Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.

The Road to Hell Is Paved with Good Interventions : A Pragmatic Examination of Humanitarian Intervention with Special Reference to Kosovo

Kansainvälisen oikeuden alaan kuuluvassa tutkielmassa käsitellään humanitaarisen intervention oikeutusta ja laillisuutta. Tutkimuskysymyksenä on, missä määrin humanitaarisilla näkökohdilla perusteltuja sotilaallisia toimia tai niillä uhkaamista voi pitää kansainvälisoikeudellisesti hyväksyttävänä ja millainen painoarvo ennakkotapauksena olisi annettava NATO-maiden Kosovossa toteuttamalle väliintulolle. Tutkielmassa perehdytään ihmisoikeusajattelun tiettyjen taustaoletusten kritiikkiin. Tarkastelun kohteena ovat erityisesti kannanotot, joiden mukaan ihmisoikeuksia ei voi pitää luonteeltaan universaaleina, sekä kyseiseen kritiikkiin liittyvät väitteet siitä, että ns. hegemonisessa asemassa olevat valtiot hyödyntävät ihmisoikeusargumentteja oikeuttaakseen voimankäyttönsä. Universaalisuuskritiikkiä voidaan pitää pitkälti perusteltuna, mutta nykyinen kansainvälinen yhteisö tarvitsee kuitenkin tietynlaisia yleismaailmallisia normeja voidakseen toimia tehokkaasti. Kritiikin ei voikaan katsoa pätevän humanitaarisen intervention kannalta keskeisiin ihmisoikeusnormeihin kuten kansanmurhan kieltoon, sillä kyseiset velvoitteet suojaavat kansainvälisen yhteisön toimivuutta ja uskottavuutta. Humanitaarisiin argumentteihin liittyy kuitenkin muita ongelmia: niillä on esimerkiksi aika ajoin pyritty oikeuttamaan sotilaallisia toimia, joissa ihmisoikeusnäkökohdat eivät välttämättä ole olleet etusijalla. Ihmisoikeuksille ei ole syytä antaa kansainvälisessä oikeudessa asemaa universaaleina "superargumentteina", jotka eivät olisi kyseenalaistettavissa. YK:n peruskirjan ja kansainvälisen tapaoikeuden näkökulmasta humanitaarisen intervention kaltaiseen voimankäyttöön vaaditaan turvallisuusneuvoston hyväksyntä, jota ei Kosovo-operaatioon saatu. Interventiota voi tässä suhteessa pitää yksiselitteisesti laittomana, sillä sen tueksi esitetyt oikeudelliset argumentit eivät ole vakuuttavia. Tapaukseen liittyvät ihmisoikeusnäkökohdat ovat kuitenkin siinä määrin merkittäviä, että ongelmaan ei ole perusteltua suhtautua tiukan legalistisesti. Operaation hyväksyminen moraaliargumenttien nojalla voisi kuitenkin johtaa nykyisten voimankäyttörajoitusten marginalisoitumiseen, mikä olisi yllä käsitellyn kritiikin valossa ongelmallista. Tutkielmassa nostetaan suositeltavaksi ratkaisuksi lähestymistapa, jossa Kosovon tapaus ymmärretään yksittäisenä oikeudenvastaisena mutta samalla oikeudenulkoisena poikkeustapauksena. Tällöin peruskirjan mukainen voimankäytön sääntely säilyy entisellään ilman että humanitaariset näkökohdat jäisivät tyystin huomiotta. Ratkaisu ei sulje pois mahdollisuutta suhtautua positiivisesti Kosovo-operaation mahdollisesti luomaan "poliittiseen normiin": suuren mittakaavan ihmisoikeusloukkaukset eivät jää Euroopassa seurauksitta. Ilman turvallisuusneuvoston suostumusta toteutettaviin humanitaarisiin interventioihin liittyvien käytännöllisten ja kansainvälisoikeudellisten riskien vuoksi niihin on kuitenkin aihetta suhtautua suurella varauksella.

