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  • Reproducibility of Results  (484)
  • Nature Publishing Group (NPG)  (484)
  • American Institute of Physics (AIP)
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  • 201
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    Nature Publishing Group (NPG)
    Publication Date: 2012-03-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2012 Mar 28;483(7391):509. doi: 10.1038/483509a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22460859" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Science Disciplines/standards ; Humans ; Periodicals as Topic/standards ; Quality Control ; Reproducibility of Results ; Research/*standards ; Research Design/standards/*statistics & numerical data ; Research Personnel/*standards ; Treatment Failure
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 202
    Publication Date: 2012-04-13
    Description: Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cancers. Here we show in 104 TNBC cases that at the time of diagnosis these cancers exhibit a wide and continuous spectrum of genomic evolution, with some having only a handful of coding somatic aberrations in a few pathways, whereas others contain hundreds of coding somatic mutations. High-throughput RNA sequencing (RNA-seq) revealed that only approximately 36% of mutations are expressed. Using deep re-sequencing measurements of allelic abundance for 2,414 somatic mutations, we determine for the first time-to our knowledge-in an epithelial tumour subtype, the relative abundance of clonal frequencies among cases representative of the population. We show that TNBCs vary widely in their clonal frequencies at the time of diagnosis, with the basal subtype of TNBC showing more variation than non-basal TNBC. Although p53 (also known as TP53), PIK3CA and PTEN somatic mutations seem to be clonally dominant compared to other genes, in some tumours their clonal frequencies are incompatible with founder status. Mutations in cytoskeletal, cell shape and motility proteins occurred at lower clonal frequencies, suggesting that they occurred later during tumour progression. Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863681/" 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/PMC3863681/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shah, Sohrab P -- Roth, Andrew -- Goya, Rodrigo -- Oloumi, Arusha -- Ha, Gavin -- Zhao, Yongjun -- Turashvili, Gulisa -- Ding, Jiarui -- Tse, Kane -- Haffari, Gholamreza -- Bashashati, Ali -- Prentice, Leah M -- Khattra, Jaswinder -- Burleigh, Angela -- Yap, Damian -- Bernard, Virginie -- McPherson, Andrew -- Shumansky, Karey -- Crisan, Anamaria -- Giuliany, Ryan -- Heravi-Moussavi, Alireza -- Rosner, Jamie -- Lai, Daniel -- Birol, Inanc -- Varhol, Richard -- Tam, Angela -- Dhalla, Noreen -- Zeng, Thomas -- Ma, Kevin -- Chan, Simon K -- Griffith, Malachi -- Moradian, Annie -- Cheng, S-W Grace -- Morin, Gregg B -- Watson, Peter -- Gelmon, Karen -- Chia, Stephen -- Chin, Suet-Feung -- Curtis, Christina -- Rueda, Oscar M -- Pharoah, Paul D -- Damaraju, Sambasivarao -- Mackey, John -- Hoon, Kelly -- Harkins, Timothy -- Tadigotla, Vasisht -- Sigaroudinia, Mahvash -- Gascard, Philippe -- Tlsty, Thea -- Costello, Joseph F -- Meyer, Irmtraud M -- Eaves, Connie J -- Wasserman, Wyeth W -- Jones, Steven -- Huntsman, David -- Hirst, Martin -- Caldas, Carlos -- Marra, Marco A -- Aparicio, Samuel -- 5U01ES017154-02/ES/NIEHS NIH HHS/ -- R01 GM084875/GM/NIGMS NIH HHS/ -- R01GM084875/GM/NIGMS NIH HHS/ -- Cancer Research UK/United Kingdom -- England -- Nature. 2012 Apr 4;486(7403):395-9. doi: 10.1038/nature10933.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada. sshah@bccrc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22495314" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Breast Neoplasms/diagnosis/*genetics/*pathology ; Clone Cells/metabolism/pathology ; DNA Copy Number Variations/genetics ; DNA Mutational Analysis ; Disease Progression ; *Evolution, Molecular ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/genetics ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; INDEL Mutation/genetics ; Mutation/*genetics ; Point Mutation/genetics ; Precision Medicine ; Reproducibility of Results ; Sequence Analysis, RNA
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 203
    Publication Date: 2012-02-10
    Description: Cancer immunoediting, the process by which the immune system controls tumour outgrowth and shapes tumour immunogenicity, is comprised of three phases: elimination, equilibrium and escape. Although many immune components that participate in this process are known, its underlying mechanisms remain poorly defined. A central tenet of cancer immunoediting is that T-cell recognition of tumour antigens drives the immunological destruction or sculpting of a developing cancer. However, our current understanding of tumour antigens comes largely from analyses of cancers that develop in immunocompetent hosts and thus may have already been edited. Little is known about the antigens expressed in nascent tumour cells, whether they are sufficient to induce protective antitumour immune responses or whether their expression is modulated by the immune system. Here, using massively parallel sequencing, we characterize expressed mutations in highly immunogenic methylcholanthrene-induced sarcomas derived from immunodeficient Rag2(-/-) mice that phenotypically resemble nascent primary tumour cells. Using class I prediction algorithms, we identify mutant spectrin-beta2 as a potential rejection antigen of the d42m1 sarcoma and validate this prediction by conventional antigen expression cloning and detection. We also demonstrate that cancer immunoediting of d42m1 occurs via a T-cell-dependent immunoselection process that promotes outgrowth of pre-existing tumour cell clones lacking highly antigenic mutant spectrin-beta2 and other potential strong antigens. These results demonstrate that the strong immunogenicity of an unedited tumour can be ascribed to expression of highly antigenic mutant proteins and show that outgrowth of tumour cells that lack these strong antigens via a T-cell-dependent immunoselection process represents one mechanism of cancer immunoediting.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874809/" 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/PMC3874809/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsushita, Hirokazu -- Vesely, Matthew D -- Koboldt, Daniel C -- Rickert, Charles G -- Uppaluri, Ravindra -- Magrini, Vincent J -- Arthur, Cora D -- White, J Michael -- Chen, Yee-Shiuan -- Shea, Lauren K -- Hundal, Jasreet -- Wendl, Michael C -- Demeter, Ryan -- Wylie, Todd -- Allison, James P -- Smyth, Mark J -- Old, Lloyd J -- Mardis, Elaine R -- Schreiber, Robert D -- R01 CA043059/CA/NCI NIH HHS/ -- U01 CA141541/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Feb 8;482(7385):400-4. doi: 10.1038/nature10755.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22318521" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Carrier Proteins/genetics/immunology ; DNA-Binding Proteins/deficiency/genetics ; Exome/*genetics/*immunology ; Histocompatibility Antigens Class I/immunology ; Humans ; Immunologic Surveillance/*immunology ; Male ; Methylcholanthrene ; Mice ; Microfilament Proteins/genetics/immunology ; Models, Immunological ; Neoplasms/chemically induced/*genetics/*immunology/pathology ; Reproducibility of Results ; Sarcoma/chemically induced/genetics/immunology/pathology ; T-Lymphocytes/*immunology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
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  • 204
    Publication Date: 2012-05-19
    Description: The opioid receptor family comprises three members, the micro-, delta- and kappa-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coupled receptor (GPCR) superfamily, and are excellent therapeutic targets for pain control. The delta-opioid receptor (delta-OR) has a role in analgesia, as well as in other neurological functions that remain poorly understood. The structures of the micro-OR and kappa-OR have recently been solved. Here we report the crystal structure of the mouse delta-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the micro-OR and kappa-OR, the delta-OR structure provides insights into conserved elements of opioid ligand recognition while also revealing structural features associated with ligand-subtype selectivity. The binding pocket of opioid receptors can be divided into two distinct regions. Whereas the lower part of this pocket is highly conserved among opioid receptors, the upper part contains divergent residues that confer subtype selectivity. This provides a structural explanation and validation for the 'message-address' model of opioid receptor pharmacology, in which distinct 'message' (efficacy) and 'address' (selectivity) determinants are contained within a single ligand. Comparison of the address region of the delta-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523198/" 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/PMC3523198/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Granier, Sebastien -- Manglik, Aashish -- Kruse, Andrew C -- Kobilka, Tong Sun -- Thian, Foon Sun -- Weis, William I -- Kobilka, Brian K -- DA031418/DA/NIDA NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- R01 GM083118/GM/NIGMS NIH HHS/ -- R01 NS028471/NS/NINDS NIH HHS/ -- R21 DA031418/DA/NIDA NIH HHS/ -- England -- Nature. 2012 May 16;485(7398):400-4. doi: 10.1038/nature11111.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA. granier@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22596164" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; Mice ; Models, Molecular ; Molecular Sequence Data ; Naltrexone/*analogs & derivatives/chemistry/metabolism/pharmacology ; Protein Structure, Tertiary ; Receptors, Opioid, delta/antagonists & inhibitors/*chemistry/metabolism ; Reproducibility of Results ; Structure-Activity Relationship ; Substrate Specificity
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  • 205
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    Nature Publishing Group (NPG)
    Publication Date: 2012-09-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maxmen, Amy -- England -- Nature. 2012 Sep 20;489(7416):349-50. doi: 10.1038/489349a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22996526" target="_blank"〉PubMed〈/a〉
    Keywords: Humans ; Kidney/pathology/virology ; Kidney Diseases/*etiology/pathology/prevention & control/*virology ; Models, Biological ; RNA, Viral/urine ; Reproducibility of Results ; United States/epidemiology ; West Nile Fever/*complications/epidemiology/therapy ; West Nile virus/genetics/isolation & purification/*pathogenicity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
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  • 206
    Publication Date: 2013-01-22
    Description: Interferon-induced proteins with tetratricopeptide repeats (IFITs) are innate immune effector molecules that are thought to confer antiviral defence through disruption of protein-protein interactions in the host translation-initiation machinery. However, it was recently discovered that IFITs can directly recognize viral RNA bearing a 5'-triphosphate group (PPP-RNA), which is a molecular signature that distinguishes it from host RNA. Here we report crystal structures of human IFIT5, its complex with PPP-RNAs, and an amino-terminal fragment of IFIT1. The structures reveal a new helical domain that houses a positively charged cavity designed to specifically engage only single-stranded PPP-RNA, thus distinguishing it from the canonical cytosolic sensor of double-stranded viral PPP-RNA, retinoic acid-inducible gene I (RIG-I, also known as DDX58). Mutational analysis, proteolysis and gel-shift assays reveal that PPP-RNA is bound in a non-sequence-specific manner and requires a 5'-overhang of approximately three nucleotides. Abrogation of PPP-RNA binding in IFIT1 and IFIT5 was found to cause a defect in the antiviral response by human embryonic kidney cells. These results demonstrate the mechanism by which IFIT proteins selectively recognize viral RNA, and lend insight into their downstream effector function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbas, Yazan M -- Pichlmair, Andreas -- Gorna, Maria W -- Superti-Furga, Giulio -- Nagar, Bhushan -- MOP-82929/Canadian Institutes of Health Research/Canada -- England -- Nature. 2013 Feb 7;494(7435):60-4. doi: 10.1038/nature11783. Epub 2013 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Groupe de Recherche Axe sur la Structure des Proteines, McGill University, Montreal, Quebec H3G 0B1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23334420" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; Humans ; Immunity, Innate/immunology ; Models, Molecular ; Neoplasm Proteins/*chemistry/*metabolism ; Phosphorylation ; Protein Conformation ; RNA, Viral/*chemistry/genetics/*metabolism ; Reproducibility of Results ; Substrate Specificity
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  • 207
    Publication Date: 2013-06-19
    Description: Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919509/" 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/PMC3919509/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawrence, Michael S -- Stojanov, Petar -- Polak, Paz -- Kryukov, Gregory V -- Cibulskis, Kristian -- Sivachenko, Andrey -- Carter, Scott L -- Stewart, Chip -- Mermel, Craig H -- Roberts, Steven A -- Kiezun, Adam -- Hammerman, Peter S -- McKenna, Aaron -- Drier, Yotam -- Zou, Lihua -- Ramos, Alex H -- Pugh, Trevor J -- Stransky, Nicolas -- Helman, Elena -- Kim, Jaegil -- Sougnez, Carrie -- Ambrogio, Lauren -- Nickerson, Elizabeth -- Shefler, Erica -- Cortes, Maria L -- Auclair, Daniel -- Saksena, Gordon -- Voet, Douglas -- Noble, Michael -- DiCara, Daniel -- Lin, Pei -- Lichtenstein, Lee -- Heiman, David I -- Fennell, Timothy -- Imielinski, Marcin -- Hernandez, Bryan -- Hodis, Eran -- Baca, Sylvan -- Dulak, Austin M -- Lohr, Jens -- Landau, Dan-Avi -- Wu, Catherine J -- Melendez-Zajgla, Jorge -- Hidalgo-Miranda, Alfredo -- Koren, Amnon -- McCarroll, Steven A -- Mora, Jaume -- Lee, Ryan S -- Crompton, Brian -- Onofrio, Robert -- Parkin, Melissa -- Winckler, Wendy -- Ardlie, Kristin -- Gabriel, Stacey B -- Roberts, Charles W M -- Biegel, Jaclyn A -- Stegmaier, Kimberly -- Bass, Adam J -- Garraway, Levi A -- Meyerson, Matthew -- Golub, Todd R -- Gordenin, Dmitry A -- Sunyaev, Shamil -- Lander, Eric S -- Getz, Gad -- ES065073/ES/NIEHS NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- T32 CA009216/CA/NCI NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- U24 CA143845/CA/NCI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- England -- Nature. 2013 Jul 11;499(7457):214-8. doi: 10.1038/nature12213. Epub 2013 Jun 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23770567" target="_blank"〉PubMed〈/a〉
    Keywords: Artifacts ; DNA Replication Timing ; Exome/genetics ; False Positive Reactions ; Gene Expression ; *Genetic Heterogeneity ; Genome, Human/genetics ; Humans ; Lung Neoplasms/genetics ; Mutation/*genetics ; Mutation Rate ; Neoplasms/classification/*genetics/pathology ; Neoplasms, Squamous Cell/genetics ; Oncogenes/*genetics ; Reproducibility of Results ; Sample Size
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  • 208
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    Nature Publishing Group (NPG)
    Publication Date: 2013-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2013 Jul 25;499(7459):390. doi: 10.1038/499390a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23887410" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Separation ; *Cell Size ; Embryo, Mammalian/cytology ; Humans ; Mice ; Reproducibility of Results ; Stem Cell Transplantation ; Stem Cells/*cytology ; *Uncertainty
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  • 209
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    Nature Publishing Group (NPG)
    Publication Date: 2013-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Callaway, Ewen -- England -- Nature. 2013 Nov 7;503(7474):18-9. doi: 10.1038/503018a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24201261" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaeology/methods ; Collagen/analysis/genetics ; Elephants/*classification/metabolism ; Evolution, Molecular ; Fossils ; Humans ; Mass Spectrometry ; Phylogeny ; Proteomics/*methods ; Reproducibility of Results ; Sequence Analysis, DNA
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  • 210
    Publication Date: 2013-05-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2013 May 2;497(7447):16. doi: 10.1038/497016a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23636371" target="_blank"〉PubMed〈/a〉
    Keywords: *Cues ; Humans ; *Intelligence Tests ; Psychology/standards ; Reproducibility of Results ; Scientific Misconduct ; Sociology/standards ; *Unconscious (Psychology)
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  • 211
    Publication Date: 2013-10-15
    Description: The mechanisms by which genetic variation affects transcription regulation and phenotypes at the nucleotide level are incompletely understood. Here we use natural genetic variation as an in vivo mutagenesis screen to assess the genome-wide effects of sequence variation on lineage-determining and signal-specific transcription factor binding, epigenomics and transcriptional outcomes in primary macrophages from different mouse strains. We find substantial genetic evidence to support the concept that lineage-determining transcription factors define epigenetic and transcriptomic states by selecting enhancer-like regions in the genome in a collaborative fashion and facilitating binding of signal-dependent factors. This hierarchical model of transcription factor function suggests that limited sets of genomic data for lineage-determining transcription factors and informative histone modifications can be used for the prioritization of disease-associated regulatory variants.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994126/" 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/PMC3994126/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heinz, S -- Romanoski, C E -- Benner, C -- Allison, K A -- Kaikkonen, M U -- Orozco, L D -- Glass, C K -- 5T32DK007494/DK/NIDDK NIH HHS/ -- CA17390/CA/NCI NIH HHS/ -- DK063491/DK/NIDDK NIH HHS/ -- DK091183/DK/NIDDK NIH HHS/ -- P01 DK074868/DK/NIDDK NIH HHS/ -- P30 CA023100/CA/NCI NIH HHS/ -- P30 DK063491/DK/NIDDK NIH HHS/ -- R01 CA173903/CA/NCI NIH HHS/ -- R01 DK091183/DK/NIDDK NIH HHS/ -- T32 AR059033/AR/NIAMS NIH HHS/ -- England -- Nature. 2013 Nov 28;503(7477):487-92. doi: 10.1038/nature12615. Epub 2013 Oct 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24121437" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs/genetics ; Animals ; Base Sequence ; Cell Lineage/genetics ; DNA-Binding Proteins/metabolism ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation/*genetics ; Genetic Variation/*genetics ; Histones/chemistry/metabolism ; Macrophages/metabolism ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Models, Biological ; Mutation/genetics ; NF-kappa B/metabolism ; Protein Binding ; Reproducibility of Results ; Selection, Genetic/*genetics ; Transcription Factor RelA/metabolism ; Transcription Factors/*metabolism
