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  • Reproducibility of Results  (484)
  • Nature Publishing Group (NPG)  (484)
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  • 1
    Publication Date: 2016-04-29
    Description: The meaning of language is represented in regions of the cerebral cortex collectively known as the 'semantic system'. However, little of the semantic system has been mapped comprehensively, and the semantic selectivity of most regions is unknown. Here we systematically map semantic selectivity across the cortex using voxel-wise modelling of functional MRI (fMRI) data collected while subjects listened to hours of narrative stories. We show that the semantic system is organized into intricate patterns that seem to be consistent across individuals. We then use a novel generative model to create a detailed semantic atlas. Our results suggest that most areas within the semantic system represent information about specific semantic domains, or groups of related concepts, and our atlas shows which domains are represented in each area. This study demonstrates that data-driven methods--commonplace in studies of human neuroanatomy and functional connectivity--provide a powerful and efficient means for mapping functional representations in the brain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852309/" 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/PMC4852309/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huth, Alexander G -- de Heer, Wendy A -- Griffiths, Thomas L -- Theunissen, Frederic E -- Gallant, Jack L -- EY019684/EY/NEI NIH HHS/ -- R01 EY019684/EY/NEI NIH HHS/ -- England -- Nature. 2016 Apr 28;532(7600):453-8. doi: 10.1038/nature17637.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA. ; Department of Psychology, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27121839" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Auditory Perception ; *Brain Mapping ; Cerebral Cortex/*anatomy & histology/*physiology ; Female ; Humans ; Magnetic Resonance Imaging ; Male ; Narration ; Principal Component Analysis ; Reproducibility of Results ; *Semantics ; *Speech
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    Electronic ISSN: 1476-4687
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  • 2
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    Nature Publishing Group (NPG)
    Publication Date: 2016-05-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bender, Eric -- England -- Nature. 2016 May 11;533(7602):S62-4. doi: 10.1038/533S62a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27167394" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amyotrophic Lateral Sclerosis/diagnosis ; *Awards and Prizes ; Biomedical Research/economics/*manpower/*methods ; Breast Neoplasms/diagnosis/pathology ; *Competitive Behavior ; Cooperative Behavior ; Crowdsourcing/economics/*methods ; Datasets as Topic ; Drug Industry/economics/methods ; Humans ; Information Dissemination ; *Interdisciplinary Communication ; Internet/utilization ; Male ; Models, Biological ; Monitoring, Physiologic/instrumentation ; Prognosis ; Reproducibility of Results ; Smartphone/utilization ; Statistics as Topic ; Systems Biology/manpower/methods ; Time Factors
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  • 3
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    Nature Publishing Group (NPG)
    Publication Date: 2016-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldacre, Ben -- England -- Nature. 2016 Feb 4;530(7588):7. doi: 10.1038/530007a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26842021" target="_blank"〉PubMed〈/a〉
    Keywords: Bias (Epidemiology) ; Clinical Trials as Topic/*methods/*standards ; *Editorial Policies ; Evidence-Based Medicine/methods/standards ; Guidelines as Topic ; Humans ; Periodicals as Topic/*standards ; Reproducibility of Results ; Research Report/*standards ; Treatment Outcome
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  • 4
    Publication Date: 2016-01-07
    Description: CRISPR-Cas9 nucleases are widely used for genome editing but can induce unwanted off-target mutations. Existing strategies for reducing genome-wide off-target effects of the widely used Streptococcus pyogenes Cas9 (SpCas9) are imperfect, possessing only partial or unproven efficacies and other limitations that constrain their use. Here we describe SpCas9-HF1, a high-fidelity variant harbouring alterations designed to reduce non-specific DNA contacts. SpCas9-HF1 retains on-target activities comparable to wild-type SpCas9 with 〉85% of single-guide RNAs (sgRNAs) tested in human cells. Notably, with sgRNAs targeted to standard non-repetitive sequences, SpCas9-HF1 rendered all or nearly all off-target events undetectable by genome-wide break capture and targeted sequencing methods. Even for atypical, repetitive target sites, the vast majority of off-target mutations induced by wild-type SpCas9 were not detected with SpCas9-HF1. With its exceptional precision, SpCas9-HF1 provides an alternative to wild-type SpCas9 for research and therapeutic applications. More broadly, our results suggest a general strategy for optimizing genome-wide specificities of other CRISPR-RNA-guided nucleases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kleinstiver, Benjamin P -- Pattanayak, Vikram -- Prew, Michelle S -- Tsai, Shengdar Q -- Nguyen, Nhu T -- Zheng, Zongli -- Joung, J Keith -- DP1 GM105378/DP/NCCDPHP CDC HHS/ -- R01 GM088040/GM/NIGMS NIH HHS/ -- R01 GM107427/GM/NIGMS NIH HHS/ -- England -- Nature. 2016 Jan 28;529(7587):490-5. doi: 10.1038/nature16526. Epub 2016 Jan 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA. ; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26735016" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; CRISPR-Associated Proteins/*genetics/*metabolism ; CRISPR-Cas Systems/*physiology ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Endonucleases/genetics/*metabolism ; *Genetic Engineering ; Genome, Human/*genetics ; Humans ; Mutation ; Protein Binding ; RNA/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Streptococcus pyogenes/enzymology/genetics ; Substrate Specificity
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  • 5
    Publication Date: 2016-01-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2016 Jan 7;529(7584):9-10. doi: 10.1038/529009a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26738574" target="_blank"〉PubMed〈/a〉
    Keywords: China ; *Federal Government ; Genome, Human/genetics ; Genomics/economics/manpower/trends ; Humans ; Physicians/supply & distribution ; Population Density ; Precision Medicine/economics/*trends ; Reproducibility of Results
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  • 6
    Publication Date: 2016-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nardone, Roland M -- MacLeod, Roderick A F -- Capes-Davis, Amanda -- England -- Nature. 2016 Apr 21;532(7599):313.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27127813" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; DNA Contamination ; Databases, Factual ; *Disease Models, Animal ; Guidelines as Topic ; Heterografts/*standards ; Humans ; National Cancer Institute (U.S.) ; Neoplasms/*pathology ; Quality Control ; Reproducibility of Results ; United States ; Xenograft Model Antitumor Assays/*standards
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  • 7
    Publication Date: 2016-01-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Landry, Matt -- Gomes, Aldrin V -- England -- Nature. 2016 Jan 7;529(7584):25. doi: 10.1038/529025c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Aviva Systems Biology, San Diego, California, USA. ; University of California, Davis, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26738583" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies/*immunology ; Biotechnology/*standards ; Blotting, Western/*methods/*standards ; Buffers ; Calibration ; Indicators and Reagents/standards ; Reproducibility of Results
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  • 8
    Publication Date: 2016-04-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hsu, Angel -- Cheng, Yaping -- Weinfurter, Amy -- Xu, Kaiyang -- Yick, Cameron -- England -- Nature. 2016 Apr 21;532(7599):303-6. doi: 10.1038/532303a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yale-NUS College and Yale School of Forestry and Environmental Studies, Singapore. ; Yale Data-Driven Environmental Solutions Group, New Haven, Connecticut, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27111615" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/analysis ; Cities/*legislation & jurisprudence ; Environmental Pollution/analysis/legislation & jurisprudence/prevention & control ; Global Warming/*legislation & jurisprudence/*prevention & control ; *Government Regulation ; Greenhouse Effect/legislation & jurisprudence/prevention & control ; Industry/*legislation & jurisprudence ; International Cooperation/legislation & jurisprudence ; Private Sector/*legislation & jurisprudence ; Renewable Energy/legislation & jurisprudence ; Reproducibility of Results ; *Research Report/legislation & jurisprudence/standards ; Temperature ; Uncertainty
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  • 9
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    Nature Publishing Group (NPG)
    Publication Date: 2016-03-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edwards, Aled -- England -- Nature. 2016 Mar 17;531(7594):299-301. doi: 10.1038/531299a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Genomics Consortium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26983524" target="_blank"〉PubMed〈/a〉
    Keywords: *Cooperative Behavior ; Drug Industry/economics/manpower/*organization & administration/*standards ; Efficiency, Organizational ; Goals ; Humans ; Information Dissemination ; Reproducibility of Results ; Research/economics/manpower/*organization & administration/*standards
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  • 10
    Publication Date: 2016-01-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewandowsky, Stephan -- Bishop, Dorothy -- England -- Nature. 2016 Jan 28;529(7587):459-61. doi: 10.1038/529459a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Bristol, UK, who focuses on the public understanding of science. ; University of Oxford, UK; she chaired a symposium at the Wellcome Trust in London in April 2015 on improving scientific reliability.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26819029" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Censorship, Research ; Confidentiality ; Conflict of Interest ; Dual Use Research/legislation & jurisprudence ; Humans ; *Information Dissemination ; Peer Review, Research ; Reproducibility of Results ; Research/*standards ; Research Personnel/psychology/standards ; Retraction of Publication as Topic ; Social Behavior ; Social Media ; Violence
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  • 11
    Publication Date: 2016-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Allison, David B -- Brown, Andrew W -- George, Brandon J -- Kaiser, Kathryn A -- England -- Nature. 2016 Feb 4;530(7588):27-9. doi: 10.1038/530027a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Alabama, USA. ; Office of Energetics and the Nutrition Obesity Research Center, University of Alabama at Birmingham, Alabama, USA. ; Office of Energetics, University of Alabama at Birmingham, Alabama, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26842041" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; *Editorial Policies ; Humans ; Peer Review, Research/*methods/*standards ; Periodicals as Topic/economics/*standards ; Reproducibility of Results ; Research Design/*statistics & numerical data ; *Retraction of Publication as Topic
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  • 12
    Publication Date: 2016-03-31
    Description: Transected axons fail to regrow in the mature central nervous system. Astrocytic scars are widely regarded as causal in this failure. Here, using three genetically targeted loss-of-function manipulations in adult mice, we show that preventing astrocyte scar formation, attenuating scar-forming astrocytes, or ablating chronic astrocytic scars all failed to result in spontaneous regrowth of transected corticospinal, sensory or serotonergic axons through severe spinal cord injury (SCI) lesions. By contrast, sustained local delivery via hydrogel depots of required axon-specific growth factors not present in SCI lesions, plus growth-activating priming injuries, stimulated robust, laminin-dependent sensory axon regrowth past scar-forming astrocytes and inhibitory molecules in SCI lesions. Preventing astrocytic scar formation significantly reduced this stimulated axon regrowth. RNA sequencing revealed that astrocytes and non-astrocyte cells in SCI lesions express multiple axon-growth-supporting molecules. Our findings show that contrary to the prevailing dogma, astrocyte scar formation aids rather than prevents central nervous system axon regeneration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anderson, Mark A -- Burda, Joshua E -- Ren, Yilong -- Ao, Yan -- O'Shea, Timothy M -- Kawaguchi, Riki -- Coppola, Giovanni -- Khakh, Baljit S -- Deming, Timothy J -- Sofroniew, Michael V -- MH099559A/MH/NIMH NIH HHS/ -- MH104069/MH/NIMH NIH HHS/ -- NS057624/NS/NINDS NIH HHS/ -- NS060677/NS/NINDS NIH HHS/ -- NS084030/NS/NINDS NIH HHS/ -- P30 NS062691/NS/NINDS NIH HHS/ -- England -- Nature. 2016 Apr 14;532(7598):195-200. doi: 10.1038/nature17623. Epub 2016 Mar 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095-1763, USA. ; Departments of Psychiatry and Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095-1761, USA. ; Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095-1751, USA. ; Departments of Bioengineering, Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095-1600, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27027288" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Astrocytes/*pathology ; Axons/*physiology ; Central Nervous System/cytology/*pathology/*physiology ; Chondroitin Sulfate Proteoglycans/biosynthesis ; Cicatrix/*pathology/prevention & control ; Female ; Genomics ; Mice ; *Models, Biological ; *Nerve Regeneration ; Reproducibility of Results ; Spinal Cord Injuries/genetics/pathology
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  • 13
    Publication Date: 2016-01-29
