Managing memory and reducing I/O cost for correlation matrix calculation in bioinformatics

The generation of a correlation matrix from a large set of long gene sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. The generation is not only computationally intensive but also requires significant memory resources as, typically, few gene sequences can be simultaneously stored in primary memory. The standard practice in such computation is to use frequent input/output (I/O) operations. Therefore, minimizing the number of these operations will yield much faster run-times. This paper develops an approach for the faster and scalable computing of large-size correlation matrices through the full use of available memory and a reduced number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different problems with different correlation matrix sizes. The significant performance improvement of the approach over the existing approaches is demonstrated through benchmark examples.

Quality Assessment Matrix : A Collaborative Evaluation Using Multiple Lines of Evidence

Welcome to the Quality assessment matrix. This matrix is designed for highly qualified discipline experts to evaluate their course, major or unit in a systematic manner. The primary purpose of the Quality assessment matrix is to provide a tool that a group of academic staff at universities can collaboratively review the assessment within a course, major or unit annually. The annual review will result in you being read for an external curricula review at any point in time. This tool is designed for use in a workshop format with one, two or more academic staff, and will lead to an action plan for implementation.

Ruptures in the heterosexual matrix through teenage flows and multiplicities

This article analyzes a series of stories and artworks that were produced in a collective biography workshop. It explores Judith Butler’s concept of the heterosexual matrix combined with a Deleuzian theoretical framework. The article begins with an overview of Butler’s concept of the heterosexual matrix and her theorizations on how it might be disrupted. It then suggests how a Deleuzian framework offers other tools for analyzing these ruptures at the micro level of girls’ everyday interactions.

Matrix metalloproteinase biosensor based on a porous silicon reflector

Matrix metalloproteinases (MMPs) are proteolytic enzymes important to wound healing. In non-healing wounds, it has been suggested that MMP levels become dysfunctional, hence it is of great interest to develop sensors to detect MMP biomarkers. This study presents the development of a label-free optical MMP biosensor based on a functionalised porous silicon (pSi) thin film. The biosensor is fabricated by immobilising a peptidomimetic MMP inhibitor in the porous layer using hydrosilylation followed by amide coupling. The binding of MMP to the immobilised inhibitor translates into a change of effective optical thickness (EOT) over the time. We investigate the effect of surface functionalisation on the stability of pSi surface and evaluate the sensing performance. We successfully demonstrate MMP detection in buffer solution and human wound fluid at physiologically relevant concentrations. This biosensor may find application as a point-of-care device that is prognostic of the healing trajectory of chronic wounds.

Development of a large scale flexible LED display matrix for the screen industry

This project addresses the viability of lightweight, low power consumption, flexible, large format LED screens. The investigation encompasses all aspects of the electrical and mechanical design, individually and as a system, and achieves a successful full scale prototype. The prototype implements novel techniques to achieve large displacement colour aliasing, a purely passive thermal management solution, a rapid deployment system, individual seven bit LED current control with two way display communication, auto-configuration and complete signal redundancy, all of which are in direct response to industry needs.

Matrix metalloproteinase localisation by in situ-RT-PCR in archival human breast biopsy material

Utilising archival human breast cancer biopsy material we examined the stromal/epithelial interactions of several matrix metalloproteinases (MMPs) using in situ-RT-PCR (IS-RT-PCR). In breast cancer, the stromal/epithelial interactions that occur, and the site of production of these proteases, are central to understanding their role in invasive and metastatic processes. We examined MT1-MMP (MMP-14, membrane type-1-MMP), MMP-1 (interstitial collagenase) and MMP-3 (stromelysin-1) for their localisation profile in progressive breast cancer biopsy material (poorly differentiated invasive breast carcinoma (PDIBC), invasive breast carcinomas (IBC) and lymph node metastases (LNM)). Expression of MT1-MMP, MMP-1 and MMP-3 was observed in both the tumour epithelial and surrounding stromal cells in most tissue sections examined. MT1-MMP expression was predominantly localised to the tumour component in the pre-invasive lesions. MMP-1 gene expression was relatively well distributed between both tissue compartments, while MMP-3 demonstrated highest expression levels in the stromal tissue surrounding the epithelial tumour cells. The results demonstrate the ability to distinguish compartmental gene expression profiles using IS-RT-PCR. Further, we suggest a role for MT1-MMP in early tumour progression, expression of MMP-1 during metastasis and focal expression pattern of MMP-3 in areas of expansion. These expression profiles may provide markers for early breast cancer diagnoses and present potential therapeutic targets.

