A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer

Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of > 10 million SNPs in 43,303 prostate cancer cases and 43,737 controls from studies in populations of European, African, Japanese and Latino ancestry. Twenty-three new susceptibility loci were identified at association P < 5 × 10(-8); 15 variants were identified among men of European ancestry, 7 were identified in multi-ancestry analyses and 1 was associated with early-onset prostate cancer. These 23 variants, in combination with known prostate cancer risk variants, explain 33% of the familial risk for this disease in European-ancestry populations. These findings provide new regions for investigation into the pathogenesis of prostate cancer and demonstrate the usefulness of combining ancestrally diverse populations to discover risk loci for disease.

Outdated journal rankings and the ERA exercise

As the results of the latest Excellence in Research Australia (ERA) exercise come closer to being announced, universities around Australia are holding their collective breaths. The ERA claims to be an assessment of research strengths and quality at Australian universities. While it is not supposed to produce a set of league tables, ultimately that is what tends to happen...

The Role of the Law in Communicating Patient Safety

This chapter considers the role of the law in communicating patient safety. Downie, Lahey, Ford, et al’s (2006) preventing, knowing and responding theoretical framework is adopted to classify the different elements of patient safety law. Rather than setting out all relevant patient safety laws in detail, this chapter highlights key legal strategies which are employed to: prevent the occurrence of patient safety incidents (preventing); support the discovery and open discussion of patient safety incidents when they do occur (knowing),; and guide responses after they occur (responding) (Downie, Lahey, Ford, et al 2006). The law is increasingly being invoked to facilitate open discussion of and communication surrounding patient safety. After highlighting some legal strategies used to communicate patient safety, two practice examples are presented. The practice examples highlight different aspects of patient safety law and are indicative of communication issues commonly faced in practice. The first practice example focuses on the role of the Ccoroner in communicating patient safety. This example highlights the investigative role of the law in relation to patient safety (knowing). It also showcases the preventing responding and preventing elements in respect of the significant number of communication errors that can occur in a multi-disciplinary, networked health system. The main focus of the second practice example is responding example illustrates how the law responds to health service providers’ and professionals’ miscommunication (and subsequent incidents) during treatment, however it also touches upon knowing and preventing.

Nature and extent of genetic diversity of dengue viruses determined by 454 pyrosequencing

Dengue virus (DENV) populations are characteristically highly diverse. Regular lineage extinction and replacement is an important dynamic DENV feature, and most DENV lineage turnover events are associated with increased incidence of disease. The role of genetic diversity in DENV lineage extinctions is not understood. We investigated the nature and extent of genetic diversity in the envelope (E) gene of DENV serotype 1 representing different lineages histories. A region of the DENV genome spanning the E gene was amplified and sequenced by Roche/454 pyrosequencing. The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene. A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences, and the sequences of each constructed haplotype showed that the haplotypes segregated with the Sanger consensus sequence of the population from which they were drawn. Haplotypes determined through pyrosequencing identified a recombinant DENV genome that could not be identified through Sanger sequencing. Nucleotide level sequence diversities of DENV-1 populations determined from SNP analysis were very low, estimated from 0.009-0.01. There were also no stop codon, frameshift or non-frameshift mutations observed in the E genes of any lineage. No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5). Although our hypothesis that accumulation of deleterious mutations over time led to the extinction and replacement of DENV lineages was ultimately not supported by the data, our data does highlight the significant technical issues that must be resolved in the way in which population diversity is measured for DENV and other viruses. The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.