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  • 212
    Publication Date: 2013-10-15
    Description: The design of G-protein-coupled receptor (GPCR) allosteric modulators, an active area of modern pharmaceutical research, has proved challenging because neither the binding modes nor the molecular mechanisms of such drugs are known. Here we determine binding sites, bound conformations and specific drug-receptor interactions for several allosteric modulators of the M2 muscarinic acetylcholine receptor (M2 receptor), a prototypical family A GPCR, using atomic-level simulations in which the modulators spontaneously associate with the receptor. Despite substantial structural diversity, all modulators form cation-pi interactions with clusters of aromatic residues in the receptor extracellular vestibule, approximately 15 A from the classical, 'orthosteric' ligand-binding site. We validate the observed modulator binding modes through radioligand binding experiments on receptor mutants designed, on the basis of our simulations, either to increase or to decrease modulator affinity. Simulations also revealed mechanisms that contribute to positive and negative allosteric modulation of classical ligand binding, including coupled conformational changes of the two binding sites and electrostatic interactions between ligands in these sites. These observations enabled the design of chemical modifications that substantially alter a modulator's allosteric effects. Our findings thus provide a structural basis for the rational design of allosteric modulators targeting muscarinic and possibly other GPCRs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dror, Ron O -- Green, Hillary F -- Valant, Celine -- Borhani, David W -- Valcourt, James R -- Pan, Albert C -- Arlow, Daniel H -- Canals, Meritxell -- Lane, J Robert -- Rahmani, Raphael -- Baell, Jonathan B -- Sexton, Patrick M -- Christopoulos, Arthur -- Shaw, David E -- England -- Nature. 2013 Nov 14;503(7475):295-9. doi: 10.1038/nature12595. Epub 2013 Oct 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] D. E. Shaw Research, 120 West 45th Street, 39th Floor, New York, New York 10036, USA [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24121438" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/physiology ; Animals ; Binding Sites ; CHO Cells ; Cricetulus ; *Drug Design ; Humans ; Models, Chemical ; Molecular Conformation ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; Receptors, G-Protein-Coupled/*antagonists & inhibitors/*chemistry/genetics ; Reproducibility of Results
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  • 213
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    Nature Publishing Group (NPG)
    Publication Date: 2013-02-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2013 Feb 14;494(7436):155-6. doi: 10.1038/494155a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23407515" target="_blank"〉PubMed〈/a〉
    Keywords: Crowdsourcing ; Data Mining/*methods ; *Epidemiological Monitoring ; Humans ; Influenza A Virus, H3N2 Subtype/isolation & purification/pathogenicity ; Influenza, Human/*epidemiology/mortality/virology ; *Internet ; Reproducibility of Results ; Social Media ; United States/epidemiology
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  • 214
    Publication Date: 2013-11-12
    Description: Myocardial infarction, a leading cause of death in the Western world, usually occurs when the fibrous cap overlying an atherosclerotic plaque in a coronary artery ruptures. The resulting exposure of blood to the atherosclerotic material then triggers thrombus formation, which occludes the artery. The importance of genetic predisposition to coronary artery disease and myocardial infarction is best documented by the predictive value of a positive family history. Next-generation sequencing in families with several affected individuals has revolutionized mutation identification. Here we report the segregation of two private, heterozygous mutations in two functionally related genes, GUCY1A3 (p.Leu163Phefs*24) and CCT7 (p.Ser525Leu), in an extended myocardial infarction family. GUCY1A3 encodes the alpha1 subunit of soluble guanylyl cyclase (alpha1-sGC), and CCT7 encodes CCTeta, a member of the tailless complex polypeptide 1 ring complex, which, among other functions, stabilizes soluble guanylyl cyclase. After stimulation with nitric oxide, soluble guanylyl cyclase generates cGMP, which induces vasodilation and inhibits platelet activation. We demonstrate in vitro that mutations in both GUCY1A3 and CCT7 severely reduce alpha1-sGC as well as beta1-sGC protein content, and impair soluble guanylyl cyclase activity. Moreover, platelets from digenic mutation carriers contained less soluble guanylyl cyclase protein and consequently displayed reduced nitric-oxide-induced cGMP formation. Mice deficient in alpha1-sGC protein displayed accelerated thrombus formation in the microcirculation after local trauma. Starting with a severely affected family, we have identified a link between impaired soluble-guanylyl-cyclase-dependent nitric oxide signalling and myocardial infarction risk, possibly through accelerated thrombus formation. Reversing this defect may provide a new therapeutic target for reducing the risk of myocardial infarction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erdmann, Jeanette -- Stark, Klaus -- Esslinger, Ulrike B -- Rumpf, Philipp Moritz -- Koesling, Doris -- de Wit, Cor -- Kaiser, Frank J -- Braunholz, Diana -- Medack, Anja -- Fischer, Marcus -- Zimmermann, Martina E -- Tennstedt, Stephanie -- Graf, Elisabeth -- Eck, Sebastian -- Aherrahrou, Zouhair -- Nahrstaedt, Janja -- Willenborg, Christina -- Bruse, Petra -- Braenne, Ingrid -- Nothen, Markus M -- Hofmann, Per -- Braund, Peter S -- Mergia, Evanthia -- Reinhard, Wibke -- Burgdorf, Christof -- Schreiber, Stefan -- Balmforth, Anthony J -- Hall, Alistair S -- Bertram, Lars -- Steinhagen-Thiessen, Elisabeth -- Li, Shu-Chen -- Marz, Winfried -- Reilly, Muredach -- Kathiresan, Sekar -- McPherson, Ruth -- Walter, Ulrich -- CARDIoGRAM -- Ott, Jurg -- Samani, Nilesh J -- Strom, Tim M -- Meitinger, Thomas -- Hengstenberg, Christian -- Schunkert, Heribert -- British Heart Foundation/United Kingdom -- England -- Nature. 2013 Dec 19;504(7480):432-6. doi: 10.1038/nature12722. Epub 2013 Nov 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institut fur Integrative und Experimentelle Genomik, Universitat zu Lubeck, 23562 Lubeck, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lubeck/Kiel, 23562 Lubeck, Germany [3]. ; 1] Klinik und Poliklinik fur Innere Medizin II, Universitatsklinikum Regensburg, 93053 Regensburg, Germany [2] Department of Genetic Epidemiology, University of Regensburg, 93053 Regensburg, Germany [3]. ; 1] Klinik und Poliklinik fur Innere Medizin II, Universitatsklinikum Regensburg, 93053 Regensburg, Germany [2] Institut National de la Sante et de la Recherche Medicale (INSERM), UMR-S937 Paris, France [3]. ; 1] Deutsches Herzzentrum Munchen and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universitat Munchen, 80636 Munchen, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80636 Munich, Germany [3]. ; Department of Pharmacology and Toxicology, Ruhr-University Bochum, 44801 Bochum, Germany. ; 1] German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lubeck/Kiel, 23562 Lubeck, Germany [2] Institut fur Physiologie, Universitat zu Lubeck, 23562 Lubeck, Germany. ; 1] German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lubeck/Kiel, 23562 Lubeck, Germany [2] Institut fur Humangenetik, Universitat zu Lubeck, 23562 Lubeck, Germany. ; Institut fur Humangenetik, Universitat zu Lubeck, 23562 Lubeck, Germany. ; Institut fur Integrative und Experimentelle Genomik, Universitat zu Lubeck, 23562 Lubeck, Germany. ; Klinik und Poliklinik fur Innere Medizin II, Universitatsklinikum Regensburg, 93053 Regensburg, Germany. ; 1] Institute of Human Genetics, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany [2] Institute of Human Genetics, Technische Universitat Munchen, 81675 Munchen, Germany. ; 1] Institut fur Integrative und Experimentelle Genomik, Universitat zu Lubeck, 23562 Lubeck, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lubeck/Kiel, 23562 Lubeck, Germany. ; 1] Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany [2] Department of Genomics, Research Center Life & Brain, University of Bonn, 53127 Bonn, Germany. ; 1] Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany [2] Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, 4003 Basel, Switzerland. ; 1] Department of Cardiovascular Sciences, University of Leicester, Leicester LE1 7RH, UK [2] Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester LE1 7RH, UK. ; 1] Deutsches Herzzentrum Munchen and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universitat Munchen, 80636 Munchen, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80636 Munich, Germany. ; Deutsches Herzzentrum Munchen and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universitat Munchen, 80636 Munchen, Germany. ; Institute of Clinical Molecular Biology, Christian-Albrecht-Universitat, 24105 Kiel, Germany. ; Division of Cardiovascular and Diabetes Research, Multidisciplinary Cardiovascular Research Centre, Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds LS2 9JT, UK. ; Division of Cardiovascular and Neuronal Remodelling, Multidisciplinary Cardiovascular Research Centre, Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds LS2 9JT, UK. ; Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. ; Charite Research Group on Geriatrics, Charite-Universitatsmedizin, 10117 Berlin, Germany. ; 1] Center for Lifespan Psychology, Max Planck Institute for Human Development, 14195 Berlin, Germany [2] Department of Psychology, TU Dresden, 01062 Dresden, Germany. ; 1] Synlab Academy and Business Development, synlab Services GmbH, 68165 Mannheim, Germany [2] Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, 8036 Graz, Austria [3] Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany. ; The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; 1] Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02215, USA [2] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02215, USA [3] Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02215, USA. ; University of Ottawa, Heart Institute, Ottawa, Ontario K1Y 4W7, Canada. ; 1] Centrum fur Thrombose und Hamostase (CTH), Universitatsmedizin Mainz, 55131 Mainz, Germany [2] German Centre for Cardiovascular Research (DZHK), partner site RheinMain, 55131 Mainz, Germany. ; 1] Institute of Psychology, Chinese Academy of Sciences, Beijing 100864, China [2] Laboratory of Statistical Genetics, Rockefeller University, New York 10065, USA. ; 1] Deutsches Herzzentrum Munchen and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universitat Munchen, 80636 Munchen, Germany [2] Institute of Human Genetics, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany [3] Institute of Human Genetics, Technische Universitat Munchen, 81675 Munchen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24213632" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chaperonin Containing TCP-1/genetics/metabolism ; Cyclic GMP/metabolism ; Disease Susceptibility/*metabolism ; Exome/genetics ; Female ; Genetic Predisposition to Disease ; Guanylate Cyclase/deficiency/genetics/metabolism ; HEK293 Cells ; Humans ; Male ; Mice ; Mutation/genetics ; Myocardial Infarction/genetics/*metabolism/physiopathology ; Nitric Oxide/*metabolism ; Pedigree ; Platelet Activation ; Receptors, Cytoplasmic and Nuclear/deficiency/genetics/metabolism ; Reproducibility of Results ; *Signal Transduction ; Solubility ; Thrombosis/metabolism ; Vasodilation
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  • 215
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    Nature Publishing Group (NPG)
    Publication Date: 2013-12-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Dec 19;504(7480):331.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24358504" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Bias (Epidemiology) ; Clinical Trials as Topic/adverse effects/*ethics/*legislation & jurisprudence ; Expert Testimony ; *Federal Government ; Humans ; Italy ; *Patient Advocacy ; Reproducibility of Results ; Stem Cell Transplantation/adverse effects/*ethics/*legislation & jurisprudence
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  • 216
    Publication Date: 2013-04-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Russell, Jonathan F -- England -- Nature. 2013 Apr 4;496(7443):7. doi: 10.1038/496007a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉jonathan.russell@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23552910" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/economics/manpower/*methods/*standards ; Publishing/economics/trends ; Reproducibility of Results ; Research Design/*standards ; Research Personnel/psychology ; Scientific Misconduct/ethics/statistics & numerical data ; Validation Studies as Topic
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  • 217
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    Nature Publishing Group (NPG)
    Publication Date: 2013-05-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yong, Ed -- England -- Nature. 2013 May 16;497(7449):297-9. doi: 10.1038/497297a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23676731" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Child ; China ; Eugenics ; Genome, Human/genetics ; Genomics ; Great Britain ; Humans ; Intelligence/*genetics ; Intelligence Tests ; Learning Disorders/genetics ; Male ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Sample Size ; Sequence Analysis, DNA ; Uncertainty ; United States
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  • 218
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    Nature Publishing Group (NPG)
    Publication Date: 2013-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Noorden, Richard -- England -- Nature. 2013 Jul 4;499(7456):13-4. doi: 10.1038/499013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823771" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/statistics & numerical data ; *Biofuels/supply & distribution/utilization ; Environmental Policy/economics/*legislation & jurisprudence ; *European Union/economics ; *Policy Making ; Renewable Energy/*statistics & numerical data ; Reproducibility of Results
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  • 219
    Publication Date: 2013-03-15
    Description: Magnetic resonance is an exceptionally powerful and versatile measurement technique. The basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50 years, being mainly restricted to the qualitative probing of only a limited set of the properties that can in principle be accessed by this technique. Here we introduce an approach to data acquisition, post-processing and visualization--which we term 'magnetic resonance fingerprinting' (MRF)--that permits the simultaneous non-invasive quantification of multiple important properties of a material or tissue. MRF thus provides an alternative way to quantitatively detect and analyse complex changes that can represent physical alterations of a substance or early indicators of disease. MRF can also be used to identify the presence of a specific target material or tissue, which will increase the sensitivity, specificity and speed of a magnetic resonance study, and potentially lead to new diagnostic testing methodologies. When paired with an appropriate pattern-recognition algorithm, MRF inherently suppresses measurement errors and can thus improve measurement accuracy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602925/" 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/PMC3602925/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, Dan -- Gulani, Vikas -- Seiberlich, Nicole -- Liu, Kecheng -- Sunshine, Jeffrey L -- Duerk, Jeffrey L -- Griswold, Mark A -- KL2 TR000440/TR/NCATS NIH HHS/ -- R01 HL094557/HL/NHLBI NIH HHS/ -- R01HL094557/HL/NHLBI NIH HHS/ -- England -- Nature. 2013 Mar 14;495(7440):187-92. doi: 10.1038/nature11971.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23486058" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Diagnostic Tests, Routine/*methods ; Humans ; Magnetic Resonance Spectroscopy/*methods ; Motion ; Pattern Recognition, Automated ; Phantoms, Imaging ; Reproducibility of Results ; Research Design ; Sensitivity and Specificity
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  • 220
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    Nature Publishing Group (NPG)
    Publication Date: 2013-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hughes, Virginia -- England -- Nature. 2013 May 23;497(7450):428-30. doi: 10.1038/497428a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23698426" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Body Mass Index ; Cause of Death ; Confounding Factors (Epidemiology) ; Humans ; *Life Expectancy ; Longevity/physiology ; Meta-Analysis as Topic ; Overweight/*mortality ; Public Health/*statistics & numerical data ; Reproducibility of Results ; Sex Factors ; Smoking/epidemiology
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  • 221
    Publication Date: 2013-07-05
    Description: We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4087036/" 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/PMC4087036/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galagan, James E -- Minch, Kyle -- Peterson, Matthew -- Lyubetskaya, Anna -- Azizi, Elham -- Sweet, Linsday -- Gomes, Antonio -- Rustad, Tige -- Dolganov, Gregory -- Glotova, Irina -- Abeel, Thomas -- Mahwinney, Chris -- Kennedy, Adam D -- Allard, Rene -- Brabant, William -- Krueger, Andrew -- Jaini, Suma -- Honda, Brent -- Yu, Wen-Han -- Hickey, Mark J -- Zucker, Jeremy -- Garay, Christopher -- Weiner, Brian -- Sisk, Peter -- Stolte, Christian -- Winkler, Jessica K -- Van de Peer, Yves -- Iazzetti, Paul -- Camacho, Diogo -- Dreyfuss, Jonathan -- Liu, Yang -- Dorhoi, Anca -- Mollenkopf, Hans-Joachim -- Drogaris, Paul -- Lamontagne, Julie -- Zhou, Yiyong -- Piquenot, Julie -- Park, Sang Tae -- Raman, Sahadevan -- Kaufmann, Stefan H E -- Mohney, Robert P -- Chelsky, Daniel -- Moody, D Branch -- Sherman, David R -- Schoolnik, Gary K -- HHSN272200800059C/AI/NIAID NIH HHS/ -- HHSN272200800059C/PHS HHS/ -- R01 AI 071155/AI/NIAID NIH HHS/ -- R01 AI071155/AI/NIAID NIH HHS/ -- U19 AI 076217/AI/NIAID NIH HHS/ -- U19 AI076217/AI/NIAID NIH HHS/ -- England -- Nature. 2013 Jul 11;499(7457):178-83. doi: 10.1038/nature12337. Epub 2013 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA. jgalag@bu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823726" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Anoxia/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Binding Sites ; Chromatin Immunoprecipitation ; Gene Expression Profiling ; *Gene Regulatory Networks/genetics ; Genomics ; Lipid Metabolism/genetics ; Metabolic Networks and Pathways/*genetics ; Models, Biological ; Mycobacterium tuberculosis/drug effects/*genetics/*metabolism/physiology ; Oxygen/pharmacology ; Proteolysis ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcription Factors/genetics/metabolism ; Tuberculosis/metabolism/microbiology
