Detection and use of QTL for complex traits in multiple environments.

QTL mapping methods for complex traits are challenged by new developments in marker technology, phenotyping platforms, and breeding methods. In meeting these challenges, QTL mapping approaches will need to also acknowledge the central roles of QTL by environment interactions (QEI) and QTL by trait interactions in the expression of complex traits like yield. This paper presents an overview of mixed model QTL methodology that is suitable for many types of populations and that allows predictive modeling of QEI, both for environmental and developmental gradients. Attention is also given to multi-trait QTL models which are essential to interpret the genetic basis of trait correlations. Biophysical (crop growth) model simulations are proposed as a complement to statistical QTL mapping for the interpretation of the nature of QEI and to investigate better methods for the dissection of complex traits into component traits and their genetic controls.

Adaptation and management of Australian buffalograss cultivars for shade and water conservation

Soft-leaf buffalo grass is increasing in popularity as an amenity turfgrass in Australia. This project was instigated to assess the adaptation of and establish management guidelines for its use in Australias vast array of growing environments. There is an extensive selection of soft-leaf buffalo grass cultivars throughout Australia and with the countrys changing climates from temperate in the south to tropical in the north not all cultivars are going to be adapted to all regions. The project evaluated 19 buffalo grass cultivars along with other warm-season grasses including green couch, kikuyu and sweet smother grass. The soft-leaf buffalo grasses were evaluated for their growth and adaptation in a number of regions throughout Australia including Western Australia, Victoria, ACT, NSW and Queensland. The growth habit of the individual cultivars was examined along with their level of shade tolerance, water use, herbicide tolerance, resistance to wear, response to nitrogen applications and growth potential in highly alkaline (pH) soils. The growth habit of the various cultivars currently commercially available in Australia differs considerably from the more robust type that spreads quicker and is thicker in appearance (Sir Walter, Kings Pride, Ned Kelly and Jabiru) to the dwarf types that are shorter and thinner in appearance (AusTine and AusDwarf). Soft-leaf buffalo grass types tested do not differ in water use when compared to old-style common buffalo grass. Thus, soft-leaf buffalo grasses, like other warm-season turfgrass species, are efficient in water use. These grasses also recover after periods of low water availability. Individual cultivar differences were not discernible. In high pH soils (i.e. on alkaline-side) some elements essential for plant growth (e.g. iron and manganese) may be deficient causing turfgrass to appear pale green, and visually unacceptable. When 14 soft-leaf buffalo grass genotypes were grown on a highly alkaline soil (pH 7.5-7.9), cultivars differed in leaf iron, but not in leaf manganese, concentrations. Nitrogen is critical to the production of quality turf. The methods for applying this essential element can be manipulated to minimise the maintenance inputs (mowing) during the peak growing period (summer). By applying the greatest proportion of the turfs total nitrogen requirements in early spring, peak summer growth can be reduced resulting in a corresponding reduction in mowing requirements. Soft-leaf buffalo grass cultivars are more shade and wear tolerant than other warm-season turfgrasses being used by homeowners. There are differences between the individual buffalo grass varieties however. The majority of types currently available would be classified as having moderate levels of shade tolerance and wear reasonably well with good recovery rates. The impact of wear in a shaded environment was not tested and there is a need to investigate this as this is a typical growing environment for many homeowners. The use of herbicides is required to maintain quality soft-leaf buffalo grass turf. The development of softer herbicides for other turfgrasses has seen an increase in their popularity. The buffalo grass cultivars currently available have shown varying levels of susceptibility to the chemicals tested. The majority of the cultivars evaluated have demonstrated low levels of phytotoxicity to the herbicides chlorsulfuron (Glean) and fluroxypyr (Starane and Comet). In general, soft leaf buffalo grasses are varied in their makeup and have demonstrated varying levels of tolerance/susceptibility/adaptation to the conditions they are grown under. Consequently, there is a need to choose the cultivar most suited to the environment it is expected to perform in and the management style it will be exposed to. Future work is required to assess how the structure of the different cultivars impacts on their capacity to tolerate wear, varying shade levels, water use and herbicide tolerance. The development of a growth model may provide the solution.

