X -- Berger, W H -- Bjorndal, K A -- Botsford, L W -- Bourque, B J -- Bradbury, R H -- Cooke, R -- Erlandson, J -- Estes, J A -- Hughes, T P -- Kidwell, S -- Lange, C B -- Lenihan, H S -- Pandolfi, J M -- Peterson, C H -- Steneck, R S -- Tegner, M J -- Warner, R R -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):629-37.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0244, USA. jbcj@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474098" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaeology ; Bacteria ; Cnidaria ; Conservation of Natural Resources ; *Ecosystem ; Eutrophication ; *Fishes ; Geologic Sediments ; Humans ; *Marine Biology ; Seaweed ; Shellfish ; Time Factors
    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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  • 3
    Publication Date: 2008-04-15
    Description: The Philadelphia chromosome, a chromosomal abnormality that encodes BCR-ABL1, is the defining lesion of chronic myelogenous leukaemia (CML) and a subset of acute lymphoblastic leukaemia (ALL). To define oncogenic lesions that cooperate with BCR-ABL1 to induce ALL, we performed a genome-wide analysis of diagnostic leukaemia samples from 304 individuals with ALL, including 43 BCR-ABL1 B-progenitor ALLs and 23 CML cases. IKZF1 (encoding the transcription factor Ikaros) was deleted in 83.7% of BCR-ABL1 ALL, but not in chronic-phase CML. Deletion of IKZF1 was also identified as an acquired lesion at the time of transformation of CML to ALL (lymphoid blast crisis). The IKZF1 deletions resulted in haploinsufficiency, expression of a dominant-negative Ikaros isoform, or the complete loss of Ikaros expression. Sequencing of IKZF1 deletion breakpoints suggested that aberrant RAG-mediated recombination is responsible for the deletions. These findings suggest that genetic lesions resulting in the loss of Ikaros function are an important event in the development of BCR-ABL1 ALL.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mullighan, Charles G -- Miller, Christopher B -- Radtke, Ina -- Phillips, Letha A -- Dalton, James -- Ma, Jing -- White, Deborah -- Hughes, Timothy P -- Le Beau, Michelle M -- Pui, Ching-Hon -- Relling, Mary V -- Shurtleff, Sheila A -- Downing, James R -- England -- Nature. 2008 May 1;453(7191):110-4. doi: 10.1038/nature06866. Epub 2008 Apr 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18408710" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Child ; Fusion Proteins, bcr-abl/*genetics ; *Gene Deletion ; Humans ; Ikaros Transcription Factor/chemistry/*deficiency/*genetics/metabolism ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/*genetics/pathology ; Polymorphism, Single Nucleotide/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*genetics/pathology ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Structure, Tertiary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2009-09-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rockstrom, Johan -- Steffen, Will -- Noone, Kevin -- Persson, Asa -- Chapin, F Stuart 3rd -- Lambin, Eric F -- Lenton, Timothy M -- Scheffer, Marten -- Folke, Carl -- Schellnhuber, Hans Joachim -- Nykvist, Bjorn -- de Wit, Cynthia A -- Hughes, Terry -- van der Leeuw, Sander -- Rodhe, Henning -- Sorlin, Sverker -- Snyder, Peter K -- Costanza, Robert -- Svedin, Uno -- Falkenmark, Malin -- Karlberg, Louise -- Corell, Robert W -- Fabry, Victoria J -- Hansen, James -- Walker, Brian -- Liverman, Diana -- Richardson, Katherine -- Crutzen, Paul -- Foley, Jonathan A -- England -- Nature. 2009 Sep 24;461(7263):472-5. doi: 10.1038/461472a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stockholm Resilience Centre, Stockholm University, Kraftriket 2B, 10691 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779433" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Civilization ; Conservation of Natural Resources/*methods/trends ; *Earth (Planet) ; Ecology/*methods/*trends ; *Ecosystem ; Extinction, Biological ; Fossils ; Green Chemistry Technology/*methods/trends ; Greenhouse Effect ; History, 20th Century ; History, 21st Century ; History, Ancient ; *Human Activities/history ; Humans ; Nitrogen/metabolism ; Phosphorus/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2006-05-27