    Description: Wearable sensor technologies are essential to the realization of personalized medicine through continuously monitoring an individual's state of health. Sampling human sweat, which is rich in physiological information, could enable non-invasive monitoring. Previously reported sweat-based and other non-invasive biosensors either can only monitor a single analyte at a time or lack on-site signal processing circuitry and sensor calibration mechanisms for accurate analysis of the physiological state. Given the complexity of sweat secretion, simultaneous and multiplexed screening of target biomarkers is critical and requires full system integration to ensure the accuracy of measurements. Here we present a mechanically flexible and fully integrated (that is, no external analysis is needed) sensor array for multiplexed in situ perspiration analysis, which simultaneously and selectively measures sweat metabolites (such as glucose and lactate) and electrolytes (such as sodium and potassium ions), as well as the skin temperature (to calibrate the response of the sensors). Our work bridges the technological gap between signal transduction, conditioning (amplification and filtering), processing and wireless transmission in wearable biosensors by merging plastic-based sensors that interface with the skin with silicon integrated circuits consolidated on a flexible circuit board for complex signal processing. This application could not have been realized using either of these technologies alone owing to their respective inherent limitations. The wearable system is used to measure the detailed sweat profile of human subjects engaged in prolonged indoor and outdoor physical activities, and to make a real-time assessment of the physiological state of the subjects. This platform enables a wide range of personalized diagnostic and physiological monitoring applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gao, Wei -- Emaminejad, Sam -- Nyein, Hnin Yin Yin -- Challa, Samyuktha -- Chen, Kevin -- Peck, Austin -- Fahad, Hossain M -- Ota, Hiroki -- Shiraki, Hiroshi -- Kiriya, Daisuke -- Lien, Der-Hsien -- Brooks, George A -- Davis, Ronald W -- Javey, Ali -- P01 HG000205/HG/NHGRI NIH HHS/ -- England -- Nature. 2016 Jan 28;529(7587):509-14. doi: 10.1038/nature16521.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA. ; Berkeley Sensor and Actuator Center, University of California, Berkeley, California 94720, USA. ; Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. ; Stanford Genome Technology Center, Stanford School of Medicine, Palo Alto, California 94304, USA. ; Integrative Biology, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26819044" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Bicycling/physiology ; Body Water ; Calibration ; Electrolytes/analysis ; Female ; Glucose/analysis ; Healthy Volunteers ; Humans ; Lactic Acid/analysis ; Male ; Monitoring, Physiologic/*instrumentation/*methods ; Precision Medicine/instrumentation/methods ; Reproducibility of Results ; Running/physiology ; Skin ; Skin Temperature ; Sweat/*chemistry ; Young Adult
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  • 14
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    Nature Publishing Group (NPG)
    Publication Date: 2016-01-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2016 Jan 28;529(7587):456-8. doi: 10.1038/529456a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26819028" target="_blank"〉PubMed〈/a〉
    Keywords: Accreditation ; Animals ; Calibration ; Financing, Organized/organization & administration ; Laboratories/standards ; Quality Control ; Reproducibility of Results ; Research/*standards ; *Research Design ; Scientific Misconduct
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  • 15
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    Nature Publishing Group (NPG)
    Publication Date: 2016-01-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gewin, Virginia -- England -- Nature. 2016 Jan 7;529(7584):117-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26744755" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information ; Competitive Behavior ; *Information Dissemination ; Journal Impact Factor ; Publishing ; Reproducibility of Results ; *Research/standards ; *Research Personnel/psychology/standards ; Research Support as Topic ; Software
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  • 16
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    Nature Publishing Group (NPG)
    Publication Date: 2016-03-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Makin, Simon -- England -- Nature. 2016 Mar 3;531(7592):S10-1. doi: 10.1038/531S10a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26934518" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Enhancement/*methods ; Brain/*physiology ; Child ; Cognition/physiology ; Controlled Clinical Trials as Topic ; Games, Experimental ; Humans ; Intelligence/physiology ; Memory, Short-Term/*physiology ; Meta-Analysis as Topic ; Reproducibility of Results ; *Uncertainty ; Young Adult
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  • 17
    Publication Date: 2016-03-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2016 Mar 10;531(7593):151. doi: 10.1038/nature.2016.19503.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26961635" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/*methods/*standards ; Models, Biological ; *Probability ; Reproducibility of Results ; *Research Design ; Research Personnel/*education ; Statistics as Topic/*methods/*standards ; Uncertainty
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  • 18
    Publication Date: 2016-03-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karve, Shraddha Madhav -- Mangalam, Madhur -- England -- Nature. 2016 Mar 17;531(7594):305. doi: 10.1038/531305d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Indian Institute of Science Education and Research, Pune, India. ; University of Georgia, Athens, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26983529" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Motivation ; *Publishing ; Reproducibility of Results ; Research/*standards ; Research Personnel/psychology/*standards ; Time Factors
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  • 19
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    Nature Publishing Group (NPG)
    Publication Date: 2016-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chi, Kelly Rae -- England -- Nature. 2016 Apr 14;532(7598):269-71. doi: 10.1038/532269a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27075102" target="_blank"〉PubMed〈/a〉
    Keywords: Aged, 80 and over ; Biopsy/economics/*methods ; Blood Platelets/cytology ; DNA Mutational Analysis/economics/methods ; DNA, Neoplasm/*blood/genetics ; Drug Resistance, Neoplasm/genetics ; Exosomes/genetics ; Female ; Humans ; Neoplasm Metastasis/diagnosis/genetics ; Neoplasm Recurrence, Local/blood/diagnosis/genetics ; Neoplasms/*blood/*diagnosis/drug therapy/genetics ; Neoplastic Cells, Circulating/metabolism ; Phagocytosis ; Polymerase Chain Reaction ; Reproducibility of Results ; Sensitivity and Specificity
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  • 20
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    Nature Publishing Group (NPG)
    Publication Date: 2016-03-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bourzac, Katherine -- England -- Nature. 2016 Mar 3;531(7592):S6-8. doi: 10.1038/531S6a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26934525" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Biomedical Enhancement/*methods ; Brain/*physiology ; Female ; Humans ; Intelligence Tests ; Male ; Memory/physiology ; Patient Safety ; Reproducibility of Results ; Self Care/adverse effects ; *Transcranial Direct Current Stimulation/adverse effects ; *Transcranial Magnetic Stimulation ; Uncertainty
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  • 21
    Publication Date: 2016-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boulton, Geoffrey -- England -- Nature. 2016 Feb 18;530(7590):281. doi: 10.1038/530281c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉ICSU CODATA; and University of Edinburgh, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26887481" target="_blank"〉PubMed〈/a〉
    Keywords: Datasets as Topic ; Information Dissemination/*legislation & jurisprudence ; International Cooperation/*legislation & jurisprudence ; Knowledge ; Open Access Publishing/*legislation & jurisprudence ; Reproducibility of Results ; *Research/legislation & jurisprudence
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  • 22
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    Nature Publishing Group (NPG)
    Publication Date: 2016-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reardon, Sara -- England -- Nature. 2016 Feb 18;530(7590):264. doi: 10.1038/nature.2016.19335.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26887470" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Feed/*analysis/standards ; Animal Nutritional Physiological Phenomena ; Animals ; *Animals, Laboratory/genetics/microbiology ; Confounding Factors (Epidemiology) ; Diet/standards/veterinary ; *Environment ; Female ; Gastrointestinal Microbiome ; *Housing, Animal ; Humans ; Lighting ; Male ; Mice ; Mice, Inbred Strains ; Models, Animal ; Reproducibility of Results ; *Research Design/standards
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  • 23
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    Nature Publishing Group (NPG)
    Publication Date: 2016-03-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cressey, Daniel -- England -- Nature. 2016 Mar 3;531(7592):128.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26949773" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Experimentation/*standards ; Animals ; Animals, Laboratory ; Bias (Epidemiology) ; Confidentiality ; Confounding Factors (Epidemiology) ; Feedback ; Guidelines as Topic ; *Internet ; Quality Control ; Random Allocation ; Reproducibility of Results ; *Research Design ; Sample Size ; *Software
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  • 24
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    Nature Publishing Group (NPG)
    Publication Date: 2016-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2016 Feb 18;530(7590):254. doi: 10.1038/530254a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26887455" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Feed/*analysis ; *Animal Nutritional Physiological Phenomena ; Animals ; Animals, Laboratory/*physiology ; Diet/*veterinary ; Environment ; Japan ; Longevity/*physiology ; Mice ; Models, Animal ; Reproducibility of Results ; Research Design
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  • 25
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    Nature Publishing Group (NPG)
    Publication Date: 2016-05-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buenz, Eric -- England -- Nature. 2016 May 5;533(7601):36. doi: 10.1038/533036d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nelson Marlborough Institute of Technology, Nelson, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27147021" target="_blank"〉PubMed〈/a〉
    Keywords: *Efficiency, Organizational/ethics ; *Goals ; Humans ; Industry/*ethics/organization & administration/*standards ; Reproducibility of Results ; Research/manpower/organization & administration/*standards ; Research Personnel/*ethics/organization & administration/psychology/*standards ; Scientific Misconduct/psychology
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  • 26
    Publication Date: 2016-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ward, Alyssa -- Baldwin, Thomas O -- Antin, Parker B -- England -- Nature. 2016 Apr 14;532(7598):177. doi: 10.1038/532177d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. ; University of California, Riverside, USA. ; University of Arizona, Tucson, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27075087" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Confounding Factors (Epidemiology) ; *Learning ; Mice ; Mice, Transgenic/genetics ; National Institutes of Health (U.S.)/economics ; Reproducibility of Results ; Research/*standards ; United States
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  • 27
    Publication Date: 2016-01-28
    Description: Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is lacking. Here, using H3K27ac and BRD4 chromatin immunoprecipitation followed by sequencing (ChIP-seq) coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors, validated by ChIP-seq, that is responsible for subgroup divergence, and implicates candidate cells of origin for Group 4. Our integrated analysis of enhancer elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Charles Y -- Erkek, Serap -- Tong, Yiai -- Yin, Linlin -- Federation, Alexander J -- Zapatka, Marc -- Haldipur, Parthiv -- Kawauchi, Daisuke -- Risch, Thomas -- Warnatz, Hans-Jorg -- Worst, Barbara C -- Ju, Bensheng -- Orr, Brent A -- Zeid, Rhamy -- Polaski, Donald R -- Segura-Wang, Maia -- Waszak, Sebastian M -- Jones, David T W -- Kool, Marcel -- Hovestadt, Volker -- Buchhalter, Ivo -- Sieber, Laura -- Johann, Pascal -- Chavez, Lukas -- Groschel, Stefan -- Ryzhova, Marina -- Korshunov, Andrey -- Chen, Wenbiao -- Chizhikov, Victor V -- Millen, Kathleen J -- Amstislavskiy, Vyacheslav -- Lehrach, Hans -- Yaspo, Marie-Laure -- Eils, Roland -- Lichter, Peter -- Korbel, Jan O -- Pfister, Stefan M -- Bradner, James E -- Northcott, Paul A -- England -- Nature. 2016 Feb 4;530(7588):57-62. doi: 10.1038/nature16546. Epub 2016 Jan 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Oncology, Dana Farber Cancer Institute (DFCI), Boston, Massachusetts 02215, USA. ; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany. ; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. ; Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA. ; Department of Molecular Physiology &Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA. ; Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. ; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98105, USA. ; Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. ; Department of Bone Marrow Transplantation &Cellular Therapy, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA. ; Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA. ; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany. ; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. ; Department of Translational Oncology, NCT Heidelberg, 69120 Heidelberg, Germany. ; Department of Neuropathology, NN Burdenko Neurosurgical Institute, 125047 Moscow, Russia. ; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and Department of Neuropathology University Hospital, 69120 Heidelberg, Germany. ; Department of Anatomy and Neurobiology, University of Tennessee Health Sciences Center, Memphis, Tennessee 38163, USA. ; Department of Pediatrics, Genetics Division, University of Washington, Seattle, Washington 98195, USA. ; Institute of Pharmacy and Molecular Biotechnology and BioQuant, University of Heidelberg, 69117 Heidelberg, Germany. ; Department of Pediatrics, University of Heidelberg, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26814967" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cerebellar Neoplasms/classification/*genetics/*pathology ; Enhancer Elements, Genetic/*genetics ; Female ; Gene Expression Regulation, Neoplastic/*genetics ; Gene Regulatory Networks/genetics ; Genes, Neoplasm/genetics ; Genes, Reporter/genetics ; Humans ; Male ; Medulloblastoma/*classification/genetics/*pathology ; Mice ; Reproducibility of Results ; Transcription Factors/*metabolism ; Zebrafish/genetics
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  • 28
    Publication Date: 2016-02-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2016 Feb 11;530(7589):141. doi: 10.1038/nature.2016.19269.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26863961" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/*standards ; *Biotechnology ; Drug Industry ; *Open Access Publishing ; Reproducibility of Results ; *Uncertainty ; United States
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  • 29
    Publication Date: 2015-01-17
