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

Genome-wide analysis in a murine Dnmt1 knockdown model identifies epigenetically silenced genes in primary human pituitary tumors

DNA methylation at promoter CpG islands (CGI) is an epigenetic modification associated with inappropriate gene silencing in multiple tumor types. In the absence of a human pituitary tumor cell line, small interfering RNA-mediated knockdown of the maintenance methyltransferase DNA methyltransferase (cytosine 5)-1 (Dnmt1) was used in the murine pituitary adenoma cell line AtT-20. Sustained knockdown induced reexpression of the fully methylated and normally imprinted gene neuronatin (Nnat) in a time-dependent manner. Combined bisulfite restriction analysis (COBRA) revealed that reexpression of Nnat was associated with partial CGI demethylation, which was also observed at the H19 differentially methylated region. Subsequent genome-wide microarray analysis identified 91 genes that were significantly differentially expressed in Dnmt1 knockdown cells (10% false discovery rate). The analysis showed that genes associated with the induction of apoptosis, signal transduction, and developmental processes were significantly overrepresented in this list (P < 0.05). Following validation by reverse transcription-PCR and detection of inappropriate CGI methylation by COBRA, four genes (ICAM1, NNAT, RUNX1, and S100A10) were analyzed in primary human pituitary tumors, each displaying significantly reduced mRNA levels relative to normal pituitary (P < 0.05). For two of these genes, NNAT and S100A10, decreased expression was associated with increased promoter CGI methylation. Induced expression of Nnat in stable transfected AtT-20 cells inhibited cell proliferation. To our knowledge, this is the first report of array-based "epigenetic unmasking" in combination with Dnmt1 knockdown and reveals the potential of this strategy toward identifying genes silenced by epigenetic mechanisms across species boundaries.

Augmenting and assisting model elicitation tasks with 3D virtual world context metadata

Accurate process model elicitation continues to be a time consuming task, requiring skill on the part of the interviewer to extract explicit and tacit process information from the interviewee. Many errors occur in this elicitation stage that would be avoided by better activity recall, more consistent specification methods and greater engagement in the elicitation process by interviewees. Theories of situated cognition indicate that interactive 3D representations of real work environments engage and prime the cognitive state of the viewer. In this paper, our major contribution is to augment a previous process elicitation methodology with virtual world context metadata, drawn from a 3D simulation of the workplace. We present a conceptual and formal approach for representing this contextual metadata, integrated into a process similarity measure that provides hints for the business analyst to use in later modelling steps. Finally, we conclude with examples from two use cases to illustrate the potential abilities of this approach.

Commitment to internationalisation : an extension of the internationalisation process model

Notwithstanding the interest over many years by scholars in modeling the internationalization of the firm, the initial transition for the firm from domestic to international operations remains under-researched. We identify the behavioral factors that are important at the pre-internationalization state and discuss how they may interrelate to influence a decision to commit to internationalization through export commencement. We study export commitment by proposing and constructing an index that incorporates the factors that influence a firm’s propensity to commit to export activities. Utilizing the items from this index in a logistic regression analysis, we distinguish between the pre-internationalization characteristics of exporting and non-exporting firms to better understand the key influences in export commitment. Implications are discussed.

Examining the cost efficiency of Chinese hydroelectric companies using a finite mixture model

This paper evaluates the operational activities of Chinese hydroelectric power companies over the period 2000-2010 using a finite mixture model that controls for unobserved heterogeneity. In so doing, a stochastic frontier latent class model, which allows for the existence of different technologies, is adopted to estimate cost frontiers. This procedure not only enables us to identify different groups among the hydro-power companies analysed, but also permits the analysis of their cost efficiency. The main result is that three groups are identified in the sample, each equipped with different technologies, suggesting that distinct business strategies need to be adapted to the characteristics of China's hydro-power companies. Some managerial implications are developed. © 2012 Elsevier B.V.

Sensitivity of an Elekta iView GT a-Si EPID model to delivery errors for pre-treatment verification of IMRT fields

A Monte Carlo model of an Elekta iViewGT amorphous silicon electronic portal imaging device (a-Si EPID) has been validated for pre-treatment verification of clinical IMRT treatment plans. The simulations involved the use of the BEAMnrc and DOSXYZnrc Monte Carlo codes to predict the response of the iViewGT a-Si EPID model. The predicted EPID images were compared to the measured images obtained from the experiment. The measured EPID images were obtained by delivering a photon beam from an Elekta Synergy linac to the Elekta iViewGT a-Si EPID. The a-Si EPID was used with no additional build-up material. Frame averaged EPID images were acquired and processed using in-house software. The agreement between the predicted and measured images was analyzed using the gamma analysis technique with acceptance criteria of 3% / 3 mm. The results show that the predicted EPID images for four clinical IMRT treatment plans have a good agreement with the measured EPID signal. Three prostate IMRT plans were found to have an average gamma pass rate of more than 95.0 % and a spinal IMRT plan has the average gamma pass rate of 94.3 %. During the period of performing this work a routine MLC calibration was performed and one of the IMRT treatments re-measured with the EPID. A change in the gamma pass rate for one field was observed. This was the motivation for a series of experiments to investigate the sensitivity of the method by introducing delivery errors, MLC position and dosimetric overshoot, into the simulated EPID images. The method was found to be sensitive to 1 mm leaf position errors and 10% overshoot errors.