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  • 222
    Publication Date: 2013-10-15
    Description: The biogenic amine transporters (BATs) regulate endogenous neurotransmitter concentrations and are targets for a broad range of therapeutic agents including selective serotonin reuptake inhibitors (SSRIs), serotonin-noradrenaline reuptake inhibitors (SNRIs) and tricyclic antidepressants (TCAs). Because eukaryotic BATs are recalcitrant to crystallographic analysis, our understanding of the mechanism of these inhibitors and antidepressants is limited. LeuT is a bacterial homologue of BATs and has proven to be a valuable paradigm for understanding relationships between their structure and function. However, because only approximately 25% of the amino acid sequence of LeuT is in common with that of BATs, and as LeuT is a promiscuous amino acid transporter, it does not recapitulate the pharmacological properties of BATs. Indeed, SSRIs and TCAs bind in the extracellular vestibule of LeuT and act as non-competitive inhibitors of transport. By contrast, multiple studies demonstrate that both TCAs and SSRIs are competitive inhibitors for eukaryotic BATs and bind to the primary binding pocket. Here we engineered LeuT to harbour human BAT-like pharmacology by mutating key residues around the primary binding pocket. The final LeuBAT mutant binds the SSRI sertraline with a binding constant of 18 nM and displays high-affinity binding to a range of SSRIs, SNRIs and a TCA. We determined 12 crystal structures of LeuBAT in complex with four classes of antidepressants. The chemically diverse inhibitors have a remarkably similar mode of binding in which they straddle transmembrane helix (TM) 3, wedge between TM3/TM8 and TM1/TM6, and lock the transporter in a sodium- and chloride-bound outward-facing open conformation. Together, these studies define common and simple principles for the action of SSRIs, SNRIs and TCAs on BATs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904662/" 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/PMC3904662/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Hui -- Goehring, April -- Wang, Kevin H -- Penmatsa, Aravind -- Ressler, Ryan -- Gouaux, Eric -- R37 MH070039/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Nov 7;503(7474):141-5. doi: 10.1038/nature12648. Epub 2013 Oct 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24121440" target="_blank"〉PubMed〈/a〉
    Keywords: Antidepressive Agents, Second-Generation/metabolism/*pharmacology ; Antidepressive Agents, Tricyclic/metabolism/*pharmacology ; Bacterial Proteins/antagonists & inhibitors/chemistry/genetics/metabolism ; Binding, Competitive/drug effects ; Biogenic Amines/*metabolism ; Chlorides/metabolism ; Crystallography, X-Ray ; Humans ; Mazindol/metabolism/pharmacology ; Models, Molecular ; Mutation ; Norepinephrine/metabolism ; *Plasma Membrane Neurotransmitter Transport Proteins/antagonists & ; inhibitors/chemistry/genetics/metabolism ; Protein Conformation/drug effects ; Recombinant Fusion Proteins/*chemistry/genetics/metabolism ; Reproducibility of Results ; Serotonin Plasma Membrane Transport Proteins/*chemistry/genetics/*metabolism ; Serotonin Uptake Inhibitors/metabolism/*pharmacology ; Sertraline/metabolism/pharmacology ; Sodium/metabolism ; Structure-Activity Relationship
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  • 223
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    Nature Publishing Group (NPG)
    Publication Date: 2013-04-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Vivien -- England -- Nature. 2013 Apr 11;496(7444):253-8. doi: 10.1038/496253a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23579682" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Aggregation/drug effects ; Cell Culture Techniques/instrumentation/*methods ; Cell Division/drug effects ; Cell Transdifferentiation/drug effects ; Coculture Techniques ; Collagen/chemistry ; Cryopreservation ; Culture Media/*chemistry/*pharmacology ; Drug Combinations ; Drug Evaluation, Preclinical/instrumentation/methods ; Embryoid Bodies/cytology/drug effects ; Humans ; Induced Pluripotent Stem Cells/cytology/drug effects ; Laminin/chemistry ; Magnetic Fields ; Neurons/cytology/drug effects ; Proteoglycans/chemistry ; Reproducibility of Results ; Serum/chemistry
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  • 224
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2013-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Jul 11;499(7457):125-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23858536" target="_blank"〉PubMed〈/a〉
    Keywords: Germany ; *Guidelines as Topic ; Plagiarism ; Punishment ; Reproducibility of Results ; Research Support as Topic/*organization & administration ; *Scientific Misconduct/legislation & jurisprudence ; Universities ; *Whistleblowing/legislation & jurisprudence
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  • 225
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    Nature Publishing Group (NPG)
    Publication Date: 2013-11-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Watson, Traci -- England -- Nature. 2013 Nov 21;503(7476):322-3. doi: 10.1038/503322a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24256786" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/*methods ; Dissent and Disputes ; Ecosystem ; *Lions/physiology ; Nigeria ; Population Density ; Reproducibility of Results
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  • 226
    Publication Date: 2013-11-29
    Description: Two large-scale pharmacogenomic studies were published recently in this journal. Genomic data are well correlated between studies; however, the measured drug response data are highly discordant. Although the source of inconsistencies remains uncertain, it has potential implications for using these outcome measures to assess gene-drug associations or select potential anticancer drugs on the basis of their reported results.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237165/" 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/PMC4237165/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haibe-Kains, Benjamin -- El-Hachem, Nehme -- Birkbak, Nicolai Juul -- Jin, Andrew C -- Beck, Andrew H -- Aerts, Hugo J W L -- Quackenbush, John -- CA087969/CA/NCI NIH HHS/ -- P01 CA087969/CA/NCI NIH HHS/ -- U19 CA148065/CA/NCI NIH HHS/ -- U19 CA148065-01/CA/NCI NIH HHS/ -- England -- Nature. 2013 Dec 19;504(7480):389-93. doi: 10.1038/nature12831. Epub 2013 Nov 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institut de Recherches Cliniques de Montreal, University of Montreal, Montreal, Quebec, Canada [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada. ; Institut de Recherches Cliniques de Montreal, University of Montreal, Montreal, Quebec, Canada. ; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark. ; Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, USA. ; 1] Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, USA [2]. ; 1] Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Radiation Oncology & Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA [3] Department of Radiation Oncology, Maastricht University, Maastricht 6200 MD, The Netherlands [4]. ; 1] Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [3].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24284626" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/*pharmacology ; Area Under Curve ; Cell Line ; Drug Resistance, Neoplasm/drug effects/genetics ; Gene Expression Profiling ; Genome, Human/genetics ; Humans ; Inhibitory Concentration 50 ; Neoplasms/drug therapy/genetics/pathology ; *Pharmacogenetics ; Reproducibility of Results
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  • 227
    Publication Date: 2014-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉See, Linda -- Fritz, Steffen -- McCallum, Ian -- England -- Nature. 2014 Oct 9;514(7521):168. doi: 10.1038/514168a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉International Institute for Applied Systems Analysis, Laxenburg, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25297427" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Biodiversity ; Calibration ; Environmental Monitoring ; *Information Dissemination ; Reproducibility of Results ; *Satellite Imagery ; Trees
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  • 228
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    Nature Publishing Group (NPG)
    Publication Date: 2014-03-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perrin, Steve -- England -- Nature. 2014 Mar 27;507(7493):423-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24678540" target="_blank"〉PubMed〈/a〉
    Keywords: Amyotrophic Lateral Sclerosis/genetics/pathology/therapy ; Animals ; Cause of Death ; Clinical Trials as Topic/economics/standards ; *Disease Models, Animal ; Disease Progression ; Dose-Response Relationship, Drug ; Drug Evaluation, Preclinical/economics/*methods/*standards ; False Positive Reactions ; Guidelines as Topic ; Half-Life ; Humans ; Mice ; Organ Specificity ; Reproducibility of Results ; *Research Design ; Superoxide Dismutase/deficiency/genetics/metabolism ; Survival Analysis ; Translational Medical Research/economics/*methods/*standards ; Treatment Failure
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  • 229
    Publication Date: 2013-11-29
    Description: Achieving the goal of malaria elimination will depend on targeting Plasmodium pathways essential across all life stages. Here we identify a lipid kinase, phosphatidylinositol-4-OH kinase (PI(4)K), as the target of imidazopyrazines, a new antimalarial compound class that inhibits the intracellular development of multiple Plasmodium species at each stage of infection in the vertebrate host. Imidazopyrazines demonstrate potent preventive, therapeutic, and transmission-blocking activity in rodent malaria models, are active against blood-stage field isolates of the major human pathogens P. falciparum and P. vivax, and inhibit liver-stage hypnozoites in the simian parasite P. cynomolgi. We show that imidazopyrazines exert their effect through inhibitory interaction with the ATP-binding pocket of PI(4)K, altering the intracellular distribution of phosphatidylinositol-4-phosphate. Collectively, our data define PI(4)K as a key Plasmodium vulnerability, opening up new avenues of target-based discovery to identify drugs with an ideal activity profile for the prevention, treatment and elimination of malaria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940870/" 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/PMC3940870/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McNamara, Case W -- Lee, Marcus C S -- Lim, Chek Shik -- Lim, Siau Hoi -- Roland, Jason -- Nagle, Advait -- Simon, Oliver -- Yeung, Bryan K S -- Chatterjee, Arnab K -- McCormack, Susan L -- Manary, Micah J -- Zeeman, Anne-Marie -- Dechering, Koen J -- Kumar, T R Santha -- Henrich, Philipp P -- Gagaring, Kerstin -- Ibanez, Maureen -- Kato, Nobutaka -- Kuhen, Kelli L -- Fischli, Christoph -- Rottmann, Matthias -- Plouffe, David M -- Bursulaya, Badry -- Meister, Stephan -- Rameh, Lucia -- Trappe, Joerg -- Haasen, Dorothea -- Timmerman, Martijn -- Sauerwein, Robert W -- Suwanarusk, Rossarin -- Russell, Bruce -- Renia, Laurent -- Nosten, Francois -- Tully, David C -- Kocken, Clemens H M -- Glynne, Richard J -- Bodenreider, Christophe -- Fidock, David A -- Diagana, Thierry T -- Winzeler, Elizabeth A -- 078285/Wellcome Trust/United Kingdom -- 089275/Wellcome Trust/United Kingdom -- 090534/Wellcome Trust/United Kingdom -- 096157/Wellcome Trust/United Kingdom -- R01 AI079709/AI/NIAID NIH HHS/ -- R01 AI085584/AI/NIAID NIH HHS/ -- R01 AI090141/AI/NIAID NIH HHS/ -- R01 AI103058/AI/NIAID NIH HHS/ -- R01079709/PHS HHS/ -- R01085584/PHS HHS/ -- R01AI090141/AI/NIAID NIH HHS/ -- WT078285/Wellcome Trust/United Kingdom -- WT096157/Wellcome Trust/United Kingdom -- England -- Nature. 2013 Dec 12;504(7479):248-53. doi: 10.1038/nature12782. Epub 2013 Nov 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA [2]. ; 1] Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032, USA [2]. ; Novartis Institutes for Tropical Disease, 138670 Singapore. ; Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA. ; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA. ; Department of Parasitology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands. ; TropIQ Health Sciences, 6525 GA Nijmegen, The Netherlands. ; Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032, USA. ; Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland. ; 1] Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland [2] University of Basel, CH-4003 Basel, Switzerland. ; Department of Medicine, School of Medicine, Boston University, Boston, Massachusetts 02118, USA. ; Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. ; 1] TropIQ Health Sciences, 6525 GA Nijmegen, The Netherlands [2] Department of Medical Microbiology, Radboud University, Nijmegen Medical CentrePO Box 9101, 6500 HB Nijmegen, The Netherlands. ; Laboratory of Malaria Immunobiology, Singapore Immunology Network, Agency for Science Technology and Research (A*STAR), Biopolis, 138648 Singapore. ; 1] Laboratory of Malaria Immunobiology, Singapore Immunology Network, Agency for Science Technology and Research (A*STAR), Biopolis, 138648 Singapore [2] Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 117545 Singapore. ; 1] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK [2] Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand. ; 1] Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032, USA [2] Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA. ; 1] Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA [2] Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24284631" target="_blank"〉PubMed〈/a〉
    Keywords: 1-Phosphatidylinositol 4-Kinase/*antagonists & ; inhibitors/chemistry/genetics/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Cytokinesis/drug effects ; Drug Resistance/drug effects/genetics ; Fatty Acids/metabolism ; Female ; Hepatocytes/parasitology ; Humans ; Imidazoles/metabolism/pharmacology ; Life Cycle Stages/drug effects ; Macaca mulatta ; Malaria/*drug therapy/*parasitology ; Male ; Models, Biological ; Models, Molecular ; Phosphatidylinositol Phosphates/metabolism ; Plasmodium/classification/*drug effects/*enzymology/growth & development ; Pyrazoles/metabolism/pharmacology ; Quinoxalines/metabolism/pharmacology ; Reproducibility of Results ; Schizonts/cytology/drug effects ; rab GTP-Binding Proteins/genetics/metabolism
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  • 230
    Publication Date: 2014-06-05
    Description: Transcriptional enhancers are crucial regulators of gene expression and animal development and the characterization of their genomic organization, spatiotemporal activities and sequence properties is a key goal in modern biology. Here we characterize the in vivo activity of 7,705 Drosophila melanogaster enhancer candidates covering 13.5% of the non-coding non-repetitive genome throughout embryogenesis. 3,557 (46%) candidates are active, suggesting a high density with 50,000 to 100,000 developmental enhancers genome-wide. The vast majority of enhancers display specific spatial patterns that are highly dynamic during development. Most appear to regulate their neighbouring genes, suggesting that the cis-regulatory genome is organized locally into domains, which are supported by chromosomal domains, insulator binding and genome evolution. However, 12 to 21 per cent of enhancers appear to skip non-expressed neighbours and regulate a more distal gene. Finally, we computationally identify cis-regulatory motifs that are predictive and required for enhancer activity, as we validate experimentally. This work provides global insights into the organization of an animal regulatory genome and the make-up of enhancer sequences and confirms and generalizes principles from previous studies. All enhancer patterns are annotated manually with a controlled vocabulary and all results are available through a web interface (http://enhancers.starklab.org), including the raw images of all microscopy slides for manual inspection at arbitrary zoom levels.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kvon, Evgeny Z -- Kazmar, Tomas -- Stampfel, Gerald -- Yanez-Cuna, J Omar -- Pagani, Michaela -- Schernhuber, Katharina -- Dickson, Barry J -- Stark, Alexander -- England -- Nature. 2014 Aug 7;512(7512):91-5. doi: 10.1038/nature13395. Epub 2014 Jun 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Research Institute of Molecular Pathology (IMP), Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria [2] Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147, USA (B.J.D.); Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA (E.Z.K.). ; Research Institute of Molecular Pathology (IMP), Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria. ; 1] Research Institute of Molecular Pathology (IMP), Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24896182" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila melanogaster/*embryology/*genetics ; Embryonic Development/*genetics ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation, Developmental/*genetics ; Genome, Insect/*genetics ; Internet ; Nucleotide Motifs/genetics ; Organ Specificity/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Reproducibility of Results ; User-Computer Interface
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  • 231
    Publication Date: 2014-02-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, Simon L -- England -- Nature. 2014 Feb 27;506(7489):409. doi: 10.1038/506409a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24572388" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; *Dissent and Disputes ; Floods/statistics & numerical data ; Great Britain ; Journalism/standards ; Mass Media/standards ; *Public Opinion ; Rain ; Reproducibility of Results ; Uncertainty
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  • 232
    Publication Date: 2013-12-18