    Description: The structure of water near non-polar molecular fragments or surfaces mediates the hydrophobic interactions that underlie a broad range of interfacial, colloidal and biophysical phenomena. Substantial progress over the past decade has improved our understanding of hydrophobic interactions in simple model systems, but most biologically and technologically relevant structures contain non-polar domains in close proximity to polar and charged functional groups. Theories and simulations exploring such nanometre-scale chemical heterogeneity find it can have an important effect, but the influence of this heterogeneity on hydrophobic interactions has not been tested experimentally. Here we report chemical force microscopy measurements on alkyl-functionalized surfaces that reveal a dramatic change in the surfaces' hydrophobic interaction strengths on co-immobilization of amine or guanidine groups. Protonation of amine groups doubles the strength of hydrophobic interactions, and guanidinium groups eliminate measurable hydrophobic interactions in all pH ranges investigated. We see these divergent effects of proximally immobilized cations also in single-molecule measurements on conformationally stable beta-peptides with non-polar subunits located one nanometre from either amine- or guanidine-bearing subunits. Our results demonstrate the importance of nanometre-scale chemical heterogeneity, with hydrophobicity not an intrinsic property of any given non-polar domain but strongly modulated by functional groups located as far away as one nanometre. The judicious placing of charged groups near hydrophobic domains thus provides a strategy for tuning hydrophobic driving forces to optimize molecular recognition or self-assembly processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, C Derek -- Wang, Chenxuan -- Acevedo-Velez, Claribel -- Gellman, Samuel H -- Abbott, Nicholas L -- England -- Nature. 2015 Jan 15;517(7534):347-50. doi: 10.1038/nature14018.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA. ; 1] Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA [2] Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA. ; Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25592540" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonium Compounds/chemistry ; Arginine/chemistry ; Buffers ; Cations/chemistry ; Colloids/chemistry ; Ethanolamines/chemistry ; Guanidine/chemistry ; Hydrogen-Ion Concentration ; *Hydrophobic and Hydrophilic Interactions ; Lysine/chemistry ; Methanol/chemistry ; Microscopy, Atomic Force ; Peptides/chemistry ; Protons ; Reproducibility of Results ; Surface Properties
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  • 30
    Publication Date: 2015-11-13
    Description: Neuroblastoma is a paediatric malignancy that typically arises in early childhood, and is derived from the developing sympathetic nervous system. Clinical phenotypes range from localized tumours with excellent outcomes to widely metastatic disease in which long-term survival is approximately 40% despite intensive therapy. A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility and oncogenic addiction to LMO1 in the tumour cells. Here we investigate the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation and transcription factor binding sites. We show that SNP rs2168101 G〉T is the most highly associated variant (combined P = 7.47 x 10(-29), odds ratio 0.65, 95% confidence interval 0.60-0.70), and resides in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G allele that is associated with tumour formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P = 0.028) in neuroblastoma primary tumours, and ablates GATA3 binding (P 〈 0.0001). We demonstrate allelic imbalance favouring the G-containing strand in tumours heterozygous for this SNP, as demonstrated both by RNA sequencing (P 〈 0.0001) and reporter assays (P = 0.002). These findings indicate that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumour cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775078/" 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/PMC4775078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oldridge, Derek A -- Wood, Andrew C -- Weichert-Leahey, Nina -- Crimmins, Ian -- Sussman, Robyn -- Winter, Cynthia -- McDaniel, Lee D -- Diamond, Maura -- Hart, Lori S -- Zhu, Shizhen -- Durbin, Adam D -- Abraham, Brian J -- Anders, Lars -- Tian, Lifeng -- Zhang, Shile -- Wei, Jun S -- Khan, Javed -- Bramlett, Kelli -- Rahman, Nazneen -- Capasso, Mario -- Iolascon, Achille -- Gerhard, Daniela S -- Guidry Auvil, Jaime M -- Young, Richard A -- Hakonarson, Hakon -- Diskin, Sharon J -- Look, A Thomas -- Maris, John M -- 100210/Wellcome Trust/United Kingdom -- 100210/Z/12/Z/Wellcome Trust/United Kingdom -- 1K99CA178189/CA/NCI NIH HHS/ -- R00-CA151869/CA/NCI NIH HHS/ -- R01 CA124709/CA/NCI NIH HHS/ -- R01 CA180692/CA/NCI NIH HHS/ -- R01-CA109901/CA/NCI NIH HHS/ -- R01-CA124709/CA/NCI NIH HHS/ -- R01-CA180692/CA/NCI NIH HHS/ -- RC1MD004418/MD/NIMHD NIH HHS/ -- T32 HG000046/HG/NHGRI NIH HHS/ -- T32-HG000046/HG/NHGRI NIH HHS/ -- England -- Nature. 2015 Dec 17;528(7582):418-21. doi: 10.1038/nature15540. Epub 2015 Nov 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA. ; Medical Scientist Training Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Department of Molecular Medicine and Pathology, University of Auckland, Auckland, Auckland Region 1142, New Zealand. ; Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA. ; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA. ; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA. ; Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA. ; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA. ; Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA. ; Thermo Fisher Scientific, Austin, Texas 78744, USA. ; The Institute of Cancer Research, London SM2 5NG, UK. ; University of Naples Federico II, 80131 Naples, Italy. ; CEINGE Biotecnologie Avanzate, 80131 Naples, Italy. ; Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA. ; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26560027" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Alleles ; Allelic Imbalance ; Binding Sites ; DNA-Binding Proteins/*genetics ; Enhancer Elements, Genetic/*genetics ; Epigenomics ; GATA3 Transcription Factor/metabolism ; Gene Expression Regulation, Neoplastic/genetics ; Genetic Predisposition to Disease/*genetics ; Genome-Wide Association Study ; Genotype ; Histones/chemistry/metabolism ; Humans ; Introns/genetics ; LIM Domain Proteins/*genetics ; Lysine/metabolism ; Neuroblastoma/*genetics ; Organ Specificity ; Polymorphism, Single Nucleotide/*genetics ; Reproducibility of Results ; Transcription Factors/*genetics
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  • 31
    Publication Date: 2015-11-10
    Description: Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA sequence motifs. Such sequences are very common in the human genome, and an important determinant of the specificity of gene expression is the cooperative binding of multiple TFs to closely located motifs. However, interactions between DNA-bound TFs have not been systematically characterized. To identify TF pairs that bind cooperatively to DNA, and to characterize their spacing and orientation preferences, we have performed consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have not been previously described. The observed cooperativity occurred promiscuously between TFs from diverse structural families. Structural analysis of the TF pairs, including a novel crystal structure of MEIS1 and DLX3 bound to their identified recognition site, revealed that the interactions between the TFs were predominantly mediated by DNA. Most TF pair sites identified involved a large overlap between individual TF recognition motifs, and resulted in recognition of composite sites that were markedly different from the individual TF's motifs. Together, our results indicate that the DNA molecule commonly plays an active role in cooperative interactions that define the gene regulatory lexicon.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jolma, Arttu -- Yin, Yimeng -- Nitta, Kazuhiro R -- Dave, Kashyap -- Popov, Alexander -- Taipale, Minna -- Enge, Martin -- Kivioja, Teemu -- Morgunova, Ekaterina -- Taipale, Jussi -- England -- Nature. 2015 Nov 19;527(7578):384-8. doi: 10.1038/nature15518. Epub 2015 Nov 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biosciences and Nutrition, Karolinska Institutet, SE 141 83, Sweden. ; European Synchrotron Radiation Facility, 38043 Grenoble, France. ; Genome-Scale Biology Program, University of Helsinki, P.O. Box 63, FI-00014, Finland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26550823" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites/genetics ; Crystallography, X-Ray ; DNA/*genetics/*metabolism ; Gene Expression Regulation/genetics ; Humans ; Molecular Sequence Data ; Nucleotide Motifs/genetics ; Reproducibility of Results ; *Substrate Specificity/genetics ; Transcription Factors/*metabolism
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  • 32
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    Nature Publishing Group (NPG)
    Publication Date: 2015-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2015 Jul 30;523(7562):510-1. doi: 10.1038/523510a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26223603" target="_blank"〉PubMed〈/a〉
    Keywords: Aircraft ; Atmosphere/chemistry ; Climate Change ; *Expeditions ; *Geography ; Greenland ; Ice Cover/*chemistry ; Models, Theoretical ; Oceans and Seas ; Reproducibility of Results ; *Research ; Seawater/chemistry ; Ships ; United States ; *United States National Aeronautics and Space Administration ; Water/*analysis/chemistry
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  • 33
    Publication Date: 2015-12-18
    Description: The response of the Greenland Ice Sheet (GIS) to changes in temperature during the twentieth century remains contentious, largely owing to difficulties in estimating the spatial and temporal distribution of ice mass changes before 1992, when Greenland-wide observations first became available. The only previous estimates of change during the twentieth century are based on empirical modelling and energy balance modelling. Consequently, no observation-based estimates of the contribution from the GIS to the global-mean sea level budget before 1990 are included in the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Here we calculate spatial ice mass loss around the entire GIS from 1900 to the present using aerial imagery from the 1980s. This allows accurate high-resolution mapping of geomorphic features related to the maximum extent of the GIS during the Little Ice Age at the end of the nineteenth century. We estimate the total ice mass loss and its spatial distribution for three periods: 1900-1983 (75.1 +/- 29.4 gigatonnes per year), 1983-2003 (73.8 +/- 40.5 gigatonnes per year), and 2003-2010 (186.4 +/- 18.9 gigatonnes per year). Furthermore, using two surface mass balance models we partition the mass balance into a term for surface mass balance (that is, total precipitation minus total sublimation minus runoff) and a dynamic term. We find that many areas currently undergoing change are identical to those that experienced considerable thinning throughout the twentieth century. We also reveal that the surface mass balance term shows a considerable decrease since 2003, whereas the dynamic term is constant over the past 110 years. Overall, our observation-based findings show that during the twentieth century the GIS contributed at least 25.0 +/- 9.4 millimetres of global-mean sea level rise. Our result will help to close the twentieth-century sea level budget, which remains crucial for evaluating the reliability of models used to predict global sea level rise.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kjeldsen, Kristian K -- Korsgaard, Niels J -- Bjork, Anders A -- Khan, Shfaqat A -- Box, Jason E -- Funder, Svend -- Larsen, Nicolaj K -- Bamber, Jonathan L -- Colgan, William -- van den Broeke, Michiel -- Siggaard-Andersen, Marie-Louise -- Nuth, Christopher -- Schomacker, Anders -- Andresen, Camilla S -- Willerslev, Eske -- Kjaer, Kurt H -- England -- Nature. 2015 Dec 17;528(7582):396-400. doi: 10.1038/nature16183.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen 1350, Denmark. ; Department of Earth Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada. ; DTU Space-National Space Institute, Technical University of Denmark, Department of Geodesy, Kongens Lyngby 2800, Denmark. ; Geological Survey of Denmark and Greenland, Department of Marine Geology and Glaciology, Copenhagen 1350, Denmark. ; Department of Geoscience, Aarhus University, Aarhus 8000, Denmark. ; Bristol Glaciology Centre, University of Bristol, Bristol BS8 1SS, UK. ; Department of Earth and Space Science and Engineering, York University, Toronto, Ontario M3J 1P3, Canada. ; Institute for Marine and Atmospheric Research, Utrecht University, Utrecht 80005, The Netherlands. ; Department of Geosciences, University of Oslo, Oslo 0316, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26672555" target="_blank"〉PubMed〈/a〉
    Keywords: Climate Change/*statistics & numerical data ; Greenland ; History, 20th Century ; History, 21st Century ; *Ice Cover ; Models, Theoretical ; Observation ; Photography ; Reproducibility of Results ; Seawater/analysis ; *Spatio-Temporal Analysis ; Temperature
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  • 34
    Publication Date: 2015-07-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maron, Martine -- Gordon, Ascelin -- Mackey, Brendan G -- Possingham, Hugh P -- Watson, James E M -- England -- Nature. 2015 Jul 23;523(7561):401-3. doi: 10.1038/523401a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Geography, Planning and Environmental Management at the University of Queensland, Brisbane, Australia. ; School of Global, Urban and Social Studies at RMIT University, Melbourne, Victoria. ; Griffith University, Gold Coast, Australia. ; University of Queensland, Brisbane, Australia, and professor of conservation decisions at Imperial College London, UK. ; University of Queensland, Brisbane, Australia, and director of the Science and Research Initiative at the Wildlife Conservation Society.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26201581" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Conservation of Natural Resources/economics/*methods/statistics & numerical data ; Reproducibility of Results
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  • 35
    Publication Date: 2015-01-30
