Nineteenth century narratives reveal historic catch rates for Australian snapper (Pagrus auratus)

Snapper (Pagrus auratus) is widely distributed throughout subtropical and temperate southern oceans and forms a significant recreational and commercial fishery in Queensland, Australia. Using data from government reports, media sources, popular publications and a government fisheries survey carried out in 1910, we compiled information on individual snapper fishing trips that took place prior to the commencement of fisherywide organized data collection, from 1871 to 1939. In addition to extracting all available quantitative data, we translated qualitative information into bounded estimates and used multiple imputation to handle missing values, forming 287 records for which catch rate (snapper fisher−1 h−1) could be derived. Uncertainty was handled through a parametric maximum likelihood framework (a transformed trivariate Gaussian), which facilitated statistical comparisons between data sources. No statistically significant differences in catch rates were found among media sources and the government fisheries survey. Catch rates remained stable throughout the time series, averaging 3.75 snapper fisher−1 h−1 (95% confidence interval, 3.42–4.09) as the fishery expanded into new grounds. In comparison, a contemporary (1993–2002) south-east Queensland charter fishery produced an average catch rate of 0.4 snapper fisher−1 h−1 (95% confidence interval, 0.31–0.58). These data illustrate the productivity of a fishery during its earliest years of development and represent the earliest catch rate data globally for this species. By adopting a formalized approach to address issues common to many historical records – missing data, a lack of quantitative information and reporting bias – our analysis demonstrates the potential for historical narratives to contribute to contemporary fisheries management.

STATISTICAL METHODS FOR ADVANCED ECONOMETRIC MODELS WITH APPLICATIONS TO VEHICLE HOLDING AND SPEED QUANTILES DISTRIBUTION

This dissertation proposes statistical methods to formulate, estimate and apply complex transportation models. Two main problems are part of the analyses conducted and presented in this dissertation. The first method solves an econometric problem and is concerned with the joint estimation of models that contain both discrete and continuous decision variables. The use of ordered models along with a regression is proposed and their effectiveness is evaluated with respect to unordered models. Procedure to calculate and optimize the log-likelihood functions of both discrete-continuous approaches are derived, and difficulties associated with the estimation of unordered models explained. Numerical approximation methods based on the Genz algortithm are implemented in order to solve the multidimensional integral associated with the unordered modeling structure. The problems deriving from the lack of smoothness of the probit model around the maximum of the log-likelihood function, which makes the optimization and the calculation of standard deviations very difficult, are carefully analyzed. A methodology to perform out-of-sample validation in the context of a joint model is proposed. Comprehensive numerical experiments have been conducted on both simulated and real data. In particular, the discrete-continuous models are estimated and applied to vehicle ownership and use models on data extracted from the 2009 National Household Travel Survey. The second part of this work offers a comprehensive statistical analysis of free-flow speed distribution; the method is applied to data collected on a sample of roads in Italy. A linear mixed model that includes speed quantiles in its predictors is estimated. Results show that there is no road effect in the analysis of free-flow speeds, which is particularly important for model transferability. A very general framework to predict random effects with few observations and incomplete access to model covariates is formulated and applied to predict the distribution of free-flow speed quantiles. The speed distribution of most road sections is successfully predicted; jack-knife estimates are calculated and used to explain why some sections are poorly predicted. Eventually, this work contributes to the literature in transportation modeling by proposing econometric model formulations for discrete-continuous variables, more efficient methods for the calculation of multivariate normal probabilities, and random effects models for free-flow speed estimation that takes into account the survey design. All methods are rigorously validated on both real and simulated data.

Modeling height-diameter relationship in pinus pinaster ait. in the forest intervention zone of Lomba, NE-Portugal