    Description: The protozoan parasites Trypanosoma brucei spp. cause important human and livestock diseases in sub-Saharan Africa. In mammalian blood, two developmental forms of the parasite exist: proliferative 'slender' forms and arrested 'stumpy' forms that are responsible for transmission to tsetse flies. The slender to stumpy differentiation is a density-dependent response that resembles quorum sensing in microbial systems and is crucial for the parasite life cycle, ensuring both infection chronicity and disease transmission. This response is triggered by an elusive 'stumpy induction factor' (SIF) whose intracellular signalling pathway is also uncharacterized. Laboratory-adapted (monomorphic) trypanosome strains respond inefficiently to SIF but can generate forms with stumpy characteristics when exposed to cell-permeable cAMP and AMP analogues. Exploiting this, we have used a genome-wide RNA interference library screen to identify the signalling components driving stumpy formation. In separate screens, monomorphic parasites were exposed to 8-(4-chlorophenylthio)-cAMP (pCPT-cAMP) or 8-pCPT-2'-O-methyl-5'-AMP to select cells that were unresponsive to these signals and hence remained proliferative. Genome-wide Ion Torrent based RNAi target sequencing identified cohorts of genes implicated in each step of the signalling pathway, from purine metabolism, through signal transducers (kinases, phosphatases) to gene expression regulators. Genes at each step were independently validated in cells naturally capable of stumpy formation, confirming their role in density sensing in vivo. The putative RNA-binding protein, RBP7, was required for normal quorum sensing and promoted cell-cycle arrest and transmission competence when overexpressed. This study reveals that quorum sensing signalling in trypanosomes shares similarities to fundamental quiescence pathways in eukaryotic cells, its components providing targets for quorum-sensing interference-based therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3908871/" 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/PMC3908871/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mony, Binny M -- MacGregor, Paula -- Ivens, Alasdair -- Rojas, Federico -- Cowton, Andrew -- Young, Julie -- Horn, David -- Matthews, Keith -- 088293/Wellcome Trust/United Kingdom -- 088293MA/Wellcome Trust/United Kingdom -- 095831/Wellcome Trust/United Kingdom -- 095831MA/Wellcome Trust/United Kingdom -- 100320/Wellcome Trust/United Kingdom -- 100320/Z/12/Z/Wellcome Trust/United Kingdom -- BB/I004602/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2014 Jan 30;505(7485):681-5. doi: 10.1038/nature12864. Epub 2013 Dec 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK [2]. ; Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK. ; Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336212" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cyclic AMP/metabolism ; G1 Phase ; G1 Phase Cell Cycle Checkpoints ; Gene Expression Regulation ; Genome/*genetics ; Protein Kinases/genetics ; Quorum Sensing/*genetics ; RNA Interference ; RNA-Binding Proteins/genetics/metabolism ; Reproducibility of Results ; Signal Transduction/*genetics ; Trypanosoma brucei brucei/enzymology/*genetics/growth & development/*metabolism
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  • 233
    Publication Date: 2014-08-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hanage, William P -- England -- Nature. 2014 Aug 21;512(7514):247-8. doi: 10.1038/512247a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard School of Public Health in Boston, Massachusetts, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25143098" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Humans ; *Microbiota/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Science/*standards ; *Uncertainty
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  • 234
    Publication Date: 2014-04-18
    Description: Ice volume (and hence sea level) and deep-sea temperature are key measures of global climate change. Sea level has been documented using several independent methods over the past 0.5 million years (Myr). Older periods, however, lack such independent validation; all existing records are related to deep-sea oxygen isotope (delta(18)O) data that are influenced by processes unrelated to sea level. For deep-sea temperature, only one continuous high-resolution (Mg/Ca-based) record exists, with related sea-level estimates, spanning the past 1.5 Myr. Here we present a novel sea-level reconstruction, with associated estimates of deep-sea temperature, which independently validates the previous 0-1.5 Myr reconstruction and extends it back to 5.3 Myr ago. We find that deep-sea temperature and sea level generally decreased through time, but distinctly out of synchrony, which is remarkable given the importance of ice-albedo feedbacks on the radiative forcing of climate. In particular, we observe a large temporal offset during the onset of Plio-Pleistocene ice ages, between a marked cooling step at 2.73 Myr ago and the first major glaciation at 2.15 Myr ago. Last, we tentatively infer that ice sheets may have grown largest during glacials with more modest reductions in deep-sea temperature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rohling, E J -- Foster, G L -- Grant, K M -- Marino, G -- Roberts, A P -- Tamisiea, M E -- Williams, F -- England -- Nature. 2014 Apr 24;508(7497):477-82. doi: 10.1038/nature13230. Epub 2014 Apr 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Research School of Earth Sciences, The Australian National University, Canberra 0200, Australia [2] Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton SO14 3ZH, UK. ; Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton SO14 3ZH, UK. ; Research School of Earth Sciences, The Australian National University, Canberra 0200, Australia. ; National Oceanography Centre, Joseph Proudman Building, Liverpool L3 5DA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24739960" target="_blank"〉PubMed〈/a〉
    Keywords: Foraminifera ; History, Ancient ; Ice Cover ; Mediterranean Sea ; Oxygen Isotopes ; Reproducibility of Results ; Seawater/*analysis ; *Temperature ; Time Factors
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  • 235
    Publication Date: 2014-05-09
    Description: Electromagnetic noise is emitted everywhere humans use electronic devices. For decades, it has been hotly debated whether man-made electric and magnetic fields affect biological processes, including human health. So far, no putative effect of anthropogenic electromagnetic noise at intensities below the guidelines adopted by the World Health Organization has withstood the test of independent replication under truly blinded experimental conditions. No effect has therefore been widely accepted as scientifically proven. Here we show that migratory birds are unable to use their magnetic compass in the presence of urban electromagnetic noise. When European robins, Erithacus rubecula, were exposed to the background electromagnetic noise present in unscreened wooden huts at the University of Oldenburg campus, they could not orient using their magnetic compass. Their magnetic orientation capabilities reappeared in electrically grounded, aluminium-screened huts, which attenuated electromagnetic noise in the frequency range from 50 kHz to 5 MHz by approximately two orders of magnitude. When the grounding was removed or when broadband electromagnetic noise was deliberately generated inside the screened and grounded huts, the birds again lost their magnetic orientation capabilities. The disruptive effect of radiofrequency electromagnetic fields is not confined to a narrow frequency band and birds tested far from sources of electromagnetic noise required no screening to orient with their magnetic compass. These fully double-blinded tests document a reproducible effect of anthropogenic electromagnetic noise on the behaviour of an intact vertebrate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Engels, Svenja -- Schneider, Nils-Lasse -- Lefeldt, Nele -- Hein, Christine Maira -- Zapka, Manuela -- Michalik, Andreas -- Elbers, Dana -- Kittel, Achim -- Hore, P J -- Mouritsen, Henrik -- England -- Nature. 2014 May 15;509(7500):353-6. doi: 10.1038/nature13290. Epub 2014 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institut fur Biologie und Umweltwissenschaften, Universitat Oldenburg, D-26111 Oldenburg, Germany [2] Research Centre for Neurosensory Sciences, University of Oldenburg, D-26111 Oldenburg, Germany [3]. ; 1] Institut fur Biologie und Umweltwissenschaften, Universitat Oldenburg, D-26111 Oldenburg, Germany [2] Research Centre for Neurosensory Sciences, University of Oldenburg, D-26111 Oldenburg, Germany. ; Institute of Physics, University of Oldenburg, D-26111 Oldenburg, Germany. ; Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24805233" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum ; Animal Migration/*physiology ; Animals ; Cities ; Conservation of Natural Resources ; Double-Blind Method ; Electricity/adverse effects ; Electromagnetic Fields/*adverse effects ; Electronics/instrumentation ; Germany ; Housing ; *Magnetic Fields ; Orientation/*physiology ; Radio Waves/adverse effects ; Reproducibility of Results ; Seasons ; Songbirds/*physiology ; Universities
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  • 236
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    Nature Publishing Group (NPG)
    Publication Date: 2014-01-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2014 Jan 9;505(7482):139-40. doi: 10.1038/505139a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24402259" target="_blank"〉PubMed〈/a〉
    Keywords: Child ; Clinical Trials as Topic/adverse effects/*ethics/legislation & ; jurisprudence/standards ; Confidentiality/legislation & jurisprudence ; Foundations ; Humans ; Italy ; Mesenchymal Stromal Cells/cytology ; Neural Stem Cells/cytology/transplantation ; Reproducibility of Results ; Stem Cell Transplantation/*adverse effects/*ethics/legislation & ; jurisprudence/standards ; Uncertainty
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  • 237
    Publication Date: 2013-12-03
    Description: The increasing demands placed on natural resources for fuel and food production require that we explore the use of efficient, sustainable feedstocks such as brown macroalgae. The full potential of brown macroalgae as feedstocks for commercial-scale fuel ethanol production, however, requires extensive re-engineering of the alginate and mannitol catabolic pathways in the standard industrial microbe Saccharomyces cerevisiae. Here we present the discovery of an alginate monomer (4-deoxy-L-erythro-5-hexoseulose uronate, or DEHU) transporter from the alginolytic eukaryote Asteromyces cruciatus. The genomic integration and overexpression of the gene encoding this transporter, together with the necessary bacterial alginate and deregulated native mannitol catabolism genes, conferred the ability of an S. cerevisiae strain to efficiently metabolize DEHU and mannitol. When this platform was further adapted to grow on mannitol and DEHU under anaerobic conditions, it was capable of ethanol fermentation from mannitol and DEHU, achieving titres of 4.6% (v/v) (36.2 g l(-1)) and yields up to 83% of the maximum theoretical yield from consumed sugars. These results show that all major sugars in brown macroalgae can be used as feedstocks for biofuels and value-added renewable chemicals in a manner that is comparable to traditional arable-land-based feedstocks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Enquist-Newman, Maria -- Faust, Ann Marie E -- Bravo, Daniel D -- Santos, Christine Nicole S -- Raisner, Ryan M -- Hanel, Arthur -- Sarvabhowman, Preethi -- Le, Chi -- Regitsky, Drew D -- Cooper, Susan R -- Peereboom, Lars -- Clark, Alana -- Martinez, Yessica -- Goldsmith, Joshua -- Cho, Min Y -- Donohoue, Paul D -- Luo, Lily -- Lamberson, Brigit -- Tamrakar, Pramila -- Kim, Edward J -- Villari, Jeffrey L -- Gill, Avinash -- Tripathi, Shital A -- Karamchedu, Padma -- Paredes, Carlos J -- Rajgarhia, Vineet -- Kotlar, Hans Kristian -- Bailey, Richard B -- Miller, Dennis J -- Ohler, Nicholas L -- Swimmer, Candace -- Yoshikuni, Yasuo -- England -- Nature. 2014 Jan 9;505(7482):239-43. doi: 10.1038/nature12771. Epub 2013 Dec 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2]. ; 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] Manus Biosynthesis Inc., 790 Memorial Drive, Suite 102, Cambridge, Massachusetts 02139 (C.N.S.S.); Calysta Energy, 1140 O'Brien Drive, Menlo Park, California 94025 (D.D.R.); Sutro Biopharma lnc., 310 Utah Avenue, Suite 150, South San Francisco, California 94080, USA (A.G.); Total New Energies USA, 5858 Horton Street, Emeryville, California 94560 (S.A.T.; V.R.). ; Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA. ; Department of Chemical Engineering and Materials Science, Michigan State University, 2527 Engineering Building, East Lansing, Michigan 48824-1226, USA. ; Statoil ASA, Statoil Research Centre, Arkitekt Ebbells vei 10, Rotvoll, 7005 Trondheim, Norway. ; 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] BALChile S.A., Badajoz 100, Oficina 1404, Las Condes, Santiago 7550000, Chile [3] BAL Biofuels S.A., Badajoz 100, Oficina 1404, Las Condes, Santiago 7550000, Chile.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24291791" target="_blank"〉PubMed〈/a〉
    Keywords: Alginates/metabolism ; Anaerobiosis ; Ascomycota/genetics/metabolism ; Biofuels/*supply & distribution ; Biotechnology ; *Carbohydrate Metabolism ; Carrier Proteins/genetics/metabolism ; Ethanol/*metabolism ; Evolution, Molecular ; Fermentation ; Genetic Complementation Test ; *Genetic Engineering ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; Mannitol/metabolism ; Phaeophyta/genetics/*metabolism ; Quinic Acid/metabolism ; Reproducibility of Results ; Saccharomyces cerevisiae/genetics/*metabolism ; Seaweed/genetics/metabolism ; Uronic Acids/metabolism
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  • 238
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    Nature Publishing Group (NPG)
    Publication Date: 2014-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nuzzo, Regina -- England -- Nature. 2014 Feb 13;506(7487):150-2. doi: 10.1038/506150a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gallaudet University in Washington DC.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24522584" target="_blank"〉PubMed〈/a〉
    Keywords: *Data Interpretation, Statistical ; Data Mining ; Reproducibility of Results ; Research Design/*standards
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  • 239
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    Nature Publishing Group (NPG)
    Publication Date: 2014-04-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2014 Apr 17;508(7496):299. doi: 10.1038/508299a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24740046" target="_blank"〉PubMed〈/a〉
    Keywords: Acids/pharmacology ; Cell Dedifferentiation/drug effects ; Induced Pluripotent Stem Cells/cytology/drug effects ; Japan ; Lymphocytes/cytology/drug effects ; Pressure ; Reproducibility of Results ; Research Personnel/*ethics/*psychology/standards ; *Scientific Misconduct ; Stem Cell Research/*ethics ; Uncertainty
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  • 240
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    Nature Publishing Group (NPG)
    Publication Date: 2014-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bohle, Shannon -- England -- Nature. 2014 Feb 13;506(7487):159. doi: 10.1038/506159e.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24522589" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information ; *Internet/economics ; *Laboratories ; Patents as Topic ; *Records as Topic/economics ; Reproducibility of Results ; United States
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  • 241
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    Nature Publishing Group (NPG)
    Publication Date: 2014-02-01
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058759/" 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/PMC4058759/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collins, Francis S -- Tabak, Lawrence A -- Z99 OD999999/Intramural NIH HHS/ -- England -- Nature. 2014 Jan 30;505(7485):612-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24482835" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Animals ; Biomedical Research/*standards ; Disclosure/standards ; Female ; Humans ; Male ; *National Institutes of Health (U.S.) ; Pilot Projects ; Reproducibility of Results ; Research Design/*standards ; Scientific Misconduct/statistics & numerical data ; Sex Characteristics ; United States
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  • 242
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    Nature Publishing Group (NPG)
    Publication Date: 2014-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Vivien -- England -- Nature. 2014 May 29;509(7502):645-9. doi: 10.1038/509645a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nature and Nature Methods.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24870547" target="_blank"〉PubMed〈/a〉
    Keywords: Anatomy, Artistic ; Antibodies/analysis/immunology ; Antibody Specificity ; Atlases as Topic ; Automation ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; Immunohistochemistry ; Organ Specificity ; Protein Transport ; Proteome/analysis/genetics/*metabolism/secretion ; Reproducibility of Results ; Staining and Labeling ; Tissue Array Analysis
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  • 243
    Publication Date: 2014-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barbier, Edward B -- England -- Nature. 2014 Nov 6;515(7525):32-3. doi: 10.1038/515032a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Wyoming, Laramie, Wyoming, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25373661" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/*economics/*statistics & numerical data ; *Ecosystem ; *Models, Economic ; Pilot Projects ; Reproducibility of Results ; Rhizophoraceae ; Thailand ; Wood
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  • 244
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    Nature Publishing Group (NPG)
    Publication Date: 2014-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katsnelson, Alla -- England -- Nature. 2014 Apr 3;508(7494):S8-9. doi: 10.1038/508S8a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24695336" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antipsychotic Agents/therapeutic use ; Cognition/physiology ; Cognition Disorders/drug therapy/pathology/physiopathology ; *Disease Models, Animal ; Drug Discovery/*methods/standards ; Humans ; Mice ; Mice, Transgenic ; Multifactorial Inheritance/genetics ; Rats ; Reproducibility of Results ; *Schizophrenia/chemically induced/drug therapy/etiology/physiopathology
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  • 245
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sohn, Emily -- England -- Nature. 2015 Dec 17;528(7582):S120-2. doi: 10.1038/528S120a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26672781" target="_blank"〉PubMed〈/a〉
    Keywords: Early Diagnosis ; False Positive Reactions ; Humans ; Male ; Mass Screening/trends ; Prognosis ; Prostate-Specific Antigen/*blood ; Prostatic Neoplasms/*blood/*diagnosis/psychology ; Reproducibility of Results ; Risk Assessment ; Stress, Psychological/etiology/prevention & control
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  • 246
    Publication Date: 2015-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hicks, Diana -- Wouters, Paul -- Waltman, Ludo -- de Rijcke, Sarah -- Rafols, Ismael -- England -- Nature. 2015 Apr 23;520(7548):429-31. doi: 10.1038/520429a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Georgia Institute of Technology, Atlanta, Georgia, USA. ; Centre for Science and Technology Studies, Leiden University, the Netherlands. ; Spanish National Research Council and the Polytechnic University of Valencia, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25903611" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Achievement ; *Bibliometrics/history ; Blogging/utilization ; Career Mobility ; *Guidelines as Topic ; History, 20th Century ; History, 21st Century ; Journal Impact Factor/history ; Reproducibility of Results ; Research/*standards/*statistics & numerical data ; Research Personnel/*standards/statistics & numerical data