Silvicultural decisions based on simulation-optimization systems

Forest management is facing new challenges under climate change. By adjusting thinning regimes, conventional forest management can be adapted to various objectives of utilization of forest resources, such as wood quality, forest bioenergy, and carbon sequestration. This thesis aims to develop and apply a simulation-optimization system as a tool for an interdisciplinary understanding of the interactions between wood science, forest ecology, and forest economics. In this thesis, the OptiFor software was developed for forest resources management. The OptiFor simulation-optimization system integrated the process-based growth model PipeQual, wood quality models, biomass production and carbon emission models, as well as energy wood and commercial logging models into a single optimization model. Osyczka s direct and random search algorithm was employed to identify optimal values for a set of decision variables. The numerical studies in this thesis broadened our current knowledge and understanding of the relationships between wood science, forest ecology, and forest economics. The results for timber production show that optimal thinning regimes depend on site quality and initial stand characteristics. Taking wood properties into account, our results show that increasing the intensity of thinning resulted in lower wood density and shorter fibers. The addition of nutrients accelerated volume growth, but lowered wood quality for Norway spruce. Integrating energy wood harvesting into conventional forest management showed that conventional forest management without energy wood harvesting was still superior in sparse stands of Scots pine. Energy wood from pre-commercial thinning turned out to be optimal for dense stands. When carbon balance is taken into account, our results show that changing carbon assessment methods leads to very different optimal thinning regimes and average carbon stocks. Raising the carbon price resulted in longer rotations and a higher mean annual increment, as well as a significantly higher average carbon stock over the rotation.

Improved estimation of size-transition matrices using tag-recapture data

We derive a new method for determining size-transition matrices (STMs) that eliminates probabilities of negative growth and accounts for individual variability. STMs are an important part of size-structured models, which are used in the stock assessment of aquatic species. The elements of STMs represent the probability of growth from one size class to another, given a time step. The growth increment over this time step can be modelled with a variety of methods, but when a population construct is assumed for the underlying growth model, the resulting STM may contain entries that predict negative growth. To solve this problem, we use a maximum likelihood method that incorporates individual variability in the asymptotic length, relative age at tagging, and measurement error to obtain von Bertalanffy growth model parameter estimates. The statistical moments for the future length given an individual’s previous length measurement and time at liberty are then derived. We moment match the true conditional distributions with skewed-normal distributions and use these to accurately estimate the elements of the STMs. The method is investigated with simulated tag–recapture data and tag–recapture data gathered from the Australian eastern king prawn (Melicertus plebejus).

Essays on the Economics of Intellectual Property Rights

Väitöskirjassani tarkastelen informaatiohyödykkeiden ja tekijänoikeuksien taloustiedettä kahdesta eri perspektiivistä. Niistä ensimmäinen kuuluu endogeenisen kasvuteorian alaan. Väitöskirjassani yleistän ”pool of knowledge” -tyyppisen endogeenisen kasvumallin tilanteeseen, jossa patentoitavissa olevalla innovaatiolla on minimikoko, ja jossa uudenlaisen tuotteen patentoinut yritys voi menettää monopolinsa tuotteeseen jäljittelyn johdosta. Mallin kontekstissa voidaan analysoida jäljittelyn ja innovaatioilta vaaditun ”minimikoon” vaikutuksia hyvinvointiin ja talouskasvuun. Kasvun maksimoiva imitaation määrä on mallissa aina nolla, mutta hyvinvoinnin maksimoiva imitaation määrä voi olla positiivinen. Talouskasvun ja hyvinvoinnin maksimoivalla patentoitavissa olevan innovaation ”minimikoolla” voi olla mikä tahansa teoreettista maksimia pienempi arvo. Väitöskirjani kahdessa jälkimmäisessä pääluvussa tarkastelen informaatiohyödykkeiden kaupallista piratismia mikrotaloustieteellisen mallin avulla. Informaatiohyödykkeistä laittomasti tehtyjen kopioiden tuotantokustannukset ovat pienet, ja miltei olemattomat silloin kun niitä levitetään esimerkiksi Internetissä. Koska piraattikopioilla on monta eri tuottajaa, niiden hinnan voitaisiin mikrotaloustieteen teorian perusteella olettaa laskevan melkein nollaan, ja jos näin kävisi, kaupallinen piratismi olisi mahdotonta. Mallissani selitän kaupallisen piratismin olemassaolon olettamalla, että piratismista saatavan rangaistuksen uhka riippuu siitä, kuinka monille kuluttajille piraatti tarjoaa laittomia hyödykkeitä, ja että se siksi vaikuttaa piraattikopioiden markkinoihin mainonnan kustannuksen tavoin. Kaupallisten piraattien kiinteiden kustannusten lisääminen on mallissani aina tekijänoikeuksien haltijan etujen mukaista, mutta ”mainonnan kustannuksen” lisääminen ei välttämättä ole, vaan se saattaa myös alentaa laillisten kopioiden myynnistä saatavia voittoja. Tämä tulos poikkeaa vastaavista aiemmista tuloksista sikäli, että se pätee vaikka tarkasteltuihin informaatiohyödykkeisiin ei liittyisi verkkovaikutuksia. Aiemmin ei-kaupallisen piratismin malleista on usein johdettu tulos, jonka mukaan informaatiohyödykkeen laittomat kopiot voivat kasvattaa laillisten kopioiden myynnistä saatavia voittoja jos laillisten kopioiden arvo niiden käyttäjille riippuu siitä, kuinka monet muut kuluttajat käyttävät samanlaista hyödykettä ja jos piraattikopioiden saatavuus lisää riittävästi laillisten kopioiden arvoa. Väitöskirjan viimeisessä pääluvussa yleistän mallini verkkotoimialoille, ja tutkin yleistämäni mallin avulla sitä, missä tapauksissa vastaava tulos pätee myös kaupalliseen piratismiin.

