Efficiency of parallelisation of genetic algorithms in the data analysis context

Most real-life data analysis problems are difficult to solve using exact methods, due to the size of the datasets and the nature of the underlying mechanisms of the system under investigation. As datasets grow even larger, finding the balance between the quality of the approximation and the computing time of the heuristic becomes non-trivial. One solution is to consider parallel methods, and to use the increased computational power to perform a deeper exploration of the solution space in a similar time. It is, however, difficult to estimate a priori whether parallelisation will provide the expected improvement. In this paper we consider a well-known method, genetic algorithms, and evaluate on two distinct problem types the behaviour of the classic and parallel implementations.

Building cross-scale models of epigenetic mechanisms

Epigenetic changes correspond to heritable modifications of the chromosome structure, which do not involve alteration of the DNA sequence but do affect gene expression. These mechanisms play an important role in normal cell differentiation, but aberration is associated also with several diseases, including cancer and neural disorders. In consequence, despite intensive studies in recent years, the contribution of modifications remains largely unquantified due to overall system complexity and insufficient data. Computational models can provide powerful auxiliary tools to experimentation, not least as scales from the sub-cellular through cell populations (or to networks of genes) can be spanned. In this paper, the challenges to development, of realistic cross-scale models, are discussed and illustrated with respect to current work.

The protective mechanisms of first aid training within a school-based program for early adolescents

This thesis was concerned with the protective mechanisms of first aid training in the context of peer support. Using a randomised control trial design the current program of research explores first aid training in the school setting and identifies the key components of effective school-based first aid training programs. In particular, examining whether first aid training and associated knowledge could be protective for early adolescents. This broader framing considered whether first aid impacted on increasing behaviour and attitudes towards helping an injured friend, and reducing personal risk taking and related injury.

Parallel attentive visual tracking

The research reported here addresses the problem of detecting and tracking independently moving objects from a moving observer in real-time, using corners as object tokens. Corners are detected using the Harris corner detector, and local image-plane constraints are employed to solve the correspondence problem. The approach relaxes the restrictive static-world assumption conventionally made, and is therefore capable of tracking independently moving and deformable objects. Tracking is performed without the use of any 3-dimensional motion model. The technique is novel in that, unlike traditional feature-tracking algorithms where feature detection and tracking is carried out over the entire image-plane, here it is restricted to those areas most likely to contain-meaningful image structure. Two distinct types of instantiation regions are identified, these being the “focus-of-expansion” region and “border” regions of the image-plane. The size and location of these regions are defined from a combination of odometry information and a limited knowledge of the operating scenario. The algorithms developed have been tested on real image sequences taken from typical driving scenarios. Implementation of the algorithm using T800 Transputers has shown that near-linear speedups are achievable, and that real-time operation is possible (half-video rate has been achieved using 30 processing elements).

Product stability and sequestration mechanisms in Solanum tuberosum engineered to biosynthesize high value ketocarotenoids

To produce commercially valuable ketocarotenoids in Solanum tuberosum, the 4, 4′ β-oxygenase (crtW) and 3, 3′ β-hydroxylase (crtZ) genes from Brevundimonas spp. have been expressed in the plant host under constitutive transcriptional control. The CRTW and CRTZ enzymes are capable of modifying endogenous plant carotenoids to form a range of hydroxylated and ketolated derivatives. The host (cv. Désirée) produced significant levels of nonendogenous carotenoid products in all tissues, but at the apparent expense of the economically critical metabolite, starch. Carotenoid levels increased in both wild-type and transgenic tubers following cold storage; however, stability during heat processing varied between compounds. Subcellular fractionation of leaf tissues revealed the presence of ketocarotenoids in thylakoid membranes, but not predominantly in the photosynthetic complexes. A dramatic increase in the carotenoid content of plastoglobuli was determined. These findings were corroborated by microscopic analysis of chloroplasts. In tuber tissues, esterified carotenoids, representing 13% of the total pigment found in wild-type extracts, were sequestered in plastoglobuli. In the transgenic tubers, this proportion increased to 45%, with esterified nonendogenous carotenoids in place of endogenous compounds. Conversely, nonesterified carotenoids in both wild-type and transgenic tuber tissues were associated with amyloplast membranes and starch granules.

Legal mechanisms for maximising community engagement with formal evacuation messaging: How well are these understood?