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  • 247
    Publication Date: 2014-04-04
    Description: Cancers have dysfunctional redox regulation resulting in reactive oxygen species production, damaging both DNA and free dNTPs. The MTH1 protein sanitizes oxidized dNTP pools to prevent incorporation of damaged bases during DNA replication. Although MTH1 is non-essential in normal cells, we show that cancer cells require MTH1 activity to avoid incorporation of oxidized dNTPs, resulting in DNA damage and cell death. We validate MTH1 as an anticancer target in vivo and describe small molecules TH287 and TH588 as first-in-class nudix hydrolase family inhibitors that potently and selectively engage and inhibit the MTH1 protein in cells. Protein co-crystal structures demonstrate that the inhibitors bind in the active site of MTH1. The inhibitors cause incorporation of oxidized dNTPs in cancer cells, leading to DNA damage, cytotoxicity and therapeutic responses in patient-derived mouse xenografts. This study exemplifies the non-oncogene addiction concept for anticancer treatment and validates MTH1 as being cancer phenotypic lethal.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gad, Helge -- Koolmeister, Tobias -- Jemth, Ann-Sofie -- Eshtad, Saeed -- Jacques, Sylvain A -- Strom, Cecilia E -- Svensson, Linda M -- Schultz, Niklas -- Lundback, Thomas -- Einarsdottir, Berglind Osk -- Saleh, Aljona -- Gokturk, Camilla -- Baranczewski, Pawel -- Svensson, Richard -- Berntsson, Ronnie P-A -- Gustafsson, Robert -- Stromberg, Kia -- Sanjiv, Kumar -- Jacques-Cordonnier, Marie-Caroline -- Desroses, Matthieu -- Gustavsson, Anna-Lena -- Olofsson, Roger -- Johansson, Fredrik -- Homan, Evert J -- Loseva, Olga -- Brautigam, Lars -- Johansson, Lars -- Hoglund, Andreas -- Hagenkort, Anna -- Pham, Therese -- Altun, Mikael -- Gaugaz, Fabienne Z -- Vikingsson, Svante -- Evers, Bastiaan -- Henriksson, Martin -- Vallin, Karl S A -- Wallner, Olov A -- Hammarstrom, Lars G J -- Wiita, Elisee -- Almlof, Ingrid -- Kalderen, Christina -- Axelsson, Hanna -- Djureinovic, Tatjana -- Puigvert, Jordi Carreras -- Haggblad, Maria -- Jeppsson, Fredrik -- Martens, Ulf -- Lundin, Cecilia -- Lundgren, Bo -- Granelli, Ingrid -- Jensen, Annika Jenmalm -- Artursson, Per -- Nilsson, Jonas A -- Stenmark, Pal -- Scobie, Martin -- Berglund, Ulrika Warpman -- Helleday, Thomas -- England -- Nature. 2014 Apr 10;508(7495):215-21. doi: 10.1038/nature13181. Epub 2014 Apr 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2]. ; Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden. ; Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden. ; 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden. ; Sahlgrenska Translational Melanoma Group, Sahlgrenska Cancer Center, Department of Surgery, University of Gothenburg and Sahlgrenska University Hospital, S-405 30 Gothenburg, Sweden. ; Department of Analytical Chemistry, Stockholm University, S-106 91 Stockholm, Sweden. ; 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy, Uppsala University, S-751 23 Uppsala, Sweden. ; 1] Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy, Uppsala University, S-751 23 Uppsala, Sweden. ; Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden. ; 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Clinical Pharmacology, Department of Medical and Health Sciences, Linkoping University, S-58185 Linkoping, Sweden. ; 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2] Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1006 Amsterdam, The Netherlands (B.E.); Department of Immunology, Genetics, and Pathology, Uppsala University, S-751 23 Uppsala, Sweden (T.D.). ; 1] Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden [2] Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1006 Amsterdam, The Netherlands (B.E.); Department of Immunology, Genetics, and Pathology, Uppsala University, S-751 23 Uppsala, Sweden (T.D.). ; Science for Life Laboratory, RNAi Cell Screening Facility, Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24695224" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalytic Domain ; Cell Death/drug effects ; Cell Survival/drug effects ; Crystallization ; DNA Damage ; DNA Repair Enzymes/*antagonists & inhibitors/chemistry/metabolism ; Deoxyguanine Nucleotides/metabolism ; Enzyme Inhibitors/chemistry/pharmacokinetics/pharmacology/therapeutic use ; Female ; Humans ; Male ; Mice ; Models, Molecular ; Molecular Conformation ; Molecular Targeted Therapy ; Neoplasms/*drug therapy/*metabolism/pathology ; Nucleotides/*metabolism ; Oxidation-Reduction/drug effects ; Phosphoric Monoester Hydrolases/*antagonists & inhibitors/chemistry/metabolism ; Pyrimidines/chemistry/pharmacokinetics/pharmacology/therapeutic use ; Pyrophosphatases/antagonists & inhibitors ; Reproducibility of Results ; Xenograft Model Antitumor Assays
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  • 248
    Publication Date: 2014-04-25
    Description: The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180223/" 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/PMC4180223/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉MacArthur, D G -- Manolio, T A -- Dimmock, D P -- Rehm, H L -- Shendure, J -- Abecasis, G R -- Adams, D R -- Altman, R B -- Antonarakis, S E -- Ashley, E A -- Barrett, J C -- Biesecker, L G -- Conrad, D F -- Cooper, G M -- Cox, N J -- Daly, M J -- Gerstein, M B -- Goldstein, D B -- Hirschhorn, J N -- Leal, S M -- Pennacchio, L A -- Stamatoyannopoulos, J A -- Sunyaev, S R -- Valle, D -- Voight, B F -- Winckler, W -- Gunter, C -- P30 DK020595/DK/NIDDK NIH HHS/ -- P30 DK042086/DK/NIDDK NIH HHS/ -- R01 HG007022/HG/NHGRI NIH HHS/ -- R01 HL117626/HL/NHLBI NIH HHS/ -- R01 MH101810/MH/NIMH NIH HHS/ -- U54 HG006997/HG/NHGRI NIH HHS/ -- England -- Nature. 2014 Apr 24;508(7497):469-76. doi: 10.1038/nature13127.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. ; Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland 20892, USA. ; Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA. ; 1] Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Cambridge, Massachusetts 02139, USA [2] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA. ; Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA. ; 1] NIH Undiagnosed Diseases Program, National Institutes of Health Office of Rare Diseases Research and National Human Genome Research Institute, Bethesda, Maryland 20892, USA [2] Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Departments of Bioengineering & Genetics, Stanford University, Stanford, California 94305, USA. ; 1] Department of Genetic Medicine, University of Geneva Medical School, 1211 Geneva, Switzerland [2] iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland. ; Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, California 94305, USA. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK. ; Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA. ; Departments of Genetics, Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA. ; HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA. ; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA. ; 1] Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA [2] Departments of Computer Science, Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA. ; Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina 27708, USA. ; 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [2] Divisions of Genetics and Endocrinology, Children's Hospital, Boston, Massachusetts 02115, USA. ; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA. ; 1] Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. ; Department of Genome Sciences, University of Washington, 1705 Northeast Pacific Street, Seattle, Washington 98195, USA. ; 1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [2] Harvard Medical School, Boston, Massachusetts 02115, USA. ; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA. ; Department of Pharmacology and Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA. ; 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [2] Next Generation Diagnostics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA (W.W.); Marcus Autism Center, Children's Healthcare of Atlanta, Atlanta, Georgia 30329, USA (C.G.). ; 1] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA [2] Next Generation Diagnostics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA (W.W.); Marcus Autism Center, Children's Healthcare of Atlanta, Atlanta, Georgia 30329, USA (C.G.).〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24759409" target="_blank"〉PubMed〈/a〉
    Keywords: *Disease ; False Positive Reactions ; Genes/genetics ; Genetic Predisposition to Disease/*genetics ; Genetic Variation/*genetics ; *Guidelines as Topic ; Humans ; Information Dissemination ; Publishing ; Reproducibility of Results ; Research Design ; Translational Medical Research/standards
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  • 249
    Publication Date: 2013-12-10
    Description: Bile acids are synthesized from cholesterol in hepatocytes and secreted through the biliary tract into the small intestine, where they aid in absorption of lipids and fat-soluble vitamins. Through a process known as enterohepatic recirculation, more than 90% of secreted bile acids are then retrieved from the intestine and returned to the liver for resecretion. In humans, there are two Na(+)-dependent bile acid transporters involved in enterohepatic recirculation, the Na(+)-taurocholate co-transporting polypeptide (NTCP; also known as SLC10A1) expressed in hepatocytes, and the apical sodium-dependent bile acid transporter (ASBT; also known as SLC10A2) expressed on enterocytes in the terminal ileum. In recent years, ASBT has attracted much interest as a potential drug target for treatment of hypercholesterolaemia, because inhibition of ASBT reduces reabsorption of bile acids, thus increasing bile acid synthesis and consequently cholesterol consumption. However, a lack of three-dimensional structures of bile acid transporters hampers our ability to understand the molecular mechanisms of substrate selectivity and transport, and to interpret the wealth of existing functional data. The crystal structure of an ASBT homologue from Neisseria meningitidis (ASBT(NM)) in detergent was reported recently, showing the protein in an inward-open conformation bound to two Na(+) and a taurocholic acid. However, the structural changes that bring bile acid and Na(+) across the membrane are difficult to infer from a single structure. To understand the structural changes associated with the coupled transport of Na(+) and bile acids, here we solved two structures of an ASBT homologue from Yersinia frederiksenii (ASBTYf) in a lipid environment, which reveal that a large rigid-body rotation of a substrate-binding domain gives the conserved 'crossover' region, where two discontinuous helices cross each other, alternating accessibility from either side of the cell membrane. This result has implications for the location and orientation of the bile acid during transport, as well as for the translocation pathway for Na(+).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142352/" 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/PMC4142352/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Xiaoming -- Levin, Elena J -- Pan, Yaping -- McCoy, Jason G -- Sharma, Ruchika -- Kloss, Brian -- Bruni, Renato -- Quick, Matthias -- Zhou, Ming -- R01 DK088057/DK/NIDDK NIH HHS/ -- R01 GM098878/GM/NIGMS NIH HHS/ -- R01DK088057/DK/NIDDK NIH HHS/ -- R01GM098878/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM087519/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- U54GM087519/GM/NIGMS NIH HHS/ -- U54GM095315/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Jan 23;505(7484):569-73. doi: 10.1038/nature12811. Epub 2013 Dec 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [3]. ; 1] Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2]. ; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA. ; New York Consortium on Membrane Protein Structure, New York, New York 10027, USA. ; 1] Department of Psychiatry and Center for Molecular Recognition, Columbia University, New York, New York 10032, USA [2] New York State Psychiatric Institute, Division of Molecular Therapeutics, New York, New York 10032, USA. ; 1] Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [3] Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24317697" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Bile Acids and Salts/metabolism ; Biological Transport ; Carrier Proteins/*chemistry/*metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Reproducibility of Results ; Rotation ; Sodium/metabolism ; Structure-Activity Relationship ; Yersinia/*chemistry
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  • 250
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    Nature Publishing Group (NPG)
    Publication Date: 2015-11-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoag, Hannah -- England -- Nature. 2015 Nov 19;527(7578):S114-5. doi: 10.1038/527S114a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26580160" target="_blank"〉PubMed〈/a〉
    Keywords: Biomarkers, Tumor/blood/*metabolism ; Breast Neoplasms/*diagnosis/genetics/*metabolism/pathology ; Cell Proliferation ; Disease Progression ; Female ; Genes, Neoplasm/genetics ; Humans ; Medical Overuse/*prevention & control ; Neoplasm Invasiveness/diagnosis/genetics ; Neoplasm Recurrence, Local/diagnosis/genetics ; Prognosis ; Reproducibility of Results ; Tamoxifen/therapeutic use
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  • 251
    Publication Date: 2015-09-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Begley, C Glenn -- Buchan, Alastair M -- Dirnagl, Ulrich -- England -- Nature. 2015 Sep 3;525(7567):25-7. doi: 10.1038/525025a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉TetraLogic Pharmaceuticals, Malvern, Pennsylvania, USA. ; Medical Science Division, Oxford NIHR Biomedical Research Centre, University of Oxford, UK. ; Center for Stroke Research at the Universitatsmedizin Charite Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26333454" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bias (Epidemiology) ; Humans ; Peer Review, Research/*methods/*standards ; Reproducibility of Results ; Research/*standards/statistics & numerical data ; Research Design/*standards ; Scientific Misconduct/statistics & numerical data
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  • 252
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    Nature Publishing Group (NPG)
    Publication Date: 2015-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reardon, Sara -- England -- Nature. 2015 Feb 26;518(7540):474-6. doi: 10.1038/518474a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25719648" target="_blank"〉PubMed〈/a〉
    Keywords: Acute Pain/diagnosis/physiopathology/psychology ; Aging ; Algorithms ; Bias (Epidemiology) ; *Brain Mapping ; Cerebral Cortex/physiopathology ; Chronic Pain/diagnosis/physiopathology/psychology ; Confounding Factors (Epidemiology) ; Female ; Forensic Medicine/*ethics/*methods ; Humans ; *Magnetic Resonance Imaging ; Male ; Malingering/prevention & control ; Middle Aged ; Pain/*diagnosis/physiopathology/psychology ; Pain Measurement/*ethics/*methods ; Reproducibility of Results ; Sample Size ; Sex Characteristics ; Uncertainty
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  • 253
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    Nature Publishing Group (NPG)
    Publication Date: 2014-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 Nov 6;515(7525):7. doi: 10.1038/515007a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25373636" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/*standards ; *Guidelines as Topic ; Periodicals as Topic/*standards ; Quality Control ; Reproducibility of Results ; Research Report/*standards
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  • 254
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    Nature Publishing Group (NPG)
    Publication Date: 2014-10-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2014 Oct 30;514(7524):536. doi: 10.1038/514536a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25355323" target="_blank"〉PubMed〈/a〉
    Keywords: Information Dissemination/*methods ; *Periodicals as Topic/standards ; Reproducibility of Results ; *Research ; *Software
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  • 255
    Publication Date: 2014-06-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pagan-Jimenez, Jaime R -- Rodriguez-Ramos, Reniel -- Oliver, Jose R -- England -- Nature. 2014 Jun 26;510(7506):473. doi: 10.1038/510473b.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Leiden University, the Netherlands. ; University of Puerto Rico, Utuado, Puerto Rico. ; University College London, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24965639" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeology ; Bolivia/ethnology ; Crops, Agricultural/genetics/*history ; Culture ; DNA, Plant/analysis ; Feces/chemistry ; History, Ancient ; Humans ; Phylogeography ; Puerto Rico ; Reproducibility of Results ; *Zea mays/genetics
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  • 256
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    Nature Publishing Group (NPG)
    Publication Date: 2015-07-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Jul 23;523(7561):382. doi: 10.1038/523382a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26201561" target="_blank"〉PubMed〈/a〉
    Keywords: *Communication ; Data Collection ; Reproducibility of Results ; *Research Design/standards ; *Research Personnel
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  • 257
    Publication Date: 2010-10-12
    Description: More than half of the solar energy absorbed by land surfaces is currently used to evaporate water. Climate change is expected to intensify the hydrological cycle and to alter evapotranspiration, with implications for ecosystem services and feedback to regional and global climate. Evapotranspiration changes may already be under way, but direct observational constraints are lacking at the global scale. Until such evidence is available, changes in the water cycle on land-a key diagnostic criterion of the effects of climate change and variability-remain uncertain. Here we provide a data-driven estimate of global land evapotranspiration from 1982 to 2008, compiled using a global monitoring network, meteorological and remote-sensing observations, and a machine-learning algorithm. In addition, we have assessed evapotranspiration variations over the same time period using an ensemble of process-based land-surface models. Our results suggest that global annual evapotranspiration increased on average by 7.1 +/- 1.0 millimetres per year per decade from 1982 to 1997. After that, coincident with the last major El Nino event in 1998, the global evapotranspiration increase seems to have ceased until 2008. This change was driven primarily by moisture limitation in the Southern Hemisphere, particularly Africa and Australia. In these regions, microwave satellite observations indicate that soil moisture decreased from 1998 to 2008. Hence, increasing soil-moisture limitations on evapotranspiration largely explain the recent decline of the global land-evapotranspiration trend. Whether the changing behaviour of evapotranspiration is representative of natural climate variability or reflects a more permanent reorganization of the land water cycle is a key question for earth system science.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jung, Martin -- Reichstein, Markus -- Ciais, Philippe -- Seneviratne, Sonia I -- Sheffield, Justin -- Goulden, Michael L -- Bonan, Gordon -- Cescatti, Alessandro -- Chen, Jiquan -- de Jeu, Richard -- Dolman, A Johannes -- Eugster, Werner -- Gerten, Dieter -- Gianelle, Damiano -- Gobron, Nadine -- Heinke, Jens -- Kimball, John -- Law, Beverly E -- Montagnani, Leonardo -- Mu, Qiaozhen -- Mueller, Brigitte -- Oleson, Keith -- Papale, Dario -- Richardson, Andrew D -- Roupsard, Olivier -- Running, Steve -- Tomelleri, Enrico -- Viovy, Nicolas -- Weber, Ulrich -- Williams, Christopher -- Wood, Eric -- Zaehle, Sonke -- Zhang, Ke -- England -- Nature. 2010 Oct 21;467(7318):951-4. doi: 10.1038/nature09396.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Biogeochemistry, 07745 Jena, Germany. mjung@bgc-jena.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20935626" target="_blank"〉PubMed〈/a〉
