Evaluation of a Pound Net Leader Designed to Reduce Sea Turtle Bycatch

Offshore pound net leaders in the southern portion of Chesapeake Bay in Virginia waters were documented to incidentally take protected loggerhead, Caretta caretta, and Kemp’s ridley, Lepidochelys kempii, sea turtles. Because of these losses, NOAA’s National Marine Fisheries Service (NMFS) in 2004 closed the area to offshore pound net leaders annually from 6 May to 15 July and initiated a study of an experimental leader design that replaced the top two-thirds of the traditional mesh panel leader with vertical ropes (0.95 cm) spaced 61 cm apart. This experimental leader was tested on four pound net sites on the eastern shore of Chesapeake Bay in 2004 and 2005. During the 2 trial periods, 21 loggerhead and Kemp’s ridley sea turtles were found interacting with the control leader and 1 leatherback turtle, Dermochelys coriacea, was found interacting with the experimental leader. Results of a negative binomial regression analysis comparing the two leader designs found the experimental leader significantly reduced sea turtle interactions (p=0.03). Finfish were sampled from the pound nets in the study to assess finfish catch performance differences between the two leader designs. Although the conclusions from this element of the experiment are not robust, paired t-test and Wilcoxon signed rank test results determined no significant harvest weight difference between the two leaders. Kolmogorov-Smirnov tests did not reveal any substantive size selectivity differences between the two leaders.

Mortalities induced by the copepod Sinergasilus polycolpus in farmed silver and bighead carp in a reservoir

The frequency distributions of the parasitic copepod Sinergasilus polycolpus were examined in silver carp Hypophthalmichthys molitrix and bighead carp Aristichthys nobilis during a disease outbreak of the 2 species of fish in a reservoir in China. The mean abundance of the copepod was positively related with host length and age, and the overdispersion of the copepod in both silver and bighead carp was fitted well with negative binomial distribution. Although parasite-induced host mortality was observed, a peaked age-parasite abundance curve was not detected in the present parasite-host system. It is also proposed that this peaked age-abundance curve is unlikely to be observed in its natural host populations.

Seasonal population dynamics of parasitic copepods, Sinergasilus spp. on farmed fish in China

Seasonal population dynamics of parasitic copepods in the genus Sinergasilus on fanned silver carp Hypophthalmichthys molitrix, farmed bighead carp Aristichthys nobilis, and grass carp Ctenopharyngodon idellus were investigated in China. Changes in prevalence and abundance were seasonal with higher levels observed in summer. Reproduction of the copepods occurs from spring to early autumn as indicated by the higher ratio of gravid copepods. The frequency distribution of Sinergasilus polycolpus and S. major in their host populations can be fitted well with negative binomial distribution. (C) 2000 Elsevier Science B.V. All rights reserved.

