Predicting Additive and Non-additive Genetic Effects from Trials Where Traits Are Affected by Interplot Competition

There are two key types of selection in a plant breeding program, namely selection of hybrids for potential commercial use and the selection of parents for use in future breeding. Oakey et al. (in Theoretical and Applied Genetics 113, 809-819, 2006) showed how both of these aims could be achieved using pedigree information in a mixed model analysis in order to partition genetic effects into additive and non-additive effects. Their approach was developed for field trial data subject to spatial variation. In this paper we extend the approach for data from trials subject to interplot competition. We show how the approach may be used to obtain predictions of pure stand additive and non-additive effects. We develop the methodology in the context of a single field trial using an example from an Australian sorghum breeding program.

A retrospective study of vase life determinants for cut Acacia holosericea foliage

Short and variable vase life of cut Acacia holosericea foliage stems limits its commercial potential. Retrospective evaluation of factors affecting the vase life of this cut foliage line was assessed using primary data collected from 30 individual experiments. These data had been collected by four different researchers over 17 months, from late Summer to mid Winter across two consecutive years. Vase life data of cut A. holosericea stems held in deionised water (DIW) was analysed for general vase life variation and to define the most influential factor affecting vase life of the cut stems. Meanwhile, vase life of cut stems exposed to various chemical and physical postharvest treatments was analysed using meta-analysis to evaluate their efficacy in prolonging vase life of the stems. The overall mean vase life (±standard deviation) of cut A. holosericea stems was 6.4 ± 1.2 days (n = 30 trials). Longer vase life of ≥7 days was obtained from cut stems harvested at vegetative and flowering stage, which was between Summer and Autumn. Cut stems harvested at fruiting stage, between Winter and Spring displayed shorter vase life of ≤5.5 days. Mixed model analysis indicated that vase life variation of the cut stems was mostly determined by season (P < 0.001). In averaged, postharvest treatments increased vase life 1.4-fold compared to stems in DIW, with 68.32% had a large positive treatment effect size (d). Among the treatments, nano silver (NS) and copper (Cu2+) were the most beneficial to vase life. Retrospective analysis was found to be beneficial for identifying conditions and targeting practices to maximise the vase life of cut A. holosericea and, potentially for other species.

Spectral unmixing with estimated adaptive endmember index using Extended Support Vector Machine

The most difficult operation in the flood inundation mapping using optical flood images is to separate fully inundated areas from the ‘wet’ areas where trees and houses are partly covered by water. This can be referred as a typical problem the presence of mixed pixels in the images. A number of automatic information extraction image classification algorithms have been developed over the years for flood mapping using optical remote sensing images. Most classification algorithms generally, help in selecting a pixel in a particular class label with the greatest likelihood. However, these hard classification methods often fail to generate a reliable flood inundation mapping because the presence of mixed pixels in the images. To solve the mixed pixel problem advanced image processing techniques are adopted and Linear Spectral unmixing method is one of the most popular soft classification technique used for mixed pixel analysis. The good performance of linear spectral unmixing depends on two important issues, those are, the method of selecting endmembers and the method to model the endmembers for unmixing. This paper presents an improvement in the adaptive selection of endmember subset for each pixel in spectral unmixing method for reliable flood mapping. Using a fixed set of endmembers for spectral unmixing all pixels in an entire image might cause over estimation of the endmember spectra residing in a mixed pixel and hence cause reducing the performance level of spectral unmixing. Compared to this, application of estimated adaptive subset of endmembers for each pixel can decrease the residual error in unmixing results and provide a reliable output. In this current paper, it has also been proved that this proposed method can improve the accuracy of conventional linear unmixing methods and also easy to apply. Three different linear spectral unmixing methods were applied to test the improvement in unmixing results. Experiments were conducted in three different sets of Landsat-5 TM images of three different flood events in Australia to examine the method on different flooding conditions and achieved satisfactory outcomes in flood mapping.

Factors affecting partitioning of private forest holdings in Finland.