    Keywords: Artificial Intelligence ; Atmosphere/*chemistry ; Fresh Water/*analysis ; *Global Warming/statistics & numerical data ; History, 20th Century ; History, 21st Century ; Humidity ; Plant Transpiration/*physiology ; Reproducibility of Results ; Seasons ; Soil/analysis ; Uncertainty ; Volatilization ; *Water Cycle
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  • 258
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    Nature Publishing Group (NPG)
    Publication Date: 2011-05-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Altschuler, Eric L -- England -- Nature. 2011 May 26;473(7348):452. doi: 10.1038/473452a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21614062" target="_blank"〉PubMed〈/a〉
    Keywords: Peer Review, Research/*methods/*standards ; Reproducibility of Results ; Research Personnel/economics/psychology
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  • 259
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    Nature Publishing Group (NPG)
    Publication Date: 2010-07-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2010 Jul 1;466(7302):17. doi: 10.1038/466017a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20595983" target="_blank"〉PubMed〈/a〉
    Keywords: Fibroblasts/cytology/metabolism ; Gene Expression Profiling ; Germany ; Humans ; Induced Pluripotent Stem Cells/*cytology/*metabolism ; Male ; Reproducibility of Results ; *Research Personnel/ethics/standards ; Scientific Misconduct ; Testis/*cytology
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  • 260
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    Nature Publishing Group (NPG)
    Publication Date: 2011-10-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2011 Sep 27;477(7366):517-8. doi: 10.1038/477517a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21956304" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/analysis ; Climate Change/*statistics & numerical data ; Congresses as Topic ; *Conservation of Natural Resources ; India ; *International Cooperation ; Reproducibility of Results ; South Africa
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  • 261
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    Publication Date: 2010-01-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2010 Jan 7;463(7277):17. doi: 10.1038/463017a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20054371" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/enzymology/genetics/metabolism ; Enzymes/genetics/*metabolism ; Internationality ; Metabolome/genetics/*physiology ; Metabolomics/ethics/*standards ; Microarray Analysis/ethics/*standards ; Reproducibility of Results ; Research Design ; Spain
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  • 262
    Publication Date: 2011-04-05
    Description: Methylation at the 5' position of cytosine in DNA has important roles in genome function and is dynamically reprogrammed during early embryonic and germ cell development. The mammalian genome also contains 5-hydroxymethylcytosine (5hmC), which seems to be generated by oxidation of 5-methylcytosine (5mC) by the TET family of enzymes that are highly expressed in embryonic stem (ES) cells. Here we use antibodies against 5hmC and 5mC together with high throughput sequencing to determine genome-wide patterns of methylation and hydroxymethylation in mouse wild-type and mutant ES cells and differentiating embryoid bodies. We find that 5hmC is mostly associated with euchromatin and that whereas 5mC is under-represented at gene promoters and CpG islands, 5hmC is enriched and is associated with increased transcriptional levels. Most, if not all, 5hmC in the genome depends on pre-existing 5mC and the balance between these two modifications is different between genomic regions. Knockdown of Tet1 and Tet2 causes downregulation of a group of genes that includes pluripotency-related genes (including Esrrb, Prdm14, Dppa3, Klf2, Tcl1 and Zfp42) and a concomitant increase in methylation of their promoters, together with an increased propensity of ES cells for extraembryonic lineage differentiation. Declining levels of TETs during differentiation are associated with decreased hydroxymethylation levels at the promoters of ES cell-specific genes together with increased methylation and gene silencing. We propose that the balance between hydroxymethylation and methylation in the genome is inextricably linked with the balance between pluripotency and lineage commitment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ficz, Gabriella -- Branco, Miguel R -- Seisenberger, Stefanie -- Santos, Fatima -- Krueger, Felix -- Hore, Timothy A -- Marques, C Joana -- Andrews, Simon -- Reik, Wolf -- G0801156/Medical Research Council/United Kingdom -- G0801727/Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2011 May 19;473(7347):398-402. doi: 10.1038/nature10008. Epub 2011 Apr 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21460836" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies/immunology ; Cell Differentiation/*genetics ; Cell Line ; Cell Lineage/genetics ; CpG Islands/genetics ; Cytosine/*analogs & derivatives/analysis/immunology/metabolism ; *DNA Methylation ; DNA-Binding Proteins/deficiency ; Down-Regulation ; Embryoid Bodies/cytology/metabolism ; Embryonic Stem Cells/*cytology/*metabolism ; Euchromatin/genetics/metabolism ; Exons/genetics ; *Gene Expression Regulation, Developmental ; Gene Silencing ; Genome/genetics ; Mice ; Pluripotent Stem Cells/cytology/metabolism ; Promoter Regions, Genetic/genetics ; Proto-Oncogene Proteins/deficiency ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcription, Genetic
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  • 263
    Publication Date: 2011-05-20
    Description: Gene expression is a multistep process that involves the transcription, translation and turnover of messenger RNAs and proteins. Although it is one of the most fundamental processes of life, the entire cascade has never been quantified on a genome-wide scale. Here we simultaneously measured absolute mRNA and protein abundance and turnover by parallel metabolic pulse labelling for more than 5,000 genes in mammalian cells. Whereas mRNA and protein levels correlated better than previously thought, corresponding half-lives showed no correlation. Using a quantitative model we have obtained the first genome-scale prediction of synthesis rates of mRNAs and proteins. We find that the cellular abundance of proteins is predominantly controlled at the level of translation. Genes with similar combinations of mRNA and protein stability shared functional properties, indicating that half-lives evolved under energetic and dynamic constraints. Quantitative information about all stages of gene expression provides a rich resource and helps to provide a greater understanding of the underlying design principles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schwanhausser, Bjorn -- Busse, Dorothea -- Li, Na -- Dittmar, Gunnar -- Schuchhardt, Johannes -- Wolf, Jana -- Chen, Wei -- Selbach, Matthias -- England -- Nature. 2011 May 19;473(7347):337-42. doi: 10.1038/nature10098.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Delbruck Center for Molecular Medicine, Robert-Rossle-Str. 10, D-13092 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21593866" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Gene Expression Profiling/*methods ; *Gene Expression Regulation ; Half-Life ; Mammals/genetics ; Mice ; Models, Genetic ; NIH 3T3 Cells ; Protein Biosynthesis/genetics ; Proteins/*analysis/genetics/metabolism ; RNA, Messenger/*analysis/biosynthesis/genetics/metabolism ; Reproducibility of Results ; Staining and Labeling
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  • 264
    Publication Date: 2011-07-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Losos, Jonathan B -- Pringle, Robert M -- England -- Nature. 2011 Jul 13;475(7355):E1-2; discussion E3. doi: 10.1038/nature10140.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. jlosos@oeb.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21753806" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/physiology ; Competitive Behavior/*physiology ; *Geography ; Lizards/*physiology ; Population Density ; Predatory Behavior/*physiology ; Reproducibility of Results ; Research Design ; *Selection, Genetic ; Snakes/physiology ; Survival Analysis
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  • 265
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    Publication Date: 2011-10-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2011 Oct 26;478(7370):428. doi: 10.1038/478428a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031398" target="_blank"〉PubMed〈/a〉
    Keywords: Climate Change/*statistics & numerical data ; *Peer Review, Research/methods/standards ; Periodicals as Topic/standards ; Reproducibility of Results
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  • 266
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    Nature Publishing Group (NPG)
    Publication Date: 2011-07-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seitz, Russell -- England -- Nature. 2011 Jul 6;475(7354):37. doi: 10.1038/475037b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734694" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/adverse effects/analysis ; *Cold Temperature ; Models, Theoretical ; *Nuclear Warfare ; Reproducibility of Results ; *Smoke/analysis ; Sunlight
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  • 267
    Publication Date: 2011-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mackas, David L -- England -- Nature. 2011 Apr 14;472(7342):E4-5; discussion E8-9. doi: 10.1038/nature09951.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Ocean Sciences, Fisheries and Oceans Canada, PO Box 6000, Sidney, British Columbia, V8L 4B2, Canada. Dave.Mackas@dfo-mpo.gc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21490623" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/growth & development/isolation & purification/metabolism ; Bias (Epidemiology) ; Biomass ; Chlorophyll/analysis/*metabolism ; Data Collection/methods ; Phytoplankton/growth & development/isolation & purification/metabolism ; Reproducibility of Results ; Time Factors
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  • 268
    Publication Date: 2011-11-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brassard, Gilles -- England -- Nature. 2011 Nov 16;479(7373):307-8. doi: 10.1038/479307a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departement d'informatique et de recherche operationnelle, Universite de Montreal, Montreal, Quebec H3C 3J7, Canada. brassard@iro.umontreal.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22094688" target="_blank"〉PubMed〈/a〉
    Keywords: *Geographic Information Systems ; Quantum Theory ; Reproducibility of Results ; Time Factors ; Trust ; *Uncertainty
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  • 269
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    Nature Publishing Group (NPG)
    Publication Date: 2011-07-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maxmen, Amy -- England -- Nature. 2011 Jul 6;475(7354):23-5. doi: 10.1038/475023a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734684" target="_blank"〉PubMed〈/a〉
    Keywords: Bone and Bones/metabolism/physiology ; Calcium/metabolism ; Dietary Supplements/utilization ; Evidence-Based Medicine/methods/standards ; Guidelines as Topic/standards ; Health Surveys/standards ; Humans ; Institute of Medicine (U.S.) ; *Meta-Analysis as Topic ; *Nutritional Requirements ; *Nutritional Sciences/standards ; Public Health/methods/standards ; Reproducibility of Results ; United States ; Vitamin D/blood/metabolism/*physiology ; Vitamin D Deficiency/blood/epidemiology
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  • 270
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    Nature Publishing Group (NPG)
    Publication Date: 2011-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gupta, Nitin -- Stopfer, Mark -- England -- Nature. 2011 Feb 3;470(7332):39. doi: 10.1038/470039a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21293361" target="_blank"〉PubMed〈/a〉
    Keywords: Meta-Analysis as Topic ; *Models, Biological ; Reproducibility of Results ; *Research Report
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  • 271
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    Nature Publishing Group (NPG)
    Publication Date: 2011-06-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brooks, T M -- England -- Nature. 2011 Jun 15;474(7351):284. doi: 10.1038/474284b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21677730" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Ecosystem ; Endangered Species/*statistics & numerical data ; *Extinction, Biological ; *Models, Biological ; Reproducibility of Results ; Species Specificity
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  • 272
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    Nature Publishing Group (NPG)
    Publication Date: 2011-03-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeWeerdt, Sarah -- England -- Nature. 2011 Mar 24;471(7339):S22-4. doi: 10.1038/471S22a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430718" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brassica/chemistry ; Breeding ; Cooking ; Curcumin/pharmacology ; *Diet/statistics & numerical data ; Fruit/chemistry ; Genetic Variation/genetics ; Genistein/pharmacology ; Genome, Human/genetics ; Humans ; Isothiocyanates ; Metagenome ; Mice ; Neoplasms/chemically induced/*diet therapy/*prevention & control ; Phytotherapy ; Rats ; Reproducibility of Results ; Risk Management ; Stilbenes/pharmacology ; Thiocyanates/pharmacology ; Time Factors ; Vegetables/chemistry
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  • 273
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. The paper by Nowak et al. has the evolution of eusociality as its title, but it is mostly about something else. It argues against inclusive fitness theory and offers an alternative modelling approach that is claimed to be more fundamental and general, but which, we believe, has no practical biological meaning for the evolution of eusociality. Nowak et al. overlook the robust empirical observation that eusociality has only arisen in clades where mothers are associated with their full-sibling offspring; that is, in families where the average relatedness of offspring to siblings is as high as to their own offspring, independent of population structure or ploidy. We believe that this omission makes the paper largely irrelevant for understanding the evolution of eusociality.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boomsma, Jacobus J -- Beekman, Madeleine -- Cornwallis, Charlie K -- Griffin, Ashleigh S -- Holman, Luke -- Hughes, William O H -- Keller, Laurent -- Oldroyd, Benjamin P -- Ratnieks, Francis L W -- England -- Nature. 2011 Mar 24;471(7339):E4-5; author reply E9-10. doi: 10.1038/nature09832.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430722" target="_blank"〉PubMed〈/a〉
    Keywords: *Altruism ; Animals ; *Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; Genetic Fitness ; Genetics, Population ; Male ; *Models, Biological ; Reproducibility of Results ; Reproduction/physiology ; Selection, Genetic ; Sex Ratio ; *Siblings
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  • 274
    Publication Date: 2011-02-05
    Description: Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077050/" 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/PMC3077050/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mills, Ryan E -- Walter, Klaudia -- Stewart, Chip -- Handsaker, Robert E -- Chen, Ken -- Alkan, Can -- Abyzov, Alexej -- Yoon, Seungtai Chris -- Ye, Kai -- Cheetham, R Keira -- Chinwalla, Asif -- Conrad, Donald F -- Fu, Yutao -- Grubert, Fabian -- Hajirasouliha, Iman -- Hormozdiari, Fereydoun -- Iakoucheva, Lilia M -- Iqbal, Zamin -- Kang, Shuli -- Kidd, Jeffrey M -- Konkel, Miriam K -- Korn, Joshua -- Khurana, Ekta -- Kural, Deniz -- Lam, Hugo Y K -- Leng, Jing -- Li, Ruiqiang -- Li, Yingrui -- Lin, Chang-Yun -- Luo, Ruibang -- Mu, Xinmeng Jasmine -- Nemesh, James -- Peckham, Heather E -- Rausch, Tobias -- Scally, Aylwyn -- Shi, Xinghua -- Stromberg, Michael P -- Stutz, Adrian M -- Urban, Alexander Eckehart -- Walker, Jerilyn A -- Wu, Jiantao -- Zhang, Yujun -- Zhang, Zhengdong D -- Batzer, Mark A -- Ding, Li -- Marth, Gabor T -- McVean, Gil -- Sebat, Jonathan -- Snyder, Michael -- Wang, Jun -- Ye, Kenny -- Eichler, Evan E -- Gerstein, Mark B -- Hurles, Matthew E -- Lee, Charles -- McCarroll, Steven A -- Korbel, Jan O -- 1000 Genomes Project -- 062023/Wellcome Trust/United Kingdom -- 077009/Wellcome Trust/United Kingdom -- 077014/Wellcome Trust/United Kingdom -- 077192/Wellcome Trust/United Kingdom -- 085532/Wellcome Trust/United Kingdom -- G0701805/Medical Research Council/United Kingdom -- G1000758/Medical Research Council/United Kingdom -- P01 HG004120/HG/NHGRI NIH HHS/ -- P41 HG004221/HG/NHGRI NIH HHS/ -- P41 HG004221-01/HG/NHGRI NIH HHS/ -- P41 HG004221-02/HG/NHGRI NIH HHS/ -- P41 HG004221-03/HG/NHGRI NIH HHS/ -- P41 HG004221-03S1/HG/NHGRI NIH HHS/ -- P41 HG004221-03S2/HG/NHGRI NIH HHS/ -- P41 HG004221-03S3/HG/NHGRI NIH HHS/ -- R01 GM059290/GM/NIGMS NIH HHS/ -- R01 GM081533/GM/NIGMS NIH HHS/ -- R01 GM081533-01A1/GM/NIGMS NIH HHS/ -- R01 GM081533-02/GM/NIGMS NIH HHS/ -- R01 GM081533-03/GM/NIGMS NIH HHS/ -- R01 GM081533-04/GM/NIGMS NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG004719/HG/NHGRI NIH HHS/ -- R01 HG004719-01/HG/NHGRI NIH HHS/ -- R01 HG004719-02/HG/NHGRI NIH HHS/ -- R01 HG004719-02S1/HG/NHGRI NIH HHS/ -- R01 HG004719-03/HG/NHGRI NIH HHS/ -- R01 HG004719-04/HG/NHGRI NIH HHS/ -- R01 MH091350/MH/NIMH NIH HHS/ -- RC2 HG005552/HG/NHGRI NIH HHS/ -- RC2 HG005552-01/HG/NHGRI NIH HHS/ -- RC2 HG005552-02/HG/NHGRI NIH HHS/ -- U01 HG005209/HG/NHGRI NIH HHS/ -- U01 HG005209-01/HG/NHGRI NIH HHS/ -- U01 HG005209-02/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21293372" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Copy Number Variations/*genetics ; Gene Duplication/genetics ; Genetic Predisposition to Disease/genetics ; *Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Genotype ; Humans ; Mutagenesis, Insertional/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Sequence Deletion/genetics
