Estimates of Marine Mammal, Sea Turtle, and Seabird Mortality in the California Drift Gillnet Fishery for Swordfish and Thresher Shark, 1996–2002

Estimates of incidental marine mammal, sea turtle, and seabird mortality in the California drift gillnet fishery for broadbill swordfish, Xiphias gladius, and common thresher shark, Alopias vulpinus, are summarized for the 7-year period, 1996 to 2002. Fishery observer coverage was 19% over the period (3,369 days observed/17,649 days fished). An experiment to test the effectiveness of acoustic pingers on reducing marine mammal entanglements in this fishery began in 1996 and resulted in statistically significant reductions in marine mammal bycatch. The most commonly entangled marine mammal species were the short-beaked common dolphin, Delphinus delphis; California sea lion, Zalophus californianus; and northern right whale dolphin, Lissodelphis borealis. Estimated mortality by species (CV and observed mortality in parentheses) from 1996 to 2002 is 861 (0.11, 133) short-beaked common dolphins; 553 (0.16, 103) California sea lions; 151 (0.25, 31) northern right whale dolphins; 150 (0.21, 27) northern elephant seals, Mirounga angustirostris; 54 (0.41, 10) long-beaked common dolphins, Delphinus capensis; 44 (0.53, 6) Dall’s porpoise, Phocoenoides dalli; 19 (0.60, 5) Risso’s dolphins, Grampus griseus; 11 (0.71, 2) gray whales, Eschrichtius robustus; 7 (0.83, 2) sperm whales, Physeter macrocephalus; 7 (0.96, 1) short-finned pilot whales, Globicephala macrorhychus; 12 (1.06, 1) minke whales, Balaenoptera acutorostrata; 5 (1.05, 1) fin whales, Balaenoptera physalus; 11 (0.68, 2) unidentified pinnipeds; 33 (0.52, 4) leatherback turtles, Dermochelys coriacea; 18 (0.57, 3) loggerhead turtles, Caretta caretta; 13 (0.73, 3) northern fulmars, Fulmarus glacialis; and 6 (0.86, 2) unidentified birds

Interpreting Dark Matter Direct Detection Independently of the Local Velocity and Density Distribution

We demonstrate precisely what particle physics information can be extracted from a single direct detection observation of dark matter while making absolutely no assumptions about the local velocity distribution and local density of dark matter. Our central conclusions follow from a very simple observation: the velocity distribution of dark matter is positive definite, f(v) >= 0. We demonstrate the utility of this result in several ways. First, we show a falling deconvoluted recoil spectrum (deconvoluted of the nuclear form factor), such as from ordinary elastic scattering, can be "mocked up" by any mass of dark matter above a kinematic minimum. As an example, we show that dark matter much heavier than previously considered can explain the CoGeNT excess. Specifically, m_chi < m_Ge} can be in just as good agreement as light dark matter, while m_\chi > m_Ge depends on understanding the sensitivity of Xenon to dark matter at very low recoil energies, E_R ~ 6 keVnr. Second, we show that any rise in the deconvoluted recoil spectrum represents distinct particle physics information that cannot be faked by an arbitrary f(v). As examples of resulting non-trivial particle physics, we show that inelastic dark matter and dark matter with a form factor can both yield such a rise

La ingeniería lingüística con Java

In this article the Java programming language and runtime environment is examined, with special reference being made to its applicability to the creation of applications in the area of linguistic engineering. Java has been presented by Sun Microsystems as an easy to use, secure and robust programming language, which is capable of being used to produce distributed platforrn independent applications, capable of running across the Web. Following a brief analysis of these claims, sorne of the principal requirements of linguistic applications are outlined, and the properties of Java that can be used to rneet these requirements are considered. Iii this process a few brief remarks are made regarding the comparison of Java and other programming languages like Lisp, Prolog, C and C++. Finally, an example system which is being developed by the authors is presented, in order to illustrate the main arguments contained in this article.Este artículo intenta hacer una reflexión teórica sobre Java que sea de interés y utilidad para la comunidad informática, y especialmente para los programadores de aplicaciones lingüísticas, ya que, como ocurre con muchas otras tecnologías asociadas con la Web, hay cierta confusión, falta de información y malentendidos sobre este lenguaje de programación. Aunque muchos lingüistas computacionales hayan oído hablar de Java, considerado su uso e incluso llegado hasta su primer applet (aplicación pequeña para una página Web) ‘Hola mundo quizás no se hayan planteado todas las implicaciones del uso de este lenguaje y del papel que podría desempeñar en el desarrollo de aplicaciones lingüísticas hoy en día. Es necesario clarificar de antemano que aquí no se tiene el propósito de presentar Java como sustituto absoluto de los lenguajes de programación tradicionales para aplicaciones lingüísticas ya que, entre otras cosas, la historia de Java es demasiado corta para examinar comparativamente las aplicaciones escritas en este lenguaje y en otros y extraer conclusiones definitivas

Longitudinal characterization of antimicrobial resistance genes in feces shed from cattle fed different subtherapeutic antibiotics

<p>Abstract</p> <p>Background</p> <p>Environmental transmission of antimicrobial-resistant bacteria and resistance gene determinants originating from livestock is affected by their persistence in agricultural-related matrices. This study investigated the effects of administering subtherapeutic concentrations of antimicrobials to beef cattle on the abundance and persistence of resistance genes within the microbial community of fecal deposits. Cattle (three pens per treatment, 10 steers per pen) were administered chlortetracycline, chlortetracycline plus sulfamethazine, tylosin, or no antimicrobials (control). Model fecal deposits (<it>n </it>= 3) were prepared by mixing fresh feces from each pen into a single composite sample. Real-time PCR was used to measure concentrations of <it>tet</it>, <it>sul </it>and <it>erm </it>resistance genes in DNA extracted from composites over 175 days of environmental exposure in the field. The microbial communities were analyzed by quantification and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified <it>16S-rRNA.</it></p> <p>Results</p> <p>The concentrations of <it>16S-rRNA </it>in feces were similar across treatments and increased by day 56, declining thereafter. DGGE profiles of <it>16S-rRNA </it>differed amongst treatments and with time, illustrating temporal shifts in microbial communities. All measured resistance gene determinants were quantifiable in feces after 175 days. Antimicrobial treatment differentially affected the abundance of certain resistance genes but generally not their persistence. In the first 56 days, concentrations of <it>tet</it>(B), <it>tet</it>(C), <it>sul1, sul2</it>, <it>erm</it>(A) tended to increase, and decline thereafter, whereas <it>tet</it>(M) and <it>tet</it>(W) gradually declined over 175 days. At day 7, the concentration of <it>erm</it>(X) was greatest in feces from cattle fed tylosin, compared to all other treatments.</p> <p>Conclusion</p> <p>The abundance of genes coding for antimicrobial resistance in bovine feces can be affected by inclusion of antibiotics in the feed. Resistance genes can persist in feces from cattle beyond 175 days with concentrations of some genes increasing with time. Management practices that accelerate DNA degradation such as frequent land application or composting of manure may reduce the extent to which bovine feces serves as a reservoir of antimicrobial resistance.</p

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

1. Studying fungal biodiversit y using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables. 2. Here, we introduce PIPITS, an o pen-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS e xploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables. 3. We pro vide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the MiSeq platform from Illumina MiSeq. 4. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curatedUNITE fungal data set