In this work, the relationship between diameter at breast height (d) and total height (h) of individual-tree was modeled with the aim to establish provisory height-diameter (h-d) equations for maritime pine (Pinus pinaster Ait.) stands in the Lomba ZIF, Northeast Portugal. Using data collected locally, several local and generalized h-d equations from the literature were tested and adaptations were also considered. Model fitting was conducted by using usual nonlinear least squares (nls) methods. The best local and generalized models selected, were also tested as mixed models applying a first-order conditional expectation (FOCE) approximation procedure and maximum likelihood methods to estimate fixed and random effects. For the calibration of the mixed models and in order to be consistent with the fitting procedure, the FOCE method was also used to test different sampling designs. The results showed that the local h-d equations with two parameters performed better than the analogous models with three parameters. However a unique set of parameter values for the local model can not be used to all maritime pine stands in Lomba ZIF and thus, a generalized model including covariates from the stand, in addition to d, was necessary to obtain an adequate predictive performance. No evident superiority of the generalized mixed model in comparison to the generalized model with nonlinear least squares parameters estimates was observed. On the other hand, in the case of the local model, the predictive performance greatly improved when random effects were included. The results showed that the mixed model based in the local h-d equation selected is a viable alternative for estimating h if variables from the stand are not available. Moreover, it was observed that it is possible to obtain an adequate calibrated response using only 2 to 5 additional h-d measurements in quantile (or random) trees from the distribution of d in the plot (stand). Balancing sampling effort, accuracy and straightforwardness in practical applications, the generalized model from nls fit is recommended. Examples of applications of the selected generalized equation to the forest management are presented, namely how to use it to complete missing information from forest inventory and also showing how such an equation can be incorporated in a stand-level decision support system that aims to optimize the forest management for the maximization of wood volume production in Lomba ZIF maritime pine stands.

Modelos linear e não linear em análises genéticas para sobrevivência de crias de ovinos da raça Santa Inês.

Resumo: Registros de sobrevivência do nascimento ao desmame de 3846 crias de ovinos da raça Santa Inês foram analisados por modelos de reprodutor linear e não linear (modelo de limiar), para estimar componentes de variância e herdabilidade. Os modelos usados para sobrevivência, analisada como característica da cria, incluíram os efeitos fixos de sexo, da combinação tipo de nascimento-criação da cria e da idade da ovelha ao parto, efeito da covariável peso da cria ao nascer e efeitos aleatórios de reprodutor, da classe rebanho-ano-estação e do resíduo. Componentes de variância para o modelo linear foram estimados pelo método da máxima verossimilhança restrita (REML) e para o modelo não linear por uma aproximação da máxima verossimilhança marginal (MML), pelo programa CMMAT2. O coeficiente de herdabilidade (h2) estimado pelo modelo de limiar foi de 0,29, e pelo modelo linear, 0,14. A correlação de ordem de Spearman entre as capacidades de transmissão dos reprodutores, com base nos dois modelos foi de 0,96. As estimativas de h2 obtidas indicam a possibilidade de se obter, por seleção, ganho genético para sobrevivência. [Linear and nonlinear models in genetic analyses of lamb survival in the Santa Inês hair sheep breed]. Abstract: Records of 3,846 lambs survival from birth to weaning of Santa Inês hair sheep breed, were analyzed by linear and non linear sire models (threshold model) to estimate variance components and heritability (h2). The models that were used to analyze survival, considered in this study as a lamb trait, included the fixed effects of sex of the lamb, combination of type of birth-rearing of lamb, and age of ewe, birth weight of lamb as covariate, and random effects of sire, herd-year-season and residual. Variance components were obtained using restricted maximum likelihood (REML), in linear model and marginal maximum likelihood in threshold model through CMMAT2 program. Estimate of heritability (h2) obtained by threshold model was 0.29 and by linear model was 0.14. Rank correlation of Spearman, between sire solutions based on the two models was 0.96. The obtained estimates in this study indicate that it is possible to acquire genetic gain to survival by selection.

Keeping Variables within Bounds: Using Information between Observations

This research develops an econometric framework to analyze time series processes with bounds. The framework is general enough that it can incorporate several different kinds of bounding information that constrain continuous-time stochastic processes between discretely-sampled observations. It applies to situations in which the process is known to remain within an interval between observations, by way of either a known constraint or through the observation of extreme realizations of the process. The main statistical technique employs the theory of maximum likelihood estimation. This approach leads to the development of the asymptotic distribution theory for the estimation of the parameters in bounded diffusion models. The results of this analysis present several implications for empirical research. The advantages are realized in the form of efficiency gains, bias reduction and in the flexibility of model specification. A bias arises in the presence of bounding information that is ignored, while it is mitigated within this framework. An efficiency gain arises, in the sense that the statistical methods make use of conditioning information, as revealed by the bounds. Further, the specification of an econometric model can be uncoupled from the restriction to the bounds, leaving the researcher free to model the process near the bound in a way that avoids bias from misspecification. One byproduct of the improvements in model specification is that the more precise model estimation exposes other sources of misspecification. Some processes reveal themselves to be unlikely candidates for a given diffusion model, once the observations are analyzed in combination with the bounding information. A closer inspection of the theoretical foundation behind diffusion models leads to a more general specification of the model. This approach is used to produce a set of algorithms to make the model computationally feasible and more widely applicable. Finally, the modeling framework is applied to a series of interest rates, which, for several years, have been constrained by the lower bound of zero. The estimates from a series of diffusion models suggest a substantial difference in estimation results between models that ignore bounds and the framework that takes bounding information into consideration.

