Using GIS and stakeholder involvement to innovate marine mammal bycatch risk assessment in data-limited fisheries

Fisheries bycatch has been identified as the greatest threat to marine mammals worldwide. Characterizing the impacts of bycatch on marine mammals is challenging because it is difficult to both observe and quantify, particularly in small-scale fisheries where data on fishing effort and marine mammal abundance and distribution are often limited. The lack of risk frameworks that can integrate and visualize existing data have hindered the ability to describe and quantify bycatch risk. Here, we describe the design of a new geographic information systems tool built specifically for the analysis of bycatch in small-scale fisheries, called Bycatch Risk Assessment (ByRA). Using marine mammals in Malaysia and Vietnam as a test case, we applied ByRA to assess the risks posed to Irrawaddy dolphins (Orcaella brevirostris) and dugongs (Dugong dugon) by five small-scale fishing gear types (hook and line, nets, longlines, pots and traps, and trawls). ByRA leverages existing data on animal distributions, fisheries effort, and estimates of interaction rates by combining expert knowledge and spatial analyses of existing data to visualize and characterize bycatch risk. By identifying areas of bycatch concern while accounting for uncertainty using graphics, maps and summary tables, we demonstrate the importance of integrating available geospatial data in an accessible format that taps into local knowledge and can be corroborated by and communicated to stakeholders of data-limited fisheries. Our methodological approach aims to meet a critical need of fisheries managers: to identify emergent interaction patterns between fishing gears and marine mammals and support the development of management actions that can lead to sustainable fisheries and mitigate bycatch risk for species of conservation concern

Appraisal and Diagnosis of Neurogenic Communication Disorders in Remote Settings

TB

Five years of observations of ozone profiles over Lauder, New Zealand

Altitude profiles of ozone (O3) over Lauder (45°S, 170°E) performed using a lidar, ozonesondes, and the satellite-borne Stratospheric Aerosol and Gas Experiment (SAGE II) instrument are presented. These data form one of the few long-term sets of O3 profiles at a Southern Hemisphere location. In the 5 years of data presented, the dominant variation is the annual cycle, the phase and amplitude of which differ below and above 27.5 km. Superposed are irregular episodic variations, caused by various processes. The first process studied is stratosphere-troposphere exchange, characterized by dry and O3-rich air residing in the troposphere, which was found in 21% of the measurements. The second relates to the positioning of the higher polar vortex over Lauder, often in combination with the exchange of air between midlatitude and subtropical stratospheric regions. We present examples of this which were observed over Lauder during the 1997 winter. This winter was selected for further study because of the record-low O3 amounts measured. The third process is mixing of O3-depleted vortex air with midlatitude air after the vortex breakup. We present one example, which shows that a filament originating from the depleted Antarctic vortex significantly lowers O3 amounts over Lauder around 27 November 1997. There is thus a connection between Antarctic O3 depletion and later decrease of O3 amounts at a Southern Hemisphere midlatitude location, namely Lauder

Theory and Applications of Non-Relativistic and Relativistic Turbulent Reconnection

Realistic astrophysical environments are turbulent due to the extremely high Reynolds numbers. Therefore, the theories of reconnection intended for describing astrophysical reconnection should not ignore the effects of turbulence on magnetic reconnection. Turbulence is known to change the nature of many physical processes dramatically and in this review we claim that magnetic reconnection is not an exception. We stress that not only astrophysical turbulence is ubiquitous, but also magnetic reconnection itself induces turbulence. Thus turbulence must be accounted for in any realistic astrophysical reconnection setup. We argue that due to the similarities of MHD turbulence in relativistic and non-relativistic cases the theory of magnetic reconnection developed for the non-relativistic case can be extended to the relativistic case and we provide numerical simulations that support this conjecture. We also provide quantitative comparisons of the theoretical predictions and results of numerical experiments, including the situations when turbulent reconnection is self-driven, i.e. the turbulence in the system is generated by the reconnection process itself. We show how turbulent reconnection entails the violation of magnetic flux freezing, the conclusion that has really far reaching consequences for many realistically turbulent astrophysical environments. In addition, we consider observational testing of turbulent reconnection as well as numerous implications of the theory. The former includes the Sun and solar wind reconnection, while the latter include the process of reconnection diffusion induced by turbulent reconnection, the acceleration of energetic particles, bursts of turbulent reconnection related to black hole sources as well as gamma ray bursts. Finally, we explain why turbulent reconnection cannot be explained by turbulent resistivity or derived through the mean field approach.Comment: 66 pages, 24 figures, a chapter of the book "Magnetic Reconnection - Concepts and Applications", editors W. Gonzalez, E. N. Parke

Early-onset progressive retinal atrophy associated with an IQCB1 variant in African black-footed cats (Felis nigripes)

African black-footed cats (Felis nigripes) are endangered wild felids. One male and full-sibling female African black-footed cat developed vision deficits and mydriasis as early as 3 months of age. The diagnosis of early-onset progressive retinal atrophy (PRA) was supported by reduced direct and consensual pupillary light reflexes, phenotypic presence of retinal degeneration, and a non-recordable electroretinogram with negligible amplitudes in both eyes. Whole genome sequencing, conducted on two unaffected parents and one affected offspring was compared to a variant database from 51 domestic cats and a Pallas cat, revealed 50 candidate variants that segregated concordantly with the PRA phenotype. Testing in additional affected cats confirmed that cats homozygous for a 2 base pair (bp) deletion within IQ calmodulin-binding motif-containing protein-1 (IQCB1), the gene that encodes for nephrocystin-5 (NPHP5), had vision loss. The variant segregated concordantly in other related individuals within the pedigree supporting the identification of a recessively inherited early-onset feline PRA. Analysis of the black-footed cat studbook suggests additional captive cats are at risk. Genetic testing for IQCB1 and avoidance of matings between carriers should be added to the species survival plan for captive management

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts