Stochastic modeling of bacterial protein domains distribution to predict horizontal gene transfer

In questo elaborato, abbiamo tentato di modellizzare i processi che regolano la presenza dei domini proteici. I domini proteici studiati in questa tesi sono stati ottenuti dai genomi batterici disponibili nei data base pubblici (principalmente dal National Centre for Biotechnology Information: NCBI) tramite una procedura di simulazione computazionale. Ci siamo concentrati su organismi batterici in quanto in essi la presenza di geni trasmessi orizzontalmente, ossia che parte del materiale genetico non provenga dai genitori, e assodato che sia presente in una maggiore percentuale rispetto agli organismi più evoluti. Il modello usato si basa sui processi stocastici di nascita e morte, con l'aggiunta di un parametro di migrazione, usato anche nella descrizione dell'abbondanza relativa delle specie in ambito delle biodiversità ecologiche. Le relazioni tra i parametri, calcolati come migliori stime di una distribuzione binomiale negativa rinormalizzata e adattata agli istogrammi sperimentali, ci induce ad ipotizzare che le famiglie batteriche caratterizzate da un basso valore numerico del parametro di immigrazione abbiano contrastato questo deficit con un elevato valore del tasso di nascita. Al contrario, ipotizziamo che le famiglie con un tasso di nascita relativamente basso si siano adattate, e in conseguenza, mostrano un elevato valore del parametro di migrazione. Inoltre riteniamo che il parametro di migrazione sia direttamente proporzionale alla quantità di trasferimento genico orizzontale effettuato dalla famiglia batterica.

A Nonstationary Negative Binomial Time Series with Time-Dependent Covariates: Enterococcus Counts in Boston Harbor

Boston Harbor has had a history of poor water quality, including contamination by enteric pathogens. We conduct a statistical analysis of data collected by the Massachusetts Water Resources Authority (MWRA) between 1996 and 2002 to evaluate the effects of court-mandated improvements in sewage treatment. Motivated by the ineffectiveness of standard Poisson mixture models and their zero-inflated counterparts, we propose a new negative binomial model for time series of Enterococcus counts in Boston Harbor, where nonstationarity and autocorrelation are modeled using a nonparametric smooth function of time in the predictor. Without further restrictions, this function is not identifiable in the presence of time-dependent covariates; consequently we use a basis orthogonal to the space spanned by the covariates and use penalized quasi-likelihood (PQL) for estimation. We conclude that Enterococcus counts were greatly reduced near the Nut Island Treatment Plant (NITP) outfalls following the transfer of wastewaters from NITP to the Deer Island Treatment Plant (DITP) and that the transfer of wastewaters from Boston Harbor to the offshore diffusers in Massachusetts Bay reduced the Enterococcus counts near the DITP outfalls.

Statnote 39: The binomial distribution: comparing two proportions

Many populations consist of two classes only, e.g., alive or dead, present or absent, clean or dirty, infected or non-infected, and it is the proportion or percentage of observations that fall into one of these classes that is of interest to an investigator. An observation that falls into one of the two classes is considered a ‘success’ (S), and ‘p’ is defined as the proportion of observations falling into that class. If a random sample of size ‘n’ is obtained from a population, the probability of obtaining 0, 1, 2, 3, etc., successes is then given by the binomial distribution. The binomial distribution can be used as the basis of a number of statistical tests but is most useful when comparing two proportions. This statnote describes two such scenarios in which the binomial distribution is used to compare: (1) two proportions when the samples are independent and (2) two proportions when the samples are paired.

Co-Infestation and Spatial Distribution of Bactrocera carambolae and Anastrepha spp. (Diptera: Tephritidae) in Common Guava in the Eastern Amazon.

Field infestation and spatial distribution of introduced Bactrocera carambolae Drew and Hancock and native species of Anastrepha in common guavas [Psidium guajava (L.)] were investigated in the eastern Amazon. Fruit sampling was carried out in the municipalities of Calc¸oene and Oiapoque in the state of Amapa, Brazil. The frequency distribution of larvae in fruit was fitted to the negative binomial distribution. Anastrepha striata was more abundant in both sampled areas in comparison to Anastrepha fraterculus (Wiedemann) and B. carambolae. The frequency distribution analysis of adults revealed an aggregated pattern for B. carambolae as well as for A. fraterculus and Anastrepha striata Schiner, described by the negative binomial distribution. Although the populations of Anastrepha spp. may have suffered some impact due to the presence of B. carambolae, the results are still not robust enough to indicate effective reduction in the abundance of Anastrepha spp. caused by B. carambolae in a general sense. The high degree of aggregation observed for both species suggests interspecific co-occurrence with the simultaneous presence of both species in the analysed fruit. Moreover, a significant fraction of uninfested guavas also indicated absence of competitive displacement.