Generalizability of established prostate cancer risk variants in men of African ancestry

Genome-wide association studies have identified more than 80 risk variants for prostate cancer, mainly in European or Asian populations. The generalizability of these variants in other racial/ethnic populations needs to be understood before the loci can be used widely in risk modeling. In our study, we examined 82 previously reported risk variants in 4,853 prostate cancer cases and 4,678 controls of African ancestry. We performed association testing for each variant using logistic regression adjusted for age, study and global ancestry. Of the 82 known risk variants, 68 (83%) had effects that were directionally consistent in their association with prostate cancer risk and 30 (37%) were significantly associated with risk at p < 0.05, with the most statistically significant variants being rs116041037 (p = 3.7 × 10(-26) ) and rs6983561 (p = 1.1 × 10(-16) ) at 8q24, as well as rs7210100 (p = 5.4 × 10(-8) ) at 17q21. By exploring each locus in search of better markers, the number of variants that captured risk in men of African ancestry (p < 0.05) increased from 30 (37%) to 44 (54%). An aggregate score comprised of these 44 markers was strongly associated with prostate cancer risk [per-allele odds ratio (OR) = 1.12, p = 7.3 × 10(-98) ]. In summary, the consistent directions of effects for the vast majority of variants in men of African ancestry indicate common functional alleles that are shared across populations. Further exploration of these susceptibility loci is needed to identify the underlying biologically relevant variants to improve prostate cancer risk modeling in populations of African ancestry.

Multijurisdictional fisheries performance reporting: How Australia’s nationally standardised approach to assessing stock status compares

Australian marine wild-capture fisheries are managed by eight separate jurisdictions. Traditionally, fishery status reports have been produced separately by most of these jurisdictions, assessing the fish stocks they manage, and reporting on the effectiveness of their fisheries management. However, the format, the type of stock status assessments, the thresholds and terminology used to describe stock status and the classification frameworks have varied over time and among jurisdictions. These differences complicate efforts to understand stock status on a national scale. They also create potential misunderstanding among the wider community about how to interpret information on the status of fish stocks, and the fisheries management and science processes more generally. This is especially true when considering stocks that are shared across two or more jurisdictional boundaries. A standardised approach was developed in 2011 leading to production of the first national Status of key Australian fish stocks reports in 2012, followed by a second edition in 2014 (www.fish.gov.au). Production of these reports was the first step towards a broader national approach to reporting on the performance of Australian fisheries for target species and for wider ecosystem and socioeconomic consequences. This paper outlines the challenges associated with moving towards national performance reporting for target fish stocks and Australia’s successes so far. It also outlines the challenges ahead, in particular those relating to reporting more broadly on the status of entire fisheries. Comparisons are drawn between Australia and New Zealand and more broadly between Australia and other countries.

Analog/RF Built-in-Self-Test Subsystem for a Mobile Broadcast Video Receiver in 65-nm CMOS

A built-in-self-test (BIST) subsystem embedded in a 65-nm mobile broadcast video receiver is described. The subsystem is designed to perform analog and RF measurements at multiple internal nodes of the receiver. It uses a distributed network of CMOS sensors and a low bandwidth, 12-bit A/D converter to perform the measurements with a serial bus interface enabling a digital transfer of measured data to automatic test equipment (ATE). A perturbation/correlation based BIST method is described, which makes pass/fail determination on parts, resulting in significant test time and cost reduction.

EFFECT OF OFF-STOICHIOMETRY AND TERNARY ADDITIONS ON PLANAR FAULT ENERGIES IN Ni3Al

First principles calculations were done to evaluate the lattice parameter, cohesive energy and stacking fault energies of ordered gamma' (Ll(2)) precipitates in superalloys as a function of composition. It was found that addition of Ti and Ta lead to an increase in lattice parameter and decrease in cohesive energy, while Ni antisites had the opposite effect. Ta and Ti addition to stoichiometric Ni3Al resulted in an initial increase in the energies of APB((111)), CSF(111), APB((001)) and SISF(111). However, at higher concentrations, the fault energies decreased. Addition of Ni antisites decreased the energy of all four faults monotonically. A model based on nearest neighbor bonding was used for Ni-3(Al, Ta), Ni-3(Al, Ti) and Ni-3(Al, Ni) pseudo-binary systems and extended to pseudo- ternary Ni-3(Al, Ta, Ni) and Ni-3(Al, Ti, Ni) systems. Recipes were developed for predicting lattice parameters, cohesive energies and fault energies in pseudo- ternary systems on the basis of coefficients derived from simpler pseudobinary systems. The model predictions were found to be in good agreement with first principles calculations for lattice parameters, cohesive energies, and energies of APB((111)) and CSF(111).