Mathematical modelling and numerical simulation of phosphine flow during grain fumigation in leaky cylindrical silos

The phosphine distribution in a cylindrical silo containing grain is predicted. A three-dimensional mathematical model, which accounts for multicomponent gas phase transport and the sorption of phosphine into the grain kernel is developed. In addition, a simple model is presented to describe the death of insects within the grain as a function of their exposure to phosphine gas. The proposed model is solved using the commercially available computational fluid dynamics (CFD) software, FLUENT, together with our own C code to customize the solver in order to incorporate the models for sorption and insect extinction. Two types of fumigation delivery are studied, namely, fan- forced from the base of the silo and tablet from the top of the silo. An analysis of the predicted phosphine distribution shows that during fan forced fumigation, the position of the leaky area is very important to the development of the gas flow field and the phosphine distribution in the silo. If the leak is in the lower section of the silo, insects that exist near the top of the silo may not be eradicated. However, the position of a leak does not affect phosphine distribution during tablet fumigation. For such fumigation in a typical silo configuration, phosphine concentrations remain low near the base of the silo. Furthermore, we find that half-life pressure test readings are not an indicator of phosphine distribution during tablet fumigation.

Computation of turbulent flow in an IFRF quarl burner

A computational model for isothermal axisymmetric turbulent flow in a quarl burner is set up using the CFD package FLUENT, and numerical solutions obtained from the model are compared with available experimental data. A standard k-e model and and two versions of the RNG k-e model are used to model the turbulence. One of the aims of the computational study is to investigate whether the RNG based k-e turbulence models are capable of yielding improved flow predictions compared with the standard k-e turbulence model. A difficulty is that the flow considered here features a confined vortex breakdown which can be highly sensitive to flow behaviour both upstream and downstream of the breakdown zone. Nevertheless, the relatively simple confining geometry allows us to undertake a systematic study so that both grid-independent and domain-independent results can be reported. The systematic study includes a detailed investigation of the effects of upstream and downstream conditions on the predictions, in addition to grid refinement and other tests to ensure that numerical error is not significant. Another important aim is to determine to what extent the turbulence model predictions can provide us with new insights into the physics of confined vortex breakdown flows. To this end, the computations are discussed in detail with reference to known vortex breakdown phenomena and existing theories. A major conclusion is that one of the RNG k-e models investigated here is able to correctly capture the complex forward flow region inside the recirculating breakdown zone. This apparently pathological result is in stark contrast to the findings of previous studies, most of which have concluded that either algebraic or differential Reynolds stress modelling is needed to correctly predict the observed flow features. Arguments are given as to why an isotropic eddy-viscosity turbulence model may well be able to capture the complex flow structure within the recirculating zone for this flow setup. With regard to the flow physics, a major finding is that the results obtained here are more consistent with the view that confined vortex breakdown is a type of axisymmetric boundary layer separation, rather than a manifestation of a subcritical flow state.

Recapitulation in generating spatial layouts: Representations of embryogenesis in evolutionary design modelling

The noted 19th century biologist, Ernst Haeckel, put forward the idea that the growth (ontogenesis) of an organism recapitulated the history of its evolutionary development. While this idea is defunct within biology, the idea has been promoted in areas such as education (the idea of an education being the repetition of the civilizations before). In the research presented in this paper, recapitulation is used as a metaphor within computer-aided design as a way of grouping together different generations of spatial layouts. In most CAD programs, a spatial layout is represented as a series of objects (lines, or boundary representations) that stand in as walls. The relationships between spaces are not usually explicitly stated. A representation using Lindenmayer Systems (originally designed for the purpose of modelling plant morphology) is put forward as a way of representing the morphology of a spatial layout. The aim of this research is not just to describe an individual layout, but to find representations that link together lineages of development. This representation can be used in generative design as a way of creating more meaningful layouts which have particular characteristics. The use of genetic operators (mutation and crossover) is also considered, making this representation suitable for use with genetic algorithms.

Adsorption isotherms-microscopic modelling

The phenomenon of adsorption is governed by the various interactions among the constituents of the interface and the forms of adsorption isotherms hold the clue to the nature of the se in teractions. An understanding of this phenomenon may be said to be complete only when the parameters occurring in such expres - sions for isotherms are interpretable in terms of molecular/electronic interactions.This objective viz. expressing the composition of the isotherm parameters through a microscopic modelling is by no means a simple one. Such a task is particularly made difficult in the case of charged interfaces where idealisation is difficult to make and, when made, not so easy to justify.

Theory of Non-linear Waves in Multi-dimensions: with Special Reference to Surface Water Waves

The surface water waves are "modal" waves in which the "physical space" (t, x, y, z) is the product of a propagation space (t, x, y) and a cross space, the z-axis in the vertical direction. We have derived a new set of equations for the long waves in shallow water in the propagation space. When the ratio of the amplitude of the disturbance to the depth of the water is small, these equations reduce to the equations derived by Whitham (1967) by the variational principle. Then we have derived a single equation in (t, x, y)-space which is a generalization of the fourth order Boussinesq equation for one-dimensional waves. In the neighbourhood of a wave froat, this equation reduces to the multidimensional generalization of the KdV equation derived by Shen & Keller (1973). We have also included a systematic discussion of the orders of the various non-dimensional parameters. This is followed by a presentation of a general theory of approximating a system of quasi-linear equations following one of the modes. When we apply this general method to the surface water wave equations in the propagation space, we get the Shen-Keller equation.

