A-SCALA: an age-structured statistical catch-at-length analysis for assessing tuna stocks in the eastern tropical Pacific Ocean

English: We describe an age-structured statistical catch-at-length analysis (A-SCALA) based on the MULTIFAN-CL model of Fournier et al. (1998). The analysis is applied independently to both the yellowfin and the bigeye tuna populations of the eastern Pacific Ocean (EPO). We model the populations from 1975 to 1999, based on quarterly time steps. Only a single stock for each species is assumed for each analysis, but multiple fisheries that are spatially separate are modeled to allow for spatial differences in catchability and selectivity. The analysis allows for error in the effort-fishing mortality relationship, temporal trends in catchability, temporal variation in recruitment, relationships between the environment and recruitment and between the environment and catchability, and differences in selectivity and catchability among fisheries. The model is fit to total catch data and proportional catch-at-length data conditioned on effort. The A-SCALA method is a statistical approach, and therefore recognizes that the data collected from the fishery do not perfectly represent the population. Also, there is uncertainty in our knowledge about the dynamics of the system and uncertainty about how the observed data relate to the real population. The use of likelihood functions allow us to model the uncertainty in the data collected from the population, and the inclusion of estimable process error allows us to model the uncertainties in the dynamics of the system. The statistical approach allows for the calculation of confidence intervals and the testing of hypotheses. We use a Bayesian version of the maximum likelihood framework that includes distributional constraints on temporal variation in recruitment, the effort-fishing mortality relationship, and catchability. Curvature penalties for selectivity parameters and penalties on extreme fishing mortality rates are also included in the objective function. The mode of the joint posterior distribution is used as an estimate of the model parameters. Confidence intervals are calculated using the normal approximation method. It should be noted that the estimation method includes constraints and priors and therefore the confidence intervals are different from traditionally calculated confidence intervals. Management reference points are calculated, and forward projections are carried out to provide advice for making management decisions for the yellowfin and bigeye populations. Spanish: Describimos un análisis estadístico de captura a talla estructurado por edad, A-SCALA (del inglés age-structured statistical catch-at-length analysis), basado en el modelo MULTIFAN- CL de Fournier et al. (1998). Se aplica el análisis independientemente a las poblaciones de atunes aleta amarilla y patudo del Océano Pacífico oriental (OPO). Modelamos las poblaciones de 1975 a 1999, en pasos trimestrales. Se supone solamente una sola población para cada especie para cada análisis, pero se modelan pesquerías múltiples espacialmente separadas para tomar en cuenta diferencias espaciales en la capturabilidad y selectividad. El análisis toma en cuenta error en la relación esfuerzo-mortalidad por pesca, tendencias temporales en la capturabilidad, variación temporal en el reclutamiento, relaciones entre el medio ambiente y el reclutamiento y entre el medio ambiente y la capturabilidad, y diferencias en selectividad y capturabilidad entre pesquerías. Se ajusta el modelo a datos de captura total y a datos de captura a talla proporcional condicionados sobre esfuerzo. El método A-SCALA es un enfoque estadístico, y reconoce por lo tanto que los datos obtenidos de la pesca no representan la población perfectamente. Además, hay incertidumbre en nuestros conocimientos de la dinámica del sistema e incertidumbre sobre la relación entre los datos observados y la población real. El uso de funciones de verosimilitud nos permite modelar la incertidumbre en los datos obtenidos de la población, y la inclusión de un error de proceso estimable nos permite modelar las incertidumbres en la dinámica del sistema. El enfoque estadístico permite calcular intervalos de confianza y comprobar hipótesis. Usamos una versión bayesiana del marco de verosimilitud máxima que incluye constreñimientos distribucionales sobre la variación temporal en el reclutamiento, la relación esfuerzo-mortalidad por pesca, y la capturabilidad. Se incluyen también en la función objetivo penalidades por curvatura para los parámetros de selectividad y penalidades por tasas extremas de mortalidad por pesca. Se usa la moda de la distribución posterior conjunta como estimación de los parámetros del modelo. Se calculan los intervalos de confianza usando el método de aproximación normal. Cabe destacar que el método de estimación incluye constreñimientos y distribuciones previas y por lo tanto los intervalos de confianza son diferentes de los intervalos de confianza calculados de forma tradicional. Se calculan puntos de referencia para el ordenamiento, y se realizan proyecciones a futuro para asesorar la toma de decisiones para el ordenamiento de las poblaciones de aleta amarilla y patudo.