Proceedings of the 1998 Science Board Symposium on The Impacts of the 1997/98 El Niño Event on the North Pacific Ocean and Its Marginal Seas

Preface [pdf, 0.01 Mb] James J. O'Brien The big picture - The ENSO of 1997-98 [pdf, 0.01 Mb] James E. Overland, Nicholas A. Bond & Jennifer Miletta Adams Atmospheric anomalies in 1997: Links to ENSO? [pdf, 0.54 Mb] Vladimir I. Ponomarev, Olga Trusenkova, Serge Trousenkov, Dmitry Kaplunenko, Elena Ustinova & Antonina Polyakova The ENSO signal in the northwest Pacific [pdf, 0.47 Mb] Robert L. Smith, A. Huyer, P.M. Kosro & J.A. Barth Observations of El Niño off Oregon: July 1997 to present (October 1998) [pdf, 1.31 Mb] Patrica A. Wheeler & Jon Hill Biological effects of the 1997-1998 El Niño event off Oregon: Nutrient and chlorophyll distributions [pdf, 1.13 Mb] William T. Peterson Hydrography and zooplankton off the central Oregon coast during the 1997-1998 El Niño event [pdf, 0.26 Mb] William Crawford, Josef Cherniawsky, Michael Foreman & Peter Chandler El Niño sea level signal along the west coast of Canada [pdf, 1.25 Mb] Howard J. Freeland & Rick Thomson The El Niño signal along the west coast of Canada - temperature, salinity and velocity [pdf, 0.49 Mb] Frank A. Whitney, David L. Mackas, David W. Welch & Marie Robert Impact of the 1990s El Niños on nutrient supply and productivity of Gulf of Alaska waters [pdf, 0.06 Mb] Craig McNeil, David Farmer & Mark Trevorrow Dissolved gas measurements at Stn. P4 during the 97-98 El Niño [pdf, 0.13 Mb] Kristen L.D. Milligan, Colin D. Levings & Robert E. DeWreede Data compilation and preliminary time series analysis of abundance of a dominant intertidal kelp species in relation to the 1997/1998 El Niño event [pdf, 0.05 Mb] S.M. McKinnell, C.C. Wood, M. Lapointe, J.C. Woodey, K.E. Kostow, J. Nelson & K.D. Hyatt Reviewing the evidence that adult sockeye salmon strayed from the Fraser River and spawned in other rivers in 1997 [pdf,0.03 Mb] G.A. McFarlane & R.J. Beamish Sardines return to British Columbia waters [pdf, 0.34 Mb] Ken H. Morgan Impact of the 1997/98 El Niño on seabirds of the northeast Pacific [pdf, 0.06 Mb] Thomas C. Royer & Thomas Weingartner Coastal hydrographic responses in the northern Gulf of Alaska to the 1997-98 ENSO event [pdf, 0.76 Mb] John F. Piatt, Gary Drew, Thomas Van Pelt, Alisa Abookire, April Nielsen, Mike Shultz & Alexander Kitaysky Biological effects of the 1997/98 ENSO in Cook Inlet, Alaska [pdf, 0.22 Mb] H.J. Niebauer The 1997-98 El Niño in the Bering Sea as compared with previous ENSO events and the "regime shift" of the late 1970s [pdf, 0.10 Mb] A.S. Krovnin, G.P. Nanyushin, M.Yu. Kruzhalov, G.V. Khen, M.A. Bogdanov, E.I. Ustinova, V.V. Maslennikov, A.M. Orlov, B.N. Kotenev, V.V. Bulanov & G.P. Muriy The state of the Far East seas during the 1997/98 El Niño event [pdf, 0.15 Mb] Stacy Smith & Susan Henrichs Phytoplankton collected by a time-series sediment trap deployed in the southeast Bering Sea during 1997 [pdf, 0.21 Mb] Cynthia T. Tynan Redistributions of cetaceans in the southeast Bering Sea relative to anomalous oceanographic conditions during the 1997 El Niño [pdf, 0.02 Mb] Akihiko Yatsu, Junta Mori, Hiroyuki Tanaka, Tomowo Watanabe, Kazuya Nagasawa, Yikimasa Ishida, Toshimi Meguro, Yoshihiko Kamei & Yasunori Sakurai Stock abundance and size compositions of the neon flying squid in the central North Pacific Ocean during 1979-1998 [pdf, 0.11 Mb] O.B. Feschenko A new point of view concerning the El Niño mechanism [pdf, 0.01 Mb] Nathan Mantua 97/98 Ocean climate variability in the northeast Pacific: How much blame does El Niño deserve? [pdf, 0.01 Mb] Vadim P. Pavlychev Sharp changes of hydrometeorological conditions in the northwestern Pacific during the 1997/1998 El Niño event [pdf, 0.01 Mb] Jingyi Wang Predictability and forecast verification of El Niño events [pdf, 0.01 Mb] (Document contains 110 pages)

