Pairwise balanced designs covered by bounded flats

We prove that for any $K$ and $d$, there exist, for all sufficiently large admissible $v$, a pairwise balanced design PBD$(v,K)$ of dimension $d$ for which all $d$-point-generated flats are bounded by a constant independent of $v$. We also tighten a prior upper bound for $K = \{3,4,5\}$, in which case there are no divisibility restrictions on the number of points. One consequence of this latter result is the construction of latin squares `covered' by small subsquares

Mismatches in scale between highly mobile marine megafauna and marine protected areas

Marine protected areas (MPAs), particularly large MPAs, are increasing in number and size around the globe in part to facilitate the conservation of marine megafauna under the assumption that large-scale MPAs better align with vagile life histories; however, this alignment is not well established. Using a global tracking dataset from 36 species across five taxa, chosen to reflect the span of home range size in highly mobile marine megafauna, we show most MPAs are too small to encompass complete home ranges of most species. Based on size alone, 40% of existing MPAs could encompass the home ranges of the smallest ranged species, while only \u3c 1% of existing MPAs could encompass those of the largest ranged species. Further, where home ranges and MPAs overlapped in real geographic space, MPAs encompassed \u3c 5% of core areas used by all species. Despite most home ranges of mobile marine megafauna being much larger than existing MPAs, we demonstrate how benefits from MPAs are still likely to accrue by targeting seasonal aggregations and critical life history stages and through other management techniques

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

Mismatches in scale between highly mobile marine megafauna and marine protected areas

Marine protected areas (MPAs), particularly large MPAs, are increasing in number and size around the globe in part to facilitate the conservation of marine megafauna under the assumption that large-scale MPAs better align with vagile life histories; however, this alignment is not well established. Using a global tracking dataset from 36 species across five taxa, chosen to reflect the span of home range size in highly mobile marine megafauna, we show most MPAs are too small to encompass complete home ranges of most species. Based on size alone, 40% of existing MPAs could encompass the home ranges of the smallest ranged species, while only < 1% of existing MPAs could encompass those of the largest ranged species. Further, where home ranges and MPAs overlapped in real geographic space, MPAs encompassed < 5% of core areas used by all species. Despite most home ranges of mobile marine megafauna being much larger than existing MPAs, we demonstrate how benefits from MPAs are still likely to accrue by targeting seasonal aggregations and critical life history stages and through other management techniques.Fil: Conners, Melinda G.. University of Washington; Estados Unidos. State University of New York. Stony Brook University; Estados UnidosFil: Sisson, Nicholas B.. Old Dominion University; Estados UnidosFil: Agamboue, Pierre D.. Wildlife Conservation Society; GabónFil: Atkinson, Philip W.. British Trust For Ornithology; Reino UnidoFil: Baylis, Alastair M. M.. Macquarie University; Australia. South Atlantic Environmental Research Institute; Reino UnidoFil: Benson, Scott R.. Noaa National Marine Fisheries Service Southwest Regional Office; Estados Unidos. Moss Landing Marine Laboratories; Estados UnidosFil: Block, Barbara A.. University of Stanford; Estados UnidosFil: Bograd, Steven J.. Noaa National Marine Fisheries Service Southwest Regional Office; Estados UnidosFil: Bordino, Pablo. Mote Marine Laboratory; Estados UnidosFil: Bowen, W.D.. Bedford Institute Of Oceanography, Fisheries And Oceans Canada; Canadá. Dalhousie University Halifax; CanadáFil: Brickle, Paul. South Atlantic Environmental Research Institute; Reino Unido. University of Aberdeen; Reino Unido. University Of Aberdeeen; Reino UnidoFil: Bruno, Ignacio Matias. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: González Carman, Victoria. Instituto Nacional de Investigaciones y Desarrollo Pesquero; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Champagne, Cory D.. University of Washington; Estados UnidosFil: Crocker, Daniel E.. Sonoma State University; Estados UnidosFil: Costa, Daniel P.. University of California; Estados UnidosFil: Dawson, Tiffany M.. University Of Central Florida; Estados Unidos. Old Dominion University; Estados UnidosFil: Deguchi, Tomohiro. Yamashina Institute For Ornithology; JapónFil: Dewar, Heidi. Noaa National Marine Fisheries Service Southwest Regional Office; Estados UnidosFil: Doherty, Philip D.. University of Exeter; Reino UnidoFil: Eguchi, Tomo. Noaa National Marine Fisheries Service Southwest Regional Office; Estados UnidosFil: Formia, Angela. Wildlife Conservation Society; Gabón. African Aquatic Conservation Fund; Estados UnidosFil: Godley, Brendan J.. University of Exeter; Reino UnidoFil: Graham, Rachel T.. Maralliance; PanamáFil: Gredzens, Christian. Padre Island National Seashore; Estados UnidosFil: Hart, Kristen M.. United States Geological Survey; Estados UnidosFil: Hawkes, Lucy A.. University of Exeter; Reino UnidoFil: Henderson, Suzanne. Scottish Natural Heritage; Reino UnidoFil: Henry, Robert William. Groundswell Coastal Ecology; Estados UnidosFil: Hückstädt, Luis A.. University of Exeter; Reino Unido. University of California; Estados Unido