    Description: Most present-generation climate models simulate an increase in global-mean surface temperature (GMST) since 1998, whereas observations suggest a warming hiatus. It is unclear to what extent this mismatch is caused by incorrect model forcing, by incorrect model response to forcing or by random factors. Here we analyse simulations and observations of GMST from 1900 to 2012, and show that the distribution of simulated 15-year trends shows no systematic bias against the observations. Using a multiple regression approach that is physically motivated by surface energy balance, we isolate the impact of radiative forcing, climate feedback and ocean heat uptake on GMST--with the regression residual interpreted as internal variability--and assess all possible 15- and 62-year trends. The differences between simulated and observed trends are dominated by random internal variability over the shorter timescale and by variations in the radiative forcings used to drive models over the longer timescale. For either trend length, spread in simulated climate feedback leaves no traceable imprint on GMST trends or, consequently, on the difference between simulations and observations. The claim that climate models systematically overestimate the response to radiative forcing from increasing greenhouse gas concentrations therefore seems to be unfounded.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marotzke, Jochem -- Forster, Piers M -- England -- Nature. 2015 Jan 29;517(7536):565-70. doi: 10.1038/nature14117.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Meteorology, Bundesstrasse 53, 20146 Hamburg, Germany. ; School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25631444" target="_blank"〉PubMed〈/a〉
    Keywords: Bias (Epidemiology) ; *Feedback ; Global Warming/history/*statistics & numerical data ; History, 20th Century ; History, 21st Century ; *Models, Theoretical ; Multivariate Analysis ; Regression Analysis ; Reproducibility of Results ; *Temperature ; Time Factors
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  • 36
    Publication Date: 2015-02-20
    Description: Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515363/" 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/PMC4515363/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dixon, Jesse R -- Jung, Inkyung -- Selvaraj, Siddarth -- Shen, Yin -- Antosiewicz-Bourget, Jessica E -- Lee, Ah Young -- Ye, Zhen -- Kim, Audrey -- Rajagopal, Nisha -- Xie, Wei -- Diao, Yarui -- Liang, Jing -- Zhao, Huimin -- Lobanenkov, Victor V -- Ecker, Joseph R -- Thomson, James A -- Ren, Bing -- R01 ES024984/ES/NIEHS NIH HHS/ -- T32 GM007198/GM/NIGMS NIH HHS/ -- U01 ES017166/ES/NIEHS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Feb 19;518(7539):331-6. doi: 10.1038/nature14222.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] Medical Scientist Training Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. ; Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA. ; 1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. ; The Morgridge Institute for Research, 309 North Orchard Street, Madison, Wisconsin 53715, USA. ; Tsinghua University-Peking University Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. ; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. ; Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Twinbrook I NIAID Facility, Room 1417, 5640 Fishers Lane, Rockville, Maryland 20852, USA. ; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA. ; 1] The Morgridge Institute for Research, 309 North Orchard Street, Madison, Wisconsin 53715, USA [2] Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA [3] Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA. ; 1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25693564" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Allelic Imbalance/genetics ; *Cell Differentiation/genetics ; Cell Lineage/genetics ; Chromatin/*chemistry/genetics/*metabolism ; *Chromatin Assembly and Disassembly/genetics ; Embryonic Stem Cells/*cytology/*metabolism ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/*genetics ; Epigenomics ; Gene Regulatory Networks ; Humans ; Promoter Regions, Genetic/genetics ; Reproducibility of Results
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  • 37
    Publication Date: 2015-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Victor, David G -- England -- Nature. 2015 Apr 2;520(7545):27-9. doi: 10.1038/520027a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory on International Law and Regulation, University of California, San Diego, USA. He is also chairman of the Global Agenda Council on Governance for Sustainability at the World Economic Forum.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25832390" target="_blank"〉PubMed〈/a〉
    Keywords: Advisory Committees/*organization & administration ; *Climate Change/statistics & numerical data ; Consensus ; Environmental Policy/legislation & jurisprudence/*trends ; *Policy Making ; Reproducibility of Results ; *Research Report ; Social Sciences/*trends ; Time Factors ; Uncertainty
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  • 38
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    Nature Publishing Group (NPG)
    Publication Date: 2015-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2015 Jan 29;517(7536):537-8. doi: 10.1038/517537a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25631423" target="_blank"〉PubMed〈/a〉
    Keywords: *Decision Making/physiology ; Humans ; Psychology/standards ; Reproducibility of Results ; *Unconscious (Psychology)
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  • 39
    Publication Date: 2015-08-20
    Description: Understanding the development and function of an organ requires the characterization of all of its cell types. Traditional methods for visualizing and isolating subpopulations of cells are based on messenger RNA or protein expression of only a few known marker genes. The unequivocal identification of a specific marker gene, however, poses a major challenge, particularly if this cell type is rare. Identifying rare cell types, such as stem cells, short-lived progenitors, cancer stem cells, or circulating tumour cells, is crucial to acquire a better understanding of normal or diseased tissue biology. To address this challenge we first sequenced the transcriptome of hundreds of randomly selected cells from mouse intestinal organoids, cultured self-organizing epithelial structures that contain all cell lineages of the mammalian intestine. Organoid buds, like intestinal crypts, harbour stem cells that continuously differentiate into a variety of cell types, occurring at widely different abundances. Since available computational methods can only resolve more abundant cell types, we developed RaceID, an algorithm for rare cell type identification in complex populations of single cells. We demonstrate that this algorithm can resolve cell types represented by only a single cell in a population of randomly sampled organoid cells. We use this algorithm to identify Reg4 as a novel marker for enteroendocrine cells, a rare population of hormone-producing intestinal cells. Next, we use Reg4 expression to enrich for these rare cells and investigate the heterogeneity within this population. RaceID confirmed the existence of known enteroendocrine lineages, and moreover discovered novel subtypes, which we subsequently validated in vivo. Having validated RaceID we then applied the algorithm to ex vivo-isolated Lgr5-positive stem cells and their direct progeny. We find that Lgr5-positive cells represent a homogenous abundant population of stem cells mixed with a rare population of Lgr5-positive secretory cells. We envision broad applicability of our method for discovering rare cell types and the corresponding marker genes in healthy and diseased organs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grun, Dominic -- Lyubimova, Anna -- Kester, Lennart -- Wiebrands, Kay -- Basak, Onur -- Sasaki, Nobuo -- Clevers, Hans -- van Oudenaarden, Alexander -- England -- Nature. 2015 Sep 10;525(7568):251-5. doi: 10.1038/nature14966. Epub 2015 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584 CT Utrecht, The Netherlands. ; University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CG Utrecht, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26287467" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Biomarkers/analysis ; Cell Differentiation/genetics ; Cell Lineage ; Cell Separation/*methods ; In Situ Hybridization, Fluorescence ; Intestine, Small/*cytology ; Mice ; Neoplasm Proteins/genetics ; Organoids/cytology ; Paneth Cells/cytology/metabolism ; RNA, Messenger/*genetics ; Receptors, G-Protein-Coupled/genetics ; Reproducibility of Results ; *Sequence Analysis, RNA ; *Single-Cell Analysis ; Stem Cells/cytology/metabolism ; Transcriptome/genetics
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  • 40
    Publication Date: 2015-12-18
    Description: Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727831/" 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/PMC4727831/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doyle, Lindsey -- Hallinan, Jazmine -- Bolduc, Jill -- Parmeggiani, Fabio -- Baker, David -- Stoddard, Barry L -- Bradley, Philip -- R01 GM049857/GM/NIGMS NIH HHS/ -- R01 GM115545/GM/NIGMS NIH HHS/ -- R01GM49857/GM/NIGMS NIH HHS/ -- R21 GM106117/GM/NIGMS NIH HHS/ -- R21GM106117/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Dec 24;528(7583):585-8. doi: 10.1038/nature16191. Epub 2015 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, Washington 98109, USA. ; Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA. ; Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA. ; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA. ; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, Washington 98019, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26675735" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Motifs ; *Bioengineering ; *Computer Simulation ; Crystallography, X-Ray ; Databases, Protein ; Models, Molecular ; *Protein Structure, Secondary ; Proteins/*chemistry ; Reproducibility of Results
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  • 41
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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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  • 42
    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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  • 43
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    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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  • 44
    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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  • 45
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    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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  • 46
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    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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  • 47
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    Nature Publishing Group (NPG)
    Publication Date: 2015-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2015 Nov 26;527(7579):545-51. doi: 10.1038/527545a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nature in San Francisco, California.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26607547" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies/*immunology ; Antibody Specificity/*immunology ; Cross Reactions/immunology ; Humans ; Immunoassay/*methods/*standards ; Indicators and Reagents/standards ; International Cooperation ; Mice ; National Institutes of Health (U.S.) ; Neuroanatomy/methods/standards ; Periodicals as Topic ; Reproducibility of Results ; United States
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  • 48
    Publication Date: 2015-05-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2015 May 21;521(7552):274-6. doi: 10.1038/521274a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25993940" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies/chemistry/economics/genetics/*immunology ; Antibody Specificity/*immunology ; *Artifacts ; Cross Reactions/immunology ; Humans ; Indicators and Reagents/economics/standards ; Membrane Proteins/immunology ; Quality Control ; Reagent Kits, Diagnostic/standards ; Reproducibility of Results
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  • 49
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    Nature Publishing Group (NPG)
    Publication Date: 2015-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Sep 24;525(7570):426. doi: 10.1038/525426a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26399791" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Cellular Reprogramming ; Embryonic Stem Cells/cytology/*metabolism ; Genotype ; Induced Pluripotent Stem Cells/cytology/*metabolism ; Peer Review, Research ; *Periodicals as Topic ; Reproducibility of Results ; Research/*standards ; *Retraction of Publication as Topic ; Sequence Analysis, DNA
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  • 50
    Publication Date: 2015-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Werner, Reinhard -- England -- Nature. 2015 Jan 15;517(7534):245. doi: 10.1038/517245a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25592498" target="_blank"〉PubMed〈/a〉
    Keywords: Decision Making ; *Journal Impact Factor ; *Motivation ; Personnel Selection/methods ; Reproducibility of Results ; Research Personnel/*psychology/*standards
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  • 51
    Publication Date: 2015-12-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- Callaway, Ewen -- Castelvecchi, Davide -- Morello, Lauren -- Reardon, Sara -- Schiermeier, Quirin -- Witze, Alexandra -- England -- Nature. 2015 Dec 24;528(7583):448-51. doi: 10.1038/528448a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26701034" target="_blank"〉PubMed〈/a〉
    Keywords: CRISPR-Cas Systems/genetics ; Congresses as Topic ; Cryoelectron Microscopy ; Dengue Vaccines/supply & distribution ; Earthquakes/statistics & numerical data ; Ebola Vaccines/immunology ; Genetic Engineering/ethics/legislation & jurisprudence ; Global Warming/legislation & jurisprudence/prevention & control ; Humans ; Hydraulic Fracking/statistics & numerical data ; International Cooperation ; Malaria Vaccines/immunology ; Paris ; Physics ; Pluto ; Precision Medicine ; Reproducibility of Results ; Research/standards ; *Science ; Sexism/statistics & numerical data ; Space Flight
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  • 52
    Publication Date: 2015-11-05
