Evaluating methods for estimating rare events with zero-heavy data: a simulation model estimating sea turtle bycatch in the pelagic longline fishery

Estimating rare events from zero-heavy data (data with many zero values) is a common challenge in fisheries science and ecology. For example, loggerhead sea turtles (Caretta caretta) and leatherback sea turtles (Dermochelys coriacea) account for less than 1% of total catch in the U.S. Atlantic pelagic longline fishery. Nevertheless, the Southeast Fisheries Science Center (SEFSC) of the National Marine Fisheries Service (NMFS) is charged with assessing the effect of this fishery on these federally protected species. Annual estimates of loggerhead and leatherback bycatch in a fishery can affect fishery management and species conservation decisions. However, current estimates have wide confidence intervals, and their accuracy is unknown. We evaluate 3 estimation methods, each at 2 spatiotemporal scales, in simulations of 5 spatial scenarios representing incidental capture of sea turtles by the U.S. Atlantic pelagic longline fishery. The delta-log normal method of estimating bycatch for calendar quarter and fishing area strata was the least biased estimation method in the spatial scenarios believed to be most realistic. This result supports the current estimation procedure used by the SEFSC.

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.

Prevalência e fatores relacionados à infecção por HPV em mulheres assistidas pela Estratégia Saúde da Família em Juiz de Fora, Minas Gerais.

O câncer do colo do útero ocasiona 7% dos óbitos por câncer na população feminina brasileira, com taxa de incidência estimada em 15,33/100 mil, sendo a infecção pelo papilomavírus humano (HPV) causa necessária. O rastreamento com citologia do esfregaço cervical convencional é ação escolhida no Brasil e em outros países para prevenir e controlar o câncer, através da detecção precoce das lesões pré-neoplásicas. Porém, apresenta falhas na cobertura, com desigualdade de acesso, e na qualidade, devido aos problemas nas etapas operacionais, desde a coleta na unidade até a interpretação dos resultados. O rastreamento é oportunístico, e uma alternativa organizada pode ser a utilização de cadastros populacionais, como os disponíveis pela Estratégia Saúde da Família (ESF). A efetividade do rastreamento pode ser aumentada com a incorporação de novas técnicas, destacando-se aquelas de biologia molecular, que testam o HPV nas mulheres, em acréscimo ao rastreamento com citologia ou a substituindo integralmente. O conhecimento acerca dos fatores relacionados à infecção vem sendo ampliado para compreender por que mulheres que se encontram em risco semelhante de transmissão apresentam infecção e outras, não. A inexistência de um sistema de vigilância dos tipos circulantes de HPV prejudica a avaliação do cenário atual, inclusive no que se refere à recente implantação da vacinação contra o HPV no calendário básico de vacinação. Neste estudo, o objetivo foi estimar a prevalência de infecção pelo HPV no grupo de mulheres estudadas, relacionando estes achados aos fatores relacionados à infecção, que podem auxiliar na identificação de mulheres mais vulneráveis à infecção e à presença de lesões pré-neoplásicas. 2062 mulheres da periferia de Juiz de Fora, após serem convocadas para rastreamento, participaram do estudo, desenvolvido em duas unidades com a ESF, tendo respondido a um questionário padronizado, submetidas ao exame citológico cervical convencional e testadas para o HPV com o teste cobas 4800 (Roche). A adesão das mulheres convocadas foi semelhante àquela observada em estudos de outros delineamentos, os quais podem contribuir para o seu entendimento. Foram calculadas estimativas de prevalência de infecção pelo HPV segundo características selecionadas. A prevalência global de infecção pelo HPV foi 12,61%. A análise multivariada por regressão de Poisson com variância robusta mostrou associação estatisticamente significativa para ser solteira, consumir bebida alcoólica e ter três ou mais parceiros sexuais ao longo da vida, com razões de prevalência ajustadas de 1,40, 1,44 e 1,35, respectivamente. A prevalência de lesões precursoras do câncer do colo do útero foi 7,27%. A qualidade do esfregaço, avaliada pela representatividade dos epitélios coletados, mostrou que há variação da prevalência de lesões pré-neoplásicas mediante qualidade do esfregaço, porém, não há variação nos resultados do teste HPV mediante a representatividade celular, achado que consistente com uma sensibilidade maior e possivelmente um melhor valor preditivo positivo. A testagem do HPV mostrou ser útil, especialmente entre mulheres com resultado de citologia normal.