A matrix for appropriate assessment of workplace learning in stem disciplines

With increasing interest shown by Universities in workplace learning, especially in STEM disciplines, an issue has arisen amongst educators and industry partners regarding authentic assessment tasks for work integrated learning (WIL) subjects. This paper describes the use of a matrix, which is also available as a decision-tree, based on the features of the WIL experience, in order to facilitate the selection of appropriate assessment strategies. The matrix divides the WIL experiences into seven categories, based on such factors as: the extent to which the experience is compulsory, required for membership of a professional body or elective; whether the student is undertaking a project, or embedding in a professional culture; and other key aspects of the WIL experience. One important variable is linked to the fundamental purpose of the assessment. This question revolves around the focus of the assessment: whether on the person (student development); the process (professional conduct/language); or the product (project, assignment, literature review, report, software). The matrix has been trialed at QUT in the Faculty of Science and Technology, and also at the University of Surrey, UK, and has proven to have good applicability in both universities.

Mainstreaming therapeutic jurisprudence and the adversarial paradigm—incommensurability and the possibility of a shared disciplinary matrix

Problem-solving courts appear to achieve outcomes that are not common in mainstream courts. There are increasing calls for the adoption of more therapeutic and problem-solving practices by mainstream judges in civil and criminal courts in a number of jurisdictions, most notably in the United States and Australia. Currently, a judge who sets out to exercise a significant therapeutic function is likely to be doing so in a specialist court or jurisdiction, outside the mainstream court system, and arguably, outside the adversarial paradigm itself. To some extent, this work is tolerated but marginalised. However, do therapeutic and problem-solving functions have the potential to help define, rather than simply complement, the role of judicial officers? The core question addressed in this thesis is whether the judicial role could evolve to be not just less adversarial, but fundamentally non-adversarial. In other words, could we see—or are we seeing—a juristic paradigm shift not just in the colloquial, casual sense of the word, but in the strong, worldview changing sense meant by Thomas Kuhn? This thesis examines the current relationship between adversarialism and therapeutic jurisprudence in the context of Kuhn’s conception of the transition from periods of ‘normal science’, through periods of anomaly and disciplinary crises to paradigm shifts. It considers whether therapeutic jurisprudence and adversarialism are incommensurable in the Kuhnian sense, and if so, what this means for the relationship between the two, and for the agenda to mainstream therapeutic jurisprudence. The thesis asserts that Kuhnian incommensurability is, in fact, a characteristic of the relationship between adversarialism and therapeutic jurisprudence, but that the possibility of a therapeutic paradigm shift in law can be reconciled with many adversarial and due process principles by relating this incommensurability to a broader disciplinary matrix.

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.

A case study analysis of Israeli Organised Crime (IOC) (1990-2005) : applying the Crime Business Analysis Matrix (CBAM)

Israeli Organised Crime (IOC) gained prominence in the 1990s for its involvement in the manufacturing and wholesale distribution of MDMA through traditional trafficking networks across Europe. Equipped with astute business acumen and an entrepreneurial spirit, IOC dominated MDMA trafficking in Europe for more than a decade and remains as a major participant in this drug market. The paper analyses the entrepreneurial activities of IOC within the context of the MDMA market in Europe between 1990 and 2005 using the Crime Business Analysis Matrix (CBAM) as proffered by Dean, et al (2010). The study is in two parts. Part A provides a review of the literature as it pertains to IOC and its involvement in the European drug market, while Part B provides a qualitative analysis of their criminal business practices and entrepreneurialism of IOC within this context.