    Description: It is estimated that more than 170 million people are infected with hepatitis C virus (HCV) worldwide. Clinical trials have demonstrated that, for the first time in human history, the potential exists to eradicate a chronic viral disease using combination therapies that contain only direct-acting antiviral agents. HCV non-structural protein 5A (NS5A) is a multifunctional protein required for several stages of the virus replication cycle. NS5A replication complex inhibitors, exemplified by daclatasvir (DCV; also known as BMS-790052 and Daklinza), belong to the most potent class of direct-acting anti-HCV agents described so far, with in vitro activity in the picomolar (pM) to low nanomolar (nM) range. The potency observed in vitro has translated into clinical efficacy, with HCV RNA declining by ~3-4 log10 in infected patients after administration of single oral doses of DCV. Understanding the exceptional potency of DCV was a key objective of this study. Here we show that although DCV and an NS5A inhibitor analogue (Syn-395) are inactive against certain NS5A resistance variants, combinations of the pair enhance DCV potency by 〉1,000-fold, restoring activity to the pM range. This synergistic effect was validated in vivo using an HCV-infected chimaeric mouse model. The cooperative interaction of a pair of compounds suggests that NS5A protein molecules communicate with each other: one inhibitor binds to resistant NS5A, causing a conformational change that is transmitted to adjacent NS5As, resensitizing resistant NS5A so that the second inhibitor can act to restore inhibition. This unprecedented synergistic anti-HCV activity also enhances the resistance barrier of DCV, providing additional options for HCV combination therapy and new insight into the role of NS5A in the HCV replication cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Jin-Hua -- O'Boyle, Donald R 2nd -- Fridell, Robert A -- Langley, David R -- Wang, Chunfu -- Roberts, Susan B -- Nower, Peter -- Johnson, Benjamin M -- Moulin, Frederic -- Nophsker, Michelle J -- Wang, Ying-Kai -- Liu, Mengping -- Rigat, Karen -- Tu, Yong -- Hewawasam, Piyasena -- Kadow, John -- Meanwell, Nicholas A -- Cockett, Mark -- Lemm, Julie A -- Kramer, Melissa -- Belema, Makonen -- Gao, Min -- England -- Nature. 2015 Nov 12;527(7577):245-8. doi: 10.1038/nature15711. Epub 2015 Nov 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, USA. ; Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, USA. ; Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, USA. ; Leads Discovery and Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, USA. ; Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26536115" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/drug effects ; Animals ; Antiviral Agents/*pharmacology ; Biphenyl Compounds/*pharmacology ; Cell Line ; Drug Resistance, Viral/*drug effects ; Drug Synergism ; Drug Therapy, Combination ; Hepacivirus/*drug effects/*genetics/metabolism ; Hepatitis C/virology ; Hepatocytes/transplantation ; Humans ; Imidazoles/*pharmacology ; Mice ; Models, Molecular ; Protein Conformation/drug effects ; Protein Multimerization/drug effects ; Protein Structure, Quaternary/drug effects ; Reproducibility of Results ; Viral Nonstructural Proteins/chemistry/genetics/*metabolism ; Virus Replication/drug effects
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  • 53
    Publication Date: 2015-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Check Hayden, Erika -- England -- Nature. 2015 Apr 16;520(7547):276-7. doi: 10.1038/520276a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25877185" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Algorithms ; Computational Biology/methods/*standards ; Datasets as Topic ; Peer Review, Research/*methods/*standards ; Periodicals as Topic/*standards ; Reproducibility of Results ; Research Design/*standards ; Software/*standards
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  • 54
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    Nature Publishing Group (NPG)
    Publication Date: 2015-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reardon, Sara -- England -- Nature. 2015 Jul 16;523(7560):266. doi: 10.1038/523266a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26178942" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biotechnology/methods ; Clinical Trials as Topic ; Drug Discovery/*methods ; Drug Industry/*methods ; Humans ; *Models, Biological ; Organ Specificity/*drug effects ; Rats ; Reproducibility of Results ; Tissue Array Analysis/*methods
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  • 55
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    Nature Publishing Group (NPG)
    Publication Date: 2015-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Oct 8;526(7572):163. doi: 10.1038/526163a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26450020" target="_blank"〉PubMed〈/a〉
    Keywords: *Bias (Epidemiology) ; *Cognition ; Crowdsourcing ; Humans ; Reproducibility of Results ; Research Design ; Research Personnel/*psychology ; Statistics as Topic/*standards ; *Thinking
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  • 56
    Publication Date: 2015-04-08
    Description: Regulation of protein synthesis is fundamental for all aspects of eukaryotic biology by controlling development, homeostasis and stress responses. The 13-subunit, 800-kilodalton eukaryotic initiation factor 3 (eIF3) organizes initiation factor and ribosome interactions required for productive translation. However, current understanding of eIF3 function does not explain genetic evidence correlating eIF3 deregulation with tissue-specific cancers and developmental defects. Here we report the genome-wide discovery of human transcripts that interact with eIF3 using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). eIF3 binds to a highly specific program of messenger RNAs involved in cell growth control processes, including cell cycling, differentiation and apoptosis, via the mRNA 5' untranslated region. Surprisingly, functional analysis of the interaction between eIF3 and two mRNAs encoding the cell proliferation regulators c-JUN and BTG1 reveals that eIF3 uses different modes of RNA stem-loop binding to exert either translational activation or repression. Our findings illuminate a new role for eIF3 in governing a specialized repertoire of gene expression and suggest that binding of eIF3 to specific mRNAs could be targeted to control carcinogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603833/" 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/PMC4603833/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Amy S Y -- Kranzusch, Philip J -- Cate, Jamie H D -- P50 GM102706/GM/NIGMS NIH HHS/ -- S10 RR027303/RR/NCRR NIH HHS/ -- S10 RR029668/RR/NCRR NIH HHS/ -- S10RR025622/RR/NCRR NIH HHS/ -- S10RR027303/RR/NCRR NIH HHS/ -- S10RR029668/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Jun 4;522(7554):111-4. doi: 10.1038/nature14267. Epub 2015 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Molecular &Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [2] Center for RNA Systems Biology, University of California, Berkeley, Berkeley, California 94720, USA. ; 1] Department of Molecular &Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [2] Howard Hughes Medical Institute (HHMI), University of California, Berkeley, Berkeley, California 94720, USA. ; 1] Department of Molecular &Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [2] Center for RNA Systems Biology, University of California, Berkeley, Berkeley, California 94720, USA [3] Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA [4] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25849773" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions/genetics ; Apoptosis ; Binding Sites ; Cell Differentiation ; Cell Line ; Cell Proliferation/genetics ; Cross-Linking Reagents ; *Down-Regulation ; Eukaryotic Initiation Factor-3/chemistry/*metabolism ; Humans ; Immunoprecipitation ; Neoplasm Proteins/metabolism ; Neoplasms/metabolism/pathology ; Organ Specificity ; *Peptide Chain Initiation, Translational ; Phenotype ; Proto-Oncogene Proteins c-jun/metabolism ; RNA, Messenger/*genetics/*metabolism ; Reproducibility of Results ; Ribonucleosides ; Ribosomes/metabolism ; Substrate Specificity ; Transcriptome
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  • 57
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    Nature Publishing Group (NPG)
    Publication Date: 2015-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Jul 30;523(7562):502. doi: 10.1038/523502a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26223589" target="_blank"〉PubMed〈/a〉
    Keywords: *Communication ; Contact Tracing ; Coronavirus Infections/epidemiology/psychology/*transmission ; Disease Outbreaks/prevention & control/*statistics & numerical data ; *Fear ; Hemorrhagic Fever, Ebola/epidemiology/psychology/transmission ; Hospitals ; Humans ; Patient Isolation ; *Public Opinion ; Quarantine ; Reproducibility of Results ; Republic of Korea/epidemiology ; Risk Assessment
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  • 58
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    Nature Publishing Group (NPG)
    Publication Date: 2015-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Jun 18;522(7556):256. doi: 10.1038/522256a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26085234" target="_blank"〉PubMed〈/a〉
    Keywords: National Institutes of Health (U.S.) ; Periodicals as Topic/standards ; Public Opinion ; Quality Control ; Reproducibility of Results ; Research/*economics/*standards ; *Risk Management ; United States
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  • 59
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Dec 24;528(7583):459-67. doi: 10.1038/528459a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26701036" target="_blank"〉PubMed〈/a〉
    Keywords: Analgesics, Opioid/metabolism ; Astronomy ; Benzylisoquinolines/chemistry/metabolism ; Bias (Epidemiology) ; CRISPR-Cas Systems/genetics ; Diplomacy ; Electric Conductivity ; Electronics/instrumentation ; Embryo Research/ethics ; Genetic Engineering/ethics ; Genome, Human/genetics ; Genomics ; Global Warming/economics/*legislation & jurisprudence/prevention & control ; History, 21st Century ; History, Ancient ; Human Migration/history ; Humans ; Iran ; Language/history ; Nanotubes, Carbon ; Nuclear Weapons/legislation & jurisprudence ; Paris ; Pluto ; Prejudice ; Psychology/standards ; Reproducibility of Results ; Reproductive Medicine/ethics ; Sexual Harassment/prevention & control ; Space Flight/economics/trends ; Synthetic Biology/methods ; Temperature ; Yeasts/genetics/metabolism
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  • 60
    Publication Date: 2015-05-15
    Description: Recursive splicing is a process in which large introns are removed in multiple steps by re-splicing at ratchet points--5' splice sites recreated after splicing. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing. Here we identify 197 zero nucleotide exon ratchet points in 130 introns of 115 Drosophila genes from total RNA sequencing data generated from developmental time points, dissected tissues and cultured cells. The sequential nature of recursive splicing was confirmed by identification of lariat introns generated by splicing to and from the ratchet points. We also show that recursive splicing is a constitutive process, that depletion of U2AF inhibits recursive splicing, and that the sequence and function of ratchet points are evolutionarily conserved in Drosophila. Finally, we identify four recursively spliced human genes, one of which is also recursively spliced in Drosophila. Together, these results indicate that recursive splicing is commonly used in Drosophila, occurs in humans, and provides insight into the mechanisms by which some large introns are removed.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529404/" 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/PMC4529404/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duff, Michael O -- Olson, Sara -- Wei, Xintao -- Garrett, Sandra C -- Osman, Ahmad -- Bolisetty, Mohan -- Plocik, Alex -- Celniker, Susan E -- Graveley, Brenton R -- R01 GM095296/GM/NIGMS NIH HHS/ -- R01GM095296/GM/NIGMS NIH HHS/ -- U54 HG006994/HG/NHGRI NIH HHS/ -- U54HG006994/HG/NHGRI NIH HHS/ -- England -- Nature. 2015 May 21;521(7552):376-9. doi: 10.1038/nature14475. Epub 2015 May 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA. ; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25970244" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cells, Cultured ; Drosophila melanogaster/*genetics ; Exons/genetics ; Female ; Genes, Insect/genetics ; Genome, Insect/*genetics ; Humans ; Introns/genetics ; Male ; Nuclear Proteins/deficiency/genetics/metabolism ; Nucleotides/*genetics ; RNA Splice Sites/genetics ; RNA Splicing/*genetics ; Reproducibility of Results ; Ribonucleoproteins/deficiency/genetics/metabolism
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  • 61
    Publication Date: 2015-01-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haunschild, Robin -- Bornmann, Lutz -- England -- Nature. 2015 Jan 1;517(7532):21. doi: 10.1038/517021d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Solid State Research, Stuttgart, Germany. ; Max Planck Society, Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25557707" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/standards/statistics & numerical data ; *Bibliometrics ; Germany ; *Internationality ; Periodicals as Topic/*standards/statistics & numerical data ; Reproducibility of Results ; Research/*standards/*statistics & numerical data ; Research Report/standards
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  • 62
    Publication Date: 2015-05-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eisenstein, Michael -- England -- Nature. 2015 May 21;521(7552):S52-5. doi: 10.1038/521S52a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25992672" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*methods ; Animals ; Bees/*drug effects/*physiology ; Conflict of Interest ; European Union ; Evaluation Studies as Topic ; Female ; Guanidines/administration & dosage/*adverse effects/toxicity ; Homing Behavior/drug effects ; Humans ; Imidazoles/administration & dosage/*adverse effects/toxicity ; Insecticides/administration & dosage/*adverse effects/toxicity ; Male ; Mammals ; Nitro Compounds/administration & dosage/*adverse effects/toxicity ; Orientation/drug effects ; Oxazines/administration & dosage/*adverse effects/toxicity ; Pollination/drug effects ; Reproducibility of Results ; Spatial Navigation/drug effects ; Thiazoles/administration & dosage/*adverse effects/toxicity ; *Uncertainty ; United States ; Varroidae/pathogenicity
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  • 63
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    Nature Publishing Group (NPG)
    Publication Date: 2015-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Savage, Neil -- England -- Nature. 2015 Nov 5;527(7576):S12-3. doi: 10.1038/527S12a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26536217" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Cell Phones/*utilization ; Datasets as Topic ; Health Surveys/instrumentation/*methods/*trends ; Humans ; Mobile Applications/*utilization ; Motor Activity/physiology ; Patient Selection ; Reproducibility of Results ; Sample Size ; Telemedicine/*instrumentation/*methods/trends
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  • 64
    Publication Date: 2015-07-23