Study/Objective This program of research examines the effectiveness of legal mechanisms as motivators to maximise engagement and compliance with evacuation messages. This study is based on the understanding that the presence of legislative requirements, as well as sanctions and incentives encapsulated in law, can have a positive impact in achieving compliance. Our objective is to examine whether the current Australian legal frameworks, which incorporate evacuation during disasters, are an effective structure that is properly understood by those who enforce and those who are required to comply. Background In Australia, most jurisdictions have enacted legislation that encapsulates the power to evacuate and the ability to enforce compliance, either by the use of force or imposition of penalty. However, citizens still choose to not evacuate. Methods This program of research incorporates theoretical and doctrinal methodologies for reviewing literature and legislation in the Australia context. The aim of the research is to determine whether further clarity is required to create an understanding of the powers to evacuate, as well as greater public awareness of these powers. Results & Conclusion Legislators suggest that powers of evacuation can be ineffective if they are impractical to enforce. In Australia, there may also be confusion about from which legislative instrument the power to evacuate derives, and therefore whether there is a corresponding ability to enforce compliance through the use of force or imposition of a penalty. Equally, communities may lack awareness and understanding of the powers of agencies to enforce compliance. We seek to investigate whether this is the case, and whether even if greater awareness existed, it would act as an incentive to comply.

Sectionalizing strategies for minimizing outage durations of critical loads in parallel power system restoration with bi-level programming

Fast restoration of critical loads and non-black-start generators can significantly reduce the economic losses caused by power system blackouts. In a parallel power system restoration scenario, the sectionalization of restoration subsystems plays a very important role in determining the pickup of critical loads before synchronization. Most existing research mainly focuses on the startup of non-black-start generators. The restoration of critical loads, especially the loads with cold load characteristics, has not yet been addressed in optimizing the subsystem divisions. As a result, sectionalized restoration subsystems cannot achieve the best coordination between the pickup of loads and the ramping of generators. In order to generate sectionalizing strategies considering the pickup of critical loads in parallel power system restoration scenarios, an optimization model considering power system constraints, the characteristics of the cold load pickup and the features of generator startup is proposed in this paper. A bi-level programming approach is employed to solve the proposed sectionalizing model. In the upper level the optimal sectionalizing problem for the restoration subsystems is addressed, while in the lower level the objective is to minimize the outage durations of critical loads. The proposed sectionalizing model has been validated by the New-England 39-bus system and the IEEE 118-bus system. Further comparisons with some existing methods are carried out as well.

Deriving information systems innovation execution mechanisms

Despite a wealth of studies focusing on innovation, types of innovations and their outcomes, the process of innovation has largely been under studied. In 2010, Swanson calls for researchers to address the ‘innovation process black box’, to better understand how IT innovation potential can be exploited upon. This study derives and instantiates three unique and mutually exclusive innovation execution mechanisms: Continual, Progressive and Plug and Play. The innovation execution mechanisms of this study are developed with reference to Swanson (1994) Information Systems innovation types.

Parallel streaming signature EM-tree: A clustering algorithm for web scale applications

The proliferation of the web presents an unsolved problem of automatically analyzing billions of pages of natural language. We introduce a scalable algorithm that clusters hundreds of millions of web pages into hundreds of thousands of clusters. It does this on a single mid-range machine using efficient algorithms and compressed document representations. It is applied to two web-scale crawls covering tens of terabytes. ClueWeb09 and ClueWeb12 contain 500 and 733 million web pages and were clustered into 500,000 to 700,000 clusters. To the best of our knowledge, such fine grained clustering has not been previously demonstrated. Previous approaches clustered a sample that limits the maximum number of discoverable clusters. The proposed EM-tree algorithm uses the entire collection in clustering and produces several orders of magnitude more clusters than the existing algorithms. Fine grained clustering is necessary for meaningful clustering in massive collections where the number of distinct topics grows linearly with collection size. These fine-grained clusters show an improved cluster quality when assessed with two novel evaluations using ad hoc search relevance judgments and spam classifications for external validation. These evaluations solve the problem of assessing the quality of clusters where categorical labeling is unavailable and unfeasible.

Mechanisms underlying the effect of acupuncture on cognitive improvement: A systematic review of animal studies

Acupuncture has been reported to be beneficial in treating cognitive impairment in various pathological conditions. This review describes the effort to understand the signaling pathways that underlie the acupunctural therapeutic effect on cognitive function. We searched the literature in 12 electronic databases from their inception to November 2013, with full text available and language limited to English. Twenty-three studies were identified under the selection criteria. All recruited animal studies demonstrate a significant positive effect of acupuncture on cognitive impairment. Findings suggest acupuncture may improve cognitive function through modulation of signaling pathways involved in neuronal survival and function, specifically, through promoting cholinergic neural transmission, facilitating dopaminergic synaptic transmission, enhancing neurotrophin signaling, suppressing oxidative stress, attenuating apoptosis, regulating glycometabolic enzymes and reducing microglial activation. However, the quality of reviewed studies has room for improvement. Further high-quality animal studies with randomization, blinding and estimation of sample size are needed to strengthen the recognition of group differences.

