Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Organic non-fullerene acceptors for organic photovoltaics

Heterojunction organic photovoltaics have been the subject of intensive academic interest over the past two decades, and significant commercial efforts have been directed towards this area with the vision of developing the next generation of low-cost solar cells. Materials development has played a vital role in the dramatic improvement of organic solar cell performance in recent years, and this is driven primarily by the advancement of p-type semiconductors as donor materials. With the highest performing solar cells today dominated by acceptors based on members of the fullerene family, much less attention has been devoted to other classes of n-type acceptors. In this review, we will provide an overview of the progress in the synthesis, characterization and implementation of the various classes of non-fullerenebased n-type organic acceptors for photovoltaic applications.

Biodiesel production from non-edible beauty leaf (Calophyllum Inophyllum) oil : process optimization using response surface methodology (RSM)

In recent years, the beauty leaf plant (Calophyllum Inophyllum) is being considered as a potential 2nd generation biodiesel source due to high seed oil content, high fruit production rate, simple cultivation and ability to grow in a wide range of climate conditions. However, however, due to the high free fatty acid (FFA) content in this oil, the potential of this biodiesel feedstock is still unrealized, and little research has been undertaken on it. In this study, transesterification of beauty leaf oil to produce biodiesel has been investigated. A two-step biodiesel conversion method consisting of acid catalysed pre-esterification and alkali catalysed transesterification has been utilized. The three main factors that drive the biodiesel (fatty acid methyl ester (FAME)) conversion from vegetable oil (triglycerides) were studied using response surface methodology (RSM) based on a Box-Behnken experimental design. The factors considered in this study were catalyst concentration, methanol to oil molar ratio and reaction temperature. Linear and full quadratic regression models were developed to predict FFA and FAME concentration and to optimize the reaction conditions. The significance of these factors and their interaction in both stages was determined using analysis of variance (ANOVA). The reaction conditions for the largest reduction in FFA concentration for acid catalysed pre-esterification was 30:1 methanol to oil molar ratio, 10% (w/w) sulfuric acid catalyst loading and 75 °C reaction temperature. In the alkali catalysed transesterification process 7.5:1 methanol to oil molar ratio, 1% (w/w) sodium methoxide catalyst loading and 55 °C reaction temperature were found to result in the highest FAME conversion. The good agreement between model outputs and experimental results demonstrated that this methodology may be useful for industrial process optimization for biodiesel production from beauty leaf oil and possibly other industrial processes as well.

World emissions and economic growth: Application of non-parametric methods

The Environmental Kuznets Curve (EKC) hypothesises an inverse U-shaped relationship between a measure of environmental pollution and per capita income levels. In this study, we apply non-parametric estimation of local polynomial regression (local quadratic fitting) to allow more flexibility in local estimation. This study uses a larger and globally representative sample of many local and global pollutants and natural resources including Biological Oxygen Demand (BOD) emission, CO2 emission, CO2 damage, energy use, energy depletion, mineral depletion, improved water source, PM10, particulate emission damage, forest area and net forest depletion. Copyright © 2009 Inderscience Enterprises Ltd.

The technical efficiency of the Japanese banks : non-radial directional performance measurement with undesirable output

The paper analyses technical efficiency of the Japanese banks from 2000 to 2007. The estimation technique is based on the Russell directional distance function that takes into consideration not only desirable outputs but also an undesirable output that is represented by non-performing loans (NPLs). The results indicate that NPLs remain a significant burden as for banks' performance. We show that banks' inputs have to be utilised more efficiently, particularly labour and premises. We also argue that a further restructuring process is needed in the segment of Regional Banks. We conclude that the Japanese banking system is still far away from being fully consolidated and restructured.

Non-separability and substitutability among water pollutants : evidence from India

The design and implementation of environmental policy often involve more than one pollutant, and must consider pollution as a byproduct of the production of marketable output. In this paper, we test the implicit assumption in the empirical literature that (1) production of marketable output, pollution and abatement are separable, and (2) different pollutants can be abated separately. Using unique plant-level data in India, we reject the null hypotheses of separability between marketable output and pollutants, and between different pollutants. Firms must incur abatement costs for reducing pollution levels. In addition, complement and substitute relationships between water pollutants are demonstrated with statistical significance.