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  • 275
    Publication Date: 2011-08-05
    Description: Dust has the potential to modify global climate by influencing the radiative balance of the atmosphere and by supplying iron and other essential limiting micronutrients to the ocean. Indeed, dust supply to the Southern Ocean increases during ice ages, and 'iron fertilization' of the subantarctic zone may have contributed up to 40 parts per million by volume (p.p.m.v.) of the decrease (80-100 p.p.m.v.) in atmospheric carbon dioxide observed during late Pleistocene glacial cycles. So far, however, the magnitude of Southern Ocean dust deposition in earlier times and its role in the development and evolution of Pleistocene glacial cycles have remained unclear. Here we report a high-resolution record of dust and iron supply to the Southern Ocean over the past four million years, derived from the analysis of marine sediments from ODP Site 1090, located in the Atlantic sector of the subantarctic zone. The close correspondence of our dust and iron deposition records with Antarctic ice core reconstructions of dust flux covering the past 800,000 years (refs 8, 9) indicates that both of these archives record large-scale deposition changes that should apply to most of the Southern Ocean, validating previous interpretations of the ice core data. The extension of the record beyond the interval covered by the Antarctic ice cores reveals that, in contrast to the relatively gradual intensification of glacial cycles over the past three million years, Southern Ocean dust and iron flux rose sharply at the Mid-Pleistocene climatic transition around 1.25 million years ago. This finding complements previous observations over late Pleistocene glacial cycles, providing new evidence of a tight connection between high dust input to the Southern Ocean and the emergence of the deep glaciations that characterize the past one million years of Earth history.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martinez-Garcia, Alfredo -- Rosell-Mele, Antoni -- Jaccard, Samuel L -- Geibert, Walter -- Sigman, Daniel M -- Haug, Gerald H -- England -- Nature. 2011 Aug 3;476(7360):312-5. doi: 10.1038/nature10310.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Geological Institute, ETH Zurich, Zurich 8092, Switzerland. alfredo.martinez-garcia@erdw.ethz.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21814203" target="_blank"〉PubMed〈/a〉
    Keywords: Alkanes/analysis ; Atlantic Ocean ; Atmosphere/chemistry ; Carbon Cycle ; Carbon Dioxide/analysis ; *Climate ; Diatoms/metabolism ; Dust/*analysis ; Ecosystem ; Geologic Sediments/chemistry ; History, Ancient ; Ice/analysis ; Iron/analysis ; Nitrates/analysis ; Oceans and Seas ; Reproducibility of Results ; Seawater/*chemistry ; Uncertainty ; Wind
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  • 276
    Publication Date: 2011-11-25
    Description: Arctic sea ice extent is now more than two million square kilometres less than it was in the late twentieth century, with important consequences for the climate, the ocean and traditional lifestyles in the Arctic. Although observations show a more or less continuous decline for the past four or five decades, there are few long-term records with which to assess natural sea ice variability. Until now, the question of whether or not current trends are potentially anomalous has therefore remained unanswerable. Here we use a network of high-resolution terrestrial proxies from the circum-Arctic region to reconstruct past extents of summer sea ice, and show that-although extensive uncertainties remain, especially before the sixteenth century-both the duration and magnitude of the current decline in sea ice seem to be unprecedented for the past 1,450 years. Enhanced advection of warm Atlantic water to the Arctic seems to be the main factor driving the decline of sea ice extent on multidecadal timescales, and may result from nonlinear feedbacks between sea ice and the Atlantic meridional overturning circulation. These results reinforce the assertion that sea ice is an active component of Arctic climate variability and that the recent decrease in summer Arctic sea ice is consistent with anthropogenically forced warming.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kinnard, Christophe -- Zdanowicz, Christian M -- Fisher, David A -- Isaksson, Elisabeth -- de Vernal, Anne -- Thompson, Lonnie G -- England -- Nature. 2011 Nov 23;479(7374):509-12. doi: 10.1038/nature10581.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centro de Estudios Avanzados en Zonas Aridas, Benavente 980, Casilla 554, La Serena, 1720170, Chile. christophe.kinnard@ceaza.cl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22113692" target="_blank"〉PubMed〈/a〉
    Keywords: Arctic Regions ; Atmosphere ; Geologic Sediments/chemistry ; Global Warming/*statistics & numerical data ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Human Activities ; *Ice Cover ; Reproducibility of Results ; Seasons ; Seawater
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  • 277
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    Publication Date: 2011-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dolgin, Elie -- England -- Nature. 2011 Feb 3;470(7332):13. doi: 10.1038/470013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21293343" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cellular Reprogramming/genetics ; DNA Methylation/genetics ; Embryonic Stem Cells/cytology/*metabolism ; Epigenesis, Genetic/*genetics ; Humans ; Induced Pluripotent Stem Cells/cytology/*metabolism ; Mice ; Models, Biological ; Reproducibility of Results
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  • 278
    Publication Date: 2011-08-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Motluk, Alison -- England -- Nature. 2011 Aug 23;476(7361):382-3. doi: 10.1038/476382a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21866132" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Cryopreservation/economics/methods/*statistics & numerical data/trends ; Female ; *Human Experimentation/statistics & numerical data ; Humans ; Infant, Newborn ; Maternal Age ; Oocyte Retrieval/statistics & numerical data ; *Oocytes ; Pregnancy ; Pregnancy Outcome ; Reproducibility of Results ; Reproductive Medicine/economics/methods/standards/*statistics & numerical data ; Vitrification
    Print ISSN: 0028-0836
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  • 279
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    Publication Date: 2011-03-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stirling, Andy -- England -- Nature. 2011 Mar 17;471(7338):305. doi: 10.1038/471305a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21412323" target="_blank"〉PubMed〈/a〉
    Keywords: Great Britain ; *Policy Making ; Public Opinion ; Reproducibility of Results ; *Science
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 280
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Hamilton described a selective process in which individuals affect kin (kin selection), developed a novel modelling strategy for it (inclusive fitness), and derived a rule to describe it (Hamilton's rule). Nowak et al. assert that inclusive fitness is not the best modelling strategy, and also that its production has been "meagre". The former may be debated by theoreticians, but the latter is simply incorrect. There is abundant evidence to demonstrate that inclusive fitness, kin selection and Hamilton's rule have been extraordinarily productive for understanding the evolution of sociality.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strassmann, Joan E -- Page, Robert E Jr -- Robinson, Gene E -- Seeley, Thomas D -- England -- Nature. 2011 Mar 24;471(7339):E5-6; author reply E9-10. doi: 10.1038/nature09833.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430723" target="_blank"〉PubMed〈/a〉
    Keywords: *Altruism ; Animals ; Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; Genetic Fitness ; Genetics, Population ; Genomic Imprinting ; *Heredity ; Humans ; Male ; *Models, Biological ; Reproducibility of Results ; *Selection, Genetic ; Sex Ratio
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  • 281
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    Publication Date: 2011-10-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2011 Oct 26;478(7370):439-40. doi: 10.1038/478439a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031413" target="_blank"〉PubMed〈/a〉
    Keywords: Clinical Trials, Phase III as Topic ; Controlled Clinical Trials as Topic ; Humans ; Infant ; Malaria Vaccines/adverse effects/*immunology ; Malaria, Falciparum/epidemiology/mortality/parasitology/prevention & control ; *Mass Media ; Plasmodium falciparum/immunology ; Reproducibility of Results ; Time Factors ; World Health Organization
    Print ISSN: 0028-0836
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  • 282
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    Publication Date: 2011-10-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Callaway, Ewen -- England -- Nature. 2011 Oct 25;478(7370):444-6. doi: 10.1038/478444a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031418" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA Contamination ; Disease Outbreaks ; Evolution, Molecular ; Genome, Bacterial/*genetics ; History, 19th Century ; History, Ancient ; History, Medieval ; Humans ; Insect Vectors/microbiology ; London/epidemiology ; Phylogeny ; Plague/epidemiology/history/*microbiology/transmission ; Polymerase Chain Reaction ; Rats ; Reproducibility of Results ; Yersinia pestis/classification/*genetics/isolation & purification
    Print ISSN: 0028-0836
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  • 283
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. For over fifty years, the evolution of social behaviour has been guided by the concept of inclusive fitness as a measure of evolutionary success. Nowak et al. argue that inclusive fitness should be abandoned. In so doing, however, they misrepresent the role that inclusive fitness has played in the theory of social evolution by which understanding social behaviour in a variety of disciplines has developed and flourished. By discarding inclusive fitness on the basis of its limitations, they create a conceptual tension which, we argue, is unnecessary, and potentially dangerous for evolutionary biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferriere, Regis -- Michod, Richard E -- England -- Nature. 2011 Mar 24;471(7339):E6-8; author reply E9-10. doi: 10.1038/nature09834.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430724" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Altruism ; Animals ; *Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; *Genetic Fitness/genetics ; Genetics, Population ; Heredity/genetics ; Male ; *Models, Biological ; Phenotype ; Reproducibility of Results ; Selection, Genetic/genetics ; Sex Ratio
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  • 284
    Publication Date: 2012-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anderson, James A -- Eijkholt, Marleen -- Illes, Judy -- England -- Nature. 2012 Jul 25;487(7408):432. doi: 10.1038/487432a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22836987" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/*ethics/methods/*standards ; *Ethics, Research ; Guidelines as Topic ; Publishing/*standards/trends ; Reproducibility of Results
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  • 285
    Publication Date: 2012-09-22
    Description: Cooperation is central to human social behaviour. However, choosing to cooperate requires individuals to incur a personal cost to benefit others. Here we explore the cognitive basis of cooperative decision-making in humans using a dual-process framework. We ask whether people are predisposed towards selfishness, behaving cooperatively only through active self-control; or whether they are intuitively cooperative, with reflection and prospective reasoning favouring 'rational' self-interest. To investigate this issue, we perform ten studies using economic games. We find that across a range of experimental designs, subjects who reach their decisions more quickly are more cooperative. Furthermore, forcing subjects to decide quickly increases contributions, whereas instructing them to reflect and forcing them to decide slowly decreases contributions. Finally, an induction that primes subjects to trust their intuitions increases contributions compared with an induction that promotes greater reflection. To explain these results, we propose that cooperation is intuitive because cooperative heuristics are developed in daily life where cooperation is typically advantageous. We then validate predictions generated by this proposed mechanism. Our results provide convergent evidence that intuition supports cooperation in social dilemmas, and that reflection can undermine these cooperative impulses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rand, David G -- Greene, Joshua D -- Nowak, Martin A -- England -- Nature. 2012 Sep 20;489(7416):427-30. doi: 10.1038/nature11467.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts 02138, USA. drand@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22996558" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; *Cooperative Behavior ; Cost-Benefit Analysis ; *Decision Making ; *Ego ; Female ; *Game Theory ; *Gift Giving ; Humans ; *Impulsive Behavior ; *Intuition ; Male ; *Models, Psychological ; Reproducibility of Results ; Time Factors ; Young Adult
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  • 286
    Publication Date: 2012-05-25
    Description: Warming experiments are increasingly relied on to estimate plant responses to global climate change. For experiments to provide meaningful predictions of future responses, they should reflect the empirical record of responses to temperature variability and recent warming, including advances in the timing of flowering and leafing. We compared phenology (the timing of recurring life history events) in observational studies and warming experiments spanning four continents and 1,634 plant species using a common measure of temperature sensitivity (change in days per degree Celsius). We show that warming experiments underpredict advances in the timing of flowering and leafing by 8.5-fold and 4.0-fold, respectively, compared with long-term observations. For species that were common to both study types, the experimental results did not match the observational data in sign or magnitude. The observational data also showed that species that flower earliest in the spring have the highest temperature sensitivities, but this trend was not reflected in the experimental data. These significant mismatches seem to be unrelated to the study length or to the degree of manipulated warming in experiments. The discrepancy between experiments and observations, however, could arise from complex interactions among multiple drivers in the observational data, or it could arise from remediable artefacts in the experiments that result in lower irradiance and drier soils, thus dampening the phenological responses to manipulated warming. Our results introduce uncertainty into ecosystem models that are informed solely by experiments and suggest that responses to climate change that are predicted using such models should be re-evaluated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolkovich, E M -- Cook, B I -- Allen, J M -- Crimmins, T M -- Betancourt, J L -- Travers, S E -- Pau, S -- Regetz, J -- Davies, T J -- Kraft, N J B -- Ault, T R -- Bolmgren, K -- Mazer, S J -- McCabe, G J -- McGill, B J -- Parmesan, C -- Salamin, N -- Schwartz, M D -- Cleland, E E -- England -- Nature. 2012 May 2;485(7399):494-7. doi: 10.1038/nature11014.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive 0116, La Jolla, California 92093, USA. wolkovich@biodiversity.ubc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22622576" target="_blank"〉PubMed〈/a〉
    Keywords: Artifacts ; Ecosystem ; Flowers/growth & development/physiology ; *Global Warming ; *Models, Biological ; *Periodicity ; Plant Development ; Plant Leaves/growth & development/physiology ; *Plant Physiological Phenomena ; Plants/classification ; Reproducibility of Results ; Soil/chemistry ; Temperature ; Time Factors ; *Uncertainty
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  • 287
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    Nature Publishing Group (NPG)
    Publication Date: 2012-08-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2012 Aug 2;488(7409):13-4. doi: 10.1038/488013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22859177" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain Neoplasms/drug therapy/pathology ; Cell Tracking/*methods ; Glioblastoma/drug therapy/pathology ; Intestinal Neoplasms/drug therapy/pathology ; Mice ; Neoplastic Stem Cells/*cytology/drug effects/*pathology ; Reproducibility of Results ; Skin Neoplasms/drug therapy/pathology
    Print ISSN: 0028-0836
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  • 288
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    Nature Publishing Group (NPG)
    Publication Date: 2012-05-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yong, Ed -- England -- Nature. 2012 May 16;485(7398):298-300. doi: 10.1038/485298a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22596136" target="_blank"〉PubMed〈/a〉
    Keywords: Bias (Epidemiology) ; Humans ; Psychology/*standards ; Publishing/standards ; Reproducibility of Results ; Scientific Misconduct/statistics & numerical data
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  • 289
    Publication Date: 2012-03-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ledford, Heidi -- England -- Nature. 2012 Mar 28;483(7391):519. doi: 10.1038/483519a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22460874" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/pharmacology/therapeutic use ; Benzamides/*pharmacology/therapeutic use ; Breast Neoplasms/drug therapy ; Clinical Trials as Topic/*statistics & numerical data ; Drug Discovery/standards/*statistics & numerical data ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Hereditary Breast and Ovarian Cancer Syndrome/drug therapy/genetics ; Humans ; Ovarian Neoplasms/drug therapy ; Phthalazines/pharmacology/therapeutic use ; Piperazines/pharmacology/therapeutic use ; *Poly(ADP-ribose) Polymerase Inhibitors ; Reproducibility of Results ; Research Design/*statistics & numerical data ; Treatment Failure
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  • 290