Hierarchical modelling of acclimatory processesstar, open

The term acclimation has been used with several connotations in the field of acclimatory physiology. An attempt has been made, in this paper, to define precisely the term “acclimation” for effective modelling of acclimatory processes. Acclimation is defined with respect to a specific variable, as cumulative experience gained by the organism when subjected to a step change in the environment. Experimental observations on a large number of variables in animals exposed to sustained stress, show that after initial deviation from the basal value (defined as “growth”), the variables tend to return to basal levels (defined as “decay”). This forms the basis for modelling biological responses in terms of their growth and decay. Hierarchical systems theory as presented by Mesarovic, Macko & Takahara (1970) facilitates modelling of complex and partially characterized systems. This theory, in conjunction with “growth-decay” analysis of biological variables, is used to model temperature regulating system in animals exposed to cold. This approach appears to be applicable at all levels of biological organization. Regulation of hormonal activity which forms a part of the temperature regulating system, and the relationship of the latter with the “energy” system of the animal of which it forms a part, are also effectively modelled by this approach. It is believed that this systematic approach would eliminate much of the current circular thinking in the area of acclimatory physiology.

Modelling user profiles for recommender systems

Recommender systems assist users in finding what they want. The challenging issue is how to efficiently acquire user preferences or user information needs for building personalized recommender systems. This research explores the acquisition of user preferences using data taxonomy information to enhance personalized recommendations for alleviating cold-start problem. A concept hierarchy model is proposed, which provides a two-dimensional hierarchy for acquiring user preferences. The language model is also extended for the proposed hierarchy in order to generate an effective recommender algorithm. Both Amazon.com book and music datasets are used to evaluate the proposed approach, and the experimental results show that the proposed approach is promising.

New structural insights and molecular-modelling studies of 4-methyl-5-beta-hydroxyethylthiazole kinase from Pyrococcus horikoshii OT3 (PhThiK)

4-Methyl-5-beta-hydroxyethylthiazole kinase (ThiK) catalyses the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole. This work reports the first crystal structure of an archaeal ThiK: that from Pyrococcus horikoshii OT3 (PhThiK) at 1.85 angstrom resolution with a phosphate ion occupying the position of the beta-phosphate of the nucleotide. The topology of this enzyme shows the typical ribokinase fold of an alpha/beta protein. The overall structure of PhThiK is similar to those of Bacillus subtilis ThiK (BsThiK) and Enterococcus faecalis V583 ThiK (EfThiK). Sequence analysis of ThiK enzymes from various sources indicated that three-quarters of the residues involved in interfacial regions are conserved. It also revealed that the amino-acid residues in the nucleotide-binding, magnesium ion-binding and substrate-binding sites are conserved. Binding of the nucleotide and substrate to the ThiK enzyme do not influence the quaternary association (trimer) as revealed by the crystal structure of PhThiK.

Conceptual and statistical modelling of environmental effects in population dynamics

Population dynamics are generally viewed as the result of intrinsic (purely density dependent) and extrinsic (environmental) processes. Both components, and potential interactions between those two, have to be modelled in order to understand and predict dynamics of natural populations; a topic that is of great importance in population management and conservation. This thesis focuses on modelling environmental effects in population dynamics and how effects of potentially relevant environmental variables can be statistically identified and quantified from time series data. Chapter I presents some useful models of multiplicative environmental effects for unstructured density dependent populations. The presented models can be written as standard multiple regression models that are easy to fit to data. Chapters II IV constitute empirical studies that statistically model environmental effects on population dynamics of several migratory bird species with different life history characteristics and migration strategies. In Chapter II, spruce cone crops are found to have a strong positive effect on the population growth of the great spotted woodpecker (Dendrocopos major), while cone crops of pine another important food resource for the species do not effectively explain population growth. The study compares rate- and ratio-dependent effects of cone availability, using state-space models that distinguish between process and observation error in the time series data. Chapter III shows how drought, in combination with settling behaviour during migration, produces asymmetric spatially synchronous patterns of population dynamics in North American ducks (genus Anas). Chapter IV investigates the dynamics of a Finnish population of skylark (Alauda arvensis), and point out effects of rainfall and habitat quality on population growth. Because the skylark time series and some of the environmental variables included show strong positive autocorrelation, the statistical significances are calculated using a Monte Carlo method, where random autocorrelated time series are generated. Chapter V is a simulation-based study, showing that ignoring observation error in analyses of population time series data can bias the estimated effects and measures of uncertainty, if the environmental variables are autocorrelated. It is concluded that the use of state-space models is an effective way to reach more accurate results. In summary, there are several biological assumptions and methodological issues that can affect the inferential outcome when estimating environmental effects from time series data, and that therefore need special attention. The functional form of the environmental effects and potential interactions between environment and population density are important to deal with. Other issues that should be considered are assumptions about density dependent regulation, modelling potential observation error, and when needed, accounting for spatial and/or temporal autocorrelation.

