ALBERT

Description: starbench is a project focused on benchmarking and validating different star formation and stellar feedback codes. In this first starbench paper we perform a comparison study of the D-type expansion of an H ii region. The aim of this work is to understand the differences observed between the 12 participating numerical codes against the various analytical expressions examining the D-type phase of H ii region expansion. To do this, we propose two well-defined tests which are tackled by 1D and 3D grid- and smoothed particle hydrodynamics-based codes. The first test examines the ‘early phase’ D-type scenario during which the mechanical pressure driving the expansion is significantly larger than the thermal pressure of the neutral medium. The second test examines the ‘late phase’ D-type scenario during which the system relaxes to pressure equilibrium with the external medium. Although they are mutually in excellent agreement, all 12 participating codes follow a modified expansion law that deviates significantly from the classical Spitzer solution in both scenarios. We present a semi-empirical formula combining the two different solutions appropriate to both early and late phases that agrees with high-resolution simulations to  2 per cent. This formula provides a much better benchmark solution for code validation than the Spitzer solution. The present comparison has validated the participating codes and through this project we provide a data set for calibrating the treatment of ionizing radiation hydrodynamics codes.

Description: N-linked glycans play key roles in protein folding, stability, and function. Biosynthetic modification of N-linked glycans, within the endoplasmic reticulum, features sequential trimming and readornment steps. One unusual enzyme, endo-α-mannosidase, cleaves mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. Here, using two bacterial orthologs, we present the first structural and mechanistic dissection of endo-α-mannosidase. Structures solved at resolutions 1.7–2.1 Å reveal a (β/α)8 barrel fold in which the catalytic center is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain. Enzymatic cleavage of authentic Glc1/3Man9GlcNAc2 yields Glc1/3-Man. Using the bespoke substrate α-Glc-1,3-α-Man fluoride, the enzyme was shown to act with retention of anomeric configuration. Complexes with the established endo-α-mannosidase inhibitor α-Glc-1,3-deoxymannonojirimycin and a newly developed inhibitor, α-Glc-1,3-isofagomine, and with the reducing-end product α-1,2-mannobiose structurally define the -2 to +2 subsites of the enzyme. These structural and mechanistic data provide a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.

Description: When modelling an ionized plasma, all spectral synthesis codes need the thermally averaged free–free Gaunt factor defined over a very wide range of parameter space in order to produce an accurate prediction for the spectrum. Until now no data set exists that would meet these needs completely. We have therefore produced a table of relativistic Gaunt factors over a much wider range of parameter space than has ever been produced before. We present tables of the thermally averaged Gaunt factor covering the range 10 log 2  = –6 to 10 and 10 log u  = –16 to 13 for all atomic numbers Z  = 1 through 36. The data were calculated using the relativistic Bethe–Heitler–Elwert (BHE) approximation and were subsequently merged with accurate non-relativistic results in those parts of the parameter space where the BHE approximation is not valid. These data will be incorporated in the next major release of the spectral synthesis code cloudy . We also produced tables of the frequency integrated Gaunt factor covering the parameter space 10 log 2  = –6 to +10 for all values of Z between 1 and 36. All the data presented in this paper are available online.

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Matthew J -- Williams, Richard J -- Purves, Drew W -- New York, N.Y. -- Science. 2011 Feb 18;331(6019):857; author reply 857-8. doi: 10.1126/science.331.6019.857-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21330515" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, R J -- Heymann, D L -- New York, N.Y. -- Science. 1998 Feb 20;279(5354):1153-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Emerging and Other Communicable Diseases Surveillance and Control, World Health Organization (WHO), Geneva, Switzerland. williamsr@who.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9508688" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brose, Ulrich -- Williams, Richard J -- Martinez, Neo D -- New York, N.Y. -- Science. 2003 Aug 15;301(5635):918; author reply 918.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Romberg Tiburon Center, Department of Biology, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA. brose@sfsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12920282" target="_blank"〉PubMed〈/a〉