A chemical survey of standing waters in south-east England, with reference to acidification and eutrophication

This study looks at the distribution and magnitude of acidification and eutrophication in south-east England where there are no natural lakes but a large number of shallow artificial ponds. The study area is defined as the region lying within a 100 km radius of central London but excluding the area within the M25 motorway. Water samples were taken from 120 sites between mid-January and the end of February 1990, with a subsequent monthly survey of a subset of 31 of these waters. Twelve chemical variables were measured in the laboratory using standard techniques. PH values for the full dataset ranged from 3.2 to 8.4, although the majority of sites had pH values in the range 7.0 to 8.5; only five sites had a pH of less than 6.0. The five low pH sites expectedly had low alkalinities and are the only sites with values below 0.1 meq per litre. Concentrations of calcium, sodium, potassium, magnesium, chloride, sulphate and nitrate had normal distributions. The majority of sites had total phosphorus concentrations in the range 25 to 200 mu g per litre, although 10 sites had concentrations above 400 mu g per litre. The low number of acid sites suggests that surface water acidity is not a widespread regional problem in south-east England. However the survey shows that a large number of standing waters in the region have high total phosphorus and nitrate concentrations, and 89% may be considered moderately to considerably eutrophic.

Vulnerabilidade de enfermeiros no cuidado a pacientes com HIV/Aids: um estudo de representações sociais

Vulnerabilidade e empoderamento apresentam-se como elementos presentes na vida profissional e pessoal dos enfermeiros. Delimitou-se como objeto de estudo as representações sociais elaboradas por enfermeiros que cuidam de pacientes com HIV/Aids acerca de sua vulnerabilidade no contexto do cuidar em enfermagem. O objetivo geral foi analisar as representações sociais construídas por enfermeiros acerca de sua vulnerabilidade no contexto do cuidado que exercem. Trata-se de pesquisa qualitativa, descritiva e exploratória, orientada pelo referencial teórico-metodológico das Representações Sociais em sua abordagem processual. Participaram do estudo trinta enfermeiros de um hospital público municipal do Rio de Janeiro. Como técnicas de coleta de dados foram utilizados o questionário sociodemográfico e a entrevista semiestruturada em profundidade. Como técnica de análise de dados adotou-se a análise de conteúdo temático-categorial proposta por Bardin, sistematizada por Oliveira e operacionalizada pelo software QSR NVivo 9.0. Entre os sujeitos, há predomínio do gênero feminino, da faixa etária de 41 a 45 anos, da realização de pós-graduação lato sensu e de tempo de atuação mínimo de 16 anos em HIV/Aids. Sete categorias emergiram na segmentação do material discursivo: 1) O acesso a informações, a formação profissional e o desenvolvimento da naturalização da aids através da experiência: elementos de vulnerabilidade e de empoderamento; 2) A instituição hospitalar e sua infraestrutura como polo de vulnerabilidade e de empoderamento nas construções simbólicas de enfermeiros que cuidam de pacientes com HIV/Aids; 3) Entre o risco e a prevenção: a vulnerabilidade e o empoderamento no contexto dos acidentes ocupacionais biológicos e as práticas preventivas adotadas por enfermeiros frente ao HIV/Aids no cotidiano hospitalar; 4) Relações interpessoais entre enfermeiro e paciente soropositivo para o HIV enquanto mediadoras da vulnerabilidade e do empoderamento de ambos; 5) As limitações psíquicas enfrentadas por enfermeiros no vivenciar do trabalho junto a portadores do HIV/Aids; 6) A busca pela espiritualidade e pela religiosidade como bases de apoio para a vida profissional contextualizada na aids; e 7) O HIV e a aids no contexto de diferentes modalidades de relacionamento: a presença do risco como elemento organizador da discursividade. Na vida profissional, as representações sociais da vulnerabilidade são compostas pela fragilidade, pelo risco e pela dificuldade. O empoderamento, por sua vez, emerge sustentado por um tripéformado pela proteção, suporte e satisfação como elementosdo bem-estar. Na vida pessoal, o risco possui centralidade nas representações. Já o empoderamento se mostra oriundo do bem-estar e da proteção. Conclui-se que a reconstrução sociocognitiva da vulnerabilidade e do empoderamento permitiu o acesso ao arsenal simbólico do qual o grupo dispõe para a superação do que o ameaça. Vulnerabilidade e empoderamento são, portanto, diversificados e mutáveis em suas bases e produtos e, em movimentos de balanço e contrabalanço, corporificam a díade vulnerabilidade-empoderamento.