Production process of Scots pine.

The accompanying collective research report is the result of the research project in 1986­90 between The Finnish Academy and the former Soviet Academy of Sciences. The project was organized around common field work in Finland and in the former Soviet Union and theoretical analyses of tree growth determining processes. Based on theoretical analyses, dynamic stand growth models were made and their parameters were determined utilizing the field results. Annual cycle affects the tree growth. Our theoretical approach was based on adaptation to local climate conditions from Lapland to South Russia. The initiation of growth was described as a simple low and high temperature accumulation driven model. Linking the theoretical model with long term temperature data allowed us to analyze what type of temperature response produced favorable outcome in different climates. Initiation of growth consumes the carbohydrate reserves in plants. We measured the dynamics of insoluble and soluble sugars in the very northern and Karelian conditions. Clear cyclical pattern was observed but the differences between locations were surprisingly small. Analysis of field measurements of CO2 exchange showed that irradiance is the dominating factor causing variation in photosynthetic rate in natural conditions during summer. The effect of other factors is so small that they can be omitted without any considerable loss of accuracy. A special experiment carried out in Hyytiälä showed that the needle living space, defined as the ratio between the shoot cylindric volume and needle surface area, correlates with the shoot photosynthesis. The penetration of irradiance into Scots pine canopy is a complicated phenomenon because of the movement of the sun on the sky and the complicated structure of branches and needles. A moderately simple but balanced forest radiation regime submodel was constructed. It consists of the tree crown and forest structure, the gap probability calculation and the consideration of spatial and temporal variation of radiation inside the forest. The common field excursions in different geographical regions resulted in a lot of experimental data of regularities of woody structures. The water transport seems to be a good common factor to analyse these properties of tree structure. There are evident regressions between cross-sectional areas measured at different locations along the water pathway from fine roots to needles. The observed regressions have clear geographical trends. For example, the same cross-sectional area can support three times higher needle mass in South Russia than in Lapland. Geographical trends can also be seen in shoot and needle structure. Analysis of data published by several Russian authors show, that one ton of needles transpire 42 ton of water a year. This annual amount of transpiration seems to be independent of geographical location, year and site conditions. The produced theoretical and experimental material is utilised in the development of stand growth model that describes the growth and development of Scots pine stands in Finland and the former Soviet Union. The core of the model is carbon and nutrient balances. This means that carbon obtained in photosynthesis is consumed for growth and maintenance and nutrients are taken according to the metabolic needs. The annual photosynthetic production by trees in the stand is determined as a function of irradiance and shading during the active period. The utilisation of the annual photosynthetic production to the growth of different components of trees is based on structural regularities. Since the fundamental metabolic processes are the same in all locations the same growth model structure can be applied in the large range of Scots pine. The annual photosynthetic production and structural regularities determining the allocation of resources have geographical features. The common field measurements enable the application of the model to the analysis of growth and development of stands growing on the five locations of experiments. The model enables the analysis of geographical differences in the growth of Scots pine. For example, the annual photosynthetic production of a 100-year-old stand at Voronez is 3.5 times higher than in Lapland. The share consumed to needle growth (30 %) and to growth of branches (5 %) seems to be the same in all locations. In contrast, the share of fine roots is decreasing when moving from north to south. It is 20 % in Lapland, 15 % in Hyytiälä Central Finland and Kentjärvi Karelia and 15 % in Voronez South Russia. The stem masses (115­113 ton/ha) are rather similar in Hyytiälä, Kentjärvi and Voronez, but rather low (50 ton/ha) in Lapland. In Voronez the height of the trees reach 29 m being in Hyytiälä and Kentjärvi 22 m and in Lapland only 14 m. The present approach enables utilization of structural and functional knowledge, gained in places of intensive research, in the analysis of growth and development of any stand. This opens new possibilities for growth research and also for applications in forestry practice.