Non-invasive techniques for imaging in-vivo human corneal sub basal nerve mapping and migration rate in diabetic neuropathy

Purpose Corneal confocal microscopy (CCM) is a rapid non-invasive ophthalmic technique, which has been shown to diagnose and stratify the severity of diabetic neuropathy. Current morphometric techniques assess individual static images of the subbasal nerve plexus; this work explores the potential for non-invasive assessment of the wide-field morphology and dynamic changes of this plexus in vivo. Methods In this pilot study, laser scanning CCM was used to acquire maps (using a dynamic fixation target and semi-automated tiling software) of the central corneal sub-basal nerve plexus in 4 diabetic patients with and 6 without neuropathy and in 2 control subjects. Nerve migration was measured in an additional 7 diabetic patients with neuropathy, 4 without neuropathy and in 2 control subjects by repeating a modified version of the mapping procedure within 2-8 weeks, thus facilitating re-identification of distinctive nerve landmarks in the 2 montages. The rate of nerve movement was determined from these data and normalised to a weekly rate (µm/week), using customised software. Results Wide-field corneal nerve fibre length correlated significantly with the Neuropathy Disability Score (r = -0.58, p < 0.05), vibration perception (r = -0.66, p < 0.05) and peroneal conduction velocity (r = 0.67, p < 0.05). Central corneal nerve fibre length did not correlate with any of these measures of neuropathy (p > 0.05 for all). The rate of corneal nerve migration was 14.3 ± 1.1 µm/week in diabetic patients with neuropathy, 19.7 ± 13.3µm/week in diabetic patients without neuropathy, and 24.4 ± 9.8µm/week in control subjects; however, these differences were not significantly different (p = 0.543). Conclusions Our data demonstrate that it is possible to capture wide-field images of the corneal nerve plexus, and to quantify the rate of corneal nerve migration by repeating this procedure over a number of weeks. Further studies on larger sample sizes are required to determine the utility of this approach for the diagnosis and monitoring of diabetic neuropathy.

PTRF/cavin-1 neutralizes non-caveolar caveolin-1 microdomains in prostate cancer

Caveolin-1 has a complex role in prostate cancer and has been suggested to be a potential biomarker and therapeutic target. As mature caveolin-1 resides in caveolae, invaginated lipid raft domains at the plasma membrane, caveolae have been suggested as a tumor-promoting signaling platform in prostate cancer. However, caveola formation requires both caveolin-1 and cavin-1 (also known as PTRF; polymerase I and transcript release factor). Here, we examined the expression of cavin-1 in prostate epithelia and stroma using tissue microarray including normal, non-malignant and malignant prostate tissues. We found that caveolin-1 was induced without the presence of cavin-1 in advanced prostate carcinoma, an expression pattern mirrored in the PC-3 cell line. In contrast, normal prostate epithelia expressed neither caveolin-1 nor cavin-1, while prostate stroma highly expressed both caveolin-1 and cavin-1. Utilizing PC-3 cells as a suitable model for caveolin-1-positive advanced prostate cancer, we found that cavin-1 expression in PC-3 cells inhibits anchorage-independent growth, and reduces in vivo tumor growth and metastasis in an orthotopic prostate cancer xenograft mouse model. The expression of α-smooth muscle actin in stroma along with interleukin-6 (IL-6) in cancer cells was also decreased in tumors of mice bearing PC-3-cavin-1 tumor cells. To determine whether cavin-1 acts by neutralizing caveolin-1, we expressed cavin-1 in caveolin-1-negative prostate cancer LNCaP and 22Rv1 cells. Caveolin-1 but not cavin-1 expression increased anchorage-independent growth in LNCaP and 22Rv1 cells. Cavin-1 co-expression reversed caveolin-1 effects in caveolin-1-positive LNCaP cells. Taken together, these results suggest that caveolin-1 in advanced prostate cancer is present outside of caveolae, because of the lack of cavin-1 expression. Cavin-1 expression attenuates the effects of non-caveolar caveolin-1 microdomains partly via reduced IL-6 microenvironmental function. With circulating caveolin-1 as a potential biomarker for advanced prostate cancer, identification of the molecular pathways affected by cavin-1 could provide novel therapeutic targets.

The effect of hip muscle strengthening on pain and disability for individuals with non-specific low back pain : a randomized controlled trial

Introduction Clinical guidelines for the treatment of chronic low back pain suggest the use of supervised exercise. Motor control (MC) based exercise is widely used within clinical practice but its efficacy is equivalent to general exercise therapy. MC exercise targets the trunk musculature. Considering the mechanical links between the hip, pelvis, and lumbar spine, surprisingly little focus has been on investigating the contribution of the hip musculature to lumbopelvic support. The purpose of this study is to compare the efficacy of two exercise programs for the treatment of non-specific low back pain (NSLBP). Methods Eighty individuals aged 18-65 years of age were randomized into two groups to participate in this trial. The primary outcome measures included self-reported pain intensity (0-100mm VAS) and percent disability (Oswestry Disability Index V2). Bilateral measures of hip strength (N/kg) and two dimensional frontal plane mechanics (º) were the secondary outcomes. Outcomes were measured at baseline and following a six-week home based exercise program including weekly sessions of real-time ultrasound imaging. Results Within group comparisons revealed clinically meaningful reductions in pain for both groups. The MC exercise only (N= 40, xˉ =-20.9mm, 95%CI -25.7, -16.1) and the combined MC and hip exercise (N= 40, xˉ = -24.9mm, 95%CI -30.8, -19.0). There was no statistical difference in the change of pain (xˉ =-4.0mm, t= -1.07, p=0.29, 95%CI -11.5, 3.5) or disability (xˉ =-0.3%, t=-0.19, p=0.85, 95%CI -11.5, 3.5) between groups. Conclusion Both exercise programs had similar and positive effects on NSLBP which support the use of the home based exercise programs with weekly supervised visits. However, the addition of specific hip strengthening exercises to a MC based exercise program did not result in significantly greater reductions in pain or disability. Trial Registration NCTO1567566 Funding: Worker’s Compensation Board Alberta Research Grant.

