An effective non-parametric method for globally clustering genes from expression profiles

Clustering is widely used in bioinformatics to find gene correlation patterns. Although many algorithms have been proposed, these are usually confronted with difficulties in meeting the requirements of both automation and high quality. In this paper, we propose a novel algorithm for clustering genes from their expression profiles. The unique features of the proposed algorithm are twofold: it takes into consideration global, rather than local, gene correlation information in clustering processes; and it incorporates clustering quality measurement into the clustering processes to implement non-parametric, automatic and global optimal gene clustering. The evaluation on simulated and real gene data sets demonstrates the effectiveness of the algorithm.

Parametric conditional frailty models for recurrent cardiovascular events in the lipid study

Background Analysis of recurrent event data is frequently needed in clinical and epidemiological studies. An important issue in such analysis is how to account for the dependence of the events in an individual and any unobserved heterogeneity of the event propensity across individuals.Methods We applied a number of conditional frailty and nonfrailty models in an analysis involving recurrent myocardial infarction events in the Long-Term Intervention with Pravastatin in Ischaemic Disease study. A multiple variable risk prediction model was developed for both males and females. Results A Weibull model with a gamma frailty term fitted the data better than other frailty models for each gender. Among nonfrailty models the stratified survival model fitted the data best for each gender. The relative risk estimated by the elapsed time model was close to that estimated by the gap time model. We found that a cholesterol-lowering drug, pravastatin (the intervention being tested in the trial) had significant protective effect against the occurrence of myocardial infarction in men (HR¼0.71, 95% CI0.60–0.83). However, the treatment effect was not significant in women due to smaller sample size (HR¼0.75, 95% CI 0.51–1.10). There were no significant interactions between the treatment effect and each recurrent MI event (p¼0.24 for men and p¼0.55 for women). The risk of developing an MI event for a male who had an MI event during follow-up was about 3.4 (95% CI 2.6–4.4) times the risk compared with those who did not have an MI event. The corresponding relative risk for a female was about 7.8 (95% CI 4.4–13.6). Limitations The number of female patients was relatively small compared with their male counterparts, which may result in low statistical power to find real differences in the effect of treatment and other potential risk factors.Conclusions The conditional frailty model suggested that after accounting for all the risk factors in the model, there was still unmeasured heterogeneity of the risk for myocardial infarction, indicating the effect of subject-specific risk factors. These risk prediction models can be used to classify cardiovascular disease patients into different risk categories and may be useful for the most effective targeting of preventive therapies for cardiovascular disease.

Parametric modelling and the tessellation of architectural surfaces

Parametric modelling is gaining in popularity as both a fabrication and design tool, but its application in the architectural design industry has not been widely explored. This form of modelling has the ability to generate complex forms with intuitively reactive components, allowing designers to express and
fabricate structures previously too laborious and geometrically complex to realise. The key aim of the paper is to address the increasing need for seamless and bi-directional connectivity between the design, modelling and
fabrication ambit.

A simple parametric method for reducing sample sizes in gut passage time trials

Seed dispersal is now regularly analyzed using spatially explicit models, relying in part on frugivore gut passage times to produce model outputs. In determining species-specific gut passage times, there is a trade-off in sample size between minimizing collection effort and maintaining statistical reliability. Here we demonstrate that a two-parameter lognormal parametric distribution reliably fits empirical gut passage time distributions and is easily parameterized using relatively small data sets of approximately 30 defecations. We suggest this approach as a statistically reliable substitute for larger empirical gut passage data sets in seed dispersal modeling, and also as a way of using published gut passage data sets to parameterize new models.

Non-Deterministic Exploration through Parametric Design

This paper explores non-deterministic parametric modelling as a design tool. Specifically, it addresses the application of parametric variables to the generation of a conceptual bridge design and the use of repeatable discrete components to the conceptual form. In order to control the generation of the bridge form, a set of design variables based on the concept of a law curve have been developed.These design variables are applied and tested through interactive modelling and variation, driven by manipulating the law curve. Combining this process with the application and control of a repeatable element, known as a Representative Volumetric Element (RVE), allows for the development and exploration of a design solution that could not be achieved through the use of conventional computer modelling.The competition brief for the Australian Institute of Architects (AIA) ‘Dialectical Bridge’ has been used as a case study to demonstrate the use of non-deterministic parametric modelling as a design tool.The results of the experimentation with parametric variables, the law curve and representative volumetric elements (RVE) are presented in the paper.