Questions of the small size of non-industrial private forest (NIPF) holdings in Finland are considered and factors affecting their partitioning are analyzed. This work arises out of Finnish forest policy statements in which the small average size of holdings has been seen to have a negative influence on the economics of forestry. A survey of the literature indicates that the size of holdings is an important factor determining the costs of logging and silvicultural operations, while its influence on the timber supply is slight. The empirical data are based on a sample of 314 holdings collected by interviewing forest owners in the years 1980-86. In 1990-91 the same holdings were resurveyed by means of a postal inquiry and partly by interviewing forest owners. The principal objective in compiling the data is to assist in quantifying ownership factors that influence partitioning among different kinds of NIPF holdings. Thus the mechanism of partitioning were described and a maximum likelihood logistic regression model was constructed using seven independent holding and ownership variables. One out of four holdings had undergone partitioning in conjunction with a change in ownership, one fifth among family owned holdings and nearly a half among jointly owned holdings. The results of the logistic regression model indicate, for instance, that the odds on partitioning is about three times greater for jointly owned holdings than for family owned ones. Also, the probabilities of partitioning were estimated and the impact of independent dichotomous variables on the probability of partitioning ranged between 0.02 and 0.10. The low value of the Hosmer-Lemeshow test statistic indicates a good fit of the model and the rate of correct classification was estimated to be 88 per cent with a cutoff point of 0.5. The average size of holdings undergoing ownership changes decreased from 29.9 ha to 28.7 ha over the approximate interval 1983-90. In addition, the transition probability matrix showed that the trends towards smaller size categories mostly involved in the small size categories, less than 20 ha. The results of the study can be used in considering the effects of the small size of holdings for forestry and if the purpose is to influence partitioning through forest or rural policy.

Awakening a sleeping giant: The riddle of Latino political participation

For some time now, the Latino voice has been gradually gaining strength in American politics, particularly in such states as California, Florida, Illinois, New York, and Texas, where large numbers of Latino immigrants have settled and large numbers of electoral votes are at stake. Yet the issues public officials in these states espouse and the laws they enact often do not coincide with the interests and preferences of Latinos. The fact that Latinos in California and elsewhere have not been able to influence the political agenda in a way that is commensurate with their numbers may reflect their failure to participate fully in the political process by first registering to vote and then consistently turning out on election day to cast their ballots.

To understand Latino voting behavior, I first examine Latino political participation in California during the ten general elections of the 1980s and 1990s, seeking to understand what percentage of the eligible Latino population registers to vote, with what political party they register, how many registered Latinos to go the polls on election day, and what factors might increase their participation in politics. To ensure that my findings are not unique to California, I also consider Latino voter registration and turnout in Texas for the five general elections of the 1990s and compare these results with my California findings.

I offer a new approach to studying Latino political participation in which I rely on county-level aggregate data, rather than on individual survey data, and employ the ecological inference method of generalized bounds. I calculate and compare Latino and white voting-age populations, registration rates, turnout rates, and party affiliation rates for California's fifty-eight counties. Then, in a secondary grouped logit analysis, I consider the factors that influence these Latino and white registration, turnout, and party affiliation rates.

I find that California Latinos register and turn out at substantially lower rates than do whites and that these rates are more volatile than those of whites. I find that Latino registration is motivated predominantly by age and education, with older and more educated Latinos being more likely to register. Motor voter legislation, which was passed to ease and simplify the registration process, has not encouraged Latino registration . I find that turnout among California's Latino voters is influenced primarily by issues, income, educational attainment, and the size of the Spanish-speaking communities in which they reside. Although language skills may be an obstacle to political participation for an individual, the number of Spanish-speaking households in a community does not encourage or discourage registration but may encourage turnout, suggesting that cultural and linguistic assimilation may not be the entire answer.

With regard to party identification, I find that Democrats can expect a steady Latino political identification rate between 50 and 60 percent, while Republicans attract 20 to 30 percent of Latino registrants. I find that education and income are the dominant factors in determining Latino political party identification, which appears to be no more volatile than that of the larger electorate.

Next, when I consider registration and turnout in Texas, I find that Latino registration rates are nearly equal to those of whites but that Texas Latino turnout rates are volatile and substantially lower than those of whites.

Low turnout rates among Latinos and the volatility of these rates may explain why Latinos in California and Texas have had little influence on the political agenda even though their numbers are large and increasing. Simply put, the voices of Latinos are little heard in the halls of government because they do not turn out consistently to cast their votes on election day.