CMB-S4 Science Book, First Edition

This book lays out the scientific goals to be addressed by the next-generation ground-based cosmic microwave background experiment, CMB-S4, envisioned to consist of dedicated telescopes at the South Pole, the high Chilean Atacama plateau and possibly a northern hemisphere site, all equipped with new superconducting cameras. CMB-S4 will dramatically advance cosmological studies by crossing critical thresholds in the search for the B-mode polarization signature of primordial gravitational waves, in the determination of the number and masses of the neutrinos, in the search for evidence of new light relics, in constraining the nature of dark energy, and in testing general relativity on large scales

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine

While wine fermentation has long been known to involve complex microbial communities, the composition and role of bacteria other than a select set of lactic acid bacteria (LAB) has often been assumed either negligible or detrimental. This study served as a pilot study for using barcoded amplicon next-generation sequencing to profile bacterial community structure in wines and grape musts, comparing the taxonomic depth achieved by sequencing two different domains of prokaryotic 16S rDNA (V4 and V5). This study was designed to serve two goals: 1) to empirically determine the most taxonomically informative 16S rDNA target region for barcoded amplicon sequencing of wine, comparing V4 and V5 domains of bacterial 16S rDNA to terminal restriction fragment length polymorphism (TRFLP) of LAB communities; and 2) to explore the bacterial communities of wine fermentation to better understand the biodiversity of wine at a depth previously unattainable using other techniques. Analysis of amplicons from the V4 and V5 provided similar views of the bacterial communities of botrytized wine fermentations, revealing a broad diversity of low-abundance taxa not traditionally associated with wine, as well as atypical LAB communities initially detected by TRFLP. The V4 domain was determined as the more suitable read for wine ecology studies, as it provided greater taxonomic depth for profiling LAB communities. In addition, targeted enrichment was used to isolate two species of Alphaproteobacteria from a finished fermentation. Significant differences in diversity between inoculated and uninoculated samples suggest that Saccharomyces inoculation exerts selective pressure on bacterial diversity in these fermentations, most notably suppressing abundance of acetic acid bacteria. These results determine the bacterial diversity of botrytized wines to be far higher than previously realized, providing further insight into the fermentation dynamics of these wines, and demonstrate the utility of next-generation sequencing for wine ecology studies

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

In order to understand the evolution of enzyme reactions and to gain an overview of biological catalysis we have combined sequence and structural data to generate phylogenetic trees in an analysis of 276 structurally defined enzyme superfamilies, and used these to study how enzyme functions have evolved. We describe in detail the analysis of two superfamilies to illustrate different paradigms of enzyme evolution. Gathering together data from all the superfamilies supports and develops the observation that they have all evolved to act on a diverse set of substrates, whilst the evolution of new chemistry is much less common. Despite that, by bringing together so much data, we can provide a comprehensive overview of the most common and rare types of changes in function. Our analysis demonstrates on a larger scale than previously studied, that modifications in overall chemistry still occur, with all possible changes at the primary level of the Enzyme Commission (E.C.) classification observed to a greater or lesser extent. The phylogenetic trees map out the evolutionary route taken within a superfamily, as well as all the possible changes within a superfamily. This has been used to generate a matrix of observed exchanges from one enzyme function to another, revealing the scale and nature of enzyme evolution and that some types of exchanges between and within E.C. classes are more prevalent than others. Surprisingly a large proportion (71%) of all known enzyme functions are performed by this relatively small set of 276 superfamilies. This reinforces the hypothesis that relatively few ancient enzymatic domain superfamilies were progenitors for most of the chemistry required for life