Poisson, Poisson-gamma and zero-inflated regression models of motor vehicle crashes: balancing statistical fit and theory

There has been considerable research conducted over the last 20 years focused on predicting motor vehicle crashes on transportation facilities. The range of statistical models commonly applied includes binomial, Poisson, Poisson-gamma (or negative binomial), zero-inflated Poisson and negative binomial models (ZIP and ZINB), and multinomial probability models. Given the range of possible modeling approaches and the host of assumptions with each modeling approach, making an intelligent choice for modeling motor vehicle crash data is difficult. There is little discussion in the literature comparing different statistical modeling approaches, identifying which statistical models are most appropriate for modeling crash data, and providing a strong justification from basic crash principles. In the recent literature, it has been suggested that the motor vehicle crash process can successfully be modeled by assuming a dual-state data-generating process, which implies that entities (e.g., intersections, road segments, pedestrian crossings, etc.) exist in one of two states—perfectly safe and unsafe. As a result, the ZIP and ZINB are two models that have been applied to account for the preponderance of “excess” zeros frequently observed in crash count data. The objective of this study is to provide defensible guidance on how to appropriate model crash data. We first examine the motor vehicle crash process using theoretical principles and a basic understanding of the crash process. It is shown that the fundamental crash process follows a Bernoulli trial with unequal probability of independent events, also known as Poisson trials. We examine the evolution of statistical models as they apply to the motor vehicle crash process, and indicate how well they statistically approximate the crash process. We also present the theory behind dual-state process count models, and note why they have become popular for modeling crash data. A simulation experiment is then conducted to demonstrate how crash data give rise to “excess” zeros frequently observed in crash data. It is shown that the Poisson and other mixed probabilistic structures are approximations assumed for modeling the motor vehicle crash process. Furthermore, it is demonstrated that under certain (fairly common) circumstances excess zeros are observed—and that these circumstances arise from low exposure and/or inappropriate selection of time/space scales and not an underlying dual state process. In conclusion, carefully selecting the time/space scales for analysis, including an improved set of explanatory variables and/or unobserved heterogeneity effects in count regression models, or applying small-area statistical methods (observations with low exposure) represent the most defensible modeling approaches for datasets with a preponderance of zeros

Using simulation techniques to investigate methods to determine resistance of helminths to anthelmintic treatment

The widespread and increasing resistance of internal parasites to anthelmintic control is a serious problem for the Australian sheep and wool industry. As part of control programmes, laboratories use the Faecal Egg Count Reduction Test (FECRT) to determine resistance to anthelmintics. It is important to have confidence in the measure of resistance, not only for the producer planning a drenching programme but also for companies investigating the efficacy of their products. The determination of resistance and corresponding confidence limits as given in anthelmintic efficacy guidelines of the Standing Committee on Agriculture (SCA) is based on a number of assumptions. This study evaluated the appropriateness of these assumptions for typical data and compared the effectiveness of the standard FECRT procedure with the effectiveness of alternative procedures. Several sets of historical experimental data from sheep and goats were analysed to determine that a negative binomial distribution was a more appropriate distribution to describe pre-treatment helminth egg counts in faeces than a normal distribution. Simulated egg counts for control animals were generated stochastically from negative binomial distributions and those for treated animals from negative binomial and binomial distributions. Three methods for determining resistance when percent reduction is based on arithmetic means were applied. The first was that advocated in the SCA guidelines, the second similar to the first but basing the variance estimates on negative binomial distributions, and the third using Wadley’s method with the distribution of the response variate assumed negative binomial and a logit link transformation. These were also compared with a fourth method recommended by the International Co-operation on Harmonisation of Technical Requirements for Registration of Veterinary Medicinal Products (VICH) programme, in which percent reduction is based on the geometric means. A wide selection of parameters was investigated and for each set 1000 simulations run. Percent reduction and confidence limits were then calculated for the methods, together with the number of times in each set of 1000 simulations the theoretical percent reduction fell within the estimated confidence limits and the number of times resistance would have been said to occur. These simulations provide the basis for setting conditions under which the methods could be recommended. The authors show that given the distribution of helminth egg counts found in Queensland flocks, the method based on arithmetic not geometric means should be used and suggest that resistance be redefined as occurring when the upper level of percent reduction is less than 95%. At least ten animals per group are required in most circumstances, though even 20 may be insufficient where effectiveness of the product is close to the cut off point for defining resistance.