Description: With Low-Frequency Array (LOFAR) observations, we have discovered a diverse assembly of steep spectrum emission that is apparently associated with the intracluster medium (ICM) of the merging galaxy cluster Abell 2034. Such a rich variety of complex emission associated with the ICM has been observed in few other clusters. This not only indicates that Abell 2034 is a more interesting and complex system than previously thought but it also demonstrates the importance of sensitive and high-resolution, low-frequency observations. These observations can reveal emission from relativistic particles which have been accelerated to sufficient energy to produce observable emission or have had their high energy maintained by mechanisms in the ICM. The most prominent feature in our maps is a bright bulb of emission connected to two steep spectrum filamentary structures, the longest of which extends perpendicular to the merger axis for 0.5 Mpc across the south of the cluster. The origin of these objects is unclear, with no shock detected in the X-ray images and no obvious connection with cluster galaxies or AGNs. We also find that the X-ray bright region of the cluster coincides with a giant radio halo with an irregular morphology and a very steep spectrum. In addition, the cluster hosts up to three possible radio relics, which are misaligned with the cluster X-ray emission. Finally, we have identified multiple regions of emission with a very steep spectral index that seem to be associated with either tailed radio galaxies or a shock.

Description: Human alterations to nutrient cycles and herbivore communities are affecting global biodiversity dramatically. Ecological theory predicts these changes should be strongly counteractive: nutrient addition drives plant species loss through intensified competition for light, whereas herbivores prevent competitive exclusion by increasing ground-level light, particularly in productive systems. Here we use experimental data spanning a globally relevant range of conditions to test the hypothesis that herbaceous plant species losses caused by eutrophication may be offset by increased light availability due to herbivory. This experiment, replicated in 40 grasslands on 6 continents, demonstrates that nutrients and herbivores can serve as counteracting forces to control local plant diversity through light limitation, independent of site productivity, soil nitrogen, herbivore type and climate. Nutrient addition consistently reduced local diversity through light limitation, and herbivory rescued diversity at sites where it alleviated light limitation. Thus, species loss from anthropogenic eutrophication can be ameliorated in grasslands where herbivory increases ground-level light.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borer, Elizabeth T -- Seabloom, Eric W -- Gruner, Daniel S -- Harpole, W Stanley -- Hillebrand, Helmut -- Lind, Eric M -- Adler, Peter B -- Alberti, Juan -- Anderson, T Michael -- Bakker, Jonathan D -- Biederman, Lori -- Blumenthal, Dana -- Brown, Cynthia S -- Brudvig, Lars A -- Buckley, Yvonne M -- Cadotte, Marc -- Chu, Chengjin -- Cleland, Elsa E -- Crawley, Michael J -- Daleo, Pedro -- Damschen, Ellen I -- Davies, Kendi F -- DeCrappeo, Nicole M -- Du, Guozhen -- Firn, Jennifer -- Hautier, Yann -- Heckman, Robert W -- Hector, Andy -- HilleRisLambers, Janneke -- Iribarne, Oscar -- Klein, Julia A -- Knops, Johannes M H -- La Pierre, Kimberly J -- Leakey, Andrew D B -- Li, Wei -- MacDougall, Andrew S -- McCulley, Rebecca L -- Melbourne, Brett A -- Mitchell, Charles E -- Moore, Joslin L -- Mortensen, Brent -- O'Halloran, Lydia R -- Orrock, John L -- Pascual, Jesus -- Prober, Suzanne M -- Pyke, David A -- Risch, Anita C -- Schuetz, Martin -- Smith, Melinda D -- Stevens, Carly J -- Sullivan, Lauren L -- Williams, Ryan J -- Wragg, Peter D -- Wright, Justin P -- Yang, Louie H -- England -- Nature. 2014 Apr 24;508(7497):517-20. doi: 10.1038/nature13144. Epub 2014 Mar 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota 55108, USA. ; Department of Entomology, University of Maryland, College Park, Maryland 20742, USA. ; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA. ; Institute for Chemistry and Biology of the Marine Environment, Carl-von- Ossietzky University, 26382 Wilhelmshaven, Oldenburg, Germany. ; Department of Wildland Resources and the Ecology Center, Utah State University, Logan, Utah 84322, USA. ; Instituto de Investigaciones Marinas y Costeras (IIMyC), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Mar del Plata 7600 , Argentina. ; Department of Biology, Wake Forest University, Winston-Salem, North Carolina 27109, USA. ; School of Environmental and Forest Sciences, University of Washington, Seattle, Washington 98195, USA. ; Agricultural Research Service (ARS), United States Department of Agriculture, Fort Collins, Colorado 80526, USA. ; Deptartment of Forest, Rangeland and Watershed Stewardship, Colorado State University, Fort Collins, Colorado 80523, USA. ; Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA. ; 1] ARC Centre of Excellence for Environmental Decisions, School of Biological Sciences, The University of Queensland, Queensland 4072, Australia [2] School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland. ; Department of Ecology and Evolutionary Biology, University of Toronto Scarborough, Ontario M1C 1A4, Canada. ; State Key Laboratory of Grassland and Agro-Ecosystems, Research Station of Alpine Meadow and Wetland Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 Gansu, China. ; Division of Biological Sciences, University of California, San Diego, California 92093, USA. ; Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire SL5 7PY, UK. ; Department of Zoology, University of Wisconsin, Madison, Wisconsin 53706, USA. ; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder Colorado 80309, USA. ; US Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, Oregon 97331, USA. ; Queensland University of Technology, Biogeosciences, Brisbane, Queensland 4001, Australia. ; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA. ; Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK. ; School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA. ; Berkeley Initiative for Global Change Biology, University of California, Berkeley 94704, USA. ; Department of Plant Biology, University of Illinois at Urbana-Champaign, llinois 61820, USA. ; Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada. ; Department of Plant & Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, USA. ; Australian Research Center for Urban Ecology, c/o School of Botany, University of Melbourne, Victoria 3010, Australia, and School of Biological Sciences, Monash University, Victoria 3800, Australia. ; Department of Zoology, Oregon State University, Corvallis, Oregon 97331, USA. ; CSIRO Ecosystem Sciences, Wembley, West Australia 6913, Australia. ; Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf 8903, Switzerland. ; Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK. ; Department of Biology, Duke University, Durham, North Carolina 27708, USA. ; Department of Entomology, University of California, Davis, California 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24670649" target="_blank"〉PubMed〈/a〉