Effect of inclusion or non-inclusion of short lactations and cow and/or dam genetic group on genetic evaluation of Girolando dairy cattle.

The objective of this study was to evaluate the effects of inclusion or non-inclusion of short lactations and cow (CGG) and/or dam (DGG) genetic group on the genetic evaluation of 305-day milk yield (MY305), age at first calving (AFC), and first calving interval (FCI) of Girolando cows. Covariance components were estimated by the restricted maximum likelihood method in an animal model of single trait analyses. The heritability estimates for MY305, AFC, and FCI ranged from 0.23 to 0.29, 0.40 to 0.44, and 0.13 to 0.14, respectively, when short lactations were not included, and from 0.23 to 0.28, 0.39 to 0.43, and 0.13 to 0.14, respectively, when short lactations were included. The inclusion of short lactations caused little variation in the variance components and heritability estimates of traits, but their non-inclusion resulted in the re-ranking of animals. Models with CGG or DGG fixed effects had higher heritability estimates for all traits compared with models that consider these two effects simultaneously. We recommend using the model with fixed effects of CGG and inclusion of short lactations for the genetic evaluation of Girolando cattle.

Mapeamento de semeaduras de soja (Glycine max (L.)Merr.) mediante dados MODIS/Terra E TM/Landsat 5: um comparativo

The objective of this work was to compare the soybean crop mapping in the western of Parana State by MODIS/Terra and TM/Landsat 5 images. Firstly, it was generated a soybean crop mask using six TM images covering the crop season, which was used as a reference. The images were submitted to Parallelepiped and Maximum Likelihood digital classification algorithms, followed by visual inspection. Four MODIS images, covering the vegetative peak, were classified using the Parallelepiped method. The quality assessment of MODIS and TM classification was carried out through an Error Matrix, considering 100 sample points between soybean or not soybean, randomly allocated in each of the eight municipalities within the study area. The results showed that both the Overall Classification (OC) and the Kappa Index (KI) have produced values ranging from 0.55 to 0.80, considered good to very good performances, either in TM or MODIS images. When OC and KI, from both sensors were compared, it wasn't found no statistical difference between them. The soybean mapping, using MODIS, has produced 70% of reliance in terms of users. The main conclusion is that the mapping of soybean by MODIS is feasible, with the advantage to have better temporal resolution than Landsat, and to be available on the internet, free of charge.

Maximum inhibitory dilution of mouthwashes containing chlorhexidine and polyhexamethylene biguanide against salivary staphylococcus aureus

OBJECTIVE: The aim of the present study was to determine the in vitro maximum inhibitory dilution (MID) of two chlorhexidinebased oral mouthwashes (CHX): Noplak®, Periogard®, and one polyhexamethylene biguanide-based mouthwash (PHMB): Sanifill Premium® against 28 field Staphylococcus aureus strains using the agar dilution method. MATERIALS AND METHODS: For each product, decimal dilutions ranging from 1/10 to 1/655,360 were prepared in distilled water and added to Mueller Hinton Agar culture medium. After homogenization, the culture medium was poured onto Petri dishes. Strains were inoculated using a Steers multipoint inoculator and dishes were incubated at 37ºC for 24hours. For reading, MID was considered as the maximum dilution of the mouthwash still capable of inhibiting microbial growth. RESULTS: Sanifill Premium® inhibited the growth of all strains at 1/40 dilution and of 1 strain at 1/80 dilution. Noplak® inhibited the growth of 23 strains at 1/640 dilution and of all 28 strains at 1/320 dilution. Periogard® showed inhibited growth of 7 strains at 1/640 dilution and of all 28 strains at 1/320 dilution. Data were submitted to Kruskal-Wallis statistical test, showing significant differences between the mouthwashes evaluated (p<0.05). No significant difference was found between Noplak® and Periogard® (p>0.05). Sanifill Premium® was the least effective (p<0.05). CONCLUSION: It was concluded that CHX-based mouthwashes present better antimicrobial activity against S. Aureus than the PHMB-based mouthwash.