PICES Press, Vol. 18, No. 2, Summer 2010

•The 2010 Inter-sessional Science Board Meeting: A Note from the Science Board Chairman (pp. 1-3) •2010 Symposium on “Effects of Climate Change on Fish and Fisheries” (pp. 4-11) •2009 Mechanism of North Pacific Low Frequency Variability Workshop (pp. 12-14) •The Fourth China-Japan-Korea GLOBEC/IMBER Symposium (pp. 15-17, 23) •2010 Sendai Ocean Acidification Workshop (pp. 18-19, 31) •2010 Sendai Coupled Climate-to-Fish-to-Fishers Models Workshop (pp. 20-21) •2010 Sendai Salmon Workshop on Climate Change (pp. 22-23) •2010 Sendai Zooplankton Workshop (pp. 24-25, 28) •2010 Sendai Workshop on “Networking across Global Marine Hotspots” (pp. 26-28) •The Ocean, Salmon, Ecology and Forecasting in 2010 (pp. 29, 44) •The State of the Northeast Pacific during the Winter of 2009/2010 (pp. 30-31) •The State of the Western North Pacific in the Second Half of 2009 (pp. 32-33) •The Bering Sea: Current Status and Recent Events (pp. 34-35, 39) •PICES Seafood Safety Project: Guatemala Training Program (pp. 36-39) •The Pacific Ocean Boundary Ecosystem and Climate Study (POBEX) (pp. 40-43) •PICES Calendar (p. 44)

PICES Press, Vol. 19, No. 1, Winter 2011

•2010 PICES Science: A Note from the Former Science Board Chairman (pp. 1-4) •2010 PICES Awards (pp. 5-7) •The First Year of FUTURE: A Progress Report (pp. 8-13) •New Chairmen in PICES (pp. 14-19) •Pacific Ocean Interior Carbon Data Synthesis, PACIFICA, in Progress (pp. 20-23) •2011 PICES Calendar (p. 23) •Ecosystems 2010: Global Progress on Ecosystem-based Fisheries Management (pp. 24-26) •PICES 2010 Rapid Assessment Survey (pp. 27-29) •PICES Workshop on “An Introduction to Rapid Assessment Survey Methodologies for Application in Developing Countries” (pp. 30-31) •The State of the Western North Pacific in the First Half of 2010 (pp. 32-34) •PICES Interns (p. 34) •The State of the Bering Sea in 2010 (pp. 35-37) •The State of the Northeast Pacific in 2010 (pp. 38-40)

PICES Press, Vol. 19, No. 2, Summer 2011

•The 2011 Inter-sessional Science Board Meeting: A Note from Science Board Chairman (pp. 1-4) •Indicators for Status and Change within North Pacific Marine Ecosystems: A FUTURE Workshop (pp. 5-8) •PICES Calendar (p. 8) •2011 ESSAS Open Science Meeting (pp. 9-13) •The 5th Zooplankton Production Symposium (pp. 14-17) •Workshop on "Individual-Based Models of Zooplankton” (pp. 18-21) •New Book Release on the 100th Anniversary of the T/S Osharu Maru (p. 21) •Workshop on “Advances in Genomic and Molecular Studies of Zooplankton” (pp. 22-24) •Workshop on “Updates and Comparisons of Zooplankton Time Series” (pp. 25-27) •Workshop on “Impacts of Ocean Acidification on Zooplankton” (pp. 28-29) •Workshop on “Automated Visual Plankton Identification” (p. 30) •Professor Plum in the Dining Room with a Knife (p. 31) •PICES and ICES on the River Elbe (p. 32) •The State of the Western North Pacific in the Second Half of 2010 (pp. 33-34) •The Bering Sea: Current Status and Recent Events (pp. 35-37) •Northeast Pacific News (pp. 38-39) •PICES Advice on Marine Ecology at a Canadian Judicial Inquiry (p. 40)