Description: Ecologists have long sought to understand the factors controlling the structure of savanna vegetation. Using data from 2154 sites in savannas across Africa, Australia, and South America, we found that increasing moisture availability drives increases in fire and tree basal area, whereas fire reduces tree basal area. However, among continents, the magnitude of these effects varied substantially, so that a single model cannot adequately represent savanna woody biomass across these regions. Historical and environmental differences drive the regional variation in the functional relationships between woody vegetation, fire, and climate. These same differences will determine the regional responses of vegetation to future climates, with implications for global carbon stocks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lehmann, Caroline E R -- Anderson, T Michael -- Sankaran, Mahesh -- Higgins, Steven I -- Archibald, Sally -- Hoffmann, William A -- Hanan, Niall P -- Williams, Richard J -- Fensham, Roderick J -- Felfili, Jeanine -- Hutley, Lindsay B -- Ratnam, Jayashree -- San Jose, Jose -- Montes, Ruben -- Franklin, Don -- Russell-Smith, Jeremy -- Ryan, Casey M -- Durigan, Giselda -- Hiernaux, Pierre -- Haidar, Ricardo -- Bowman, David M J S -- Bond, William J -- New York, N.Y. -- Science. 2014 Jan 31;343(6170):548-52. doi: 10.1126/science.1247355.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Macquarie University, New South Wales 2109, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24482480" target="_blank"〉PubMed〈/a〉

Description: Fraser et al. (Reports, 17 July 2015, p. 302) report a unimodal relationship between productivity and species richness at regional and global scales, which they contrast with the results of Adler et al. (Reports, 23 September 2011, p. 1750). However, both data sets, when analyzed correctly, show clearly and consistently that productivity is a poor predictor of local species richness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tredennick, Andrew T -- Adler, Peter B -- Grace, James B -- Harpole, W Stanley -- Borer, Elizabeth T -- Seabloom, Eric W -- Anderson, T Michael -- Bakker, Jonathan D -- Biederman, Lori A -- Brown, Cynthia S -- Buckley, Yvonne M -- Chu, Chengjin -- Collins, Scott L -- Crawley, Michael J -- Fay, Philip A -- Firn, Jennifer -- Gruner, Daniel S -- Hagenah, Nicole -- Hautier, Yann -- Hector, Andy -- Hillebrand, Helmut -- Kirkman, Kevin -- Knops, Johannes M H -- Laungani, Ramesh -- Lind, Eric M -- MacDougall, Andrew S -- McCulley, Rebecca L -- Mitchell, Charles E -- Moore, Joslin L -- Morgan, John W -- Orrock, John L -- Peri, Pablo L -- Prober, Suzanne M -- Risch, Anita C -- Schutz, Martin -- Speziale, Karina L -- Standish, Rachel J -- Sullivan, Lauren L -- Wardle, Glenda M -- Williams, Ryan J -- Yang, Louie H -- New York, N.Y. -- Science. 2016 Jan 29;351(6272):457. doi: 10.1126/science.aad6236.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Wildland Resources and the Ecology Center, Utah State University, 5230 Old Main, Logan, UT 84322, USA. atredenn@gmail.com. ; Department of Wildland Resources and the Ecology Center, Utah State University, 5230 Old Main, Logan, UT 84322, USA. ; U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Boulevard, Lafayette, LA 70506, USA. ; Department of Physiological Diversity, Helmholtz Center for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany. ; Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA. ; Department of Biology, Wake Forest University, Box 7325 Reynolda Station, Winston-Salem, NC 27109, USA. ; School of Environmental and Forest Sciences, University of Washington, 3501 NE 41st Street, Box 354115, Seattle, WA 98195, USA. ; Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50010, USA. ; Department of Bioagricultural Sciences and Pest Management, Colorado State University, 307 University Avenue, Fort Collins, CO 80523, USA. ; School of Natural Sciences, Trinity College Dublin, University of Dublin, Zoology, Dublin 2, Ireland. ; School of Life Sciences, Sun Yat-sen University, Xingang Xi Road 135, Guangzhou, 510275, China. ; Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA. ; Department of Biology, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK. ; Grassland, Soil, and Water Research Laboratory, USDA-ARS, 808 East Blackland Road, Temple, TX 76502, USA. ; School of Earth, Environmental and Biological 42 Sciences, Queensland University of Technology (QUT), Gardens Point, Brisbane, Queensland, Australia, 4001. ; Department of Entomology, University of Maryland, 4112 Plant Sciences, College Park, MD 20742, USA. ; School of Life Sciences, University of KwaZulu-Natal, 1 Carbis Road, Pietermaritzburg, 3201, South Africa. ; Department of Biology, Ecology and Biodiversity group, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. ; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK. ; Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstrasse 1, 26382 Wihlhemshaven, Germany. ; School of Biological Sciences, University of Nebraska, 211 Manter Hall, Lincoln, NE 68588, USA. ; Biology Department, Doane College, 1014 Boswell Avenue, Crete, NE 68333, USA. ; Department of Integrative Biology, University of Guelph, 50 Stone Road, Guelph, Ontario, Canada N1G 2W1. ; Department of Plant and Soil Science, University of Kentucky, N-222D Ag Science North, Lexington, KY 40546-0091, USA. ; Department of Biology, University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC 27599, USA. ; School of Biological Sciences, Monash University, Clayton Campus, Wellington Road, Clayton 3800, Victoria, Australia. ; Department of Ecology, Environment and Evolution, La Trobe University, Kingsbury Drive, Bundoora 3086, Victoria, Australia. ; Department of Zoology, University of Wisconsin, 430 Lincoln Drive, Madison, WI 53706, USA. ; Department of Forestry, Agriculture and Water, Southern Patagonia National University-INTA-CONICET, CC 332 (CP 9400), Rio Gallegos, Santa Cruz, Patagonia, Argentina. ; Commonwealth Scientific and Industrial Research Organisation Land and Water, Private Bag 5, Wembley, WA 6913, Australia. ; Community Ecology, Swiss Federal Institute for Forest, Snow and Landscape Research, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland. ; Department of Ecology, INIBIOMA (CONICET-UNCO), Quintral 1250, Bariloche (8400), Rio Negro, Argentina. ; School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, 90 South Street, Murdoch, Western Australia 6150. ; School of Biological Sciences, University of Sydney, Heydon-Laurence Building, A08, University of Sydney, Sydney, NSW, 2006, Australia. ; Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA. ; Department of Entomology and Nematology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26823418" target="_blank"〉PubMed〈/a〉