Use of stereo camera systems for assessment of rockfish abundance in untrawlable areas and for recording pollock behavior during midwater trawls

We describe the application of two types of stereo camera systems in fisheries research, including the design, calibration, analysis techniques, and precision of the data obtained with these systems. The first is a stereo video system deployed by using a quick-responding winch with a live feed to provide species- and size- composition data adequate to produce acoustically based biomass estimates of rockfish. This system was tested on the eastern Bering Sea slope where rockfish were measured. Rockfish sizes were similar to those sampled with a bottom trawl and the relative error in multiple measurements of the same rockfish in multiple still-frame images was small. Measurement errors of up to 5.5% were found on a calibration target of known size. The second system consisted of a pair of still-image digital cameras mounted inside a midwater trawl. Processing of the stereo images allowed fish length, fish orientation in relation to the camera platform, and relative distance of the fish to the trawl netting to be determined. The video system was useful for surveying fish in Alaska, but it could also be used broadly in other situations where it is difficult to obtain species-composition or size-composition information. Likewise, the still-image system could be used for fisheries research to obtain data on size, position, and orientation of fish.

Spatial and temporal distribution and the potential for estuarine interactions between wild and hatchery chum salmon (Oncorhynchus keta) in Taku Inlet, Alaska

We investigated estuarine spatial and temporal overlap of wild and marked hatchery chum salmon (Oncorhynchus keta) fry; the latter included two distinct size groups released near the Taku River estuary (Taku Inlet) in Southeast Alaska (early May releases of ~ 1.9 g and late May releases of ~ 3.9 g wet weight). Our objectives were to compare abundance, body size, and condition of wild chum salmon fry and hatchery chum salmon fry raised under early and late rearing strategies in different habitats of Taku Inlet and to document environmental factors that could potentially explain the distribution, size, and abundance of these chum salmon fr y. We used a sampling design stratified into inner and outer inlet and neritic and littoral habitats. Hatchery fry were rare in the inner estuary in both years but outnumbered wild fry 20:1 in the outer estuary. Hatchery fry were significantly larger than wild fry in both littoral and neritic samples. Abundances of wild and hatchery fry were positively correlated in the outer inlet, indicating the formation of mixed schools of hatchery and wild fry. Spatial and temporal overlap was greatest between wild and early hatchery fry in the outer inlet in both habitats. The early hatchery release coincided with peak abundances of wild fry in the outer inlet, and the distribution of wild and early hatchery fry overlapped for about three weeks. Our results demonstrate that the timing of release of hatchery fry may affect interactions with wild fry.