Numerical modelling of rivet fastened rectangular hollow flange channel beams subject to shear

The intermittently rivet fastened Rectangular Hollow Flange Channel Beam (RHFCB) is a new cold-formed hollow section proposed as an alternative to welded hollow flange beams. Many experimental and numerical studies have been carried out in the past to investigate the shear behaviour of lipped channel beams. However, no research has been undertaken on the shear behaviour of rivet fastened RHFCBs. Therefore experimental and numerical studies were undertaken to investigate the shear behaviour and strength of rivet fastened RHFCBs. In this research finite element models of rivet fastened RHFCBs were developed to investigate their nonlinear shear behaviour including their buckling characteristics and ultimate shear strength. This paper presents the details of the finite element models of rivet fastened RHFCBs and the results. Both finite element analysis and experimental results showed that the current design rules are very conservative for the shear design of rivet fastened RHFCBs. Appropriate improvements have been proposed for the design rules of shear strength of rivet fastened RHFCBs within the Direct Strength Method format.

Thermal performance of magnesium oxide wall board using numerical modelling

Fire resistance of light-gauge steel frame (LSF) walls can be enhanced by lining them with single or multiple layers of wall boards. This research is focused on the thermal per-formance of Magnesium Oxide (MgO) wall boards in comparison to the conventional gypsum plasterboards exposed to standard fire on one side. Thermal properties of MgO board and gypsum plasterboard were measured first and then used in the finite element heat transfer models of the two types of panels. The measured thermal property results show that MgO board will perform better than the gypsum plasterboards due to its higher specific heat values at elevated temperatures. However, MgO board loses 50% of its ini-tial mass at about 500 °C compared to 16% for gypsum plasterboard. The developed finite element models were validated using the fire test results of gypsum plasterboards and then used to study the thermal performance of MgO board panels. Finite element analysis re-sults show that when MgO board panels are exposed to standard fire on one side the rate of temperature rise on the ambient side is significantly reduced compared to gypsum plas-terboard. This has the potential to improve the overall thermal performance of MgO board lined LSF walls and their fire resistance levels (FRL). However, full scale fire tests are needed to confirm this. This paper presents the details of this investigation and the results.

Material characterisation and numerical modelling of gypsum plasterboards in fire

The fire resistance characteristic of LSF wall systems mainly depends on the protective linings in use, commonly gypsum plasterboards. However, unclassified boards with varying composition and more notably with ambiguous thermal properties are increasingly becoming available in the market. Therefore a study was undertaken with an aim to set minimum standards for fire protective boards used in LSF wall applications. This paper presents the details of this study based on material characterisation and finite element thermal modelling of the most commonly used fire protective board, gypsum plasterboards, to address these critical issues related to fire safety design. In the material characterisation phase of this study, thermal properties of three different gypsum plasterboards manufactured in Australia were measured, analysed and compared. Subsequently, it proposes a thermal property based “k-factor” capable of giving an overall measure of the fire performance of boards, so that it can be used in appropriately classifying fire protective boards. As it is not known how this factor relates to the overall fire performance of LSF wall systems, numerical models were also developed and used to simulate the performance of LSF walls exposed to the standard fire. Finally, a correlation between time-temperature profiles from numerical analyses and calculated k-factors was established.

A Control Strategy for Reference Wave Adaptive Current Generation

Speed control of ac motors requires variable frequency, variable current, or variable voltage supply. Variable frequency supply can be obtained directly from a fixed frequency supply by using a frequency converter or from a dc source using inverters. In this paper a control technique for reference wave adaptive-current generation by modulating the inverter voltage is explained. Extension of this technique for three-phase induction-motor speed control is briefly explained. The oscillograms of the current waveforms obtained from the experimental setup are also shown.