    Description: G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a approximately 20 degrees rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521999/" 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/PMC4521999/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Yanyong -- Zhou, X Edward -- Gao, Xiang -- He, Yuanzheng -- Liu, Wei -- Ishchenko, Andrii -- Barty, Anton -- White, Thomas A -- Yefanov, Oleksandr -- Han, Gye Won -- Xu, Qingping -- de Waal, Parker W -- Ke, Jiyuan -- Tan, M H Eileen -- Zhang, Chenghai -- Moeller, Arne -- West, Graham M -- Pascal, Bruce D -- Van Eps, Ned -- Caro, Lydia N -- Vishnivetskiy, Sergey A -- Lee, Regina J -- Suino-Powell, Kelly M -- Gu, Xin -- Pal, Kuntal -- Ma, Jinming -- Zhi, Xiaoyong -- Boutet, Sebastien -- Williams, Garth J -- Messerschmidt, Marc -- Gati, Cornelius -- Zatsepin, Nadia A -- Wang, Dingjie -- James, Daniel -- Basu, Shibom -- Roy-Chowdhury, Shatabdi -- Conrad, Chelsie E -- Coe, Jesse -- Liu, Haiguang -- Lisova, Stella -- Kupitz, Christopher -- Grotjohann, Ingo -- Fromme, Raimund -- Jiang, Yi -- Tan, Minjia -- Yang, Huaiyu -- Li, Jun -- Wang, Meitian -- Zheng, Zhong -- Li, Dianfan -- Howe, Nicole -- Zhao, Yingming -- Standfuss, Jorg -- Diederichs, Kay -- Dong, Yuhui -- Potter, Clinton S -- Carragher, Bridget -- Caffrey, Martin -- Jiang, Hualiang -- Chapman, Henry N -- Spence, John C H -- Fromme, Petra -- Weierstall, Uwe -- Ernst, Oliver P -- Katritch, Vsevolod -- Gurevich, Vsevolod V -- Griffin, Patrick R -- Hubbell, Wayne L -- Stevens, Raymond C -- Cherezov, Vadim -- Melcher, Karsten -- Xu, H Eric -- DK071662/DK/NIDDK NIH HHS/ -- EY005216/EY/NEI NIH HHS/ -- EY011500/EY/NEI NIH HHS/ -- GM073197/GM/NIGMS NIH HHS/ -- GM077561/GM/NIGMS NIH HHS/ -- GM095583/GM/NIGMS NIH HHS/ -- GM097463/GM/NIGMS NIH HHS/ -- GM102545/GM/NIGMS NIH HHS/ -- GM103310/GM/NIGMS NIH HHS/ -- GM104212/GM/NIGMS NIH HHS/ -- GM108635/GM/NIGMS NIH HHS/ -- P30EY000331/EY/NEI NIH HHS/ -- P41 GM103310/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073210/GM/NIGMS NIH HHS/ -- R01 DK066202/DK/NIDDK NIH HHS/ -- R01 DK071662/DK/NIDDK NIH HHS/ -- R01 EY011500/EY/NEI NIH HHS/ -- R01 GM087413/GM/NIGMS NIH HHS/ -- R01 GM109955/GM/NIGMS NIH HHS/ -- S10 RR027270/RR/NCRR NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54 GM094599/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Jul 30;523(7562):561-7. doi: 10.1038/nature14656. Epub 2015 Jul 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA. ; Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA. ; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA. ; Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany. ; Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA. ; 1] Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA [2] Department of Obstetrics &Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. ; The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, New York 10027, USA. ; Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, USA. ; Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA. ; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, USA. ; Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA. ; 1] Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA [2] BioXFEL, NSF Science and Technology Center, 700 Ellicott Street, Buffalo, New York 14203, USA. ; 1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Department of Physics, Arizona State University, Tempe, Arizona 85287, USA. ; 1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Beijing Computational Science Research Center, Haidian District, Beijing 10084, China. ; 1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA. ; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. ; Department of Obstetrics &Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. ; Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland. ; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA. ; School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland. ; 1] BioXFEL, NSF Science and Technology Center, 700 Ellicott Street, Buffalo, New York 14203, USA [2] Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, USA. ; Laboratory of Biomolecular Research at Paul Scherrer Institute, CH-5232 Villigen, Switzerland. ; Department of Biology, Universitat Konstanz, 78457 Konstanz, Germany. ; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China. ; 1] Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany [2] Centre for Ultrafast Imaging, 22761 Hamburg, Germany. ; 1] Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; 1] Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA [2] Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA [3] iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China. ; 1] Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA [2] VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26200343" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arrestin/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Disulfides/chemistry/metabolism ; Humans ; Lasers ; Mice ; Models, Molecular ; Multiprotein Complexes/biosynthesis/chemistry/metabolism ; Protein Binding ; Reproducibility of Results ; Rhodopsin/*chemistry/*metabolism ; Signal Transduction ; X-Rays
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  • 65
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2015-04-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Savage, Neil -- England -- Nature. 2015 Apr 16;520(7547):395-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25884061" target="_blank"〉PubMed〈/a〉
    Keywords: Altitude ; Archives ; Arctic Regions ; Artifacts ; *Freezing ; Global Warming/*statistics & numerical data ; Ice Cover/*chemistry ; Meteorology/economics/*methods/*trends ; Mountaineering ; Reproducibility of Results ; Research/economics/manpower/*trends ; *Research Design ; Research Personnel ; Research Support as Topic
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  • 66
    Publication Date: 2015-11-17
    Description: Large cancer cell line collections broadly capture the genomic diversity of human cancers and provide valuable insight into anti-cancer drug response. Here we show substantial agreement and biological consilience between drug sensitivity measurements and their associated genomic predictors from two publicly available large-scale pharmacogenomics resources: The Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer databases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cancer Cell Line Encyclopedia Consortium -- Genomics of Drug Sensitivity in Cancer Consortium -- 086357/Wellcome Trust/United Kingdom -- 102696/Wellcome Trust/United Kingdom -- 1U54HG006097-01/HG/NHGRI NIH HHS/ -- A16629/Cancer Research UK/United Kingdom -- England -- Nature. 2015 Dec 3;528(7580):84-7. doi: 10.1038/nature15736. Epub 2015 Nov 16.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26570998" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor/*drug effects ; *Databases, Factual ; Datasets as Topic ; Humans ; Inhibitory Concentration 50 ; Neoplasms/drug therapy/*genetics/*pathology ; *Pharmacogenetics ; Reproducibility of Results
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  • 67
    Publication Date: 2015-03-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anderson, Warwick P -- England -- Nature. 2015 Mar 12;519(7542):158. doi: 10.1038/519158a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Health and Medical Research Council of Australia, Canberra, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25762270" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/economics/*methods/*standards ; Humans ; International Cooperation ; Reproducibility of Results ; Scientific Misconduct
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  • 68
    Publication Date: 2015-12-04
    Description: Mass-screen-and-treat and targeted mass-drug-administration strategies are being considered as a means to interrupt transmission of Plasmodium falciparum malaria. However, the effectiveness of such strategies will depend on the extent to which current and future diagnostics are able to detect those individuals who are infectious to mosquitoes. We estimate the relationship between parasite density and onward infectivity using sensitive quantitative parasite diagnostics and mosquito feeding assays from Burkina Faso. We find that a diagnostic with a lower detection limit of 200 parasites per microlitre would detect 55% of the infectious reservoir (the combined infectivity to mosquitoes of the whole population weighted by how often each individual is bitten) whereas a test with a limit of 20 parasites per microlitre would detect 83% and 2 parasites per microlitre would detect 95% of the infectious reservoir. Using mathematical models, we show that increasing the diagnostic sensitivity from 200 parasites per microlitre (equivalent to microscopy or current rapid diagnostic tests) to 2 parasites per microlitre would increase the number of regions where transmission could be interrupted with a mass-screen-and-treat programme from an entomological inoculation rate below 1 to one of up to 4. The higher sensitivity diagnostic could reduce the number of treatment rounds required to interrupt transmission in areas of lower prevalence. We predict that mass-screen-and-treat with a highly sensitive diagnostic is less effective than mass drug administration owing to the prophylactic protection provided to uninfected individuals by the latter approach. In low-transmission settings such as those in Southeast Asia, we find that a diagnostic tool with a sensitivity of 20 parasites per microlitre may be sufficient for targeted mass drug administration because this diagnostic is predicted to identify a similar village population prevalence compared with that currently detected using polymerase chain reaction if treatment levels are high and screening is conducted during the dry season. Along with other factors, such as coverage, choice of drug, timing of the intervention, importation of infections, and seasonality, the sensitivity of the diagnostic can play a part in increasing the chance of interrupting transmission.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Slater, Hannah C -- Ross, Amanda -- Ouedraogo, Andre Lin -- White, Lisa J -- Nguon, Chea -- Walker, Patrick G T -- Ngor, Pengby -- Aguas, Ricardo -- Silal, Sheetal P -- Dondorp, Arjen M -- La Barre, Paul -- Burton, Robert -- Sauerwein, Robert W -- Drakeley, Chris -- Smith, Thomas A -- Bousema, Teun -- Ghani, Azra C -- 106698/Z/14/Z/Wellcome Trust/United Kingdom -- England -- Nature. 2015 Dec 3;528(7580):S94-101. doi: 10.1038/nature16040.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, Norfolk Place, London W2 1PG, UK. ; Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland. ; University of Basel, Petersplatz 1, 4001 Basel, Switzerland. ; Institute for Disease Modelling, Bellevue, Washington 98005, USA. ; Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, 01 B.P. 2208, Ouagadougou, Burkina Faso. ; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand. ; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK. ; National Malaria Center, Ministry of Health, Phnom Penh 12302, Cambodia. ; Department of Statistical Sciences, University of Cape Town, Rondebosch 7701, Cape Town, South Africa. ; PATH, 2201 Westlake Avenue, Seattle, Washington 98121, USA. ; Radboud University Medical Center, 6525 HP Nijmegen, the Netherlands. ; London School of Hygiene &Tropical Medicine, Keppel St, London WC1E 7HT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26633771" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Animals ; Child ; Child, Preschool ; *Diagnostic Tests, Routine ; Female ; Humans ; Malaria, Falciparum/*diagnosis/*drug therapy/epidemiology/parasitology ; Male ; Plasmodium falciparum/*drug effects/*isolation & purification ; Polymerase Chain Reaction ; Prevalence ; Reproducibility of Results ; Young Adult
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  • 69
    Publication Date: 2015-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anthes, Emily -- England -- Nature. 2015 Jul 30;523(7562):516-8. doi: 10.1038/523516a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26223609" target="_blank"〉PubMed〈/a〉
    Keywords: Checklist/standards/*utilization ; Clinical Competence/statistics & numerical data ; General Surgery/*methods/*standards ; *Hospitals ; Humans ; Medical Errors/*mortality/*prevention & control ; Pilot Projects ; *Program Evaluation ; Reproducibility of Results ; Treatment Failure ; World Health Organization
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  • 70
    Publication Date: 2015-12-18
    Description: Recent research has highlighted a strong correlation between tissue-specific cancer risk and the lifetime number of tissue-specific stem-cell divisions. Whether such correlation implies a high unavoidable intrinsic cancer risk has become a key public health debate with the dissemination of the 'bad luck' hypothesis. Here we provide evidence that intrinsic risk factors contribute only modestly (less than ~10-30% of lifetime risk) to cancer development. First, we demonstrate that the correlation between stem-cell division and cancer risk does not distinguish between the effects of intrinsic and extrinsic factors. We then show that intrinsic risk is better estimated by the lower bound risk controlling for total stem-cell divisions. Finally, we show that the rates of endogenous mutation accumulation by intrinsic processes are not sufficient to account for the observed cancer risks. Collectively, we conclude that cancer risk is heavily influenced by extrinsic factors. These results are important for strategizing cancer prevention, research and public health.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Song -- Powers, Scott -- Zhu, Wei -- Hannun, Yusuf A -- England -- Nature. 2016 Jan 7;529(7584):43-7. doi: 10.1038/nature16166. Epub 2015 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA. ; Stony Brook Cancer Center, Stony Brook University, Health Sciences Center, Stony Brook, New York 11794, USA. ; Department of Pathology, Stony Brook University, Health Sciences Center, Stony Brook, New York 11794, USA. ; Department of Medicine, Stony Brook University, Health Sciences Center, Stony Brook, New York 11794, USA. ; Department of Biochemistry, Stony Brook University, Health Sciences Center, Stony Brook, New York 11794, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26675728" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Self Renewal ; Cell Transformation, Neoplastic/pathology ; Disease Progression ; Humans ; *Models, Biological ; Mutagenesis/genetics ; Mutation Accumulation ; Neoplasms/epidemiology/genetics/*pathology/*prevention & control ; Organ Specificity ; Reproducibility of Results ; Risk Assessment ; Stem Cells/*cytology/pathology
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  • 71
    Publication Date: 2015-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bradbury, Andrew -- Pluckthun, Andreas -- England -- Nature. 2015 Feb 5;518(7537):27-9. doi: 10.1038/518027a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA. ; Biochemistry Department of the University of Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25652980" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies/*chemistry/economics/*immunology/isolation & purification ; Antibodies, Monoclonal/biosynthesis/chemistry/immunology/isolation & purification ; *Antibody Specificity ; Biomedical Research/*standards ; Hybridomas/cytology/immunology/metabolism ; Immune Sera/immunology ; Indicators and Reagents/economics ; Quality Control ; Recombinant Proteins/*biosynthesis/economics/immunology/*isolation & purification ; Reproducibility of Results
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  • 72
    Publication Date: 2015-04-17
