ALBERT

Description: : We describe BiopLib, a mature C programming library for manipulating protein structure, and BiopTools, a set of command-line tools which exploit BiopLib. The library also provides a small number of functions for handling protein sequence and general purpose programming and mathematics. BiopLib transparently handles PDBML (XML) format and standard PDB files. BiopTools provides facilities ranging from renumbering atoms and residues to calculation of solvent accessibility. Availability and implementation: BiopLib and BiopTools are implemented in standard ANSI C. The core of the BiopLib library is a reliable PDB parser that handles alternate occupancies and deals with compressed PDB files and PDBML files automatically. The library is designed to be as flexible as possible, allowing users to handle PDB data as a simple list of atoms, or in a structured form using chains, residues and atoms. Many of the BiopTools command-line tools act as filters, taking a PDB (or PDBML) file as input and producing a PDB (or PDBML) file as output. All code is open source and documented using Doxygen. It is provided under the GNU Public Licence and is available from the authors’ web site or from GitHub. Contact: andrew@bioinf.org.uk

Description: The light emitted by all galaxies over the history of the Universe produces the extragalactic background light (EBL) at ultraviolet, optical, and infrared wavelengths. The EBL is a source of opacity for gamma rays via photon-photon interactions, leaving an imprint in the spectra of distant gamma-ray sources. We measured this attenuation using 739 active galaxies and one gamma-ray burst detected by the Fermi Large Area Telescope. This allowed us to reconstruct the evolution of the EBL and determine the star formation history of the Universe over 90% of cosmic time. Our star formation history is consistent with independent measurements from galaxy surveys, peaking at redshift z ~ 2. Upper limits of the EBL at the epoch of reionization suggest a turnover in the abundance of faint galaxies at z ~ 6.

