Using crop simulation to generate genotype by environment interaction effects for sorghum in water-limited environments

Multi-environment trials (METs) used to evaluate breeding lines vary in the number of years that they sample. We used a cropping systems model to simulate the target population of environments (TPE) for 6 locations over 108 years for 54 'near-isolines' of sorghum in north-eastern Australia. For a single reference genotype, each of 547 trials was clustered into 1 of 3 'drought environment types' (DETs) based on a seasonal water stress index. Within sequential METs of 2 years duration, the frequencies of these drought patterns often differed substantially from those derived for the entire TPE. This was reflected in variation in the mean yield of the reference genotype. For the TPE and for 2-year METs, restricted maximum likelihood methods were used to estimate components of genotypic and genotype by environment variance. These also varied substantially, although not in direct correlation with frequency of occurrence of different DETs over a 2-year period. Combined analysis over different numbers of seasons demonstrated the expected improvement in the correlation between MET estimates of genotype performance and the overall genotype averages as the number of seasons in the MET was increased.

Conditional simulation of random fields by successive residuals

This paper presents a new approach to the LU decomposition method for the simulation of stationary and ergodic random fields. The approach overcomes the size limitations of LU and is suitable for any size simulation. The proposed approach can facilitate fast updating of generated realizations with new data, when appropriate, without repeating the full simulation process. Based on a novel column partitioning of the L matrix, expressed in terms of successive conditional covariance matrices, the approach presented here demonstrates that LU simulation is equivalent to the successive solution of kriging residual estimates plus random terms. Consequently, it can be used for the LU decomposition of matrices of any size. The simulation approach is termed conditional simulation by successive residuals as at each step, a small set (group) of random variables is simulated with a LU decomposition of a matrix of updated conditional covariance of residuals. The simulated group is then used to estimate residuals without the need to solve large systems of equations.

A novel bioassay for human somatogenic activity in serum samples supports the clinical reliability of immunoassays

OBJECTIVE Because there is discordance between different immunoassay values for serum hGH, and because clinical state may not correlate with immunoreactive hGH, we have developed an assay to accurately measure serum hGH somatogenic bioactivity. The results of this assay were compared with the Elegance two-site ELISA assay across 135 patient samples in a variety of clinical states. DESIGN The somatogenic assay was based on stable expression of hGH receptor in the murine BaF line, allowing these cells to proliferate in response to hGH. To eliminate interference by other growth factors in serum, we created a specific antagonist of the hGH receptor (similar to Trovert or Pegvisomant) which allowed us to obtain a true measure of hGH somatogenic activity by subtraction of the activity in the presence of the antagonist. The assay was carried out in microtiter plates over 24 h, with oxidation of a chromogenic tetrazolium salt (MTT) as the endpoint. PATIENTS These encompassed a number of different clinical conditions related to short stature, including idiopathic short stature, neurosecretory dysfunction and renal failure, as well as obese patients on dietary restriction and normal volunteers. MEASUREMENTS In addition to the colourimetric (MTT) response to hGH, we measured free hGH by stripping out GHBP-bound hGH using beads coupled to a monoclonal antibody to the GHBP (GH binding protein). All samples were measured in both bioassay and ELISA assay. RESULTS This bioassay was sensitive (5 mU/l or 2 mug/l) and precise, and not subject to interference by the GHBP. There was a good correlation (r = 0.95) between bioactivity and immunoactivity across clinical states. There was, however, an increased bioactivity during secretory peaks (over 25 mU/l), which has been reported previously for the Nb2 bioassay. Free hGH did not correlate with clinical state. CONCLUSIONS Because the results of the Elegance ELISA and the bioassay correlate well, even though there is greater bioactivity at higher hormone concentrations, it is evident that an appropriate immunoassay is able to act as a reliable indicator for clinical assessment. In those rare cases where bio-inactive GH exists, our bioassay should provide an appropriate means to demonstrate this.