    Description: We describe a pathogenetic mechanism underlying a variant form of the inherited blood disorder alpha thalassemia. Association studies of affected individuals from Melanesia localized the disease trait to the telomeric region of human chromosome 16, which includes the alpha-globin gene cluster, but no molecular defects were detected by conventional approaches. After resequencing and using a combination of chromatin immunoprecipitation and expression analysis on a tiled oligonucleotide array, we identified a gain-of-function regulatory single-nucleotide polymorphism (rSNP) in a nongenic region between the alpha-globin genes and their upstream regulatory elements. The rSNP creates a new promoterlike element that interferes with normal activation of all downstream alpha-like globin genes. Thus, our work illustrates a strategy for distinguishing between neutral and functionally important rSNPs, and it also identifies a pathogenetic mechanism that could potentially underlie other genetic diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De Gobbi, Marco -- Viprakasit, Vip -- Hughes, Jim R -- Fisher, Chris -- Buckle, Veronica J -- Ayyub, Helena -- Gibbons, Richard J -- Vernimmen, Douglas -- Yoshinaga, Yuko -- de Jong, Pieter -- Cheng, Jan-Fang -- Rubin, Edward M -- Wood, William G -- Bowden, Don -- Higgs, Douglas R -- MC_U137961143/Medical Research Council/United Kingdom -- MC_U137961145/Medical Research Council/United Kingdom -- MC_U137961147/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 May 26;312(5777):1215-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16728641" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cells, Cultured ; Chromatin Immunoprecipitation ; Chromosomes, Human, Pair 16/*genetics ; Erythroblasts ; GATA1 Transcription Factor/metabolism ; Gene Expression ; Gene Expression Profiling ; Globins/*genetics ; Haplotypes ; Humans ; Melanesia ; Minisatellite Repeats ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; *Polymorphism, Single Nucleotide ; *Promoter Regions, Genetic ; Regulatory Elements, Transcriptional ; Transcription, Genetic ; alpha-Thalassemia/*genetics
    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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  • 6
    Publication Date: 2007-10-27
    Description: The melanocortin 1 receptor (MC1R) regulates pigmentation in humans and other vertebrates. Variants of MC1R with reduced function are associated with pale skin color and red hair in humans of primarily European origin. We amplified and sequenced a fragment of the MC1R gene (mc1r) from two Neanderthal remains. Both specimens have a mutation that was not found in approximately 3700 modern humans analyzed. Functional analyses show that this variant reduces MC1R activity to a level that alters hair and/or skin pigmentation in humans. The impaired activity of this variant suggests that Neanderthals varied in pigmentation levels, potentially on the scale observed in modern humans. Our data suggest that inactive MC1R variants evolved independently in both modern humans and Neanderthals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lalueza-Fox, Carles -- Rompler, Holger -- Caramelli, David -- Staubert, Claudia -- Catalano, Giulio -- Hughes, David -- Rohland, Nadin -- Pilli, Elena -- Longo, Laura -- Condemi, Silvana -- de la Rasilla, Marco -- Fortea, Javier -- Rosas, Antonio -- Stoneking, Mark -- Schoneberg, Torsten -- Bertranpetit, Jaume -- Hofreiter, Michael -- New York, N.Y. -- Science. 2007 Nov 30;318(5855):1453-5. Epub 2007 Oct 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departament de Biologia Animal, Universitat de Barcelona, Spain. clalueza@ub.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962522" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Substitution ; Animals ; Biological Evolution ; Cell Line ; DNA/genetics ; *Fossils ; Hair Color/*genetics ; Hominidae/*genetics ; Humans ; Molecular Sequence Data ; *Mutation ; Polymerase Chain Reaction ; Receptor, Melanocortin, Type 1/chemistry/*genetics/metabolism ; Sequence Analysis, DNA ; Skin Pigmentation/*genetics