While these findings suggest that there may not be any short-term or quick fixes to Latino participation, they also suggest that Latinos should be encouraged to participate more fully in the political process and that additional education may be one means of achieving this goal. Candidates should speak more directly to the issues that concern Latinos. Political parties should view Latinos as crossover voters rather than as potential converts. In other words, if Latinos were "a sleeping giant," they may now be a still-drowsy leviathan waiting to be wooed by either party's persuasive political messages and relevant issues.

Efeito da exposição ao tabagismo e da mobilidade social sobre o crescimento e ganho de peso do nascimento à adolescência em uma coorte de base populacional de Cuiabá-MT

Esta tese é composta por três artigos que permitiram avaliar o efeito da exposição ao tabagismo durante a gestação e no início da infância sobre o crescimento linear e ganho de peso do nascimento à adolescência, além de verificar o efeito do nível socioeconômico no início da infância e da mobilidade social sobre a adiposidade até a adolescência. Foram utilizados para este fim os dados de uma coorte de crianças nascidas entre 1994 e 1999 na cidade de Cuiabá-MT. Essas crianças fizeram parte de um estudo de base populacional realizado na cidade de Cuiabá, entre 1999 e 2000, com 2405 crianças (0 a 5 anos) e foram selecionadas aleatoriamente em unidades básicas de saúde quando da vacinação. As mães foram entrevistadas após a vacinação, quando foram obtidos dados relativos à exposição ao tabagismo gestacional, tabagismo passivo, nível socioeconômico das famílias e dados antropométricos. Entre 2009 e 2011, após aproximadamente 11 anos, essas crianças foram localizadas por meio do Censo Escolar e então 1716 adolescentes entre 10 e 17 anos de idade (71,4% da população) foram reavaliados nas escolas da rede pública e privada de Cuiabá, de 18 municípios do estado e outras 5 capitais do país. A análise por modelos lineares de efeitos mistos permitiu verificar a mudança de estatura e Índice de Massa Corporal (IMC) entre o nascimento e a adolescência. O primeiro e o segundo artigo desta tese avaliaram o efeito da exposição ao tabagismo materno durante a gestação e no início da infância sobre o crescimento linear e o IMC entre o nascimento e a adolescência. Crianças expostas ao tabagismo materno durante a gestação e no início da infância apresentaram menor estatura desde o nascimento até a adolescência quando comparadas às crianças não expostas. Quanto à adiposidade, entre o nascimento e a infância a mudança do IMC foi similar entre as crianças expostas e não expostas ao tabagismo materno, porém, entre a infância e a adolescência, aquelas expostas apenas durante a gestação mostraram maior ganho de IMC. Em conjunto, os dados corroboram o efeito deletério do tabagismo sobre o crescimento, efeito já bastante estudado, mas também indicam que avaliar e comparar exposição gestacional com pós-gestacional é importante, dado que seus efeitos parecem ser diferentes. O terceiro artigo avaliou o efeito do nível socioeconômico no início da infância e da mobilidade social entre a infância e a adolescência sobre o IMC do nascimento à adolescência. Para avaliar o nível socioeconômico, as famílias foram classificadas em nível econômico alto, médio e baixo, a partir do Critério de Classificação Econômica Brasil. Foi observada expressiva mobilidade social na população, principalmente entre os de menor nível econômico. Houve maior aumento do IMC entre o nascimento e a adolescência entre aqueles de maior nível econômico na infância e aqueles que permaneceram nas classes mais elevadas, indicando que a posição inicial foi o maior determinante das mudanças observadas no IMC.

Juvenile salmonid distribution, growth, condition, origin, and environmental and species associations in the Northern California Current

Information is summarized on juvenile salmonid distribution, size, condition, growth, stock origin, and species and environmental associations from June and August 2000 GLOBEC cruises with particular emphasis on differences related to the regions north and south of Cape Blanco off Southern Oregon. Juvenile salmon were more abundant during the August cruise as compared to the June cruise and were mainly distributed northward from Cape Blanco. There were distinct differences in distribution patterns between salmon species: chinook salmon were found close inshore in cooler water all along the coast and coho salmon were rarely found south of Cape Blanco. Distance offshore and temperature were the dominant explanatory variables related to coho and chinook salmon distribution. The nekton assemblages differed significantly between cruises. The June cruise was dominated by juvenile rockfishes, rex sole, and sablefish, which were almost completely absent in August. The forage fish community during June comprised Pacific herring and whitebait smelt north of Cape Blanco and surf smelt south of Cape Blanco. The fish community in August was dominated by Pacific sardines and highly migratory pelagic species. Estimated growth rates of juvenile coho salmon were higher in the GLOBEC study area than in areas farther north. An unusually high percentage of coho salmon in the study area were precocious males. Significant differences in growth and condition of juvenile coho salmon indicated different oceanographic environments north and south of Cape Blanco. The condition index was higher in juvenile coho salmon to the north but no significant differences were found for yearling chinook salmon. Genetic mixed stock analysis indicated that during June, most of the Chinook salmon in our sample originated from rivers along the central coast of Oregon. In August, chinook salmon sampled south of Cape Blanco were largely from southern Oregon and northern California; whereas most chinook salmon north of Cape Blanco were from the Central Valley in California.