A experiência de visita dirigida a múltiplas atrações: análise do comportamento espacial do turista e da sua satisfação

Esta investigação teve como objetivo central averiguar se o comportamento espaciotemporal do turista urbano influencia a sua satisfação com a experiência de visita multiatração. Apesar de a mobilidade ser uma condição sine qua non do turismo, e, por outro lado, a visita a múltiplas atrações o contexto habitual em que se desenvolve a experiência turística em contexto urbano, a investigação neste domínio tende a ignorar a dimensão espaciotemporal e multiatração dessa experiência. O modelo conceptual proposto visa a sistematização da análise do comportamento espaciotemporal do turista bem como o estudo da sua relação com a satisfação, enquanto satisfação global e satisfação com dimensões da experiência. A partir deste, foi definido o modelo da pesquisa que, modelizando a questão central em estudo, teve por base dois instrumentos principais: estudo de rastreamento através de equipamento GPS e inquérito por questionário, realizados junto de hóspedes de dez hotéis de Lisboa (n= 413). A análise dos dados assume, por sua vez, dupla natureza: espacial e estatística. Em termos de análise espacial, a metodologia SIG em que se baseou a concretização dos mapas foi executada tendo como suporte a solução ArcGIS for Desktop 10.1, permitindo gerar visualizações úteis do ponto de vista da questão em estudo. A análise estatística dos dados compreendeu métodos descritivos, exploratórios e inferenciais, tendo como principal instrumento de teste das hipóteses formuladas a modelação PLS-PM, complementada pela análise PLS-MGA, com recurso ao programa SmartPLS 2.0. Entre as várias relações significativas encontradas, a conclusão mais importante que se pode retirar da investigação empírica é que, de facto, o comportamento espaciotemporal do turista urbano influencia a sua satisfação com a experiência de visita multiatração, afigurando-se particularmente importante neste contexto, em termos científicos e empíricos, investigar a heterogeneidade subjacente à população em estudo.

Sudden cardiac death in forensic medicine - Swiss recommendations for a multidisciplinary approach.

Sudden cardiac death (SCD) is by definition unexpected and cardiac in nature. The investigation is almost invariably performed by a forensic pathologist. Under these circumstances the role of the forensic pathologist is twofold: (1.) to determine rapidly and efficiently the cause and manner of death and (2.) to initiate a multidisciplinary process in order to prevent further deaths in existing family members. If the death is determined to be due to "natural" causes the district attorney in charge often refuses further examinations. However, additional examinations, i.e. extensive histopathological investigations and/or molecular genetic analyses, are necessary in many cases to clarify the cause of death. The Swiss Society of Legal Medicine created a multidisciplinary working group together with clinical and molecular geneticists and cardiologists in the hope of harmonising the approach to investigate SCD. The aim of this paper is to close the gap between the Swiss recommendations for routine forensic post-mortem cardiac examination and clinical recommendations for genetic testing of inherited cardiac diseases; this is in order to optimise the diagnostic procedures and preventive measures for living family members. The key points of the recommendations are (1.) the forensic autopsy procedure for all SCD victims under 40 years of age, (2.) the collection and storage of adequate samples for genetic testing, (3.) communication with the families, and (4.) a multidisciplinary approach including cardiogenetic counselling.

Intrinsic test of independence in contingency tables

A condition needed for testing nested hypotheses from a Bayesian viewpoint is that the prior for the alternative model concentrates mass around the small, or null, model. For testing independence in contingency tables, the intrinsic priors satisfy this requirement. Further, the degree of concentration of the priors is controlled by a discrete parameter m, the training sample size, which plays an important role in the resulting answer regardless of the sample size. In this paper we study robustness of the tests of independence in contingency tables with respect to the intrinsic priors with different degree of concentration around the null, and compare with other “robust” results by Good and Crook. Consistency of the intrinsic Bayesian tests is established. We also discuss conditioning issues and sampling schemes, and argue that conditioning should be on either one margin or the table total, but not on both margins. Examples using real are simulated data are given

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

Background: Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Results: Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion: The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Bayesian estimation of ancestral character states on phylogenies

Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods ( BayesMultiState) is available from the authors.

Formalizing the concept of entrepreneurial capacity

This study develops a definition of the concept of entrepreneurial capacity and formalizes it in two models explaining how value is created in the innovation process. The formalization integrates the influential opportunity-based definition of entrepreneurship research offered by Shane and Venkataraman (2000) with the consensus prevailing in the management, strategy, economics and entrepreneurship literatures that innovation is a process for transforming the inherent economic value of new knowledge into realized economic value for identified stakeholders. The linear flow and mathematical models presented in the study possess the clarity and richness required of a theoretical framework for generating and testing insightful hypotheses. This study, regarding Penrose (1959) more as theorist of entrepreneurship than of resources, deepens scepticism about the relevance to entrepreneurship of the literatures on the resource-based view of the firm (RBV) and dynamic capabilities (DC). Finally, the arguments and perspectives of the study imply several pedagogic possibilities and challenges for entrepreneurship educators.