    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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  • 7
    Publication Date: 2007-04-28
    Description: New strategies for prevention and treatment of type 2 diabetes (T2D) require improved insight into disease etiology. We analyzed 386,731 common single-nucleotide polymorphisms (SNPs) in 1464 patients with T2D and 1467 matched controls, each characterized for measures of glucose metabolism, lipids, obesity, and blood pressure. With collaborators (FUSION and WTCCC/UKT2D), we identified and confirmed three loci associated with T2D-in a noncoding region near CDKN2A and CDKN2B, in an intron of IGF2BP2, and an intron of CDKAL1-and replicated associations near HHEX and in SLC30A8 found by a recent whole-genome association study. We identified and confirmed association of a SNP in an intron of glucokinase regulatory protein (GCKR) with serum triglycerides. The discovery of associated variants in unsuspected genes and outside coding regions illustrates the ability of genome-wide association studies to provide potentially important clues to the pathogenesis of common diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research -- Saxena, Richa -- Voight, Benjamin F -- Lyssenko, Valeriya -- Burtt, Noel P -- de Bakker, Paul I W -- Chen, Hong -- Roix, Jeffrey J -- Kathiresan, Sekar -- Hirschhorn, Joel N -- Daly, Mark J -- Hughes, Thomas E -- Groop, Leif -- Altshuler, David -- Almgren, Peter -- Florez, Jose C -- Meyer, Joanne -- Ardlie, Kristin -- Bengtsson Bostrom, Kristina -- Isomaa, Bo -- Lettre, Guillaume -- Lindblad, Ulf -- Lyon, Helen N -- Melander, Olle -- Newton-Cheh, Christopher -- Nilsson, Peter -- Orho-Melander, Marju -- Rastam, Lennart -- Speliotes, Elizabeth K -- Taskinen, Marja-Riitta -- Tuomi, Tiinamaija -- Guiducci, Candace -- Berglund, Anna -- Carlson, Joyce -- Gianniny, Lauren -- Hackett, Rachel -- Hall, Liselotte -- Holmkvist, Johan -- Laurila, Esa -- Sjogren, Marketa -- Sterner, Maria -- Surti, Aarti -- Svensson, Margareta -- Svensson, Malin -- Tewhey, Ryan -- Blumenstiel, Brendan -- Parkin, Melissa -- Defelice, Matthew -- Barry, Rachel -- Brodeur, Wendy -- Camarata, Jody -- Chia, Nancy -- Fava, Mary -- Gibbons, John -- Handsaker, Bob -- Healy, Claire -- Nguyen, Kieu -- Gates, Casey -- Sougnez, Carrie -- Gage, Diane -- Nizzari, Marcia -- Gabriel, Stacey B -- Chirn, Gung-Wei -- Ma, Qicheng -- Parikh, Hemang -- Richardson, Delwood -- Ricke, Darrell -- Purcell, Shaun -- F32 DK079466/DK/NIDDK NIH HHS/ -- F32 DK079466-01/DK/NIDDK NIH HHS/ -- K23 DK067288/DK/NIDDK NIH HHS/ -- K23 DK080145/DK/NIDDK NIH HHS/ -- K23 DK080145-01/DK/NIDDK NIH HHS/ -- K23 DK65978-04/DK/NIDDK NIH HHS/ -- K23-HL083102/HL/NHLBI NIH HHS/ -- U01 HG004171/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1331-6. Epub 2007 Apr 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17463246" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/genetics ; Aged ; Alleles ; Blood Glucose/analysis ; Case-Control Studies ; Chromosome Mapping ; Chromosomes, Human, Pair 9/genetics ; Diabetes Mellitus, Type 2/*genetics ; Female ; Genetic Markers ; *Genetic Predisposition to Disease ; *Genome, Human ; Genotype ; Haplotypes ; Humans ; Insulin Resistance/genetics ; Insulin-Like Growth Factor Binding Proteins/genetics ; Introns ; Male ; Meta-Analysis as Topic ; Middle Aged ; *Polymorphism, Single Nucleotide ; Quantitative Trait, Heritable ; Triglycerides/*blood