Surface modification of PDMS using atmospheric glow discharge polymerization of tetrafluoroethane for immobilization of biomolecules

In this study an atmospheric glow discharge with a fluorocarbon gas as precursor was used to modify the surface of polydimethyl siloxane (PDMS -(CH3)(2)SiO](n)-). The variation in protein immobilizing capability of PDMS was studied for different times of exposure. It was observed that the concentration of proteins adsorbed on the surface varied in an irregular manner with treatment time. The fluorination results in the formation of a thin film of fluorocarbon on the PDMS surface. The AFM and XPS data suggest that the film cracks due to stress and regains its uniformity thereafter. This Stranski-Krastanov growth model of the film was due to the high growth rate offered by atmospheric glow discharge. (C) 2011 Elsevier B. V. All rights reserved.

Microstructural evolution in laser-ablation-deposited Fe–25 at.% Ge thin film

Films with Fe–25 at.% Ge composition are deposited by the process of laser ablation on single crystal NaCl and Cu substrates at room temperature. Both the vapor and liquid droplets generated in this process are quenched on the substrate. The microstructures of the embedded droplets show size as well as composition dependence. The hierarchy of phase evolution from amorphous to body-centered cubic (bcc) to DO3 has been observed as a function of size. Some of the medium-sized droplets also show direct formation of ordered DO19 phase from the starting liquid. The evolution of disordered bcc structure in some of the droplets indicates disorder trapping during liquid to solid transformation. The microstructural evolution is analyzed on the basis of heat transfer mechanisms and continuous growth model in the solidifying droplets.

Spatial Data Mining and Modeling for visualisation of Rapid Urbanisation

Rapid urbanisation in India has posed serious challenges to the decision makers in regional planning involving plethora of issues including provision of basic amenities (like electricity, water, sanitation, transport, etc.). Urban planning entails an understanding of landscape and urban dynamics with causal factors. Identifying, delineating and mapping landscapes on temporal scale provide an opportunity to monitor the changes, which is important for natural resource management and sustainable planning activities. Multi-source, multi-sensor, multi-temporal, multi-frequency or multi-polarization remote sensing data with efficient classification algorithms and pattern recognition techniques aid in capturing these dynamics. This paper analyses the landscape dynamics of Greater Bangalore by: (i) characterisation of direct impervious surface, (ii) computation of forest fragmentation indices and (iii) modeling to quantify and categorise urban changes. Linear unmixing is used for solving the mixed pixel problem of coarse resolution super spectral MODIS data for impervious surface characterisation. Fragmentation indices were used to classify forests – interior, perforated, edge, transitional, patch and undetermined. Based on this, urban growth model was developed to determine the type of urban growth – Infill, Expansion and Outlying growth. This helped in visualising urban growth poles and consequence of earlier policy decisions that can help in evolving strategies for effective land use policies.

Modeling harvest rates and numbers from age and sex ratios: A demonstration for elephant populations

Illegal harvest rates of wildlife populations are often unknown or difficult to estimate from field data due to under-reporting or incomplete detection of carcasses. This is especially true for elephants that are killed for ivory or in conflicts with people. We describe a method to infer harvest rates from coarse field data of three population parameters, namely, adult female to male ratio, male old-adult to young-adult ratio, and proportion of adult males in the population using Jensen's (2000) 2-sex, density-dependent Leslie matrix model. The specific combination of male and female harvest rates and numbers can be determined from the history of harvest and estimate of population size. We applied this technique to two populations of elephants for which data on age structure and records of mortality were available-a forest-dwelling population of the Asian elephant (at Nagarahole, India) and an African savannah elephant population (at Samburu, Kenya) that had experienced male-biased harvest regimes over 2-3 decades. For the Nagarahole population, the recorded numbers of male and female elephants killed illegally during 1981-2000 were 64% and 88% of the values predicted by the model, respectively, implying some non-detection or incomplete reporting while for the Samburu population the recorded and modeled numbers of harvest during 1990-1999 closely matched. This technique, applicable to any animal population following logistic growth model, can be especially useful for inferring illegal harvest numbers of forest elephants in Africa and Asia.