    Description: Cell line misidentification, contamination and poor annotation affect scientific reproducibility. Here we outline simple measures to detect or avoid cross-contamination, present a framework for cell line annotation linked to short tandem repeat and single nucleotide polymorphism profiles, and provide a catalogue of synonymous cell lines. This resource will enable our community to eradicate the use of misidentified lines and generate credible cell-based data.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Mamie -- Selvaraj, Suresh K -- Liang-Chu, May M Y -- Aghajani, Sahar -- Busse, Matthew -- Yuan, Jean -- Lee, Genee -- Peale, Franklin -- Klijn, Christiaan -- Bourgon, Richard -- Kaminker, Joshua S -- Neve, Richard M -- England -- Nature. 2015 Apr 16;520(7547):307-11. doi: 10.1038/nature14397.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Discovery Oncology, Genentech Inc., South San Francisco, California 94080, USA. ; Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California 94080, USA. ; Department of Pathology, Genentech Inc., South San Francisco, California 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25877200" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line/*classification/*metabolism ; Cell Separation ; *Data Curation ; Genotype ; *Guidelines as Topic ; Microsatellite Repeats/genetics ; Polymorphism, Single Nucleotide/genetics ; Quality Control ; Reproducibility of Results ; Species Specificity ; Terminology as Topic
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  • 73
    Publication Date: 2015-11-13
    Description: The role of epithelial-to-mesenchymal transition (EMT) in metastasis is a longstanding source of debate, largely owing to an inability to monitor transient and reversible EMT phenotypes in vivo. Here we establish an EMT lineage-tracing system to monitor this process in mice, using a mesenchymal-specific Cre-mediated fluorescent marker switch system in spontaneous breast-to-lung metastasis models. We show that within a predominantly epithelial primary tumour, a small proportion of tumour cells undergo EMT. Notably, lung metastases mainly consist of non-EMT tumour cells that maintain their epithelial phenotype. Inhibiting EMT by overexpressing the microRNA miR-200 does not affect lung metastasis development. However, EMT cells significantly contribute to recurrent lung metastasis formation after chemotherapy. These cells survived cyclophosphamide treatment owing to reduced proliferation, apoptotic tolerance and increased expression of chemoresistance-related genes. Overexpression of miR-200 abrogated this resistance. This study suggests the potential of an EMT-targeting strategy, in conjunction with conventional chemotherapies, for breast cancer treatment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662610/" 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/PMC4662610/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischer, Kari R -- Durrans, Anna -- Lee, Sharrell -- Sheng, Jianting -- Li, Fuhai -- Wong, Stephen T C -- Choi, Hyejin -- El Rayes, Tina -- Ryu, Seongho -- Troeger, Juliane -- Schwabe, Robert F -- Vahdat, Linda T -- Altorki, Nasser K -- Mittal, Vivek -- Gao, Dingcheng -- 1 F31 CA186510-01/CA/NCI NIH HHS/ -- F31 CA186510/CA/NCI NIH HHS/ -- R01 CA135417/CA/NCI NIH HHS/ -- U01 CA188388/CA/NCI NIH HHS/ -- U54 CA149196-05/CA/NCI NIH HHS/ -- England -- Nature. 2015 Nov 26;527(7579):472-6. doi: 10.1038/nature15748. Epub 2015 Nov 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cardiothoracic Surgery, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA. ; Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA. ; Neuberger Berman Lung Cancer Center, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA. ; Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA. ; Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas 77030, USA. ; Methodist Cancer Center, Houston Methodist Hospital, Houston, Texas, 77030 USA. ; Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25 Bongjeong-ro Cheonan-Si, Chungcheongnam-do 31151, South Korea. ; Department of Medicine, Columbia University, College of Physicians and Surgeons, New York, New York 10032, USA. ; Institute of Human Nutrition, Columbia University, New York, New York 10032, USA. ; Department of Medicine, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26560033" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents, Alkylating/pharmacology/therapeutic use ; Apoptosis/drug effects ; Cell Lineage ; Cell Proliferation/drug effects ; Cell Tracking ; Cyclophosphamide/pharmacology/therapeutic use ; Disease Models, Animal ; Disease Progression ; *Drug Resistance, Neoplasm/drug effects/genetics ; *Epithelial-Mesenchymal Transition/drug effects/genetics ; Female ; Lung Neoplasms/drug therapy/genetics/*pathology/*secondary ; Male ; Mammary Neoplasms, Experimental/*drug therapy/genetics/*pathology ; Mice ; MicroRNAs/genetics ; Neoplasm Metastasis/drug therapy/genetics/*pathology ; Reproducibility of Results
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  • 74
    Publication Date: 2015-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cressey, Daniel -- England -- Nature. 2015 Apr 16;520(7547):271-2. doi: 10.1038/520271a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25877180" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Experimentation/ethics/*standards ; Animal Rights/standards ; Animals ; Data Interpretation, Statistical ; Great Britain ; Guidelines as Topic ; Mice ; Models, Animal ; Rats ; Reproducibility of Results ; Research Support as Topic/methods/*organization & administration ; Sample Size
    Print ISSN: 0028-0836
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  • 75
    Publication Date: 2015-09-04
    Description: The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crowther, T W -- Glick, H B -- Covey, K R -- Bettigole, C -- Maynard, D S -- Thomas, S M -- Smith, J R -- Hintler, G -- Duguid, M C -- Amatulli, G -- Tuanmu, M-N -- Jetz, W -- Salas, C -- Stam, C -- Piotto, D -- Tavani, R -- Green, S -- Bruce, G -- Williams, S J -- Wiser, S K -- Huber, M O -- Hengeveld, G M -- Nabuurs, G-J -- Tikhonova, E -- Borchardt, P -- Li, C-F -- Powrie, L W -- Fischer, M -- Hemp, A -- Homeier, J -- Cho, P -- Vibrans, A C -- Umunay, P M -- Piao, S L -- Rowe, C W -- Ashton, M S -- Crane, P R -- Bradford, M A -- England -- Nature. 2015 Sep 10;525(7568):201-5. doi: 10.1038/nature14967. Epub 2015 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yale School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06511, USA. ; Department of Environmental Sciences, University of Helsinki, Helsinki 00014, Finland. ; Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA. ; Department of Life Sciences, Silwood Park, Imperial College, London SL5 7PY, UK. ; Departamento de Ciencias Forestales, Universidad de La Frontera, Temuco 4811230, Chile. ; RedCastle Resources, Salt Lake City, Utah 84103, USA. ; Universidade Federal do Sul da Bahia, Ferradas, Itabuna 45613-204, Brazil. ; Forestry Department, Food and Agriculture Organization of the United Nations, Rome 00153, Italy. ; Operation Wallacea, Spilbsy, Lincolnshire PE23 4EX, UK. ; Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation (SAC), University of Kent, Canterbury ME4 4AG, UK. ; Molecular Imaging Research Center MIRCen/CEA, CNRS URA 2210, 91401 Orsay Cedex, France. ; Landcare Research, Lincoln 7640, New Zealand. ; WSL, Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland. ; Environmental Science Group, Wageningen University &Research Centre, 6708 PB, The Netherlands. ; Center for Forest Ecology and Productivity RAS, Moscow 117997, Russia. ; CEN Center for Earth System Research and Sustainability, Institute of Geography, University of Hamburg, Hamburg 20146, Germany. ; Department of Botany and Zoology, Masaryk University, Brno 61137, Czech Republic. ; South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa. ; Institute of Plant Sciences, Botanical Garden, and Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland. ; Senckenberg Gesellschaft fur Naturforschung, Biodiversity and Climate Research Centre (BIK-F), 60325 Frankfurt, Germany. ; Department of Plant Systematics, University of Bayreuth, 95447 Bayreuth, Germany. ; Albrecht von Haller Institute of Plant Sciences, Georg August University of Gottingen, 37073 Gottingen, Germany. ; Tropical Ecology Research Group, Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK. ; Universidade Regional de Blumenau, Departamento de Engenharia Florestal, Blumenau/Santa Catarina 89030-000, Brazil. ; Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26331545" target="_blank"〉PubMed〈/a〉
    Keywords: Ecology/statistics & numerical data ; Ecosystem ; Forestry/statistics & numerical data ; *Forests ; *Geographic Mapping ; Population Density ; Reproducibility of Results ; Trees/*growth & development
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  • 76
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    Nature Publishing Group (NPG)
    Publication Date: 2015-05-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 May 14;521(7551):126. doi: 10.1038/521126a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25971470" target="_blank"〉PubMed〈/a〉
    Keywords: Great Britain ; Politics ; Public Opinion ; Reproducibility of Results ; *Research Design
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 77
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    Nature Publishing Group (NPG)
    Publication Date: 2015-01-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gewin, Virginia -- England -- Nature. 2015 Jan 8;517(7533):231-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25574536" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Communication ; Fisheries ; Humans ; Policy Making ; Public Opinion ; Reproducibility of Results ; *Research Personnel/psychology/standards ; Science/*education
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  • 78
    Publication Date: 2015-11-26
    Description: DNase I hypersensitive sites (DHSs) provide important information on the presence of transcriptional regulatory elements and the state of chromatin in mammalian cells. Conventional DNase sequencing (DNase-seq) for genome-wide DHSs profiling is limited by the requirement of millions of cells. Here we report an ultrasensitive strategy, called single-cell DNase sequencing (scDNase-seq) for detection of genome-wide DHSs in single cells. We show that DHS patterns at the single-cell level are highly reproducible among individual cells. Among different single cells, highly expressed gene promoters and enhancers associated with multiple active histone modifications display constitutive DHS whereas chromatin regions with fewer histone modifications exhibit high variation of DHS. Furthermore, the single-cell DHSs predict enhancers that regulate cell-specific gene expression programs and the cell-to-cell variations of DHS are predictive of gene expression. Finally, we apply scDNase-seq to pools of tumour cells and pools of normal cells, dissected from formalin-fixed paraffin-embedded tissue slides from patients with thyroid cancer, and detect thousands of tumour-specific DHSs. Many of these DHSs are associated with promoters and enhancers critically involved in cancer development. Analysis of the DHS sequences uncovers one mutation (chr18: 52417839G〉C) in the tumour cells of a patient with follicular thyroid carcinoma, which affects the binding of the tumour suppressor protein p53 and correlates with decreased expression of its target gene TXNL1. In conclusion, scDNase-seq can reliably detect DHSs in single cells, greatly extending the range of applications of DHS analysis both for basic and for translational research, and may provide critical information for personalized medicine.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697938/" 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/PMC4697938/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jin, Wenfei -- Tang, Qingsong -- Wan, Mimi -- Cui, Kairong -- Zhang, Yi -- Ren, Gang -- Ni, Bing -- Sklar, Jeffrey -- Przytycka, Teresa M -- Childs, Richard -- Levens, David -- Zhao, Keji -- Z01 HL005801-05/Intramural NIH HHS/ -- England -- Nature. 2015 Dec 3;528(7580):142-6. doi: 10.1038/nature15740.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA. ; Institute of Immunology, Third Military Medical University of the People's Liberation Army, Chongqing 400038, China. ; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China. ; Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26605532" target="_blank"〉PubMed〈/a〉
    Keywords: Adenocarcinoma, Follicular/genetics/pathology ; Animals ; Chromatin/*genetics/*metabolism ; Deoxyribonuclease I/*metabolism ; Enhancer Elements, Genetic/genetics ; *Formaldehyde ; Gene Expression Profiling ; Genome/*genetics ; Histones/metabolism ; Humans ; Mice ; Mutation/genetics ; NIH 3T3 Cells ; *Paraffin Embedding ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Single-Cell Analysis/*methods ; Thioredoxins/genetics ; Thyroid Neoplasms/genetics/pathology ; *Tissue Fixation ; Tumor Suppressor Protein p53/metabolism
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  • 79
    Publication Date: 2015-06-13
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636083/" 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/PMC4636083/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lloyd, Kent -- Franklin, Craig -- Lutz, Cat -- Magnuson, Terry -- U24 DK092993/DK/NIDDK NIH HHS/ -- U42 OD010921/OD/NIH HHS/ -- U42 OD011175/OD/NIH HHS/ -- U42 OD012210/OD/NIH HHS/ -- U42 RR033193/RR/NCRR NIH HHS/ -- U54 HG006364/HG/NHGRI NIH HHS/ -- England -- Nature. 2015 Jun 11;522(7555):151-3. doi: 10.1038/522151a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mutant Mouse Resource and Research Center (MMRRC) at the University of California, Davis, California, USA. ; MMRRC at the University of Missouri, Columbia, Missouri, USA. ; MMRRC at the Jackson Laboratory in Bar Harbor, Maine, USA. ; MMRRC at the University of North Carolina at Chapel Hill, North Carolina, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26062496" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Specimen Banks/*standards/*utilization ; DNA Mutational Analysis ; Disease Models, Animal ; Genetic Testing ; Genome/genetics ; Humans ; *Mice/classification/genetics/microbiology ; Mice, Inbred C57BL ; Microbiota/genetics ; Mutation/genetics ; Quality Control ; Reproducibility of Results
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 80
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    Nature Publishing Group (NPG)
    Publication Date: 2015-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Apr 16;520(7547):263-4. doi: 10.1038/520263b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25877166" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Experimentation/*standards ; Animals ; Financing, Organized/organization & administration/standards ; Great Britain ; Guidelines as Topic ; Periodicals as Topic/standards ; Quality Control ; Reproducibility of Results ; Research/*standards ; Sample Size
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  • 81
    Publication Date: 2015-09-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarewitz, Daniel -- England -- Nature. 2015 Sep 10;525(7568):159. doi: 10.1038/525159a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Consortium for Science, Policy and Outcomes at Arizona State University, and is based in Washington DC.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26354448" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information/*legislation & jurisprudence ; Environmental Policy/legislation & jurisprudence ; Politics ; Reproducibility of Results ; Science/*legislation & jurisprudence/*standards
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  • 82