The U.S. Gulf of Mexico Pink Shrimp, Farfantepenaeus duorarum, Fishery: 50 Years of Commercial Catch Statistics

U.S. Gulf of Mexico, pink shrimp, Farfantepenaeus duorarum, catch statistics have been collected by NOAA’s National Marine Fisheries Service, or its predecessor agency, for over 50 years. Recent events, including hurricanes and oil spills within the ecosystem of the fishery, have shown that documentation of these catch data is of primary importance. Fishing effort for this stock has fluctuated over the 50-year period analyzed, ranging from 3,376 to 31,900 days fished, with the most recent years on record, 2008 and 2009, exhibiting declines up to 90% relative to the high levels recorded in the mid 1990’s. Our quantification of F. duorarum landings and catch rates (CPUE) indicates catch have been below the long-term average of about 12 million lb for all of the last 10 years on record. In contrast to catch and effort, catch rates have increased in recent years, with record CPUE levels measured in 2008 and 2009, of 1,340 and 1,144 lb per day fished, respectively. Our regression results revealed catch was dependent upon fishing effort (F=98.48df=1, 48, p<0.001, r2=0.67), (Catch=1,623,378 + (520) × (effort)). High CPUE’s measured indicate stocks were not in decline prior to 2009, despite the decline in catch. The decrease in catch is attributed in large part to low effort levels caused by economical and not biological or habitat related conditions. Future stock assessments using these baseline data will provide further insights and management advice concerning the Gulf of Mexic

Simulation of Tail Weight Distributions in Biological Year 1986–2006 Landings of Brown Shrimp, Farfantepenaeus aztecus, from the Northern Gulf of Mexico Fishery

Size distribution within re- ported landings is an important aspect of northern Gulf of Mexico penaeid shrimp stock assessments. It reflects shrimp population characteristics such as numerical abundance of various sizes, age structure, and vital rates (e.g. recruitment, growth, and mortality), as well as effects of fishing, fishing power, fishing practices, sampling, size-grading, etc. The usual measure of shrimp size in archived landings data is count (C) the number of shrimp tails (abdomen or edible portion) per pound (0.4536 kg). Shrimp are marketed and landings reported in pounds within tail count categories. Statistically, these count categories are count class intervals or bins with upper and lower limits expressed in C. Count categories vary in width, overlap, and frequency of occurrence within the landings. The upper and lower limits of most count class intervals can be transformed to lower and upper limits (respectively) of class intervals expressed in pounds per shrimp tail, w, the reciprocal of C (i.e. w = 1/C). Age based stock assessments have relied on various algorithms to estimate numbers of shrimp from pounds landed within count categories. These algorithms required un- derlying explicit or implicit assumptions about the distribution of C or w. However, no attempts were made to assess the actual distribution of C or w. Therefore, validity of the algorithms and assumptions could not be determined. When different algorithms were applied to landings within the same size categories, they produced different estimates of numbers of shrimp. This paper demonstrates a method of simulating the distribution of w in reported biological year landings of shrimp. We used, as examples, landings of brown shrimp, Farfantepenaeus aztecus, from the northern Gulf of Mexico fishery in biological years 1986–2006. Brown shrimp biological year, Ti, is defined as beginning on 1 May of the same calendar year as Ti and ending on 30 April of the next calendar year, where subscript i is the place marker for biological year. Biological year landings encompass most if not all of the brown shrimp life cycle and life span. Simulated distributions of w reflect all factors influencing sizes of brown shrimp in the landings within a given biological year. Our method does not require a priori assumptions about the parent distributions of w or C, and it takes into account the variability in width, overlap, and frequency of occurrence of count categories within the landings. Simulated biological year distributions of w can be transformed to equivalent distributions of C. Our method may be useful in future testing of previously applied algorithms and development of new estimators based on statistical estimation theory and the underlying distribution of w or C. We also examine some applications of biological year distributions of w, and additional variables derived from them.