The use of penumbrae to define and analyse non-standard fields

Aim A new method of penumbral analysis is implemented which allows an unambiguous determination of field size and penumbra size and quality for small fields and other non-standard fields. Both source occlusion and lateral electronic disequilibrium will affect the size and shape of cross-axis profile penumbrae; each is examined in detail. Method A new method of penumbral analysis is implemented where the square of the derivative of the cross-axis profile is plotted. The resultant graph displays two peaks in the place of the two penumbrae. This allows a strong visualisation of the quality of a field penumbra, as well as a mathematically consistent method of determining field size (distance between the two peak’s maxima), and penumbra (full-widthtenth-maximum of peak). Cross-axis profiles were simulated in a water phantom at a depth of 5 cm using Monte Carlo modelling, for field sizes between 5 and 30 mm. The field size and penumbra size of each field was calculated using the method above, as well as traditional definitions set out in IEC976. The effect of source occlusion and lateral electronic disequilibrium on the penumbrae was isolated by repeating the simulations removing electron transport and using an electron spot size of 0 mm, respectively. Results All field sizes calculated using the traditional and proposed methods agreed within 0.2 mm. The penumbra size measured using the proposed method was systematically 1.8 mm larger than the traditional method at all field sizes. The size of the source had a larger effect on the size of the penumbra than did lateral electronic disequilibrium, particularly at very small field sizes. Conclusion Traditional methods of calculating field size and penumbra are proved to be mathematically adequate for small fields. However, the field size definition proposed in this study would be more robust amongst other nonstandard fields, such as flattening filter free. Source occlusion plays a bigger role than lateral electronic disequilibrium in small field penumbra size.

The sideways hourglass : establishing the lemniscate as a narrative structure for writing and reading non-linear stories

This thesis is a study in narratology that examines the pre-theoretical ideas that underlie the study of narrative and time. The thesis explores how the lemniscate can be transported from geometry to narrative in order to structure a non-linear story that breaks the rules of causality and chronology by coupling physical movement through space with the backward pull of memory. The findings offer new possibilities for understanding the nexus between shape and story and for recording non-linear narratives that are marked by simultaneity, counterpoint, and reversal.

A non-aqueous solution synthesis of boron carbide by control of in-situ carbon

Synthesis of high quality boron carbide (B4C) powder is achieved by carbothermal reduction of boron oxide (B2O3) from a condensed boric acid (H3BO3) / polyvinyl acetate (PVAc) product. Precursor solutions are prepared via polymerisation of vinyl acetate (VA) in methanol in the presence of dissolved H3BO3. With excess VA monomer being removed during evaporation of the solvent, the polymerisation time is then used to manage availability of carbon for reaction.

A non-linear interface element model for thin layer high adhesive mortared masonry

A nonlinear interface element modelling method is formulated for the prediction of deformation and failure of high adhesive thin layer polymer mortared masonry exhibiting failure of units and mortar. Plastic flow vectors are explicitly integrated within the implicit finite element framework instead of relying on predictor–corrector like approaches. The method is calibrated using experimental data from uniaxial compression, shear triplet and flexural beam tests. The model is validated using a thin layer mortared masonry shear wall, whose experimental datasets are reported in the literature and is used to examine the behaviour of thin layer mortared masonry under biaxial loading.

Interactive content analysis : evaluating interactive variants of non-negative Matrix Factorisation and Latent Dirichlet Allocation as qualitative content analysis aids

This thesis addressed issues that have prevented qualitative researchers from using thematic discovery algorithms. The central hypothesis evaluated whether allowing qualitative researchers to interact with thematic discovery algorithms and incorporate domain knowledge improved their ability to address research questions and trust the derived themes. Non-negative Matrix Factorisation and Latent Dirichlet Allocation find latent themes within document collections but these algorithms are rarely used, because qualitative researchers do not trust and cannot interact with the themes that are automatically generated. The research determined the types of interactivity that qualitative researchers require and then evaluated interactive algorithms that matched these requirements. Theoretical contributions included the articulation of design guidelines for interactive thematic discovery algorithms, the development of an Evaluation Model and a Conceptual Framework for Interactive Content Analysis.