Antidepressants, but not antipsychotics, modulate GR function in human whole blood: An insight into molecular mechanisms

Clinical studies have demonstrated an impairment of glucocorticoid receptor (GR)-mediated negative feedback on the hypothalamic-pituitary-adrenal (HPA) axis in patients with major depression (GR resistance), and its resolution by antidepressant treatment. Recently, we showed that this impairment is indeed due to a dysfunction of GR in depressed patients (Carvalho et al., 2009), and that the ability of the antidepressant clomipramine to decrease GR function in peripheral blood cells is impaired in patients with major depression who are clinically resistant to treatment (Carvalho et al. 2008). To further investigate the effect of antidepressants on GR function in humans, we have compared the effect of the antidepressants clomipramine, amytriptiline, sertraline, paroxetine and venlafaxine, and of the antipsychotics, haloperidol and risperidone, on GR function in peripheral blood cells from healthy volunteers (n=33). GR function was measured by glucocorticoid inhibition of lypopolysaccharide (LPS)-stimulated interleukin-6 (IL-6) levels. Compared to vehicle-treated cells, all antidepressants inhibited dexamethasone (DEX, 10-100nM) inhibition of LPS-stimulated IL-6 levels (p values ranging from 0.007 to 0.1). This effect was specific to antidepressants, as antipsychotics had no effect on DEX-inhibition of LPS-stimulated IL-6 levels. The phosphodiesterase (PDE) type 4 inhibitor, rolipram, potentiated the effect of antidepressants on GR function, while the GR antagonist, RU-486, inhibited the effect of antidepressants on GR function. These findings indicate that the effect of antidepressants on GR function are specific for this class of psychotropic drugs, and involve second messenger pathways relevant to GR function and inflammation. Furthermore, it also points towards a possible mechanism by which one maybe able to overcome treatment-resistant depression. Research in this field will lead to new insights into the pathophysiology and treatment of affective disorders.

Mechanisms of cisplatin resistance: DNA repair and cellular implications

Cisplatin (cis-diamminedichloroplatinum (II)), is a platinum based chemotherapeutic employed in the clinic to treat patients with lung, ovarian, colorectal or head and neck cancers. Cisplatin acts to induce tumor cell death via multiple mechanisms. The best characterized mode of action is through irreversible DNA cross-links which activate DNA damage signals leading to cell death via the intrinsic mitochondrial apoptosis pathway. However, the primary issue with cisplatin is that while patients initially respond favorably, sustained cisplatin therapy often yields chemoresistance resulting in therapeutic failure. In this chapter, we review the DNA damage and repair pathways that contribute to cisplatin resistance. We also examine the cellular implications of cisplatin resistance that may lead to selection of subpopulations of cells within a tumor. In better understanding the mechanisms conferring cisplatin resistance, novel targets may be identified to restore drug sensitivity.

The tumour-promoting receptor tyrosine kinase, EphB4, regulates expression of Integrin-β8 in prostate cancer cells

Background The EphB4 receptor tyrosine kinase is overexpressed in many cancers including prostate cancer. The molecular mechanisms by which this ephrin receptor influences cancer progression are complex as there are tumor-promoting ligand-independent mechanisms in place as well as ligand-dependent tumor suppressive pathways. Methods We employed transient knockdown of EPHB4 in prostate cancer cells, coupled with gene microarray analysis, to identify genes that were regulated by EPHB4 and may represent linked tumor-promoting factors. We validated target genes using qRT-PCR and employed functional assays to determine their role in prostate cancer migration and invasion. Results We discovered that over 500 genes were deregulated upon EPHB4 siRNA knockdown, with integrin β8 (ITGB8) being the top hit (29-fold down-regulated compared to negative non-silencing siRNA). Gene ontology analysis found that the process of cell adhesion was highly deregulated and two other integrin genes, ITGA3 and ITGA10, were also differentially expressed. In parallel, we also discovered that over-expression of EPHB4 led to a concomitant increase in ITGB8 expression. In silico analysis of a prostate cancer progression microarray publically available in the Oncomine database showed that both EPHB4 and ITGB8 are highly expressed in prostatic intraepithelial neoplasia, the precursor to prostate cancer. Knockdown of ITGB8 in PC-3 and 22Rv1 prostate cancer cells in vitro resulted in significant reduction of cell migration and invasion. Conclusions These results reveal that EphB4 regulates integrin β8 expression and that integrin β8 plays a hitherto unrecognized role in the motility of prostate cancer cells and thus targeting integrin β8 may be a new treatment strategy for prostate cancer.

Understanding the function and mechanisms of intestinal cell kinase in the growth and survival of prostate cancer cells

This project was a step forward in discovering the potential role of intestinal cell kinase in prostate cancer development. Intestinal cell kinase was shown to be upregulated in prostate cancer cells and altered expression led to changes in key cell survival proteins. This study used in vitro experiments to monitor changes in cell growth, protein and RNA expression.

Toughness and toughening mechanisms of porous thin films

Toughness is the ability of a material to deform plastically and to absorb energy before fracture. The first of its kind, this book covers the most recent developments in the toughening of hard coatings and the methodologies for measuring the toughness of thin films and coatings. The book looks at the present status of toughness for coatings and discusses high-temperature nanocomposite coatings, porous thin films, laser treated surface layers, cracking resistance, indentation techniques, sliding contact fracture, IPN hybrid composites for protection, and adhesion strength.