PICES Press, Vol. 21, No. 1, Winter 2013

•2012 PICES Science: A Note from the Science Board Chairman (pp. 1-6) ◾2012 PICES Awards (pp. 7-9) ◾GLOBEC/PICES/ICES ECOFOR Workshop (pp. 10-15) ◾ICES/PICES Symposium on “Forage Fish Interactions” (pp. 16-18) ◾The Yeosu Declaration, the Yeosu Declaration Forum and the Yeosu Project (pp. 19-23) ◾2013 PICES Calendar (p. 23) ◾Why Do We Need Human Dimensions for the FUTURE Program? (pp. 24-25) ◾New PICES MAFF-Sponsored Project on “Marine Ecosystem Health and Human Well-Being” (pp. 26-28) ◾The Bering Sea: Current Status and Recent Trends (pp. 29-31) ◾Continuing Cool in the Northeast Pacific Ocean (pp. 32, 35) ◾The State of the Western North Pacific in the First Half of 2012 (pp. 33-35) ◾New Leadership in PICES (pp. 36-39)

PICES Press, Vol. 16, No. 1, January 2008

◾PICES Science in 2007 (pdf, 0.1 Mb) ◾2007 Wooster Award (pdf, 0.1 Mb) ◾FUTURE - A milestone reached but our task is not done (pdf, < 0.1 Mb) ◾International symposium on "Reproductive and Recruitment Processes of Exploited Marine Fish Stocks" (pdf, 0.1 Mb) ◾Recent results of the micronekton sampling inter-calibration experiment (pdf, 0.1 Mb) ◾2007 PICES workshop on "Measuring and monitoring primary productivity in the North Pacific" (pdf, 0.1 Mb) ◾2007 Harmful Algal Bloom Section annual workshop events (pdf, 0.1 Mb) ◾A global approach for recovery and sustainability of marine resources in Large Marine Ecosystems (pdf, 0.3 Mb) ◾Highlights of the PICES Sixteenth Annual Meeting (pdf, 0.4 Mb) ◾Ocean acidification of the North Pacific Ocean (pdf, 0.3 Mb) ◾Workshop on NE Pacific Coastal Ecosystems (2008 Call for Salmon Survival Forecasts) (pdf, 0.1 Mb) ◾The state of the western North Pacific in the first half of 2007 (pdf, 0.4 Mb) ◾PICES Calendar (pdf, 0.4 Mb) ◾The Bering Sea: Current status and recent events (pdf, 0.3 Mb) ◾PICES Interns (pdf, 0.3 Mb) ◾Recent trends in waters of the subarctic NE Pacific (pdf, 0.3 Mb) ◾Election results at PICES (pdf, 0.2 Mb) ◾A new PICES award for monitoring and data management activities (pdf, < 0.1 Mb)

Climatic indicators in an ice core from the Yukon [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): Stable isotope data obtained from snow and ice cores retrieved from an altitude of 5340m on Mt. Logan (60°30'N; 140°36'W) indicate that "isotopic seasons" are not generally in phase with calendar seasons. The former are phase lagged with respect to the latter by up to several months and appear to be correlated with SST'S and ocean heat transfer curves and/or the position of the Aleutian low rather than with air temperature or the temperature difference between the ocean surface and the core site.

2007 biennial report to Congress on the progress and findings of studies of striped bass populations

The 1997 reauthorization of the Atlantic Striped Bass Conservation Act (Striped Bass Act) mandated biennial reports to Congress and to the Atlantic States Marine Fisheries Commission (Commission) from the secretaries of the Department of Commerce and the Department of the Interior concerning the progress and findings of studies of Atlantic striped bass (Morone saxatilis). The Striped Bass Act specifically requests updates on studies that include, but are not limited to: annual stock assessments, investigations on the causes of fluctuations in Atlantic striped bass populations, the effects of environmental factors on the recruitment, spawning potential, mortality, and abundance of Atlantic striped bass populations, and investigations of interactions between Atlantic striped bass and other fish. This document is the fifth such report to Congress and includes data available through 2007 with emphasis on the 2005 and 2006 calendar years.