Adoption of accountable-eHealth systems by future healthcare professionals: An empirical research model based on the Australian context

This paper provides a first look at the acceptance of Accountable-eHealth systems, a new genre of eHealth systems, designed to manage information privacy concerns that hinder the proliferation of eHealth. The underlying concept of AeH systems is appropriate use of information through after-the-fact accountability for intentional misuse of information by healthcare professionals. An online questionnaire survey was utilised for data collection from three educational institutions in Queensland, Australia. A total of 23 hypothesis relating to 9 constructs were tested using a structural equation modelling technique. A total of 334 valid responses were received. The cohort consisted of medical, nursing and other health related students studying at various levels in both undergraduate and postgraduate courses. The hypothesis testing disproved 7 hypotheses. The empirical research model developed was capable of predicting 47.3% of healthcare professionals’ perceived intention to use AeH systems. A validation of the model with a wider survey cohort would be useful to confirm the current findings.

Fracture load for short versus standard cemented hip stems : an experimental in vitro study

Introduction: In an attempt to reduce stress shielding in the proximal femur multiple new shorter stem design have become available. We investigated the load to fracture of a new polished tapered cemented short stem in comparison to the conventional polished tapered Exeter stem. Method: A total of forty-two stems, twenty-one short stems and twenty-one conventional stems both with three different offsets were cemented in a composite sawbone model and loaded to fracture. Results: study showed that femurs will break at a significantly lower load to failure with a shorter compared to conventional length Exeter stem. Conclusion: This Both standard and short stem design are safe to use as the torque to failure is 7–10 times as much as the torques seen in activities of daily living.

Investigating the effect of internal fixation stiffness on metaphyseal fracture healing in a mouse model

This project examined the differences in healing of metaphyseal bone, when the implants of variable stiffness are used for fracture fixation. This knowledge is important in development of novel orthopaedic implants, used in orthopaedic surgery to stabilise the fractures. Dr Koval used a mouse model to create a fracture, and then assessed its healing with a combination of mechanical testing, microcomputed tomography and histomorphometric examination.

The impact of mobile phone distraction on the braking behaviour of young drivers : a hazard-based duration model

Braking is a crucial driving task with a direct relationship with crash risk, as both excess and inadequate braking can lead to collisions. The objective of this study was to compare the braking profile of young drivers distracted by mobile phone conversations to non-distracted braking. In particular, the braking behaviour of drivers in response to a pedestrian entering a zebra crossing was examined using the CARRS-Q Advanced Driving Simulator. Thirty-two licensed drivers drove the simulator in three phone conditions: baseline (no phone conversation), hands-free, and handheld. In addition to driving the simulator, each participant completed questionnaires related to driver demographics, driving history, usage of mobile phones while driving, and general mobile phone usage history. The drivers were 18–26 years old and split evenly by gender. A linear mixed model analysis of braking profiles along the roadway before the pedestrian crossing revealed comparatively increased decelerations among distracted drivers, particularly during the initial 20 kph of deceleration. Drivers’ initial 20 kph deceleration time was modelled using a parametric accelerated failure time (AFT) hazard-based duration model with a Weibull distribution with clustered heterogeneity to account for the repeated measures experiment design. Factors found to significantly influence the braking task included vehicle dynamics variables like initial speed and maximum deceleration, phone condition, and driver-specific variables such as licence type, crash involvement history, and self-reported experience of using a mobile phone whilst driving. Distracted drivers on average appear to reduce the speed of their vehicle faster and more abruptly than non-distracted drivers, exhibiting excess braking comparatively and revealing perhaps risk compensation. The braking appears to be more aggressive for distracted drivers with provisional licenses compared to drivers with open licenses. Abrupt or excessive braking by distracted drivers might pose significant safety concerns to following vehicles in a traffic stream.

A computational model for BMP movement in sea urchin embryos

Bone morphogen proteins (BMPs) are distributed along a dorsal-ventral (DV) gradient in many developing embryos. The spatial distribution of this signaling ligand is critical for correct DV axis specification. In various species, BMP expression is spatially localized, and BMP gradient formation relies on BMP transport, which in turn requires interactions with the extracellular proteins Short gastrulation/Chordin (Chd) and Twisted gastrulation (Tsg). These binding interactions promote BMP movement and concomitantly inhibit BMP signaling. The protease Tolloid (Tld) cleaves Chd, which releases BMP from the complex and permits it to bind the BMP receptor and signal. In sea urchin embryos, BMP is produced in the ventral ectoderm, but signals in the dorsal ectoderm. The transport of BMP from the ventral ectoderm to the dorsal ectoderm in sea urchin embryos is not understood. Therefore, using information from a series of experiments, we adapt the mathematical model of Mizutani et al. (2005) and embed it as the reaction part of a one-dimensional reaction–diffusion model. We use it to study aspects of this transport process in sea urchin embryos. We demonstrate that the receptor-bound BMP concentration exhibits dorsally centered peaks of the same type as those observed experimentally when the ternary transport complex (Chd-Tsg-BMP) forms relatively quickly and BMP receptor binding is relatively slow. Similarly, dorsally centered peaks are created when the diffusivities of BMP, Chd, and Chd-Tsg are relatively low and that of Chd-Tsg-BMP is relatively high, and the model dynamics also suggest that Tld is a principal regulator of the system. At the end of this paper, we briefly compare the observed dynamics in the sea urchin model to a version that applies to the fly embryo, and we find that the same conditions can account for BMP transport in the two types of embryos only if Tld levels are reduced in sea urchin compared to fly.

Business model adaptation in new ventures: are technology-based firms different?

A firm’s business model (BM) is an important driver of its relative performance. Constructive adaptation to elements of the BM can therefore sustain the position in light of changing conditions. This study takes a configurational approach to understanding drivers of business model adaptation (BMA) in new ventures. We investigate the effect of human capital, social capital, and technological environment on BMA. We find that a universal, direct effects, analysis can provide useful information, but also risks painting a distorted picture. Contingent, two-way interactions add further explanatory power, but configurational models combining elements of all three (internal resource, external activities, environment) are superior.