Pedigree-free animal models : the relatedness matrix reloaded

Animal models typically require a known genetic pedigree to estimate quantitative genetic parameters. Here we test whether animal models can alternatively be based on estimates of relatedness derived entirely from molecular marker data. Our case study is the morphology of a wild bird population, for which we report estimates of the genetic variance-covariance matrices (G) of six morphological traits using three methods: the traditional animal model; a molecular marker-based approach to estimate heritability based on Ritland's pairwise regression method; and a new approach using a molecular genealogy arranged in a relatedness matrix (R) to replace the pedigree in an animal model. Using the traditional animal model, we found significant genetic variance for all six traits and positive genetic covariance among traits. The pairwise regression method did not return reliable estimates of quantitative genetic parameters in this population, with estimates of genetic variance and covariance typically being very small or negative. In contrast, we found mixed evidence for the use of the pedigree-free animal model. Similar to the pairwise regression method, the pedigree-free approach performed poorly when the full-rank R matrix based on the molecular genealogy was employed. However, performance improved substantially when we reduced the dimensionality of the R matrix in order to maximize the signal to noise ratio. Using reduced-rank R matrices generated estimates of genetic variance that were much closer to those from the traditional model. Nevertheless, this method was less reliable at estimating covariances, which were often estimated to be negative. Taken together, these results suggest that pedigree-free animal models can recover quantitative genetic information, although the signal remains relatively weak. It remains to be determined whether this problem can be overcome by the use of a more powerful battery of molecular markers and improved methods for reconstructing genealogies.

Impact of extracellular matrix derived from osteoarthritis subchondral bone osteoblasts on osteocytes : role of integrinβ1 and focal adhesion kinase signaling cues

INTRODUCTION: Our recent study indicated that subchondral bone pathogenesis in osteoarthritis (OA) is associated with osteocyte morphology and phenotypic abnormalities. However, the mechanism underlying this abnormality needs to be identified. In this study we investigated the effect of extracellular matrix (ECM) produced from normal and OA bone on osteocytic cells function. METHODS: De-cellularized matrices, resembling the bone provisional ECM secreted from primary human subchondral bone osteoblasts (SBOs) of normal and OA patients were used as a model to study the effect on osteocytic cells. Osteocytic cells (MLOY4 osteocyte cell line) cultured on normal and OA derived ECMs were analyzed by confocal microscopy, scanning electron microscopy (SEM), cell attachment assays, zymography, apoptosis assays, qRT-PCR and western blotting. The role of integrinβ1 and focal adhesion kinase (FAK) signaling pathways during these interactions were monitored using appropriate blocking antibodies. RESULTS: The ECM produced by OA SBOs contained less mineral content, showed altered organization of matrix proteins and matrix structure compared with the matrices produced by normal SBOs. Culture of osteocytic cells on these defective OA ECM resulted in a decrease of integrinβ1 expression and the de-activation of FAK cell signaling pathway, which subsequently affected the initial osteocytic cell's attachment and functions including morphological abnormalities of cytoskeletal structures, focal adhesions, increased apoptosis, altered osteocyte specific gene expression and increased Matrix metalloproteinases (MMP-2) and -9 expression. CONCLUSION: This study provides new insights in understanding how altered OA bone matrix can lead to the abnormal osteocyte phenotypic changes, which is typical in OA pathogenesis.

Si quantum dots embedded in an amorphous SiC matrix : nanophase control by non-equilibrium plasma hydrogenation

Nanophase nc-Si/a-SiC films that contain Si quantum dots (QDs) embedded in an amorphous SiC matrix were deposited on single-crystal silicon substrates using inductively coupled plasma-assisted chemical vapor deposition from the reactive silane and methane precursor gases diluted with hydrogen at a substrate temperature of 200 °C. The effect of the hydrogen dilution ratio X (X is defined as the flow rate ratio of hydrogen-to-silane plus methane gases), ranging from 0 to 10.0, on the morphological, structural, and compositional properties of the deposited films, is extensively and systematically studied by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, Raman spectroscopy, Fourier-transform infrared absorption spectroscopy, and X-ray photoelectron spectroscopy. Effective nanophase segregation at a low hydrogen dilution ratio of 4.0 leads to the formation of highly uniform Si QDs embedded in the amorphous SiC matrix. It is also shown that with the increase of X, the crystallinity degree and the crystallite size increase while the carbon content and the growth rate decrease. The obtained experimental results are explained in terms of the effect of hydrogen dilution on the nucleation and growth processes of the Si QDs in the high-density plasmas. These results are highly relevant to the development of next-generation photovoltaic solar cells, light-emitting diodes, thin-film transistors, and other applications.