Modeling harvest rates and numbers from age and sex ratios: A demonstration for elephant populations

Illegal harvest rates of wildlife populations are often unknown or difficult to estimate from field data due to under-reporting or incomplete detection of carcasses. This is especially true for elephants that are killed for ivory or in conflicts with people. We describe a method to infer harvest rates from coarse field data of three population parameters, namely, adult female to male ratio, male old-adult to young-adult ratio, and proportion of adult males in the population using Jensen's (2000) 2-sex, density-dependent Leslie matrix model. The specific combination of male and female harvest rates and numbers can be determined from the history of harvest and estimate of population size. We applied this technique to two populations of elephants for which data on age structure and records of mortality were available-a forest-dwelling population of the Asian elephant (at Nagarahole, India) and an African savannah elephant population (at Samburu, Kenya) that had experienced male-biased harvest regimes over 2-3 decades. For the Nagarahole population, the recorded numbers of male and female elephants killed illegally during 1981-2000 were 64% and 88% of the values predicted by the model, respectively, implying some non-detection or incomplete reporting while for the Samburu population the recorded and modeled numbers of harvest during 1990-1999 closely matched. This technique, applicable to any animal population following logistic growth model, can be especially useful for inferring illegal harvest numbers of forest elephants in Africa and Asia. (C) 2013 Elsevier Ltd. All rights reserved.

Influence of ion energy and substrate temperature on the optical and electronic properties of tetrahedral amorphous carbon (ta-C) films

The properties of amorphous carbon (a-C) deposited using a filtered cathodic vacuum arc as a function of the ion energy and substrate temperature are reported. The sp3 fraction was found to strongly depend on the ion energy, giving a highly sp3 bonded a-C denoted as tetrahedral amorphous carbon (ta-C) at ion energies around 100 eV. The optical band gap was found to follow similar trends to other diamondlike carbon films, varying almost linearly with sp2 fraction. The dependence of the electronic properties are discussed in terms of models of the electronic structure of a-C. The structure of ta-C was also strongly dependent on the deposition temperature, changing sharply to sp2 above a transition temperature, T1, of ≈200°C. Furthermore, T1 was found to decrease with increasing ion energy. Most film properties, such as compressive stress and plasmon energy, were correlated to the sp3 fraction. However, the optical and electrical properties were found to undergo a more gradual transition with the deposition temperature which we attribute to the medium range order of sp2 sites. We attribute the variation in film properties with the deposition temperature to diffusion of interstitials to the surface above T1 due to thermal activation, leading to the relaxation of density in context of a growth model. © 1997 American Institute of Physics.

Statistical and stochastic description of microvoid evolution observed in dynamic failure of ductile materials

A brief review is presented of statistical approaches on microdamage evolution. An experimental study of statistical microdamage evolution in two ductile materials under dynamic loading is carried out. The observation indicates that there are large differences in size and distribution of microvoids between these two materials. With this phenomenon in mind, kinetic equations governing the nucleation and growth of microvoids in nonlinear rate-dependent materials are combined with the balance law of void number to establish statistical differential equations that describe the evolution of microvoids' number density. The theoretical solution provides a reasonable explanation of the experimentally observed phenomenon. The effects of stochastic fluctuation which is influenced by the inhomogeneous microscopic structure of materials are subsequently examined (i.e. stochastic growth model). Based on the stochastic differential equation, a Fokker-Planck equation which governs the evolution of the transition probability is derived. The analytical solution for the transition probability is then obtained and the effects of stochastic fluctuation is discussed. The statistical and stochastic analyses may provide effective approaches to reveal the physics of damage evolution and dynamic failure process in ductile materials.

Collective evolution characteristics and computer simulation of short fatigue cracks

Fatigue testing was conducted using a kind of triangular isostress specimen to obtain the short-fatigue-crack behaviour of a weld low-carbon steel. The experimental results show that short cracks continuously initiate at slip bands within ferrite grain domains and the crack number per unit area gradually increases with increasing number of fatigue cycles. The dispersed short cracks possess an orientation preference, which is associated with the crystalline orientation of the relevant slip system. Based on the observed collective characteristics, computer modelling was carried out to simulate the evolution process of initiation, propagation and coalescence of short cracks. The simulation provides progressive displays which imitate the appearance of experimental observations. The results of simulation indicate that the crack path possesses a stable value of fractal dimension whereas the critical value of percolation covers a wide datum band, suggesting that the collective evolution process of short cracks is sensitive to the pattern of crack site distribution.

Spall damage in aluminum-alloy

A void growth relations for ductile porous materials under intense dynamic general loading condition is presented. The mathematical model includes the influence of inertial effects, material rate sensitivity, as well as the contribution of void surface energy and material work-hardening. Numerical analysis shows that inertia appears to resist the growth of voids. The inertial effects increase quickly with the loading rates. The theoretical analysis suggests that the inertial effects cannot be neglected at high loading rates. Plate-impact tests of aluminum alloy are performed with light gas gun. The processes of dynamic damage in aluminum alloy are successfully simulated with a finite-difference dynamic code in which the theoretical model presented in this paper is incorporated.