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  • Reproducibility of Results
  • Dynamics, dynamical systems, lattice effects
  • 2010-2014  (8)
  • 1
    Publication Date: 2011-07-06
    Description: Author(s): Q.-C. Sun, S. N. Baker, A. D. Christianson, and J. L. Musfeldt Phonons are exquisitely sensitive to finite length scale effects because they are intimately connected to charge, structure, and magnetism, and a quantitative analysis of their behavior can reveal microscopic aspects of spin-lattice interaction. To investigate these effects in a model correlated oxi... [Phys. Rev. B 84, 014301] Published Tue Jul 05, 2011
    Keywords: Dynamics, dynamical systems, lattice effects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 2
    Publication Date: 2012-09-21
    Description: Author(s): Christopher H. Baker, Donald A. Jordan, and Pamela M. Norris The continuous wavelet transform is employed to analyze the dynamics and time-dependent energy distribution of phonon wave-packet propagation and scattering in molecular dynamics simulations. The equations of the one-dimensional continuous wavelet transform are presented and then discretized for imp... [Phys. Rev. B 86, 104306] Published Thu Sep 20, 2012
    Keywords: Dynamics, dynamical systems, lattice effects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 3
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    Nature Publishing Group (NPG)
    Publication Date: 2012-08-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2012 Aug 2;488(7409):13-4. doi: 10.1038/488013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22859177" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain Neoplasms/drug therapy/pathology ; Cell Tracking/*methods ; Glioblastoma/drug therapy/pathology ; Intestinal Neoplasms/drug therapy/pathology ; Mice ; Neoplastic Stem Cells/*cytology/drug effects/*pathology ; Reproducibility of Results ; Skin Neoplasms/drug therapy/pathology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2013-09-06
    Description: The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition. Attempts to rationally design ligand-binding proteins have met with little success, however, and the computational design of protein-small-molecule interfaces remains an unsolved problem. Current approaches for designing ligand-binding proteins for medical and biotechnological uses rely on raising antibodies against a target antigen in immunized animals and/or performing laboratory-directed evolution of proteins with an existing low affinity for the desired ligand, neither of which allows complete control over the interactions involved in binding. Here we describe a general computational method for designing pre-organized and shape complementary small-molecule-binding sites, and use it to generate protein binders to the steroid digoxigenin (DIG). Of seventeen experimentally characterized designs, two bind DIG; the model of the higher affinity binder has the most energetically favourable and pre-organized interface in the design set. A comprehensive binding-fitness landscape of this design, generated by library selections and deep sequencing, was used to optimize its binding affinity to a picomolar level, and X-ray co-crystal structures of two variants show atomic-level agreement with the corresponding computational models. The optimized binder is selective for DIG over the related steroids digitoxigenin, progesterone and beta-oestradiol, and this steroid binding preference can be reprogrammed by manipulation of explicitly designed hydrogen-bonding interactions. The computational design method presented here should enable the development of a new generation of biosensors, therapeutics and diagnostics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898436/" 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/PMC3898436/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tinberg, Christine E -- Khare, Sagar D -- Dou, Jiayi -- Doyle, Lindsey -- Nelson, Jorgen W -- Schena, Alberto -- Jankowski, Wojciech -- Kalodimos, Charalampos G -- Johnsson, Kai -- Stoddard, Barry L -- Baker, David -- P41 GM103533/GM/NIGMS NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- T32 HG000035/HG/NHGRI NIH HHS/ -- T32 HG00035/HG/NHGRI NIH HHS/ -- England -- Nature. 