Principle components analysis with covariance matrix on regional differences for mortality and percentages of cancers in Shandong province [山东省恶性肿瘤死亡率和构成比地区差异协方差矩阵主成分分析]

Objective To explore the characteristics of regional distribution of cancer deaths in Shandong Province with the principle components analysis. Methods The principle components analysis with co-variance matrix for age-adjusted mortality rates and percentages of 20 types of cancer in 22 counties （cities） were carried out using SAS Software. Results Over 90% of the total information could be reflected by the top 3 principle components and the first principle component alone represented more than half of the overall regional variances. The first component mainly reflected the area differences of esophageal cancer. The second component mainly reflected the area differences of lung cancer， stomach cancer and liver cancer. The value of the first principal component scores showed a clear trend that the west areas possessed higher values and the east the lower values. Based on the top two components，the 22 counties （cities） could be divided into several geographical clusters. Conclusion The overall difference of regional distribution of cancers in Shandong is dominated by several major cancers including esophageal cancer， lung cancer， stomach cancer and liver cancer. Among them，esophageal cancer makes the largest contribution. If the range of counties （cities） analyzed could be further widened， the characteristics of regional distribution of cancer mortality would be better examined. Abstract in Chinese 目的 利用主成分分析探讨山东省恶性肿瘤死亡的地区分布特征. 方法 利用SAS软件对山东省22个县市区2004～2006午的20种恶性肿瘤标化死亡率和构成比分别进行协方差矩阵主成分分析. 结果 前3个主成分就反映了总体差异90%以上的信息,其中仅第1主成分就提供了总体差异一半以上的信息.第1主成分主要反映了食管癌的地区差异,第2主成分主要反映肺癌的地区差异,兼顾胃癌和肝癌.各地区第1主成分得分呈现西高东低的趋势,根据第1和第2主成分可以将调查地区分为若干类别,表现为明显的地理聚集性. 结论 山东省各地区恶性肿瘤死亡的总体差异主要取决于少数高发肿瘤,包括食管癌、肺癌、胃癌、肝癌等,其中以食管癌地位最为突出.如能进一步扩大分析范围,可更好地查明恶性肿瘤死亡的地区特征.

A novel method for finding similarities between unordered trees using matrix data model

Trees are capable of portraying the semi-structured data which is common in web domain. Finding similarities between trees is mandatory for several applications that deal with semi-structured data. Existing similarity methods examine a pair of trees by comparing through nodes and paths of two trees, and find the similarity between them. However, these methods provide unfavorable results for unordered tree data and result in yielding NP-hard or MAX-SNP hard complexity. In this paper, we present a novel method that encodes a tree with an optimal traversing approach first, and then, utilizes it to model the tree with its equivalent matrix representation for finding similarity between unordered trees efficiently. Empirical analysis shows that the proposed method is able to achieve high accuracy even on the large data sets.

Phase III study of matrix metalloproteinase inhibitor prinomastat in non-small-cell lung cancer