Determination of the maximum inhibitory dilution of cetylpyridinium chloride-based mouthwashes against staphylococcus aureus: an in vitro study

The aim of this in vitro study was to determine the maximum inhibitory dilution (MID) of four cetylpyridinium chloride (CPC)-based mouthwashes: CPC+Propolis, CPC+Malva, CPC+Eucaliptol+Juá+Romã+Propolis (Natural Honey®) and CPC (Cepacol®), against 28 Staphylococcus aureus field strains, using the agar dilution method. Decimal dilutions ranging from 1/10 to 1/655,360 were prepared and added to Mueller Hinton Agar. Strains were inoculated using Steers multipoint inoculator. The inocula were seeded onto the surface of the culture medium in Petri dishes containing different dilutions of the mouthwashes. The dishes were incubated at 37ºC for 24 h. For readings, the MID was considered as the maximum dilution of mouthwash still capable of inhibiting microbial growth. The obtained data showed that CPC+Propolis had antimicrobial activity against 27 strains at 1/320 dilution and against all 28 strains at 1/160 dilution, CPC+Malva inhibited the growth of all 28 strains at 1/320 dilution, CPC+Eucaliptol+Juá+Romã+Propolis inhibited the growth of 2 strains at 1/640 dilution and all 28 strains at 1/320 dilution, and Cepacol® showed antimicrobial activity against 3 strains at 1/320 dilution and against all 28 strains at 1/160 dilution. Data were submitted to Kruskal-Wallis test, showing that the MID of Cepacol® was lower than that determined for the other products (p<0.05). In conclusion, CPC-mouthwashes showed antimicrobial activity against S. aureus and the addition of other substances to CPC improved its antimicrobial effect.

Inclusão da epistasia em modelo de avaliação genética de bovinos de corte compostos

Dados de bovinos compostos foram analisados para avaliar o efeito da epistasia nos modelos de avaliação genética. As características analisadas foram os pesos aos 205 (P205) e 390 dias (P390) e perímetro escrotal aos 390 dias (PE390). As análises foram realizadas pela metodologia de máxima verossimilhança considerando-se dois modelos: o modelo 1 incluiu como covariáveis os efeitos aditivos diretos e maternos, e os não aditivos das heterozigoses para os efeitos diretos e para o materno total, e o modelo 2 considerou também o efeito direto de epistasia. Para comparação dos modelos, foram utilizados o critério de informação de Akaike (AIC) e o critério de informação Bayesiano de Schwartz (BIC), e o teste de razão de verossimilhança. A inclusão da epistasia no modelo de avaliação genética pouco alterou as estimativas de componentes de (co)variâncias genéticas aditivas e, consequentemente, as herdabilidades. O teste de verossimilhança e o critério de Akaike sugeriram que o modelo 2, que inclui a epistasia, apresentou maior aderência aos dados para todas as características analisadas. O critério BIC indicou este modelo como o melhor apenas para P205. Para análise genética dessa população, o modelo que considerou o efeito de epistasia foi o mais adequado.

Thaptomys Thomas 1915 (Rodentia, Sigmodontinae, Akodontini) with karyotypes 2n = 50, FN = 48, and 2n = 52, FN = 52: two monophyletic lineages recovered by molecular phylogeny

A novel karyotype with 2n = 50, FN = 48, was described for specimens of Thaptomys collected at Una, State of Bahia, Brazil, which are morphologically indistinguishable from Thaptomys nigrita, 2n = 52, FN = 52, found in other localities. It was hence proposed that the 2n = 50 karyotype could belong to a distinct species, cryptic of Thaptomys nigrita, once chromosomal rearrangements observed, along with the geographic distance, might represent a reproductive barrier between both forms. Phylogenetic analyses using maximum parsimony and maximum likelihood based on partial cytochrome b sequences with 1077 bp were performed, attempting to establish the relationships among the individuals with distinct karyotypes along the geographic distribution of the genus; the sample comprised 18 karyotyped specimens of Thaptomys, encompassing 15 haplotypes, from eight different localities of the Atlantic Rainforest. The intra-generic relationships corroborated the distinct diploid numbers, once both phylogenetic reconstructions recovered two monophyletic lineages, a northeastern clade grouping the 2n = 50 and a southeastern clade with three subclades, grouping the 2n = 52 karyotype. The sequence divergence observed between their individuals ranged from 1.9% to 3.5%.