Origin of immature loggerhead sea turtles (Caretta caretta) at Hutchinson Island, Florida: evidence from mtDNA markers

Loggerhead sea turtles (Caretta caretta) are migratory, long-lived, and slow maturing. They are difficult to study because they are seen rarely and their habitats range over vast stretches of the ocean. Movements of immature turtles between pelagic and coastal developmental habitats are particularly difficult to investigate because of inadequate tagging technologies and the difficulty in capturing significant numbers of turtles at sea. However, genetic markers found in mitochondrial DNA (mtDNA) provide a basis for predicting the origin of juvenile turtles in developmental habitats. Mixed stock analysis was used to determine which nesting populations were contributing individuals to a foraging aggregation of immature loggerhead turtles (mean 63.3 cm straight carapace length [SCL]) captured in coastal waters off Hutchinson Island, Florida. The results indicated that at least three different western Atlantic loggerhead sea turtle subpopulations contribute to this group: south Florida (69%), Mexico (20%), and northeast Florida-North Carolina (10%). The conservation and management of these immature sea turtles is complicated by their multinational genetic demographics.

Feeding habits and trophic levels of some demersal fish species in the Persian Gulf (Bushehr Province) using Ecopath model

A trophic study was carried out in February of 2012 to January 2013 on the ecosystem in the Persian Gulf, Bushehr provience. A total of 2,948 samples of stomach contents were analyzed based on the weight and number of food items and were identified about 40 preys. Crustacean and bony fish were as a main prey in most of the stomach contents . The mean average trophic level was estimated at 3.6 by Ecopath software. In this research, the mean level were studied between eight species varied from 3.47 to 4.61, Saurida tumbil occupy the highest and the Argyrops spinifer was the lowest level. The ranges of total mortality varied from 0.7 to 3.05 per years. The food consumption rate was estimated about 69.82 per year. The overlap index showed that the prey items such as fish, crustacean, bivalve and echinoderm were shared about 65, 15, 15 and 6 percent in all stomach of individual in respectively. Mixed trophic analysis indicates that benthos have a positive effect on most of the fish species. Most species have a negative impact on themselves, interpreted here as reflecting increased with in group competition for resources. This preliminary model can be helpful to determine the gaps in the present knowledge about demersal system of the Persian Gulf.

Factores determinantes del uso de Internet en la comercialización del aceite de oliva. Análisis del sector en Cataluña

Las cooperativas son entidades con una gran presencia económica y social en España, y tienen una gran influencia en la economía rural de las zonas donde están ubicadas. El principal objetivo del presente trabajo es el análisis del uso de las nuevas tecnologías por parte de las cooperativas agroalimentarias, centrándose en las productoras de aceite de oliva para determinar los principales factores que condicionan su comportamiento en la Red. En el presente estudio se analizan sus sitios web y se determina qué tipo de información aporta, tanto datos generales como datos de comercialización. A partir de los resultados obtenidos, se busca la relación que pueda existir entre el tamaño de la cooperativa, su actividad exportadora o la actividad de comercio electrónico con la presencia online, mediante una regresión logística. De esta manera podremos conocer si realmente la implantación de nuevas tecnologías en las cooperativas permite desarrollar una óptima actividad económica.