    Publication Date: 2012-12-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heuer, Rolf-Dieter -- Rosenzweig, Cynthia -- Steltzner, Adam -- Blanpain, Cedric -- Iorns, Elizabeth -- Wang, Jun -- Handelsman, Jo -- Gowers, Tim -- De Bernardinis, Bernardo -- Fouchier, Ron -- England -- Nature. 2012 Dec 20;492(7429):335-43. doi: 10.1038/492335a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23257862" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Animals ; Bioterrorism/prevention & control ; Climate Change ; Disaster Planning/history ; Earthquakes/statistics & numerical data ; Forecasting ; Genomics ; History, 20th Century ; History, 21st Century ; Humans ; Influenza A Virus, H5N1 Subtype/genetics/pathogenicity ; Influenza, Human/transmission/virology ; Mars ; Neoplastic Stem Cells/cytology ; New York City ; Physics/history ; Publishing/economics ; Reproducibility of Results ; *Research/economics/standards/statistics & numerical data ; Security Measures ; Sexism/psychology/statistics & numerical data ; Space Flight/history/instrumentation
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  • 291
    Publication Date: 2012-03-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Begley, C Glenn -- Ellis, Lee M -- England -- Nature. 2012 Mar 28;483(7391):531-3. doi: 10.1038/483531a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hematology and Oncology Research, Amgen, Thousand Oaks, California 91359, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22460880" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomedical Research/*standards ; Cell Line, Tumor ; Clinical Trials as Topic/statistics & numerical data ; Drug Evaluation, Preclinical/*standards ; Humans ; Mice ; Neoplasms/*drug therapy/genetics ; Reproducibility of Results ; Research Design/statistics & numerical data ; Survival Analysis ; Translational Medical Research/standards/*statistics & numerical data/trends ; Treatment Failure
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  • 292
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    Publication Date: 2012-04-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berglund, Jennifer -- England -- Nature. 2012 Apr 12;484(7393):S11.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22509512" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Monoclonal, Humanized/adverse effects ; Apitherapy ; Complementary Therapies/adverse effects/contraindications/economics/*utilization ; Controlled Clinical Trials as Topic ; Great Britain ; Humans ; Hygiene Hypothesis ; Multiple Sclerosis/immunology/*therapy ; Natalizumab ; Reproducibility of Results ; Therapy with Helminths/adverse effects/utilization ; Uncertainty ; Vitamin D/therapeutic use
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  • 293
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    Publication Date: 2012-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macarthur, Daniel -- England -- Nature. 2012 Jul 25;487(7408):427-8. doi: 10.1038/487427a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. macarthur@atgu.mgh.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22836983" target="_blank"〉PubMed〈/a〉
    Keywords: Aged, 80 and over ; *Artifacts ; False Positive Reactions ; Genomics/*standards ; Humans ; Longevity/genetics ; Quality Control ; Reproducibility of Results ; *Research Design
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  • 294
    Publication Date: 2012-06-23
    Description: Discovering the unintended 'off-targets' that predict adverse drug reactions is daunting by empirical methods alone. Drugs can act on several protein targets, some of which can be unrelated by conventional molecular metrics, and hundreds of proteins have been implicated in side effects. Here we use a computational strategy to predict the activity of 656 marketed drugs on 73 unintended 'side-effect' targets. Approximately half of the predictions were confirmed, either from proprietary databases unknown to the method or by new experimental assays. Affinities for these new off-targets ranged from 1 nM to 30 muM. To explore relevance, we developed an association metric to prioritize those new off-targets that explained side effects better than any known target of a given drug, creating a drug-target-adverse drug reaction network. Among these new associations was the prediction that the abdominal pain side effect of the synthetic oestrogen chlorotrianisene was mediated through its newly discovered inhibition of the enzyme cyclooxygenase-1. The clinical relevance of this inhibition was borne out in whole human blood platelet aggregation assays. This approach may have wide application to de-risking toxicological liabilities in drug discovery.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383642/" 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/PMC3383642/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lounkine, Eugen -- Keiser, Michael J -- Whitebread, Steven -- Mikhailov, Dmitri -- Hamon, Jacques -- Jenkins, Jeremy L -- Lavan, Paul -- Weber, Eckhard -- Doak, Allison K -- Cote, Serge -- Shoichet, Brian K -- Urban, Laszlo -- AG002132/AG/NIA NIH HHS/ -- GM71896/GM/NIGMS NIH HHS/ -- GM93456/GM/NIGMS NIH HHS/ -- P01 AG002132/AG/NIA NIH HHS/ -- R01 GM071896/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Jun 10;486(7403):361-7. doi: 10.1038/nature11159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22722194" target="_blank"〉PubMed〈/a〉
    Keywords: Blood Platelets/drug effects ; Chlorotrianisene/adverse effects/chemistry/pharmacology ; Cyclooxygenase 1/metabolism ; Cyclooxygenase Inhibitors/adverse effects/pharmacology ; Databases, Factual ; Drug Evaluation, Preclinical/*methods ; *Drug-Related Side Effects and Adverse Reactions ; Estrogens, Non-Steroidal/adverse effects/pharmacology ; Forecasting ; Humans ; Models, Biological ; Molecular Targeted Therapy/adverse effects ; Platelet Aggregation/drug effects ; Reproducibility of Results ; Substrate Specificity ; Toxicity Tests/*methods
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  • 295
    Publication Date: 2012-07-13
    Description: Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only approximately 100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3397394/" 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/PMC3397394/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peters, Brock A -- Kermani, Bahram G -- Sparks, Andrew B -- Alferov, Oleg -- Hong, Peter -- Alexeev, Andrei -- Jiang, Yuan -- Dahl, Fredrik -- Tang, Y Tom -- Haas, Juergen -- Robasky, Kimberly -- Zaranek, Alexander Wait -- Lee, Je-Hyuk -- Ball, Madeleine Price -- Peterson, Joseph E -- Perazich, Helena -- Yeung, George -- Liu, Jia -- Chen, Linsu -- Kennemer, Michael I -- Pothuraju, Kaliprasad -- Konvicka, Karel -- Tsoupko-Sitnikov, Mike -- Pant, Krishna P -- Ebert, Jessica C -- Nilsen, Geoffrey B -- Baccash, Jonathan -- Halpern, Aaron L -- Church, George M -- Drmanac, Radoje -- P50 HG005550/HG/NHGRI NIH HHS/ -- P50HG005550/HG/NHGRI NIH HHS/ -- England -- Nature. 2012 Jul 11;487(7406):190-5. doi: 10.1038/nature11236.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA. bpeters@completegenomics.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22785314" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Cell Line ; Female ; Gene Silencing ; Genetic Variation ; *Genome, Human ; Genomics/*methods ; Haplotypes ; Humans ; Mutation ; Reproducibility of Results ; Sequence Analysis, DNA/economics/*methods/standards
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 296
    Publication Date: 2012-11-07
    Description: Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491803/" 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/PMC3491803/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jostins, Luke -- Ripke, Stephan -- Weersma, Rinse K -- Duerr, Richard H -- McGovern, Dermot P -- Hui, Ken Y -- Lee, James C -- Schumm, L Philip -- Sharma, Yashoda -- Anderson, Carl A -- Essers, Jonah -- Mitrovic, Mitja -- Ning, Kaida -- Cleynen, Isabelle -- Theatre, Emilie -- Spain, Sarah L -- Raychaudhuri, Soumya -- Goyette, Philippe -- Wei, Zhi -- Abraham, Clara -- Achkar, Jean-Paul -- Ahmad, Tariq -- Amininejad, Leila -- Ananthakrishnan, Ashwin N -- Andersen, Vibeke -- Andrews, Jane M -- Baidoo, Leonard -- Balschun, Tobias -- Bampton, Peter A -- Bitton, Alain -- Boucher, Gabrielle -- Brand, Stephan -- Buning, Carsten -- Cohain, Ariella -- Cichon, Sven -- D'Amato, Mauro -- De Jong, Dirk -- Devaney, Kathy L -- Dubinsky, Marla -- Edwards, Cathryn -- Ellinghaus, David -- Ferguson, Lynnette R -- Franchimont, Denis -- Fransen, Karin -- Gearry, Richard -- Georges, Michel -- Gieger, Christian -- Glas, Jurgen -- Haritunians, Talin -- Hart, Ailsa -- Hawkey, Chris -- Hedl, Matija -- Hu, Xinli -- Karlsen, Tom H -- Kupcinskas, Limas -- Kugathasan, Subra -- Latiano, Anna -- Laukens, Debby -- Lawrance, Ian C -- Lees, Charlie W -- Louis, Edouard -- Mahy, Gillian -- Mansfield, John -- Morgan, Angharad R -- Mowat, Craig -- Newman, William -- Palmieri, Orazio -- Ponsioen, Cyriel Y -- Potocnik, Uros -- Prescott, Natalie J -- Regueiro, Miguel -- Rotter, Jerome I -- Russell, Richard K -- Sanderson, Jeremy D -- Sans, Miquel -- Satsangi, Jack -- Schreiber, Stefan -- Simms, Lisa A -- Sventoraityte, Jurgita -- Targan, Stephan R -- Taylor, Kent D -- Tremelling, Mark -- Verspaget, Hein W -- De Vos, Martine -- Wijmenga, Cisca -- Wilson, David C -- Winkelmann, Juliane -- Xavier, Ramnik J -- Zeissig, Sebastian -- Zhang, Bin -- Zhang, Clarence K -- Zhao, Hongyu -- International IBD Genetics Consortium (IIBDGC) -- Silverberg, Mark S -- Annese, Vito -- Hakonarson, Hakon -- Brant, Steven R -- Radford-Smith, Graham -- Mathew, Christopher G -- Rioux, John D -- Schadt, Eric E -- Daly, Mark J -- Franke, Andre -- Parkes, Miles -- Vermeire, Severine -- Barrett, Jeffrey C -- Cho, Judy H -- 068545/Z/02/Wellcome Trust/United Kingdom -- 083948/Z/07/Z/Wellcome Trust/United Kingdom -- 085475/B/08/Z/Wellcome Trust/United Kingdom -- 085475/Z/08/Z/Wellcome Trust/United Kingdom -- 089120/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- AI062773/AI/NIAID NIH HHS/ -- CA141743/CA/NCI NIH HHS/ -- CZB/4/540/Chief Scientist Office/United Kingdom -- DK043351/DK/NIDDK NIH HHS/ -- DK062413/DK/NIDDK NIH HHS/ -- DK062420/DK/NIDDK NIH HHS/ -- DK062422/DK/NIDDK NIH HHS/ -- DK062423/DK/NIDDK NIH HHS/ -- DK062429/DK/NIDDK NIH HHS/ -- DK062429-S1/DK/NIDDK NIH HHS/ -- DK062431/DK/NIDDK NIH HHS/ -- DK062432/DK/NIDDK NIH HHS/ -- DK063491/DK/NIDDK NIH HHS/ -- DK076984/DK/NIDDK NIH HHS/ -- DK084554/DK/NIDDK NIH HHS/ -- DK83756/DK/NIDDK NIH HHS/ -- ETM/137/Chief Scientist Office/United Kingdom -- ETM/75/Chief Scientist Office/United Kingdom -- G0000934/British Heart Foundation/United Kingdom -- G0600329/Medical Research Council/United Kingdom -- G0800675/Medical Research Council/United Kingdom -- G0800759/Medical Research Council/United Kingdom -- G1002033/Medical Research Council/United Kingdom -- K23 DK097142/DK/NIDDK NIH HHS/ -- M01-RR00425/RR/NCRR NIH HHS/ -- P01 DK046763/DK/NIDDK NIH HHS/ -- P01DK046763/DK/NIDDK NIH HHS/ -- P30 DK043351/DK/NIDDK NIH HHS/ -- R01 CA141743/CA/NCI NIH HHS/ -- R01 DK055731/DK/NIDDK NIH HHS/ -- T32 GM007205/GM/NIGMS NIH HHS/ -- T32GM07205/GM/NIGMS NIH HHS/ -- U01 DK062418/DK/NIDDK NIH HHS/ -- U01 DK062420/DK/NIDDK NIH HHS/ -- U01 DK062422/DK/NIDDK NIH HHS/ -- U01 DK062429/DK/NIDDK NIH HHS/ -- U01 DK062431/DK/NIDDK NIH HHS/ -- U01 DK062432/DK/NIDDK NIH HHS/ -- UL1 TR000005/TR/NCATS NIH HHS/ -- UL1 TR000124/TR/NCATS NIH HHS/ -- UL1 TR000124-01/TR/NCATS NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2012 Nov 1;491(7422):119-24. doi: 10.1038/nature11582.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23128233" target="_blank"〉PubMed〈/a〉
    Keywords: Colitis, Ulcerative/genetics/immunology/microbiology/physiopathology ; Crohn Disease/genetics/immunology/microbiology/physiopathology ; Genetic Predisposition to Disease/*genetics ; Genome, Human/genetics ; *Genome-Wide Association Study ; Haplotypes/genetics ; *Host-Pathogen Interactions/genetics/immunology ; Humans ; Inflammatory Bowel Diseases/*genetics/immunology/*microbiology/physiopathology ; Mycobacterium/*immunology/pathogenicity ; Mycobacterium Infections/genetics/microbiology ; Mycobacterium tuberculosis/immunology/pathogenicity ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 297
    Publication Date: 2012-06-23
    Description: Tumour suppressor genes encode a broad class of molecules whose mutational attenuation contributes to malignant progression. In the canonical situation, the tumour suppressor is completely inactivated through a two-hit process involving a point mutation in one allele and chromosomal deletion of the other. Here, to identify tumour suppressor genes in lymphoma, we screen a short hairpin RNA library targeting genes deleted in human lymphomas. We functionally identify those genes whose suppression promotes tumorigenesis in a mouse lymphoma model. Of the nine tumour suppressors we identified, eight correspond to genes occurring in three physically linked 'clusters', suggesting that the common occurrence of large chromosomal deletions in human tumours reflects selective pressure to attenuate multiple genes. Among the new tumour suppressors are adenosylmethionine decarboxylase 1 (AMD1) and eukaryotic translation initiation factor 5A (eIF5A), two genes associated with hypusine, a unique amino acid produced as a product of polyamine metabolism through a highly conserved pathway. Through a secondary screen surveying the impact of all polyamine enzymes on tumorigenesis, we establish the polyamine-hypusine axis as a new tumour suppressor network regulating apoptosis. Unexpectedly, heterozygous deletions encompassing AMD1 and eIF5A often occur together in human lymphomas and co-suppression of both genes promotes lymphomagenesis in mice. Thus, some tumour suppressor functions can be disabled through a two-step process targeting different genes acting in the same pathway.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530829/" 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/PMC3530829/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scuoppo, Claudio -- Miething, Cornelius -- Lindqvist, Lisa -- Reyes, Jose -- Ruse, Cristian -- Appelmann, Iris -- Yoon, Seungtai -- Krasnitz, Alexander -- Teruya-Feldstein, Julie -- Pappin, Darryl -- Pelletier, Jerry -- Lowe, Scott W -- CA087497/CA/NCI NIH HHS/ -- CA148532/CA/NCI NIH HHS/ -- MOP-106530/Canadian Institutes of Health Research/Canada -- P01 CA013106/CA/NCI NIH HHS/ -- P01 CA087497/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Jul 12;487(7406):244-8. doi: 10.1038/nature11126.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22722845" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; Disease Models, Animal ; Female ; Gene Deletion ; Gene Regulatory Networks ; Genetic Testing ; Humans ; Lymphoma, B-Cell/*genetics/physiopathology ; Lysine/*analogs & derivatives/chemistry ; Mice ; Mice, Inbred C57BL ; Polyamines/*chemistry ; RNA, Small Interfering/genetics/metabolism ; Reproducibility of Results ; Tumor Suppressor Proteins/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 298
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2012-11-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deen, Ben -- Pelphrey, Kevin -- England -- Nature. 2012 Nov 1;491(7422):S20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology, Cambridge, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23136657" target="_blank"〉PubMed〈/a〉
    Keywords: *Artifacts ; Autistic Disorder/*diagnosis/*physiopathology ; Bias (Epidemiology) ; *Brain Mapping/methods/standards ; Child ; *Head/physiology ; Humans ; Magnetic Resonance Imaging/methods/standards ; *Models, Neurological ; *Movement ; Reproducibility of Results ; Software
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 299
    Publication Date: 2012-08-04
    Description: The warmest global climates of the past 65 million years occurred during the early Eocene epoch (about 55 to 48 million years ago), when the Equator-to-pole temperature gradients were much smaller than today and atmospheric carbon dioxide levels were in excess of one thousand parts per million by volume. Recently the early Eocene has received considerable interest because it may provide insight into the response of Earth's climate and biosphere to the high atmospheric carbon dioxide levels that are expected in the near future as a consequence of unabated anthropogenic carbon emissions. Climatic conditions of the early Eocene 'greenhouse world', however, are poorly constrained in critical regions, particularly Antarctica. Here we present a well-dated record of early Eocene climate on Antarctica from an ocean sediment core recovered off the Wilkes Land coast of East Antarctica. The information from biotic climate proxies (pollen and spores) and independent organic geochemical climate proxies (indices based on branched tetraether lipids) yields quantitative, seasonal temperature reconstructions for the early Eocene greenhouse world on Antarctica. We show that the climate in lowland settings along the Wilkes Land coast (at a palaeolatitude of about 70 degrees south) supported the growth of highly diverse, near-tropical forests characterized by mesothermal to megathermal floral elements including palms and Bombacoideae. Notably, winters were extremely mild (warmer than 10 degrees C) and essentially frost-free despite polar darkness, which provides a critical new constraint for the validation of climate models and for understanding the response of high-latitude terrestrial ecosystems to increased carbon dioxide forcing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pross, Jorg -- Contreras, Lineth -- Bijl, Peter K -- Greenwood, David R -- Bohaty, Steven M -- Schouten, Stefan -- Bendle, James A -- Rohl, Ursula -- Tauxe, Lisa -- Raine, J Ian -- Huck, Claire E -- van de Flierdt, Tina -- Jamieson, Stewart S R -- Stickley, Catherine E -- van de Schootbrugge, Bas -- Escutia, Carlota -- Brinkhuis, Henk -- Integrated Ocean Drilling Program Expedition 318 Scientists -- England -- Nature. 2012 Aug 2;488(7409):73-7. doi: 10.1038/nature11300.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Paleoenvironmental Dynamics Group, Institute of Geosciences, Goethe University Frankfurt, Altenhoferallee 1, 60438 Frankfurt, Germany. joerg.pross@em.uni-frankfurt.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22859204" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; Atmosphere/chemistry ; Carbon Dioxide/analysis ; Cell Respiration ; Ecosystem ; Geologic Sediments/chemistry ; Greenhouse Effect/*history ; History, Ancient ; Human Activities ; Lipids/analysis ; Models, Theoretical ; Photosynthesis ; Pollen ; Reproducibility of Results ; Seasons ; Spores/isolation & purification ; *Temperature ; Trees/growth & development ; *Tropical Climate
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 300
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2013-03-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2013 Mar 14;495(7440):141-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23495393" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Dissent and Disputes ; Genome, Human/*genetics ; Genomics ; Humans ; *Models, Genetic ; Molecular Sequence Annotation/*standards ; Reproducibility of Results ; Semantics ; *Terminology as Topic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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