Description: Congenital heart disease (CHD) patients have an increased prevalence of extracardiac congenital anomalies (CAs) and risk of neurodevelopmental disabilities (NDDs). Exome sequencing of 1213 CHD parent-offspring trios identified an excess of protein-damaging de novo mutations, especially in genes highly expressed in the developing heart and brain. These mutations accounted for 20% of patients with CHD, NDD, and CA but only 2% of patients with isolated CHD. Mutations altered genes involved in morphogenesis, chromatin modification, and transcriptional regulation, including multiple mutations in RBFOX2, a regulator of mRNA splicing. Genes mutated in other cohorts examined for NDD were enriched in CHD cases, particularly those with coexisting NDD. These findings reveal shared genetic contributions to CHD, NDD, and CA and provide opportunities for improved prognostic assessment and early therapeutic intervention in CHD patients.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Homsy, Jason -- Zaidi, Samir -- Shen, Yufeng -- Ware, James S -- Samocha, Kaitlin E -- Karczewski, Konrad J -- DePalma, Steven R -- McKean, David -- Wakimoto, Hiroko -- Gorham, Josh -- Jin, Sheng Chih -- Deanfield, John -- Giardini, Alessandro -- Porter, George A Jr -- Kim, Richard -- Bilguvar, Kaya -- Lopez-Giraldez, Francesc -- Tikhonova, Irina -- Mane, Shrikant -- Romano-Adesman, Angela -- Qi, Hongjian -- Vardarajan, Badri -- Ma, Lijiang -- Daly, Mark -- Roberts, Amy E -- Russell, Mark W -- Mital, Seema -- Newburger, Jane W -- Gaynor, J William -- Breitbart, Roger E -- Iossifov, Ivan -- Ronemus, Michael -- Sanders, Stephan J -- Kaltman, Jonathan R -- Seidman, Jonathan G -- Brueckner, Martina -- Gelb, Bruce D -- Goldmuntz, Elizabeth -- Lifton, Richard P -- Seidman, Christine E -- Chung, Wendy K -- T32 HL007208/HL/NHLBI NIH HHS/ -- Arthritis Research UK/United Kingdom -- British Heart Foundation/United Kingdom -- Department of Health/United Kingdom -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2015 Dec 4;350(6265):1262-6. doi: 10.1126/science.aac9396.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, MA, USA. Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA. ; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. ; Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY, USA. ; Department of Genetics, Harvard Medical School, Boston, MA, USA. NIHR Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield NHS Foundation and Trust and Imperial College London, London, UK. National Heart & Lung Institute, Imperial College London, London, UK. ; Department of Genetics, Harvard Medical School, Boston, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston MA, USA. ; Department of Genetics, Harvard Medical School, Boston, MA, USA. Howard Hughes Medical Institute, Harvard University, Boston, MA, USA. ; Department of Genetics, Harvard Medical School, Boston, MA, USA. ; Department of Cardiology, University College London and Great Ormond Street Hospital, London, UK. ; Department of Pediatrics, University of Rochester Medical Center, The School of Medicine and Dentistry, Rochester, NY, USA. ; Section of Cardiothoracic Surgery, University of Southern California Keck School of Medicine, Los Angeles, CA, USA. ; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. Yale Center for Genome Analysis, Yale University, New Haven, CT, USA. ; Yale Center for Genome Analysis, Yale University, New Haven, CT, USA. ; Steven and Alexandra Cohen Children's Medical Center of New York, New Hyde Park, NY, USA. ; Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY, USA. Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA. ; Department of Neurology, Columbia University Medical Center, New York, NY, USA. ; Department of Pediatrics, Columbia University Medical Center, New York, NY, USA. ; Department of Cardiology, Children's Hospital Boston, Boston, MA, USA. ; Division of Pediatric Cardiology, University of Michigan, Ann Arbor, MI, USA. ; Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada. ; Department of Cardiology, Boston Children's Hospital, Boston, MA, USA. ; Department of Pediatric Cardiac Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. ; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. ; Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA. ; Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, MD, USA. ; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. bruce.gelb@mssm.edu goldmuntz@email.chop.edu martina.brueckner@yale.edu richard.lifton@yale.edu cseidman@genetics.med.harvard.edu wkc15@cumc.columbia.edu. ; Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. bruce.gelb@mssm.edu goldmuntz@email.chop.edu martina.brueckner@yale.edu richard.lifton@yale.edu cseidman@genetics.med.harvard.edu wkc15@cumc.columbia.edu. ; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. bruce.gelb@mssm.edu goldmuntz@email.chop.edu martina.brueckner@yale.edu richard.lifton@yale.edu cseidman@genetics.med.harvard.edu wkc15@cumc.columbia.edu. ; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. Howard Hughes Medical Institute, Yale University, New Haven, CT, USA. bruce.gelb@mssm.edu goldmuntz@email.chop.edu martina.brueckner@yale.edu richard.lifton@yale.edu cseidman@genetics.med.harvard.edu wkc15@cumc.columbia.edu. ; Department of Genetics, Harvard Medical School, Boston, MA, USA. Howard Hughes Medical Institute, Harvard University, Boston, MA, USA. Cardiovascular Division, Brigham & Women's Hospital, Harvard University, Boston, MA, USA. bruce.gelb@mssm.edu goldmuntz@email.chop.edu martina.brueckner@yale.edu richard.lifton@yale.edu cseidman@genetics.med.harvard.edu wkc15@cumc.columbia.edu. ; Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA. bruce.gelb@mssm.edu goldmuntz@email.chop.edu martina.brueckner@yale.edu richard.lifton@yale.edu cseidman@genetics.med.harvard.edu wkc15@cumc.columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26785492" target="_blank"〉PubMed〈/a〉

Description: Whereas the predominant shapes of most animal tails are cylindrical, seahorse tails are square prisms. Seahorses use their tails as flexible grasping appendages, in spite of a rigid bony armor that fully encases their bodies. We explore the mechanics of two three-dimensional-printed models that mimic either the natural (square prism) or hypothetical (cylindrical) architecture of a seahorse tail to uncover whether or not the square geometry provides any functional advantages. Our results show that the square prism is more resilient when crushed and provides a mechanism for preserving articulatory organization upon extensive bending and twisting, as compared with its cylindrical counterpart. Thus, the square architecture is better than the circular one in the context of two integrated functions: grasping ability and crushing resistance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Porter, Michael M -- Adriaens, Dominique -- Hatton, Ross L -- Meyers, Marc A -- McKittrick, Joanna -- New York, N.Y. -- Science. 2015 Jul 3;349(6243):aaa6683. doi: 10.1126/science.aaa6683. Epub 2015 Jul 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Mechanical Engineering, Clemson University, Clemson, SC 29634, USA. mmporte@clemson.edu. ; Evolutionary Morphology of Vertebrates, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium. ; School of Mechanical, Industrial, and Manufacturing Engineering, Oregon State University, Corvallis, OR 97330, USA. ; Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA. Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA. Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA. ; Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA. Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26138983" target="_blank"〉PubMed〈/a〉