Dynamic matrix control on wind-induced vibration of spatial latticed structures [Chinese title = 空间网壳结构风振抑制的动态矩阵预测控制分析]

Ameliorated strategies were put forward to improve the model predictive control in reducing the wind induced vibration of spatial latticed structures. The dynamic matrix control (DMC) predictive method was used and the reference trajectory which is called the decaying functions was suggested for the analysis of spatial latticed structure (SLS) under wind loads. The wind-induced vibration control model of SLS with improved DMC model predictive control was illustrated, then the different feedback strategies were investigated and a typical SLS was taken as example to investigate the reduction of wind-induced vibration. In addition, the robustness and reliability of DMC strategy were discussed by varying the model configurations.

Decision Matrix Compared with Partnering Principles

The ideas for this CRC research project are based directly on Sidwell, Kennedy and Chan (2002). That research examined a number of case studies to identify the characteristics of successful projects. The findings were used to construct a matrix of best practice project delivery strategies. The purpose of this literature review is to test the decision matrix against established theory and best practice in the subject of construction project management.

Report on the Development and Validation of the Best Practice Decision Matrix

The Co-operative Research Centre for Construction Innovation (CRC-CI) is funding a project known as Value Alignment Process for Project Delivery. The project consists of a study of best practice project delivery and the development of a suite of products, resources and services to guide project teams towards the best procurement approach for a specific project or group of projects. These resources will be focused on promoting the principles that underlie best practice project delivery rather than simply identifying an off-the-shelf procurement system. This project builds on earlier work by Sidwell, Kennedy and Chan (2002), on re-engineering the construction delivery process, which developed a procurement framework in the form of a Decision Matrix

Towards a rule-based matrix for evaluating distress mechanisms in bridges

The effective management of bridge stock involves making decisions as to when to repair, remedy, or do nothing, taking into account the financial and service life implications. Such decisions require a reliable diagnosis as to the cause of distress and an understanding of the likely future degradation. Such diagnoses are based on a combination of visual inspections, laboratory tests on samples and expert opinions. In addition, the choice of appropriate laboratory tests requires an understanding of the degradation mechanisms involved. Under these circumstances, the use of expert systems or evaluation tools developed from “realtime” case studies provides a promising solution in the absence of expert knowledge. This paper addresses the issues in bridge infrastructure management in Queensland, Australia. Bridges affected by alkali silica reaction and chloride induced corrosion have been investigated and the results presented using a mind mapping tool. The analysis highights that several levels of rules are required to assess the mechanism causing distress. The systematic development of a rule based approach is presented. An example of this application to a case study bridge has been used to demonstrate that preliminary results are satisfactory.

Towards a Rule-based matrix for evaluating distress mechanisms in bridges

One of the key issues facing public asset owners is the decision of refurbishing aged built assets. This decision requires an assessment of the “remaining service life” of the key components in a building. The remaining service life is significantly dependent upon the existing condition of the asset and future degradation patterns considering durability and functional obsolescence. Recently developed methods on Residual Service Life modelling, require sophisticated data that are not readily available. Most of the data available are in the form of reports prior to undertaking major repairs or in the form of sessional audit reports. Valuable information from these available sources can serve as bench marks for estimating the reference service life. The authors have acquired similar informations from a public asset building in Melbourne. Using these informations, the residual service life of a case study building façade has been estimated in this paper based on state-of-the-art approaches. These estimations have been evaluated against expert opinion. Though the results are encouraging it is clear that the state-of-the-art methodologies can only provide meaningful estimates provided the level and quality of data are available. This investigation resulted in the development of a new framework for maintenance that integrates the condition assessment procedures and factors influencing residual service life

Processing of polycaprolactone and polycaprolactone-based copolymers into 3D scaffolds and their cellular responses