西藏齿突蟾蝌蚪冷适应策略研究

本文通过对高海拔两栖类西藏齿突蟾(Scutiger boulengeri)蝌蚪在实验室特定低温条件下的冷适应微空间行为分布的动态变化分析、温度耐受性实验及在不同适应温度的乳酸脱氢酶(LDH)同工酶的酶量与活性比较分析, 探讨了高海拔两栖类蝌蚪的部分冷适应策略。 西藏齿突蟾蝌蚪在不同温度的行为分布是一连续、动态过程，需用多种检验方法综合利用才能进行判断；在15℃, 除低海拔分布的西藏齿突蟾种群外所有实验物种蝌蚪均符合负二项分布、NeymanⅡ型分布；在10℃, 高海拔两栖类蝌蚪均符合负二项分布、NeymanⅡ型分布；在5℃、0℃低温时，高海拔两栖类不同分组的西藏齿突蟾蝌蚪的负二项分布、NeymanⅡ型分布均呈现明显差异, 这可能与高海拔两栖类蝌蚪在低温条件下通过不断地改变其行为分布方式来避免自身被冻伤有关。野外观察表明：高海拔两栖类蝌蚪常选择与流动河水相连的静水水体这种微生境中生存, 蝌蚪应对环境温度极端变化会不断改变其行为分布方式来选择最佳生存温度以避免极端高、低温对自身身体的伤害, 这种对微生境的利用能力对高海拔两栖类蝌蚪耐受极端环境温度的变化极其重要。 两栖类蝌蚪的温度耐受性实验表明不同的驯化温度可以改变西藏齿突蟾蝌蚪、两栖类仙琴水蛙蝌蚪的最适温度、逃避温度，并具有显著影响。 随着驯化温度5℃、10℃逐渐升高, 其最适温度、逃避温度也在一定范围内升高，但驯化温度对低海拔的仙琴水蛙蝌蚪的最适温度、逃避温度的改变效应大于高海拔的西藏齿突蟾蝌蚪的改变效应, 仙琴水蛙蝌蚪对温度的耐受范围、最适温度和逃避温度的ARRS值都大于西藏齿突蟾蝌蚪, 这说明仙琴水蛙蝌蚪对环境温度变化的适应能力大于西藏齿突蟾蝌蚪。 高海拔地区不同分组的两栖类蝌蚪, 在0℃适应温度时, LDH5条带的酶相对含量最高，而在5℃、10℃、15℃适应温度时，LDH5条带的酶相对含量明显都降低, 这表明酵解作用是高海拔两栖类蝌蚪的一些组织在低温﹑缺氧环境中的重要供能方式。高海拔两栖类蝌蚪同一分组的LDH总酶活性总是表现为10℃适应温度的总酶活性最高，而对低海拔的两栖类蝌蚪则是0℃适应温度的总酶活性最高, 这说明高海拔两栖类蝌蚪的LDH同工酶A、B两亚基基因活性在10℃时最高, 而低海拔两栖类蝌蚪的LDH同工酶A、B两亚基基因活性在0℃时最高。同时发现在15℃适应温度组的高海拔两栖类蝌蚪的LDH电泳图谱都有第6条带,有可能由LDH - C亚基组成, 对高海拔两栖类蝌蚪的LDH - C亚基只在15℃适应温度下才表达的机理还有待进一步的研究。 高海拔两栖类西藏齿突蟾蝌蚪通过行为分布方式的改变来选择最佳的生存温度, 这种温度选择过程与野外特定的微生境的存在密切相关, 现在由于人类对河道的不合理利用正在导致高海拔两栖类蝌蚪赖以生存的这种微生境逐渐消失, 这种微生境的消失将加速高海拔的两栖类种群数量衰退的进程。高海拔两栖类物种蝌蚪在低温（0℃）上表现出的同工酶多谱带说明，其A、B两亚基都有所表达，及其参与代谢的方式也是正常的，而低海拔两栖类物种蝌蚪只有A亚基表达的LDH5存在，因此其主要参与酵解过程，这种通过动物自身生理代谢方式的改变来适应极端环境温度条件的变化是高海拔两栖类蝌蚪能适应低温环境的重要策略。但高海拔物种的适应温度变化范围显著小于低海拔物种，对环境温度的变化适应能力有限，特别是对高温区域，因此全球气候变化可能对高海拔物种影响更为显著。 The partly cold-adaptation stratagem of the high altitude amphibian tadpole were researched in the laboratory by analyzing the high altitude amphibian tadpole of Scutiger boulengeri mainly on endpoints related to the dynamic variation of the micro-spatial behavior distribution patterns, the experiment of the temperature tolerance, and the enzyme content and activity of the lactic acid dehydrogenase(LDH) isozyme in special temperature condition. The behavior distribution of the Scutiger boulengeri tadpole is continuous and variable, but it can be figured out by multple testing ways. At 15℃, all of the experiment amphibian tadpoles behavior distribution fit both for the negative binomial distribution and NeymanⅡtype distribution except for the low altitude Scutiger boulengeri tadpoles. At 10℃, all of the high altitude amphibian tadpoles behavior distribution fit both for the negative binomial distribution and NeymanⅡtype distribution. At lower temperature, 5℃ and 0℃, the high altitude amphibian tadpoles of the Scutiger boulengeri at different groups behavior distribution fit for or don’t fit for behavior distribution respectively. It is denoted that the high altitude amphibian tadpoles probably avoid frostbiting by varying the behavior distribution patterns at low temperature condition. The high altitude amphibian tadpoles often actively select the special microhabitat which has the connected still water body and the flowing water body in the wild. It is important that tadpoles can endure the extreme temperature variety in this kind of microhabitat, because tadpoles can be better survival through select temperature condition through migrating in these kinds of microhabitats by varying their own behavior distribution patterns. Different acclimation temperature causes the significant change of preferred temperature(PT)、 avoiding temperature(AT) both in high altitude amphibian Scutiger boulengeri tadpoles and in low altitude amphibian Rana daunchina tadpoles in the temperature endurance experiment. With the acclimation temperature growing from 5℃ to 10℃. the PT and the AT of them would be uprise to some extent, but the effect of acclimation temperature on the PT and the AT of the tadpoles of Rana daunchina is more significant than the ones on the tadpoles of Scutiger boulengeri, at the same, the effects on the temperature endurance range, the ARRs of the tadpoles of Rana daunchina would be stronger than the ones on the tadpoles of Scutiger boulengeri. It is implied that the adaptation ability of tadpoles of Rana daunchina to the surroundings temperature alternation preferred to tadpoles of Scutiger boulengeri. At 0℃ acclimation temperature, the LDH5 enzyme comparative content of the high altitude amphibian tadpoles at different groups was highest, but it becomes lower at 5℃、10℃、15℃ acclimation temperature. It indicated that the alcoholysis role was the important ways of applying energy for special tissue of the high altitude amphibian tadpoles in low-temperature and low-oxygen condition. The total enzyme activity of the LDH of the high altitude amphibian tadpoles in the same group always keeps the highest at 10℃ acclimation temperature, but the low altitude amphibian tadpoles’ was maximum at 0℃. It was denoted that the gene activity of LDH -A and LDH – B submit was highest at 10℃ acclimation temperature for the high altitude amphibian tadpoles, but the low altitude amphibian tadpoles’ was maximum at 0℃. Meanwhile, the LDH electrophoretogram of the high altitude amphibian tadpoles always composed of 6 stripes at 15℃ acclimation temperature，the extra stripe probably was composed by LDH-C submit。It is unknown why LDH-C expresses only under high temperature。. The high altitude amphibian tadpoles can select the most optimal temperature by changing their behavior distribution patterns ceaselessly, but this course of selecting the most suitable temperature correlated with the special microhabitat in the wild closely. Nowadays, this kind of microhabitat which the high altitude amphibian tadpoles rely on are lossing gradually for human being exploit the riverway unreasonably. The disappearing of the microhabitat would accelerate the decline of the high altitude amphibian population. Compare to one band of LDH5, which only composed by the LDH-A submit, presents in the low altitude amphibian at 0℃, the five bands which composed by the LDH-A and LDH-B are checked out, this means the species which occurred in the highland is more adaptable to the low temperature. It is an important stratagem for the high altitude amphibian tadpoles adapt to the limited low temperature depends on the animal energy metabolism change.However, this kind of adaption is restricted, the adaption range to the temperature is much norrow in the high altitude amphibian than in the low one, especially for the high temperature side. The global climate change will be more serious for the high altitude species.