Parametric modelling of architectural surfaces

Parametric modelling is gaining in popularity as both a fabrication and design tool, but its application in the architectural design industry has not been widely explored. Parametric modelling has the ability to generate complex forms with intuitively reactive components, allowing designers to express and fabricate structures previously too laborious and geometrically complex to realise. This alIows designers to address a project at both the macro and micro levels of resolution in the governing control surface and the individual repetitive component. This two level modelling control, of component and overall surface, can allow designers to explore new types of form generation subject to parametric constraints. Shading screens have been selected as the focus for this paper and are used as a medium to explore form generation within a given set of functional parameters. Screens can have many applications in a building but for the purpose of the following case studies, lighting quality and passive sun control are the main functional requirement. A set of screen components have been designed within certain shading parameters to create a generic component that can automatically adapt to any given climatic conditions. These will then be applied to surfaces of varying degrees of geometric complexity to be analysed in their ability to correctly tessellate and create a unified screening array true to the lighting requirements placed on the generic component.

Geometric and material constraints in parametric modelling : the design to fabrication process

Parametric modelling, commonly used in the automotive and aerospace industries, has recently been adopted in the architecture and construction fields. The ability to design small repeatable components and apply them to a larger governing surface geometry is one area of parametric modelling that has great design potential. This two level modelling control, of component and overall surface, can allow designers to explore new types of form generation subject to parametric constraints. This paper reports on the design to fabrication process using repeatable components over a governing or carrier surface. The paper reports on our study of the requirements and possible solutions for successfully controlling a repeatable element, known as a Representative Volumetric Element (RVE), using geometric parameters of a larger governing surface geometry and material properties. This modelling process, coupled with Rapid
Manufacturing (RM) and Computer Numerically Controlled (CNC) machines has the potential to significantly reduce the interface between design and fabrication.

Modeling and simulation of a periodic grating coupled configuration for surface plasmon excitation

The deficiencies in the design of surface plasmon resonance (SPR) systems that are reported in numerous published works consistently identify the optics assembly as the main problem in the miniaturization of SPR sensors for integration into biosensor systems. This paper presents a novel design of a grating coupled optical waveguide surface plasmon (SP) excitation mechanism, investigated with the intention of addressing the problems associated with using the traditional prism input-output light coupling approach. Computational multiphysics modeling and simulation of the design is carried out. The results are presented and discussed.

Hypothesis verification using parametric models and active vision strategies

This paper proposes a methodology for determining the shape and ultimately the functionality of objects from intensity images; 2D analytic functions are used to track 3D features during known camera motions. Three analytic functions are proposed that describe the relationship between pairs of points that are either stationary or moving depending on whether the points are on occluding boundaries or otherwise. Many of the problems of correspondence are reduced by using foveation, known camera motion, and active vision methods. The three analytic functions are shown to enable hypothesis refinement of the functionality of a number of 3D objects without full 3D information about the shape.

Obtaining functional parametric models using active vision strategies

This paper addresses the problem of determining which 3D shape is present, and more importantly, the dimensions of the shape in a scene. This is performed in an active vision system because it reduces the complexity of the problem through the use of gaze stabilization, choice of foveation point, and selective processing by adaptively processing regions of interest. In our case, only a small number of equations and parameters are needed for each shape and these are incorporated into functional descriptions of the shapes.

Photochemical formation of silver nanodecahedra : structural selection by the excitation wavelength

Silver decahedra have been successfully synthesized with high yield via a photochemical reaction using blue light-emitting diodes (LEDs) as the exciting light source. The decahedra display distinct properties with respect to the ability of light scattering. The photochemical growth process of silver decahedra was monitored by both extinction and scattering spectral evolution. A suggested formation mechanism of silver decahedron is discussed.

Parametric investigation and measurement of near end and far end crosstalk in multiconductor microstrip transmission lines

This paper investigates and measures the near end and far end crosstalk in the multiconductor transmission line (MTL) mounted on the PCB by varying the parameters which are associated with physical dimension, characteristic of the substrate and the nature of input signal. With the variation of these factors, the coupling inductance and capacitance vary causing crosstalk. By using the method of moment (MoM), the per unit length parameters are calculated for microstrip lines. Subcircuit model is used to investigate the time domain and frequency domain analysis of near field and far field crosstalk. This parametric investigation is very useful for designing high speed interconnectors on PCB substrates. Some experimental results are presented to validate the analytical findings.