Simulation of the load-unload response ratio and critical sensitivity in the lattice solid model

The Load-Unload Response Ratio (LURR) method is an intermediate-term earthquake prediction approach that has shown considerable promise. It involves calculating the ratio of a specified energy release measure during loading and unloading where loading and unloading periods are determined from the earth tide induced perturbations in the Coulomb Failure Stress on optimally oriented faults. In the lead-up to large earthquakes, high LURR values are frequently observed a few months or years prior to the event. These signals may have a similar origin to the observed accelerating seismic moment release (AMR) prior to many large earthquakes or may be due to critical sensitivity of the crust when a large earthquake is imminent. As a first step towards studying the underlying physical mechanism for the LURR observations, numerical studies are conducted using the particle based lattice solid model (LSM) to determine whether LURR observations can be reproduced. The model is initialized as a heterogeneous 2-D block made up of random-sized particles bonded by elastic-brittle links. The system is subjected to uniaxial compression from rigid driving plates on the upper and lower edges of the model. Experiments are conducted using both strain and stress control to load the plates. A sinusoidal stress perturbation is added to the gradual compressional loading to simulate loading and unloading cycles and LURR is calculated. The results reproduce signals similar to those observed in earthquake prediction practice with a high LURR value followed by a sudden drop prior to macroscopic failure of the sample. The results suggest that LURR provides a good predictor for catastrophic failure in elastic-brittle systems and motivate further research to study the underlying physical mechanisms and statistical properties of high LURR values. The results provide encouragement for earthquake prediction research and the use of advanced simulation models to probe the physics of earthquakes.

Simulation of the micro-physics of rocks using LSMearth

The particle-based Lattice Solid Model (LSM) was developed to provide a basis to study the physics of rocks and the nonlinear dynamics of earthquakes (MORA and PLACE, 1994; PLACE and MORA, 1999). A new modular and flexible LSM approach has been developed that allows different microphysics to be easily included in or removed from the model. The approach provides a virtual laboratory where numerical experiments can easily be set up and all measurable quantities visualised. The proposed approach provides a means to simulate complex phenomena such as fracturing or localisation processes, and enables the effect of different micro-physics on macroscopic behaviour to be studied. The initial 2-D model is extended to allow three-dimensional simulations to be performed and particles of different sizes to be specified. Numerical bi-axial compression experiments under different confining pressure are used to calibrate the model. By tuning the different microscopic parameters (such as coefficient of friction, microscopic strength and distribution of grain sizes), the macroscopic strength of the material and can be adjusted to be in agreement with laboratory experiments, and the orientation of fractures is consistent with the theoretical value predicted based on Mohr-Coulomb diagram. Simulations indicate that 3-D numerical models have different macroscopic properties than in 2-D and, hence, the model must be recalibrated for 3-D simulations. These numerical experiments illustrate that the new approach is capable of simulating typical rock fracture behaviour. The new model provides a basis to investigate nucleation, rupture and slip pulse propagation in complex fault zones without the previous model limitations of a regular low-level surface geometry and being restricted to two-dimensions.

Simulation of the influence of rate- and state-dependent friction on the macroscopic behavior of complex fault zones with the lattice solid model

In order to understand the earthquake nucleation process, we need to understand the effective frictional behavior of faults with complex geometry and fault gouge zones. One important aspect of this is the interaction between the friction law governing the behavior of the fault on the microscopic level and the resulting macroscopic behavior of the fault zone. Numerical simulations offer a possibility to investigate the behavior of faults on many different scales and thus provide a means to gain insight into fault zone dynamics on scales which are not accessible to laboratory experiments. Numerical experiments have been performed to investigate the influence of the geometric configuration of faults with a rate- and state-dependent friction at the particle contacts on the effective frictional behavior of these faults. The numerical experiments are designed to be similar to laboratory experiments by DIETERICH and KILGORE (1994) in which a slide-hold-slide cycle was performed between two blocks of material and the resulting peak friction was plotted vs. holding time. Simulations with a flat fault without a fault gouge have been performed to verify the implementation. These have shown close agreement with comparable laboratory experiments. The simulations performed with a fault containing fault gouge have demonstrated a strong dependence of the critical slip distance D-c on the roughness of the fault surfaces and are in qualitative agreement with laboratory experiments.

Parallel simulation system for earthquake generation: Fault analysis modules and parallel coupling analysis

Solid earth simulations have recently been developed to address issues such as natural disasters, global environmental destruction and the conservation of natural resources. The simulation of solid earth phenomena involves the analysis of complex structures including strata, faults, and heterogeneous material properties. Simulation of the generation and cycle of earthquakes is particularly important, but such simulations require the analysis of complex fault dynamics. GeoFEM is a parallel finite-element analysis system intended for solid earth field phenomena problems. This paper describes recent development in the GeoFEM project for the simulation of earthquake generation and cycles.