Risk of Several Cancers is Higher in Urban Areas after Adjusting for Socioeconomic Status. Results from a Two-Country Population-Based Study of 18 Common Cancers

Some studies suggest that there are urban-rural variations in cancer incidence but whether these simply reflect urban-rural socioeconomic variation is unclear. We investigated whether there were urban-rural variations in the incidence of 18 cancers, after adjusting for socioeconomic status. Cancers diagnosed between 1995 and 2007 were extracted from the population-based National Cancer Registry Ireland and Northern Ireland Cancer Registry and categorised by urban-rural status, based on population density of area of residence at diagnosis (rural 15 people per hectare). Relative risks (RR) were calculated by negative binomial regression, adjusting for age, country and three area-based markers of socioeconomic status. Risks were significantly higher in both sexes in urban than rural residents with head and neck (males RR urban vs. rural = 1.53, 95 % CI 1.42-1.64; females RR = 1.29, 95 % CI 1.15-1.45), esophageal (males 1.21, 1.11-1.31; females 1.21, 1.08-1.35), stomach (males 1.36, 1.27-1.46; females 1.19, 1.08-1.30), colorectal (males 1.14, 1.09-1.18; females 1.04, 1.00-1.09), lung (males 1.54, 1.47-1.61; females 1.74, 1.65-1.84), non-melanoma skin (males 1.13, 1.10-1.17; females 1.23, 1.19-1.27) and bladder (males 1.30, 1.21-1.39; females 1.31, 1.17-1.46) cancers. Risks of breast, cervical, kidney and brain cancer were significantly higher in females in urban areas. Prostate cancer risk was higher in rural areas (0.94, 0.90-0.97). Other cancers showed no significant urban-rural differences. After adjusting for socioeconomic variation, urban-rural differences were evident for 12 of 18 cancers. Variations in healthcare utilization and known risk factors likely explain some of the observed associations. Explanations for others are unclear and, in the interests of equity, warrant further investigation. © 2014 The New York Academy of Medicine.

mfx: Marginal Effects, Odds Ratios and Incidence Rate Ratios for GLMs

Estimates probit, logit, Poisson, negative binomial, and beta regression models, returning their marginal effects, odds ratios, or incidence rate ratios as an output.