Space-for-time substitution to assess likely response of aquatic ecosystems to future climate-related change

Predicting and managing ecological response to a changing climate is often limited by an incomplete understanding of response thresholds and biogeographic differences. For example, step changes in rainfall and runoff, and threshold dynamics and hysteresis in ecological response make projection of future conditions difficult. To combat these constraints we propose that biophysical data across exiting climatic gradients can be used in a space-for-time substitution to predict climate-related ecological response elsewhere. This method builds on previous attempts at space-for-time substitution by using patterns in physical and physicochemical data to explain biological differences across the spatial gradient, then using those patterns to formulate hypotheses of temporal ecological response and finally testing those hypotheses on temporal data available in a second, similar region of interest. 

An analysis of the floristic composition and diversity of Amazonian forests including those of the Guiana Shield

A large number of newly published and unpublished hectare plots in Amazonia and the Guiana Shield area allow an analysis of family composition and testing of hypotheses concerning alpha-diversity in the south American rain forest. Using data from 94 plots the family-level floristic patterns in wet tropical South America are described. To test diversity patterns, 268 plots are used in this large area. Contrary to a widely held belief, western Amazonian plots are not necessarily the most diverse. Several central Amazonian plots have equal or even higher tree diversity. Annual rainfall is not a good estimator for tree diversity in the Amazonia area and Guiana shield. Plots in the Guiana Shield area (and eastern Amazonia) usually have lower diversity than those in central or western Amazonia. It is argued that this is not because of low rainfall or low nutrient status of the soil but because of the small area of the relatively isolated rain forest area in eastern Amazonia and the Guiana Shield. The low diversity on nutrient-poor white sand soils in the Amazon basin is not necessarily due to their Low nutrient status but is, at least partly, caused by their small extent and fragmented nature.

Análise de experimentos fatoriais de dois fatores com tratamentos adicionais

Experiments using factorial arrangement of treatments are rather common and useful in agricultural research. The main advantage is the possibility of testing many hypotheses, allowing broader conclusions over different factors, studied simultaneously. Factorial arrangements are used to compare levels of each factor (main effects), and also to verify if the differences among levels of a given factor are dependent on the levels of the other factors (interacions). In the analysis of data from factorial experiments, difficulty is increased when additional treatments are included. Inclusion of one or more additional treatments is a quite common practice, since such treatments are usually taken as reference or standard for evaluation and comparasion of the remaimng treatments, or aiming complementary information. This increase of difficulty is however low, compared to the advantages. As in literature there are few references about the statistical analysis of factorial experiments with additonal treatments, and given straightforward use in experimentation, the objective of this work was the presentation of approach for the use of factorial experiments with additonal treatments trough the analysis of some examples using the SAS® software, with the corresponding theoretical development, obtaining the system of normal equations, estimators of the parameters and variance of contrasts among two treatment means. It is suggested that additional treatments should be used with caution. The analysis of variance of such kind of experiment was presented using matrix notation.

Drivers of clutch-size in Fork-tailed Flycatchers (Tyrannus savana) at temperate and tropical latitudes in South America

Many species of birds exhibit a latitudinal gradient in annual reproductive investment, laying more eggs and producing more nestlings at higher latitudes. However, few studies have evaluated the mechanisms that underlie such patterns and such differences in grassland birds specifically. We monitored nests of Fork-tailed Flycatchers (Tyrannus savana) over two breeding seasons at a tropical site in Bolivia (in 2010-11 and 2011-12) and three breeding seasons at a southern temperate site in Argentina (2010-11, 2011-12 and 2012-13), testing two hypotheses explaining variation in clutch-size among populations: the food-limitation hypothesis and the nest-predation hypothesis. Mean clutch-size and mean brood-size were significantly larger at the temperate study site than at the tropical site. Availability of arthropod food per individual bird was significantly higher at the temperate site. There was no relationship, positive or negative, between rates of nest predation and either clutch- or brood-size, and thus no support for the nest-predation hypothesis. We conclude that food availability explains much of the latitudinal variation in clutch-size in this species. We discuss avenues for future research on the mechanisms underlying geographical variation in the life histories of Neotropical birds.