The biology and ecology of the invasive Indo-Pacific lionfish

The Indo-Pacific lionfishes, Pterois miles and P. volitans, are now established along the Southeast U.S. and Caribbean and are expected to expand into the Gulf of Mexico and Central and South America. Prior to this invasion little was known regarding the biology and ecology of these lionfishes. I provide a synopsis of chronology, taxonomy, local abundance, reproduction, early life history and dispersal, venomology, feeding ecology, parasitology, potential impacts, and possible control and management strategies for the lionfish invasion. This information was collected by review of the literature and by direct field and experimental study. I confirm the existence of an unusual supraocular tentacle phenotype and suggest that the high prevalence of this phenotype in the Atlantic is not the result of selection, but likely ontogenetic change. To describe the trophic impacts of lionfish, I report a comprehensive assessment of diet that describes lionfish as a generalist piscivore that preys on over 40 species of teleost comprising more than 20 families. Next, I use the histology of gonads to describe both oogenesis and reproductive dynamics of lionfish. Lionfish mature relatively early and reproduce several times per month throughout the entire calendar year off North Carolina and the Bahamas. To investigate predation, an important component of natural mortality, I assessed the vulnerability of juvenile lionfish to predation by native serranids. Juvenile lionfish are not readily consumed by serranids, even after extreme periods of starvation. Last, I used a stage-based, matrix population model to estimate the scale of control that would be needed to reduce an invading population of lionfish. Together, this research provides the first comprehensive assessment on lionfish biology and ecology and explains a number of life history and ecological interactions that have facilitated the unprecedented and rapid establishment of this invasive finfish. Future research is needed to understand the scale of impacts that lionfish could cause, especially in coral reef ecosystems, which are already heavily stressed. This research further demonstrates the need for lionfish control strategies and more rigorous prevention and early detection and rapid response programs for marine non-native introductions.

Rice-fish culture: status and potential for increased production in the southwestern states of India

The scope of increasing production through rice-fish integration, suitable for coastal districts of Kerala, Karnataka, Goa and Maharashtra, is reviewed. The method of adopting the lowlying freshwater rice fields to raise 2 rice crops along with 4-species fish culture, followed by a third non-cereal summer crop in a year, is discussed. A calendar of operation and economics of the system are presented.

Annual Report of the Game and Fisheries Department for the period Ist July, 1957 to 30th June, 1958

This report follows the now established practice of covering the financial year although, as before, for the sake of continuity and accuracy many of the statistics refer to the calendar year. This year has again been an outstanding one in the field of research on wildlife conservation problems, and culminated in one of the largest short-term biological projects yet carried out in the Protectorate. The latter involved the removal by shooting of nearly 500 hippo from badly over-grazed areas in the Queen Elizabeth National Park, but every carcass was examined by a team of scientists, a variety of scientific data collected, and the meat disposed of for local consumption. Not one animal was wasted.

Annual Report of the Game and Fisheries Department for the period 1st July 1956 to 30th June, 1957

This report continues to cover the period of the financial year. Although, as before, for the sake of continuity and accuracy many of the statistics refer to the calendar year. The year has been notable in particular for the launching of extensive research projects on wild-life conservation problems, and much progress has already been made. This has been rendered possible by the greatly appreciated help and interest of the Fulbright Commission, who arranged for three experienced American wild-life scientists to work on these problems in Uganda. The latter have been working in conjunction with The Game and Fisheries Department's Biologist, as a team under the general Direction of the recently created Fauna Research Committee.

Technical report on the environmental monitoring of the cage area at the Source of the Nile (SON) Fish Farm for quarter 1: January-March 2015

Source of the Nile (SON) fish farm is located at Bugungu in Napoleon Gulf, northern Lake Victoria. The proprietors of the farm have a collaborative arrangement with NaFIRRI, a lead agency in fisheries research and innovations, to undertake quarterly environment monitoring surveys at the farm. The agreed areas for monitoring are: selected physico-chemical parameters (i.e. temperature, dissolved oxygen, pH, conductivity, secchi depth); total suspended solids (TSS); nutrient status; BOD5) and biological parameters (i.e. algae, zooplankton, macro-benthos and fish). Water and biological samples as well as field measurements were taken at 3 sites: within the fish cage rows (WIC/experimental), upstream (USC/control) and downstream (DSC) of the fish cages. The key research question was: Does fish cage operations have impacts on the water quality and aquatic biota in and around the SON cage fish farm? The environment monitoring surveys were projected to cover a full calendar year (i.e. from January to December). The first surveys were undertaken in 2011 and have continued on an annual basis since then. The present report presents field observations made for the fourth quarter survey undertaken in November 2014 and provides a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and the different aquatic biota in and around the fish cage site.