Using choice experiments to explore the spatial distribution of willingness to pay for rural landscape improvements

We report findings from a choice experiment survey designed to estimate the economic benefits of policy measures to improve the rural landscape in the Republic of Ireland. Using a panel mixed logit specification to account for unobserved taste heterogeneity we derived individual-specific willingness-to-pay (WTP) estimates for each respondent in the sample. We subsequently investigated the spatial dependence of these estimates. Results suggest the existence of positive spatial autocorrelation for all rural landscape attributes. As a means of benefit transfer, kriging methods were employed to interpolate WTP estimates across the whole of the Republic of Ireland. The kriged WTP surfaces confirm the existence of spatial dependence and illustrate the implied spatial variation and regional disparities in WTP for all the rural landscape improvements investigated.

Molecular approaches to the study of invasive seaweeds

A wide range of vectors is currently introducing a plethora of alien marine species into indigenous marine species assemblages. Over the past two decades, molecular studies of non-native seaweeds, including cryptic invaders, have successfully identified the species involved and their sources; we briefly review these studies. As yet, however, little research has been directed towards examining the genetic consequences of seaweed invasions. Here we provide an overview of seaweed invasions from a genetic perspective, focusing on invader species for which the greatest amount of information is available. We review invasion processes, and rationalize evolutionary and genetic consequences for the indigenous and invader species into two main groups: (1) changes in gene-pool composition, in population structure and allele frequencies; and (2) changes in genome organization at the species level through hybridization, and in individual gene expression profiles at the levels of expressed messenger RNA and the proteome (i.e., all proteins synthesized) and thus the phenotype. We draw on studies of better-known aquatic and terrestrial organisms to point the way forward in revealing the genetic consequences of seaweed invasions. We also highlight potential applications of more recent methodological and statistical approaches, such as microarray technology, assignment tests and mixed stock analysis.

Determinants of long-distance investing by business angels in the UK

The business angel market is usually identified as a local market, and the proximity of an investment has been shown to be key in the angel's investment preferences and an important filter at the screening stage of the investment decision. This is generally explained by the personal and localized networks used to identify potential investments, the hands-on involvement of the investor and the desire to minimize risk. However, a significant minority of investments are long distance. This paper is based on data from 373 investments made by 109 UK business angels. We classify the location of investments into three groups: local investments ( those made within the same county or in adjacent counties); intermediate investments ( those made in counties adjacent to the 'local' counties); and long-distance investments ( those made beyond this range). Using ordered logit analysis the paper develops and tests a number of hypotheses that relate long-distance investment to investment characteristics and investor characteristics. The paper concludes by drawing out the implications for entrepreneurs seeking business angel finance in investment-deficient regions, business angel networks seeking to match investors to entrepreneurs and firms ( which are normally their primary clients), and for policy-makers responsible for local and regional economic development.

Implications for Powering Biomarker Discovery Studies

This study examined variations in gene expression between FFPE blocks within tumors of individual patients. Microarray data were used to measure tumor heterogeneity within and between patients and disease states. Data were used to determine the number of samples needed to power biomarker discovery studies. Bias and variation in gene expression were assessed at the intrapatient and interpatient levels and between adenocarcinoma and squamous samples. A mixed-model analysis of variance was fitted to gene expression data and model signatures to assess the statistical significance of observed variations within and between samples and disease states. Sample size analysis, adjusted for sample heterogeneity, was used to determine the number of samples required to support biomarker discovery studies. Variation in gene expression was observed between blocks taken from a single patient. However, this variation was considerably less than differences between histological characteristics. This degree of block-to-block variation still permits biomarker discovery using either macrodissected tumors or whole FFPE sections, provided that intratumor heterogeneity is taken into account. Failure to consider intratumor heterogeneity may result in underpowered biomarker studies that may result in either the generation of longer gene signatures or the inability to identify a viable biomarker. Moreover, the results of this study indicate that a single biopsy sample is suitable for applying a biomarker in nonsmall-cell lung cancer. © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology.

Regret minimisation and utility maximisation in a freight transport context

This study is the first to compare random regret minimisation (RRM) and random utility maximisation (RUM) in freight transport application. This paper aims to compare RRM and RUM in a freight transport scenario involving negative shock in the reference alternative. Based on data from two stated choice experiments conducted among Swiss logistics managers, this study contributes to related literature by exploring for the first time the use of mixed logit models in the most recent version of the RRM approach. We further investigate two paradigm choices by computing elasticities and forecasting choice probability. We find that regret is important in describing the managers’ choices. Regret increases in the shock scenario, supporting the idea that a shift in reference point can cause a shift towards regret minimisation. Differences in elasticities and forecast probability are identified and discussed appropriately.