PENCALC: a program for penetrance estimation in autosomal dominant diseases

We present a computer program developed for estimating penetrance rates in autosomal dominant diseases by means of family kinship and phenotype information contained within the pedigrees. The program also determines the exact 95% credibility interval for the penetrance estimate. Both executable (PenCalc for Windows) and web versions (PenCalcWeb) of the software are available. The web version enables further calculations, such as heterozygosity probabilities and assessment of offspring risks for all individuals in the pedigrees. Both programs can be accessed and down-loaded freely at the home-page address http://www.ib.usp.br/~otto/software.htm.

Técnicas de diagnóstico de influência local na análise espacial da produtividade da soja

A modelagem da estrutura de dependência espacial pela abordagem da geoestatística é fundamental para a definição de parâmetros que definem esta estrutura, e que são utilizados na interpolação de valores em locais não amostrados pela técnica de krigagem. Entretanto, a estimação de parâmetros pode ser muito afetada pela presença de observações atípicas nos dados amostrados. O desenvolvimento deste trabalho teve por objetivo utilizar técnicas de diagnóstico de influência local em modelos espaciais lineares gaussianos, utilizados em geoestatística, para avaliar a sensibilidade dos estimadores de máxima verossimilhança e máxima verossimilhança restrita na presença de dados discrepantes. Estudos com dados experimentais mostraram que tanto a presença de valores atípicos como de valores considerados influentes, pela análise de diagnóstico, pode exercer forte influência nos mapas temáticos, alterando, assim, a estrutura de dependência espacial. As aplicações de técnicas de diagnóstico de influência local devem fazer parte de toda análise geoestatística a fim de garantir que as informações contidas nos mapas temáticos tenham maior qualidade e possam ser utilizadas com maior segurança pelo agricultor.

Per capita versus adult-equivalent estimates of calorie availability in household budget surveys

This study aims to estimate an adult-equivalent scale for calorie requirements and to determine the differences between adult-equivalent and per capita measurements of calorie availability in the Brazilian population. The study used data from the 2002-2003 Brazilian Household Budget Survey. The calorie requirement for a reference adult individual was based on the mean requirements for adult males and females (2,550kcal/day). The conversion factors were defined as the ratios between the calorie requirements for each age group and gender and that of the reference adult. The adult-equivalent calorie availability levels were higher than the per capita levels, with the largest differences in rural and low-income households. Differences in household calorie availability varied from 22kcal/day (households with adults and an adolescent) to 428kcal/day (households with elderly individuals), thus showing that per capital measurements can underestimate the real calorie availability, since they overlook differences in household composition.

Características agronômicas do Panicum maximum cv. "Mombaça" submetido a níveis crescentes de fósforo

O objetivo deste experimento foi avaliar o efeito da adição de doses crescentes de P2O5 sobre a altura do dossel, o número de perfilhos e a produção de matéria seca de folhas e de colmos do capim-Mombaça, em diferentes idades. Foi conduzido um experimento implantado em um Nitossolo Vermelho Eutrófico. O delineamento experimental usado foi o de blocos completos casualizados, com quatro repetições, cinco doses de P2O5 (30, 60, 90, 120 e 150kg ha-1) e uma testemunha. Para a primeira e segunda coletas, observou-se o efeito linear do fósforo sobre o perfilhamento. Para a terceira e quarta coletas, os dados ajustaram-se ao modelo quadrático. A participação das lâminas foliares na matéria seca da parte aérea diminuiu com as doses de P2O5. Por outro lado, a participação de colmos aumentou com as doses de P2O5. A produção de matéria seca (MS) da parte aérea para primeira, segunda e terceira coletas respondeu de forma linear à aplicação de P2O5 observando-se um aumento estimado de 7, 15 e 19kg ha-1 de MS por kg ha-1 de P2O5, respectivamente. Para a quarta coleta, os dados ajustaram-se ao modelo quadrático de regressão, sendo a máxima produção, 8,3Mg ha-1 de MS, obtida com a aplicação de 103kg ha-1 de P2O5.