    Publication Date: 2015-09-08
    Description: Macromolecular complexes are essential to conserved biological processes, but their prevalence across animals is unclear. By combining extensive biochemical fractionation with quantitative mass spectrometry, here we directly examined the composition of soluble multiprotein complexes among diverse metazoan models. Using an integrative approach, we generated a draft conservation map consisting of more than one million putative high-confidence co-complex interactions for species with fully sequenced genomes that encompasses functional modules present broadly across all extant animals. Clustering reveals a spectrum of conservation, ranging from ancient eukaryotic assemblies that have probably served cellular housekeeping roles for at least one billion years, ancestral complexes that have accrued contemporary components, and rarer metazoan innovations linked to multicellularity. We validated these projections by independent co-fractionation experiments in evolutionarily distant species, affinity purification and functional analyses. The comprehensiveness, centrality and modularity of these reconstructed interactomes reflect their fundamental mechanistic importance and adaptive value to animal cell systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wan, Cuihong -- Borgeson, Blake -- Phanse, Sadhna -- Tu, Fan -- Drew, Kevin -- Clark, Greg -- Xiong, Xuejian -- Kagan, Olga -- Kwan, Julian -- Bezginov, Alexandr -- Chessman, Kyle -- Pal, Swati -- Cromar, Graham -- Papoulas, Ophelia -- Ni, Zuyao -- Boutz, Daniel R -- Stoilova, Snejana -- Havugimana, Pierre C -- Guo, Xinghua -- Malty, Ramy H -- Sarov, Mihail -- Greenblatt, Jack -- Babu, Mohan -- Derry, W Brent -- Tillier, Elisabeth R -- Wallingford, John B -- Parkinson, John -- Marcotte, Edward M -- Emili, Andrew -- F32 GM112495/GM/NIGMS NIH HHS/ -- F32GM112495/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2015 Sep 17;525(7569):339-44. doi: 10.1038/nature14877. Epub 2015 Sep 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ; Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA. ; Department of Medical Biophysics, Toronto, Ontario M5G 1L7, Canada. ; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada. ; Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada. ; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany. ; Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26344197" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Datasets as Topic ; *Evolution, Molecular ; Humans ; Multiprotein Complexes/*chemistry/*metabolism ; Protein Interaction Mapping ; *Protein Interaction Maps ; Reproducibility of Results ; Systems Biology ; Tandem Mass Spectrometry
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  • 83
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Powell, Kendall -- England -- Nature. 2015 Dec 24;528(7583):589-90.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26709403" target="_blank"〉PubMed〈/a〉
    Keywords: Archives ; Education/statistics & numerical data ; *Information Dissemination ; Italy ; Minority Groups/psychology/statistics & numerical data ; Peer Review, Research/ethics/*methods ; Reproducibility of Results ; *Research Personnel/education/psychology ; Sexism/*prevention & control ; Software/*supply & distribution ; Work Schedule Tolerance/psychology
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  • 84
    Publication Date: 2015-05-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sims, David W -- Simpson, Samantha J -- England -- Nature. 2015 Apr 30;520(7549):623. doi: 10.1038/520623e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Biological Association of the United Kingdom, Plymouth, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25925469" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/*legislation & jurisprudence/*statistics & ; numerical data ; Endangered Species/legislation & jurisprudence/statistics & numerical data ; European Union ; Fisheries/*legislation & jurisprudence/*statistics & numerical data ; *Fishes ; Reproducibility of Results ; Skates (Fish) ; Uncertainty
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  • 85
    Publication Date: 2015-09-17
    Description: Enhancers, critical determinants of cellular identity, are commonly recognized by correlative chromatin marks and gain-of-function potential, although only loss-of-function studies can demonstrate their requirement in the native genomic context. Previously, we identified an erythroid enhancer of human BCL11A, subject to common genetic variation associated with the fetal haemoglobin level, the mouse orthologue of which is necessary for erythroid BCL11A expression. Here we develop pooled clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 guide RNA libraries to perform in situ saturating mutagenesis of the human and mouse enhancers. This approach reveals critical minimal features and discrete vulnerabilities of these enhancers. Despite conserved function of the composite enhancers, their architecture diverges. The crucial human sequences appear to be primate-specific. Through editing of primary human progenitors and mouse transgenesis, we validate the BCL11A erythroid enhancer as a target for fetal haemoglobin reinduction. The detailed enhancer map will inform therapeutic genome editing, and the screening approach described here is generally applicable to functional interrogation of non-coding genomic elements.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644101/" 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/PMC4644101/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Canver, Matthew C -- Smith, Elenoe C -- Sher, Falak -- Pinello, Luca -- Sanjana, Neville E -- Shalem, Ophir -- Chen, Diane D -- Schupp, Patrick G -- Vinjamur, Divya S -- Garcia, Sara P -- Luc, Sidinh -- Kurita, Ryo -- Nakamura, Yukio -- Fujiwara, Yuko -- Maeda, Takahiro -- Yuan, Guo-Cheng -- Zhang, Feng -- Orkin, Stuart H -- Bauer, Daniel E -- 5DP1-MH100706/DP/NCCDPHP CDC HHS/ -- 5R01-DK097768/DK/NIDDK NIH HHS/ -- F30DK103359-01A1/DK/NIDDK NIH HHS/ -- K08DK093705/DK/NIDDK NIH HHS/ -- K99 HG008171/HG/NHGRI NIH HHS/ -- K99-HG008171/HG/NHGRI NIH HHS/ -- K99HG008399/HG/NHGRI NIH HHS/ -- P01 HL032262/HL/NHLBI NIH HHS/ -- P01HL032262/HL/NHLBI NIH HHS/ -- P30DK049216/DK/NIDDK NIH HHS/ -- R01 A1084905/PHS HHS/ -- R01 HL032259/HL/NHLBI NIH HHS/ -- R01HG005085/HG/NHGRI NIH HHS/ -- R01HL119099/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Nov 12;527(7577):192-7. doi: 10.1038/nature15521. Epub 2015 Sep 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA. ; Broad Institute of MIT and Harvard, McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences and Department of Biological Engineering, MIT, Cambridge, Massachusetts 02142, USA. ; Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan. ; Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan. ; Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA. ; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26375006" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; CRISPR-Associated Proteins/*metabolism ; CRISPR-Cas Systems/genetics ; Carrier Proteins/*genetics ; Cells, Cultured ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Enhancer Elements, Genetic/*genetics ; Erythroblasts/metabolism ; Fetal Hemoglobin/genetics ; *Genetic Engineering ; Genome/genetics ; Humans ; Mice ; Molecular Sequence Data ; Mutagenesis/*genetics ; Nuclear Proteins/*genetics ; Organ Specificity ; RNA, Guide/genetics ; Reproducibility of Results ; Species Specificity
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  • 86
    Publication Date: 2014-12-24
    Description: Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signalling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells in the embryonic and adult nervous system. Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor cell stages derived from a HES5::eGFP reporter human embryonic stem cell line. Using this system, we aimed to model cell-fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape and then validated these through a pooled short hairpin RNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and suggest here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336237/" 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/PMC4336237/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ziller, Michael J -- Edri, Reuven -- Yaffe, Yakey -- Donaghey, Julie -- Pop, Ramona -- Mallard, William -- Issner, Robbyn -- Gifford, Casey A -- Goren, Alon -- Xing, Jeffrey -- Gu, Hongcang -- Cacchiarelli, Davide -- Tsankov, Alexander M -- Epstein, Charles -- Rinn, John L -- Mikkelsen, Tarjei S -- Kohlbacher, Oliver -- Gnirke, Andreas -- Bernstein, Bradley E -- Elkabetz, Yechiel -- Meissner, Alexander -- F32 DK095537/DK/NIDDK NIH HHS/ -- HG006911/HG/NHGRI NIH HHS/ -- P01 GM099117/GM/NIGMS NIH HHS/ -- P01GM099117/GM/NIGMS NIH HHS/ -- U01 ES017155/ES/NIEHS NIH HHS/ -- U01ES017155/ES/NIEHS NIH HHS/ -- U54 HG006991/HG/NHGRI NIH HHS/ -- England -- Nature. 2015 Feb 19;518(7539):355-9. doi: 10.1038/nature13990. Epub 2014 Dec 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Ramat Aviv 6997801, Israel. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA [3] Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. ; Applied Bioinformatics, Center for Bioinformatics and Quantitative Biology Center, University of Tubingen, Tubingen 72076, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25533951" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Differentiation/*genetics ; Cell Lineage/genetics ; Embryonic Stem Cells/*cytology/metabolism ; Epigenesis, Genetic/*genetics ; Epigenomics/*methods ; Humans ; Neural Stem Cells/*cytology/*metabolism ; RNA, Small Interfering/analysis/genetics ; Reproducibility of Results ; Transcription Factors/metabolism ; Transcription, Genetic/genetics
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  • 87
    Publication Date: 2014-12-11
    Description: Systematic interrogation of gene function requires the ability to perturb gene expression in a robust and generalizable manner. Here we describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. We used these engineered Cas9 activation complexes to investigate single-guide RNA (sgRNA) targeting rules for effective transcriptional activation, to demonstrate multiplexed activation of ten genes simultaneously, and to upregulate long intergenic non-coding RNA (lincRNA) transcripts. We also synthesized a library consisting of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes that, upon activation, confer resistance to a BRAF inhibitor. The top hits included genes previously shown to be able to confer resistance, and novel candidates were validated using individual sgRNA and complementary DNA overexpression. A gene expression signature based on the top screening hits correlated with markers of BRAF inhibitor resistance in cell lines and patient-derived samples. These results collectively demonstrate the potential of Cas9-based activators as a powerful genetic perturbation technology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4420636/" 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/PMC4420636/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Konermann, Silvana -- Brigham, Mark D -- Trevino, Alexandro E -- Joung, Julia -- Abudayyeh, Omar O -- Barcena, Clea -- Hsu, Patrick D -- Habib, Naomi -- Gootenberg, Jonathan S -- Nishimasu, Hiroshi -- Nureki, Osamu -- Zhang, Feng -- DP1 MH100706/MH/NIMH NIH HHS/ -- DP1-MH100706/DP/NCCDPHP CDC HHS/ -- R01 NS062849/NS/NINDS NIH HHS/ -- R01 NS073124/NS/NINDS NIH HHS/ -- R01-NS07312401/NS/NINDS NIH HHS/ -- England -- Nature. 2015 Jan 29;517(7536):583-8. doi: 10.1038/nature14136. Epub 2014 Dec 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts 02142, USA [2] McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [4] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. ; 1] Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts 02142, USA [2] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. ; Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts 02142, USA. ; 1] Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts 02142, USA [2] McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [4] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [5] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA. ; 1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi Bunkyo, Tokyo 113-0032, Japan [2] JST, PRESTO 2-11-16 Yayoi Bunkyo, Tokyo 113-0032, Japan. ; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi Bunkyo, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25494202" target="_blank"〉PubMed〈/a〉
    Keywords: CRISPR-Associated Proteins/genetics/metabolism ; CRISPR-Cas Systems/*genetics ; Cell Line, Tumor ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA, Complementary/biosynthesis/genetics ; Drug Resistance, Neoplasm/drug effects/genetics ; Gene Expression Regulation, Neoplastic/genetics ; Gene Library ; Genetic Engineering/*methods ; Genetic Loci/genetics ; Genetic Testing ; Genome, Human/*genetics ; Humans ; Indoles/pharmacology ; Melanoma/drug therapy/*genetics ; Proto-Oncogene Proteins B-raf/antagonists & inhibitors ; RNA, Untranslated/biosynthesis/genetics/metabolism ; Reproducibility of Results ; Sulfonamides/pharmacology ; Transcriptional Activation/*genetics ; Up-Regulation/genetics
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  • 88
    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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  • 89
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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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  • 90
    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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  • 91
    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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  • 92
    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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  • 93
    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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  • 94
    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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  • 95
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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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  • 96
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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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  • 97
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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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  • 98
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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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  • 99
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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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  • 100
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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
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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