2013 Sep 12;501(7466):212-6. doi: 10.1038/nature12443. Epub 2013 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24005320" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biotechnology ; *Computer Simulation ; Crystallography, X-Ray ; Digoxigenin/chemistry/*metabolism ; *Drug Design ; Estradiol/chemistry/metabolism ; Ligands ; Models, Molecular ; Progesterone/chemistry/metabolism ; Protein Binding ; Proteins/*chemistry/*metabolism ; Reproducibility of Results ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2011-07-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2011 Jul 6;475(7354):123-8. doi: 10.1038/475123a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734709" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autistic Disorder/genetics/physiopathology ; Automation ; *Behavior, Animal/physiology ; Cues ; *Disease Models, Animal ; Environment ; Fragile X Syndrome/genetics/physiopathology ; Gene Knockout Techniques ; Grooming/physiology ; Housing, Animal ; Humans ; Informatics/methods ; Mental Disorders/diagnosis/*genetics/*physiopathology ; Mice ; Motor Activity/physiology ; Muscular Atrophy, Spinal/genetics/physiopathology ; Obesity/genetics/physiopathology ; Obsessive-Compulsive Disorder/genetics/physiopathology ; Rats ; Reproducibility of Results ; Rett Syndrome/genetics/physiopathology ; Schizophrenia/genetics/physiopathology ; Video Recording/instrumentation/methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Nature Publishing Group (NPG)
    Publication Date: 2011-04-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2011 Mar 31;471(7340):661-5. doi: 10.1038/471661a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21455183" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Testing Alternatives/instrumentation/*methods ; Animals ; Bioengineering/instrumentation/*methods ; Biomimetics/instrumentation/*methods ; Cell Culture Techniques/instrumentation/methods ; Drug Evaluation, Preclinical/instrumentation/methods ; Humans ; *Lab-On-A-Chip Devices ; Liver/drug effects/pathology/physiology/physiopathology ; Lung/blood supply/cytology/drug effects/immunology/physiology ; Mice ; Models, Animal ; *Models, Biological ; Nanotechnology/instrumentation/methods ; *Organ Specificity ; Reproducibility of Results ; Silicon/chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2012-07-27
    Description: The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon. With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses. As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve 'health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laurance, William F -- Useche, D Carolina -- Rendeiro, Julio -- Kalka, Margareta -- Bradshaw, Corey J A -- Sloan, Sean P -- Laurance, Susan G -- Campbell, Mason -- Abernethy, Kate -- Alvarez, Patricia -- Arroyo-Rodriguez, Victor -- Ashton, Peter -- Benitez-Malvido, Julieta -- Blom, Allard -- Bobo, Kadiri S -- Cannon, Charles H -- Cao, Min -- Carroll, Richard -- Chapman, Colin -- Coates, Rosamond -- Cords, Marina -- Danielsen, Finn -- De Dijn, Bart -- Dinerstein, Eric -- Donnelly, Maureen A -- Edwards, David -- Edwards, Felicity -- Farwig, Nina -- Fashing, Peter -- Forget, Pierre-Michel -- Foster, Mercedes -- Gale, George -- Harris, David -- Harrison, Rhett -- Hart, John -- Karpanty, Sarah -- Kress, W John -- Krishnaswamy, Jagdish -- Logsdon, Willis -- Lovett, Jon -- Magnusson, William -- Maisels, Fiona -- Marshall, Andrew R -- McClearn, Deedra -- Mudappa, Divya -- Nielsen, Martin R -- Pearson, Richard -- Pitman, Nigel -- van der Ploeg, Jan -- Plumptre, Andrew -- Poulsen, John -- Quesada, Mauricio -- Rainey, Hugo -- Robinson, Douglas -- Roetgers, Christiane -- Rovero, Francesco -- Scatena, Frederick -- Schulze, Christian -- Sheil, Douglas -- Struhsaker, Thomas -- Terborgh, John -- Thomas, Duncan -- Timm, Robert -- Urbina-Cardona, J Nicolas -- Vasudevan, Karthikeyan -- Wright, S Joseph -- Arias-G, Juan Carlos -- Arroyo, Luzmila -- Ashton, Mark -- Auzel, Philippe -- Babaasa, Dennis -- Babweteera, Fred -- Baker, Patrick -- Banki, Olaf -- Bass, Margot -- Bila-Isia, Inogwabini -- Blake, Stephen -- Brockelman, Warren -- Brokaw, Nicholas -- Bruhl, Carsten A -- Bunyavejchewin, Sarayudh -- Chao, Jung-Tai -- Chave, Jerome -- Chellam, Ravi -- Clark, Connie J -- Clavijo, Jose -- Congdon, Robert -- Corlett, Richard -- Dattaraja, H S -- Dave, Chittaranjan -- Davies, Glyn -- Beisiegel, Beatriz de Mello -- da Silva, Rosa de Nazare Paes -- Di Fiore, Anthony -- Diesmos, Arvin -- Dirzo, Rodolfo -- Doran-Sheehy, Diane -- Eaton, Mitchell -- Emmons, Louise -- Estrada, Alejandro -- Ewango, Corneille -- Fedigan, Linda -- Feer, Francois -- Fruth, Barbara -- Willis, Jacalyn Giacalone -- Goodale, Uromi -- Goodman, Steven -- Guix, Juan C -- Guthiga, Paul -- Haber, William -- Hamer, Keith -- Herbinger, Ilka -- Hill, Jane -- Huang, Zhongliang -- Sun, I Fang -- Ickes, Kalan -- Itoh, Akira -- Ivanauskas, Natalia -- Jackes, Betsy -- Janovec, John -- Janzen, Daniel -- Jiangming, Mo -- Jin, Chen -- Jones, Trevor -- Justiniano, Hermes -- Kalko, Elisabeth -- Kasangaki, Aventino -- Killeen, Timothy -- King, Hen-biau -- Klop, Erik -- Knott, Cheryl -- Kone, Inza -- Kudavidanage, Enoka -- Ribeiro, Jose Lahoz da Silva -- Lattke, John -- Laval, Richard -- Lawton, Robert -- Leal, Miguel -- Leighton, Mark -- Lentino, Miguel -- Leonel, Cristiane -- Lindsell, Jeremy -- Ling-Ling, Lee -- Linsenmair, K Eduard -- Losos, Elizabeth -- Lugo, Ariel -- Lwanga, Jeremiah -- Mack, Andrew L -- Martins, Marlucia -- McGraw, W Scott -- McNab, Roan -- Montag, Luciano -- Thompson, Jo Myers -- Nabe-Nielsen, Jacob -- Nakagawa, Michiko -- Nepal, Sanjay -- Norconk, Marilyn -- Novotny, Vojtech -- O'Donnell, Sean -- Opiang, Muse -- Ouboter, Paul -- Parker, Kenneth -- Parthasarathy, N -- Pisciotta, Katia -- Prawiradilaga, Dewi -- Pringle, Catherine -- Rajathurai, Subaraj -- Reichard, Ulrich -- Reinartz, Gay -- Renton, Katherine -- Reynolds, Glen -- Reynolds, Vernon -- Riley, Erin -- Rodel, Mark-Oliver -- Rothman, Jessica -- Round, Philip -- Sakai, Shoko -- Sanaiotti, Tania -- Savini, Tommaso -- Schaab, Gertrud -- Seidensticker, John -- Siaka, Alhaji -- Silman, Miles R -- Smith, Thomas B -- de Almeida, Samuel Soares -- Sodhi, Navjot -- Stanford, Craig -- Stewart, Kristine -- Stokes, Emma -- Stoner, Kathryn E -- Sukumar, Raman -- Surbeck, Martin -- Tobler, Mathias -- Tscharntke, Teja -- Turkalo, Andrea -- Umapathy, Govindaswamy -- van Weerd, Merlijn -- Rivera, Jorge Vega -- Venkataraman, Meena -- Venn, Linda -- Verea, Carlos -- de Castilho, Carolina Volkmer -- Waltert, Matthias -- Wang, Benjamin -- Watts, David -- Weber, William -- West, Paige -- Whitacre, David -- Whitney, Ken -- Wilkie, David -- Williams, Stephen -- Wright, Debra D -- Wright, Patricia -- Xiankai, Lu -- Yonzon, Pralad -- Zamzani, Franky -- England -- Nature. 2012 Sep 13;489(7415):290-4. doi: 10.1038/nature11318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Tropical Environmental and Sustainability Science and School of Marine and Tropical Biology, James Cook University, Cairns, Queensland 4878, Australia. bill.laurance@jcu.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22832582" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/statistics & numerical data ; Animals ; *Biodiversity ; Conservation of Natural Resources/*statistics & numerical data ; Data Collection ; Ecology/statistics & numerical data ; Endangered Species/*statistics & numerical data ; Environmental Pollution/adverse effects/statistics & numerical data ; Fires/statistics & numerical data ; Forestry/statistics & numerical data ; Interviews as Topic ; Mining/statistics & numerical data ; Population Growth ; Rain ; Reproducibility of Results ; Research Personnel ; Surveys and Questionnaires ; Temperature ; Trees/*physiology ; *Tropical Climate
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2012-04-13
    Description: It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected beta-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350576/" 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/PMC3350576/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Roak, Brian J -- Vives, Laura -- Girirajan, Santhosh -- Karakoc, Emre -- Krumm, Niklas -- Coe, Bradley P -- Levy, Roie -- Ko, Arthur -- Lee, Choli -- Smith, Joshua D -- Turner, Emily H -- Stanaway, Ian B -- Vernot, Benjamin -- Malig, Maika -- Baker, Carl -- Reilly, Beau -- Akey, Joshua M -- Borenstein, Elhanan -- Rieder, Mark J -- Nickerson, Deborah A -- Bernier, Raphael -- Shendure, Jay -- Eichler, Evan E -- HD065285/HD/NICHD NIH HHS/ -- HHSN273200800010C/PHS HHS/ -- HL 094976/HL/NHLBI NIH HHS/ -- HL 1029230/HL/NHLBI NIH HHS/ -- HL 102924/HL/NHLBI NIH HHS/ -- HL102926/HL/NHLBI NIH HHS/ -- R01 HD065285/HD/NICHD NIH HHS/ -- R01 HD065285-02/HD/NICHD NIH HHS/ -- R01 HL094976/HL/NHLBI NIH HHS/ -- RC2 HL102923/HL/NHLBI NIH HHS/ -- RC2 HL102926/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Apr 4;485(7397):246-50. doi: 10.1038/nature10989.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22495309" target="_blank"〉PubMed〈/a〉
    Keywords: Autistic Disorder/*genetics ; DNA-Binding Proteins/genetics ; Exome/*genetics ; Exons/*genetics ; GPI-Linked Proteins/genetics ; Genetic Predisposition to Disease/genetics ; Humans ; Laminin/genetics ; NAV1.1 Voltage-Gated Sodium Channel ; Nerve Tissue Proteins/genetics ; Parents ; Point Mutation/*genetics ; Protein Interaction Maps/*genetics ; Receptors, N-Methyl-D-Aspartate/genetics ; Reproducibility of Results ; Siblings ; Signal Transduction ; Sodium Channels/genetics ; Stochastic Processes ; Transcription Factors/genetics ; Tumor Suppressor Protein p53/metabolism ; beta Catenin/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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