An overview of APSIM, a model designed for farming systems simulation

The Agricultural Production Systems Simulator (APSIM) is a modular modelling framework that has been developed by the Agricultural Production Systems Research Unit in Australia. APSIM was developed to simulate biophysical process in farming systems, in particular where there is interest in the economic and ecological outcomes of management practice in the face of climatic risk. The paper outlines APSIM's structure and provides details of the concepts behind the different plant, soil and management modules. These modules include a diverse range of crops, pastures and trees, soil processes including water balance, N and P transformations, soil pH, erosion and a full range of management controls. Reports of APSIM testing in a diverse range of systems and environments are summarised. An example of model performance in a long-term cropping systems trial is provided. APSIM has been used in a broad range of applications, including support for on-farm decision making, farming systems design for production or resource management objectives, assessment of the value of seasonal climate forecasting, analysis of supply chain issues in agribusiness activities, development of waste management guidelines, risk assessment for government policy making and as a guide to research and education activity. An extensive citation list for these model testing and application studies is provided. Crown Copyright (C) 2002 Published by Elsevier Science B.V. All rights reserved.

Measuring range of active cervical rotation in a position of full head flexion using the 3D Fastrak measurement system: an intra-tester reliability study

Most external assessments of cervical range of motion assess the upper and lower cervical regions simultaneously. This study investigated the within and between days reliability of the clinical method used to bias this movement to the upper cervical region, namely measuring rotation of the head and neck in a position of full cervical flexion. Measurements were made using the Fastrak measurement system and were conducted by one operator. Results indicated high levels of within and between days repeatability (range of ICC2,1 values: 0.85-0.95). The ranges of axial rotation to right and left, measured with the neck positioned in full flexion, were approximately 56% and 50%, respectively of total cervical rotation, which relates well to the proportional division of rotation in the upper and lower cervical regions. These results suggest that this method of measuring rotation would be appropriate for use in subject studies where movement dysfunction is present in the upper cervical region, such as those with cervicogenic headache. (C) 2003 Elsevier Science Ltd. All rights reserved.

Assessing childrens competence in computer interactions: Preliminary reliability and validity of the test of mouse proficiency

The Test of Mouse Proficiency (TOMP) was developed to assist occupational therapists and education professionals assess computer mouse competency skills in children from preschool to upper primary (elementary) school age. The preliminary reliability and validity of TOMP are reported in this paper. Methods used to examine the internal consistency, test-retest reliability, and criterion- and construct-related validity of the test are elaborated. In the continuing process of test refinement, these preliminary studies support to varying degrees the reliability and validity of TOMP. Recommendations for further validation of the assessment are discussed along with indications for potential clinical application.

Warranty and optimal reliability improvement through product development

For products sold with warranty, the warranty servicing cost can be reduced by improving product reliability through a development process. However, this increases the unit manufacturing cost. Optimal development must achieve a trade-off between these two costs. The outcome of the development process is uncertain and needs to be taken into account in the determination of the optimal development effort. The paper develops a model where this uncertainty is taken into account. (C) 2003 Elsevier Ltd. All rights reserved.

The reliability of video based time motion analysis

Time motion analysis is extensively used to assess the demands of team sports. At present there is only limited information on the reliability of measurements using this analysis tool. The aim of this study was to establish the reliability of an individual observer's time motion analysis of rugby union. Ten elite level rugby players were individually tracked in Southern Hemisphere Super 12 matches using a digital video camera. The video footage was subsequently analysed by a single researcher on two occasions one month apart. The test-retest reliability was quantified as the typical error of measurement (TEM) and rated as either good (10% TEM). The total time spent in the individual movements of walking, jogging, striding, sprinting, static exertion and being stationary had moderate to poor reliability (5.8-11.1% TEM). The frequency of individual movements had good to poor reliability (4.3-13.6% TEM), while the mean duration of individual movements had moderate reliability (7.1-9.3% TEM). For the individual observer in the present investigation, time motion analysis was shown to be moderately reliable as an evaluation tool for examining the movement patterns of players in competitive rugby. These reliability values should be considered when assessing the movement patterns of rugby players within competition.