Excess mortality in Type 1 diabetes diagnosed in childhood and adolescence: a systematic review of population-based cohorts

Aims: Systematic review of mortality in childhood-/adolescent-diagnosed Type 1 diabetes and examination of factors explaining the mortality variation between studies. 
Methods: Relevant studies were identified from systematic searches of MEDLINE and EMBASE. Observed and expected numbers of deaths were extracted, and standardised mortality ratios (SMRs) and 95 % confidence intervals (CIs) were calculated. Negative binomial regression was used to investigate association between mortality and study/country characteristics.
Results: Thirteen relevant publications with mortality data were identified describing 23 independent studies. SMRs varied markedly ranging from 0 to 854 (chi-squared = 70.68,df = 21, p<0.0001). Significant associations were observed between SMR and mid-year of follow-up [incidence rate ratio (IRR) 0.95, 95 % CI 0.91–0.99 equivalent to a 5 % decrease per year], between SMR and infant mortality rate (IRR 1.07, 95 % CI 1.02–1.12, a 7 % increase for each death per 1,000 live births) and, after omitting an outlier, between SMR and health expenditure as a percentage of gross domestic product (GDP) (IRR 0.79, 95 % CI 0.68–0.93, a 21 % decrease for each one percent increase in GDP). No relationship was detected between SMR and a country’s childhood diabetes incidence rate or GDP.
Conclusions: Excess mortality in childhood-/adolescent diagnosed Type 1 diabetes is apparent across countries worldwide. Excesses were less marked in more recent studies and in countries with lower infant mortality and higher health expenditure.

The potential utility of age, triage score, and disposition data contained in emergency department electronic records for influenza-like illness surveillance in Montreal

La surveillance de l’influenza s’appuie sur un large spectre de données, dont les données de surveillance syndromique provenant des salles d’urgences. De plus en plus de variables sont enregistrées dans les dossiers électroniques des urgences et mises à la disposition des équipes de surveillance. L’objectif principal de ce mémoire est d’évaluer l’utilité potentielle de l’âge, de la catégorie de triage et de l’orientation au départ de l’urgence pour améliorer la surveillance de la morbidité liée aux cas sévères d’influenza. Les données d’un sous-ensemble des hôpitaux de Montréal ont été utilisées, d’avril 2006 à janvier 2011. Les hospitalisations avec diagnostic de pneumonie ou influenza ont été utilisées comme mesure de la morbidité liée aux cas sévères d’influenza, et ont été modélisées par régression binomiale négative, en tenant compte des tendances séculaires et saisonnières. En comparaison avec les visites avec syndrome d’allure grippale (SAG) totales, les visites avec SAG stratifiées par âge, par catégorie de triage et par orientation de départ ont amélioré le modèle prédictif des hospitalisations avec pneumonie ou influenza. Avant d’intégrer ces variables dans le système de surveillance de Montréal, des étapes additionnelles sont suggérées, incluant l’optimisation de la définition du syndrome d’allure grippale à utiliser, la confirmation de la valeur de ces prédicteurs avec de nouvelles données et l’évaluation de leur utilité pratique.

Exam 1999

Exam and solutions in LaTex

Exam 1999 pdf

Exercises and solutions in PDF

MA348exam 1998

Exam questions and solutions in LaTex

MA348exam 1998 pdf

Exam questions and solutions in PDF

Asymptotic normality in mixtures of power series distributions

The problem of estimating the individual probabilities of a discrete distribution is considered. The true distribution of the independent observations is a mixture of a family of power series distributions. First, we ensure identifiability of the mixing distribution assuming mild conditions. Next, the mixing distribution is estimated by non-parametric maximum likelihood and an estimator for individual probabilities is obtained from the corresponding marginal mixture density. We establish asymptotic normality for the estimator of individual probabilities by showing that, under certain conditions, the difference between this estimator and the empirical proportions is asymptotically negligible. Our framework includes Poisson, negative binomial and logarithmic series as well as binomial mixture models. Simulations highlight the benefit in achieving normality when using the proposed marginal mixture density approach instead of the empirical one, especially for small sample sizes and/or when interest is in the tail areas. A real data example is given to illustrate the use of the methodology.

Extending the Lincoln–Petersen estimator for multiple identifications in one source

The Lincoln–Petersen estimator is one of the most popular estimators used in capture–recapture studies. It was developed for a sampling situation in which two sources independently identify members of a target population. For each of the two sources, it is determined if a unit of the target population is identified or not. This leads to a 2 × 2 table with frequencies f11, f10, f01, f00 indicating the number of units identified by both sources, by the first but not the second source, by the second but not the first source and not identified by any of the two sources, respectively. However, f00 is unobserved so that the 2 × 2 table is incomplete and the Lincoln–Petersen estimator provides an estimate for f00. In this paper, we consider a generalization of this situation for which one source provides not only a binary identification outcome but also a count outcome of how many times a unit has been identified. Using a truncated Poisson count model, truncating multiple identifications larger than two, we propose a maximum likelihood estimator of the Poisson parameter and, ultimately, of the population size. This estimator shows benefits, in comparison with Lincoln–Petersen’s, in terms of bias and efficiency. It is possible to test the homogeneity assumption that is not testable in the Lincoln–Petersen framework. The approach is applied to surveillance data on syphilis from Izmir, Turkey.