Catch rates and demographics of loggerhead sea turtles (Caretta caretta) captured from the Charleston, South Carolina, shipping channel during the period of mandatory use of turtle excluder devices (TEDs)

Trawling was conducted in the Charleston, South Carolina, shipping channel between May and August during 2004–07 to evaluate loggerhead sea turtle (Caretta caretta) catch rates and demographic distributions. Two hundred and twenty individual loggerheads were captured in 432 trawling events during eight sampling periods lasting 2–10 days each. Catch was analyzed by using a generalized linear model. Data were fitted to a negative binomial distribution with the log of standardized sampling effort (i.e., an hour of sampling with a net head rope length standardized to 30.5 m) for each event treated as an offset term. Among 21 variables, factors, and interactions, five terms were significant in the final model, which accounted for 45% of model deviance. Highly significant differences in catch were noted among sampling periods and sampling locations within the channel, with greatest catch furthest seaward consistent with historical observations. Loggerhead sea turtle catch rates in 2004–07 were greater than in 1991–92 when mandatory use of turtle excluder devices was beginning to be phased in. Concurrent with increased catch rates, loggerheads captured in 2004–07 were larger than in 1991–92. Eighty-five percent of loggerheads captured were ≤75.0 cm straight-line carapace length (nuchal notch to tip of carapace) and there was a 3.9:1 female-to-male bias, consistent with limited data for this location two decades earlier. Only juvenile loggerheads ≤75.0 cm possessed haplotypes other than CC-A01 or CC-A02 that dominate in the region. Six rare and one un-described haplotype were predominantly found in June 2004.

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.

Age-period-cohort effects in the incidence of hip fractures: political and economic events are coincident with changes in risk

Introduction: Healthcare improvements have allowed prevention but have also increased life expectancy, resulting in more people being at risk. Our aim was to analyse the separate effects of age, period and cohort on incidence rates by sex in Portugal, 2000–2008. Methods: From the National Hospital Discharge Register, we selected admissions (aged ≥49 years) with hip fractures (ICD9-CM, codes 820.x) caused by low/moderate trauma (falls from standing height or less), readmissions and bone cancer cases. We calculated person-years at risk using population data from Statistics Portugal. To identify period and cohort effects for all ages, we used an age–period–cohort model (1-year intervals) followed by generalised additive models with a negative binomial distribution of the observed incidence rates of hip fractures. Results: There were 77,083 hospital admissions (77.4 % women). Incidence rates increased exponentially with age for both sexes (age effect). Incidence rates fell after 2004 for women and were random for men (period effect). There was a general cohort effect similar in both sexes; risk of hip fracture altered from an increasing trend for those born before 1930 to a decreasing trend following that year. Risk alterations (not statistically significant) coincident with major political and economic change in the history of Portugal were observed around birth cohorts 1920 (stable–increasing), 1940 (decreasing–increasing) and 1950 (increasing–decreasing only among women). Conclusions: Hip fracture risk was higher for those born during major economically/politically unstable periods. Although bone quality reflects lifetime exposure, conditions at birth may determine future risk for hip fractures.

On the clustering of winter storm loss events over Germany

During the last decades, several windstorm series hit Europe leading to large aggregated losses. Such storm series are examples of serial clustering of extreme cyclones, presenting a considerable risk for the insurance industry. Clustering of events and return periods of storm series for Germany are quantified based on potential losses using empirical models. Two reanalysis data sets and observations from German weather stations are considered for 30 winters. Histograms of events exceeding selected return levels (1-, 2- and 5-year) are derived. Return periods of historical storm series are estimated based on the Poisson and the negative binomial distributions. Over 4000 years of general circulation model (GCM) simulations forced with current climate conditions are analysed to provide a better assessment of historical return periods. Estimations differ between distributions, for example 40 to 65 years for the 1990 series. For such less frequent series, estimates obtained with the Poisson distribution clearly deviate from empirical data. The negative binomial distribution provides better estimates, even though a sensitivity to return level and data set is identified. The consideration of GCM data permits a strong reduction of uncertainties. The present results support the importance of considering explicitly clustering of losses for an adequate risk assessment for economical applications.

A flexible model for survival data with a cure rate: a Bayesian approach

In this paper we deal with a Bayesian analysis for right-censored survival data suitable for populations with a cure rate. We consider a cure rate model based on the negative binomial distribution, encompassing as a special case the promotion time cure model. Bayesian analysis is based on Markov chain Monte Carlo (MCMC) methods. We also present some discussion on model selection and an illustration with a real dataset.

A hands-on approach for fitting long-term survival models under the GAMLSS framework

In many data sets from clinical studies there are patients insusceptible to the occurrence of the event of interest. Survival models which ignore this fact are generally inadequate. The main goal of this paper is to describe an application of the generalized additive models for location, scale, and shape (GAMLSS) framework to the fitting of long-term survival models. in this work the number of competing causes of the event of interest follows the negative binomial distribution. In this way, some well known models found in the literature are characterized as particular cases of our proposal. The model is conveniently parameterized in terms of the cured fraction, which is then linked to covariates. We explore the use of the gamlss package in R as a powerful tool for inference in long-term survival models. The procedure is illustrated with a numerical example. (C) 2009 Elsevier Ireland Ltd. All rights reserved.