Investigação orientada e formação inicial de professores de química: um estudo com base em uma proposta de elaboração de mini-cursos temáticos

The educational institutions need to rethink issues related to teacher training in order to seek personal construction of teaching. Oriented research has been identified as useful in the process of teacher training. Through research builds knowledge about the problems faced in teaching, producing the most effective methods. The aim of this paper is to verify the validity of the application of research activities in the form of short courses and themed play during the formation of licensees and the use and construction of knowledge of high school students who attended these short courses. This work is linked to training of undergraduates and implementation of different activities of teaching and learning for high school students. The oriented investigation was the methodology chosen for the development of activities in which, through the construction and implementation of the mini-courses Students are encouraged to participate in the construction of knowledge itself in activities that suggest the development and testing of hypotheses. The mini-courses are designed and implemented by teachers of the ninth and tenth terms of the degree in chemistry. Students of public schools were the privileged. Data were collected through observation and interview. In applying these mini-courses, associated with the daily, prospective teachers connected theory to practice, arousing the curiosity of students and leading them to raise issues related to the content of chemistry. Students showed interest in the construction of the content addressed. The student teachers sought to study different concepts and how to make them more attractive, causing the chemistry was associated with the phenomena of everyday life, including the problems faced when teaching and trying different possible solutions. Thus, there was an increase in interest in teaching and learning

The humankind genome: from genetic diversity to the origin of human diseases

Genome-wide association studies have failed to establish common variant risk for the majority of common human diseases. The underlying reasons for this failure are explained by recent studies of resequencing and comparison of over 1200 human genomes and 10 000 exomes, together with the delineation of DNA methylation patterns (epigenome) and full characterization of coding and noncoding RNAs (transcriptome) being transcribed. These studies have provided the most comprehensive catalogues of functional elements and genetic variants that are now available for global integrative analysis and experimental validation in prospective cohort studies. With these datasets, researchers will have unparalleled opportunities for the alignment, mining, and testing of hypotheses for the roles of specific genetic variants, including copy number variations, single nucleotide polymorphisms, and indels as the cause of specific phenotypes and diseases. Through the use of next-generation sequencing technologies for genotyping and standardized ontological annotation to systematically analyze the effects of genomic variation on humans and model organism phenotypes, we will be able to find candidate genes and new clues for disease’s etiology and treatment. This article describes essential concepts in genetics and genomic technologies as well as the emerging computational framework to comprehensively search websites and platforms available for the analysis and interpretation of genomic data.

Helper response to experimentally manipulated predation risk in the cooperatively breeding cichlid Neolamprologus pulcher

Background We manipulated predation risk in a field experiment with the cooperatively breeding cichlid Neolamprologus pulcher by releasing no predator, a medium- or a large-sized fish predator inside underwater cages enclosing two to three natural groups. We assessed whether helpers changed their helping behaviour, and whether within-group conflict changed, depending on these treatments, testing three hypotheses: ‘pay-to-stay’ PS, ‘risk avoidance’ RA, or (future) reproductive benefits RB. We also assessed whether helper food intake was reduced under risk, because this might reduce investments in other behaviours to save energy. Methodology/Principal Findings Medium and large helpers fed less under predation risk. Despite this effect helpers invested more in territory defence, but not territory maintenance, under the risk of predation (supporting PS). Experimentally covering only the breeding shelter with sand induced more helper digging under predation risk compared to the control treatment (supporting PS). Aggression towards the introduced predator did not differ between the two predator treatments and increased with group member size and group size (supporting PS and RA). Large helpers increased their help ratio (helping effort/breeder aggression received, ‘punishment’ by the dominant pair in the group) in the predation treatments compared to the control treatment, suggesting they were more willing to PS. Medium helpers did not show such effects. Large helpers also showed a higher submission ratio (submission/ breeder aggression received) in all treatments, compared to the medium helpers (supporting PS). Conclusions/Significance We conclude that predation risk reduces helper food intake, but despite this effect, helpers were more willing to support the breeders, supporting PS. Effects of breeder punishment suggests that PS might be more important for large compared to the medium helpers. Evidence for RA was also detected. Finally, the results were inconsistent with RB.

Sudden cardiac death in forensic medicine – Swiss recommendations for a multidisciplinary approach

Sudden cardiac death (SCD) is by definition unexpected and cardiac in nature. The investigation is almost invariably performed by a forensic pathologist. Under these circumstances the role of the forensic pathologist is twofold: (1.) to determine rapidly and efficiently the cause and manner of death and (2.) to initiate a multidisciplinary process in order to prevent further deaths in existing family members. If the death is determined to be due to "natural" causes the district attorney in charge often refuses further examinations. However, additional examinations, i.e. extensive histopathological investigations and/or molecular genetic analyses, are necessary in many cases to clarify the cause of death. The Swiss Society of Legal Medicine created a multidisciplinary working group together with clinical and molecular geneticists and cardiologists in the hope of harmonising the approach to investigate SCD. The aim of this paper is to close the gap between the Swiss recommendations for routine forensic post-mortem cardiac examination and clinical recommendations for genetic testing of inherited cardiac diseases; this is in order to optimise the diagnostic procedures and preventive measures for living family members. The key points of the recommendations are (1.) the forensic autopsy procedure for all SCD victims under 40 years of age, (2.) the collection and storage of adequate samples for genetic testing, (3.) communication with the families, and (4.) a multidisciplinary approach including cardiogenetic counselling.