Synthetic polymers have attracted much attention in tissue engineering due to their ability to modulate biomechanical properties. This study investigated the feasibility of processing poly(varepsilon-caprolactone) (PCL) homopolymer, PCL-poly(ethylene glycol) (PEG) diblock, and PCL-PEG-PCL triblock copolymers into three-dimensional porous scaffolds. Properties of the various polymers were investigated by dynamic thermal analysis. The scaffolds were manufactured using the desktop robot-based rapid prototyping technique. Gross morphology and internal three-dimensional structure of scaffolds were identified by scanning electron microscopy and micro-computed tomography, which showed excellent fusion at the filament junctions, high uniformity, and complete interconnectivity of pore networks. The influences of process parameters on scaffolds' morphological and mechanical characteristics were studied. Data confirmed that the process parameters directly influenced the pore size, porosity, and, consequently, the mechanical properties of the scaffolds. The in vitro cell culture study was performed to investigate the influence of polymer nature and scaffold architecture on the adhesion of the cells onto the scaffolds using rabbit smooth muscle cells. Light, scanning electron, and confocal laser microscopy showed cell adhesion, proliferation, and extracellular matrix formation on the surface as well as inside the structure of both scaffold groups. The completely interconnected and highly regular honeycomb-like pore morphology supported bridging of the pores via cell-to-cell contact as well as production of extracellular matrix at later time points. The results indicated that the incorporation of hydrophilic PEG into hydrophobic PCL enhanced the overall hydrophilicity and cell culture performance of PCL-PEG copolymer. However, the scaffold architecture did not significantly influence the cell culture performance in this study.

Towards automatic tree crown detection and delineation in spectral feature space using PCNN and morphological reconstruction

The application of object-based approaches to the problem of extracting vegetation information from images requires accurate delineation of individual tree crowns. This paper presents an automated method for individual tree crown detection and delineation by applying a simplified PCNN model in spectral feature space followed by post-processing using morphological reconstruction. The algorithm was tested on high resolution multi-spectral aerial images and the results are compared with two existing image segmentation algorithms. The results demonstrate that our algorithm outperforms the other two solutions with the average accuracy of 81.8%.

Inducing shades of meaning by matrix methods : a first step towards thematic analysis of opinion

This article explores two matrix methods to induce the ``shades of meaning" (SoM) of a word. A matrix representation of a word is computed from a corpus of traces based on the given word. Non-negative Matrix Factorisation (NMF) and Singular Value Decomposition (SVD) compute a set of vectors corresponding to a potential shade of meaning. The two methods were evaluated based on loss of conditional entropy with respect to two sets of manually tagged data. One set reflects concepts generally appearing in text, and the second set comprises words used for investigations into word sense disambiguation. Results show that for NMF consistently outperforms SVD for inducing both SoM of general concepts as well as word senses. The problem of inducing the shades of meaning of a word is more subtle than that of word sense induction and hence relevant to thematic analysis of opinion where nuances of opinion can arise.

The evaluation of a biphasic osteochondral implant coupled with an electrospun membrane in a large animal model

Conventional clinical therapies are unable to resolve osteochondral defects adequately, hence tissue engineering solutions are sought to address the challenge. A biphasic implant which was seeded with Mesenchymal Stem Cells (MSC) and coupled with an electrospun membrane was evaluated as an alternative. This dual phase construct comprised of a Polycaprolactone (PCL) cartilage scaffold and a Polycaprolactone - Tri Calcium Phosphate (PCL - TCP) osseous matrix. Autologous MSC was seeded into the entire implant via fibrin and the construct was inserted into critically sized osteochondral defects located at the medial condyle and patellar groove of pigs. The defect was resurfaced with a PCL - collagen electrospun mesh that served as a substitute for periosteal flap in preventing cell leakage. Controls either without implanted MSC or resurfacing membrane were included. After 6 months, cartilaginous repair was observed with a low occurrence of fibrocartilage at the medial condyle. Osteochondral repair was promoted and host cartilage degeneration was arrested as shown by the superior Glycosaminoglycan (GAG) maintenance. This positive morphological outcome was supported by a higher relative Young's modulus which indicated functional cartilage restoration. Bone in growth and remodeling occurred in all groups with a higher degree of mineralization in the experimental group. Tissue repair was compromised in the absence of the implanted cells or the resurfacing membrane. Moreover healing was inferior at the patellar groove as compared to the medial condyle and this was attributed to the native biomechanical features.