Purpose: Matrix metalloproteinases (MMPs) degrade extracellular proteins and facilitate tumor growth, invasion, metastasis, and angiogenesis. This trial was undertaken to determine the effect of prinomastat, an inhibitor of selected MMPs, on the survival of patients with advanced non-small-cell lung cancer (NSCLC), when given in combination with gemcitabine-cisplatin chemotherapy. Patients and Methods: Chemotherapy-naive patients were randomly assigned to receive prinomastat 15 mg or placebo twice daily orally continuously, in combination with gemcitabine 1,250 mg/m2 days 1 and 8 plus cisplatin 75 mg/m2 day 1, every 21 days for up to six cycles. The planned sample size was 420 patients. Results: Study results at an interim analysis and lack of efficacy in another phase III trial prompted early closure of this study. There were 362 patients randomized (181 on prinomastat and 181 on placebo). One hundred thirty-four patients had stage IIIB disease with T4 primary tumor, 193 had stage IV disease, and 34 had recurrent disease (one enrolled patient was ineligible with stage IIIA disease). Overall response rates for the two treatment arms were similar (27% for prinomastat v 26% for placebo; P = .81). There was no difference in overall survival or time to progression; for prinomastat versus placebo patients, the median overall survival times were 11.5 versus 10.8 months (P = .82), 1-year survival rates were 43% v 38% (P = .45), and progression-free survival times were 6.1 v 5.5 months (P = .11), respectively. The toxicities of prinomastat were arthralgia, stiffness, and joint swelling. Treatment interruption was required in 38% of prinomastat patients and 12% of placebo patients. Conclusion: Prinomastat does not improve the outcome of chemotherapy in advanced NSCLC. © 2005 by American Society of Clinical Oncology.

A biomimetic extracellular matrix for cartilage tissue engineering centered on photocurable gelatin, hyaluronic acid and chondroitin sulfate

The development of hydrogels tailored for cartilage tissue engineering has been a research and clinical goal for over a decade. Directing cells towards a chondrogenic phenotype and promoting new matrix formation are significant challenges that must be overcome for the successful application of hydrogels in cartilage tissue therapies. Gelatin-methacrylamide (Gel-MA) hydrogels have shown promise for the repair of some tissues, but they have not been extensively investigated for cartilage tissue engineering. We encapsulated human chondrocytes in gel-MA based hydrogels, and show that with the incorporation of small quantities of photo-crosslinkable hyaluronic acid methacrylate (HA-MA), and to a lesser extent chondroitin sulfate methacrylate (CS-MA), chondrogenesis and mechanical properties can be enhanced. The addition of HA-MA to Gel-MA constructs resulted in more rounded cell morphologies, enhanced chondrogenesis as assessed by gene expression and immunofluorescence, and increased quantity and distribution of the newly synthesised ECM throughout the construct. Consequently, while the compressive moduli of control Gel-MA constructs increased by 26 kPa after 8 weeks culture, constructs with HA-MA and CS-MA increased by 96 kPa. The enhanced chondrogenic differentiation, distribution of ECM, and improved mechanical properties make these materials potential candidates for cartilage tissue engineering applications.

Matrix metalloproteinases 2 and 9 (gelatinases A and B) expression in malignant mesothelioma and benign pleura

Matrix metalloproteinases (MMPs), in particular the gelatinases (MMP-2 and -9), play a significant role in tumour invasion and angiogenesis. The expression and activities of MMPs have not been characterised in malignant mesothelioma (MM) tumour samples. In a prospective study, gelatinase activity was evaluated in homogenised supernatants of snap frozen MM (n = 35), inflamed pleura (IP, n = 12) and uninflammed pleura (UP, n = 14) tissue specimens by semiquantitative gelatin zymography. Matrix metalloproteinases were correlated with clinicopathological factors and with survival using Kaplan-Meier and Cox proportional hazard models. In MM, pro- and active MMP-2 levels were significantly greater than for MMP-9 (P = 0.006, P<0.001). Active MMP-2 was significantly greater in MM than in UP (P=0.04). MMP-2 activity was equivalent between IP and MM, but both pro- and active MMP-9 activities were greater in IP (P=0.02, P=0.009). While there were trends towards poor survival with increasing total and pro-MMP-2 activity (P=0.08) in univariate analysis, they were both independent poor prognostic factors in multivariate analysis in conjunction with weight loss (pro-MMP-2 P = 0.03, total MMP-2 P = 0.04). Total and pro-MMP-2 also contributed to the Cancer and Leukemia Group B prognostic groups. MMP-9 activities were not prognostic. Matrix metalloproteinases, and in particular MMP-2, the most abundant gelatinase, may play an important role in MM tumour growth and metastasis. Agents that reduce MMP synthesis and/or activity may have a role to play in the management of MM. © 2003 Cancer Research UK.