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2008-07-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoegh-Guldberg, O -- Hughes, L -- McIntyre, S -- Lindenmayer, D B -- Parmesan, C -- Possingham, H P -- Thomas, C D -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):345-6. doi: 10.1126/science.1157897.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Marine Studies, Australian Research Council Centre for Excellence in Reef Studies and the Coral Reef Targeted Research Project, University of Queensland, St Lucia, Queensland (QLD) 4072, Australia. oveh@uq.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635780" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; Biodiversity ; *Climate ; *Conservation of Natural Resources ; Ecology/*methods ; *Ecosystem ; Extinction, Biological ; Geography ; Humans ; Population Dynamics ; Socioeconomic Factors
    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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  • 9
    Publication Date: 2009-05-16
    Description: Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in physiology, development, and evolution, comprehensive DNA binding specificities have been determined experimentally for only a few proteins. Here, we used microarrays containing all 10-base pair sequences to examine the binding specificities of 104 distinct mouse DNA binding proteins representing 22 structural classes. Our results reveal a complex landscape of binding, with virtually every protein analyzed possessing unique preferences. Roughly half of the proteins each recognized multiple distinctly different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905877/" 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/PMC2905877/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Badis, Gwenael -- Berger, Michael F -- Philippakis, Anthony A -- Talukder, Shaheynoor -- Gehrke, Andrew R -- Jaeger, Savina A -- Chan, Esther T -- Metzler, Genita -- Vedenko, Anastasia -- Chen, Xiaoyu -- Kuznetsov, Hanna -- Wang, Chi-Fong -- Coburn, David -- Newburger, Daniel E -- Morris, Quaid -- Hughes, Timothy R -- Bulyk, Martha L -- R01 HG003985/HG/NHGRI NIH HHS/ -- R01 HG003985-01/HG/NHGRI NIH HHS/ -- R01 HG003985-02/HG/NHGRI NIH HHS/ -- R01 HG003985-03/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19443739" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; DNA/chemistry/*metabolism ; Electrophoretic Mobility Shift Assay ; Gene Expression Regulation ; Gene Regulatory Networks ; Humans ; Mice ; Protein Array Analysis ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/*chemistry/*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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  • 10
    Publication Date: 2003-08-16
    Description: Degradation of coral reef ecosystems began centuries ago, but there is no global summary of the magnitude of change. We compiled records, extending back thousands of years, of the status and trends of seven major guilds of carnivores, herbivores, and architectural species from 14 regions. Large animals declined before small animals and architectural species, and Atlantic reefs declined before reefs in the Red Sea and Australia, but the trajectories of decline were markedly similar worldwide. All reefs were substantially degraded long before outbreaks of coral disease and bleaching. Regardless of these new threats, reefs will not survive without immediate protection from human exploitation over large spatial scales.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pandolfi, John M -- Bradbury, Roger H -- Sala, Enric -- Hughes, Terence P -- Bjorndal, Karen A -- Cooke, Richard G -- McArdle, Deborah -- McClenachan, Loren -- Newman, Marah J H -- Paredes, Gustavo -- Warner, Robert R -- Jackson, Jeremy B C -- New York, N.Y. -- Science. 2003 Aug 15;301(5635):955-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Paleobiology, MRC-121, National Museum of Natural History, Post Office Box 37012, Smithsonian Institution, Washington, DC 20013-7012, USA. pandolfi.john@nmnh.si.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12920296" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/*growth & development ; Conservation of Natural Resources ; Culture ; *Ecosystem ; Humans ; Population Dynamics ; Principal Component Analysis ; Time Factors
    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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