Use of cadavers and anthropometric test devices (ATDs) for assessing lower limb injury outcome from under‐vehicle explosions

Lower extremities are particularly susceptible to injury in an under‐vehicle explosion. Operational fitness of military vehicles is assessed through anthropometric test devices (ATDs) in full‐scale blast tests. The aim of this study was to compare the response between the Hybrid‐III ATD, the MiL‐Lx ATD and cadavers in our traumatic injury simulator, which is able to replicate the response of the vehicle floor in an under‐vehicle explosion. All specimens were fitted with a combat boot and tested on our traumatic injury simulator in a seated position. The load recorded in the ATDs was above the tolerance levels recommended by NATO in all tests; no injuries were observed in any of the 3 cadaveric specimens. The Hybrid‐III produced higher peak forces than the MiL‐Lx. The time to peak strain in the calcaneus of the cadavers was similar to the time to peak force in the ATDs. Maximum compression of the sole of the combat boot was similar for cadavers and MiL‐Lx, but significantly greater for the Hybrid‐III. These results suggest that the MiL‐Lx has a more biofidelic response to under‐vehicle explosive events compared to the Hybrid‐III. Therefore, it is recommended that mitigation strategies are assessed using the MiL‐Lx surrogate and not the Hybrid‐III.

Genomic resources notes accepted 1 December 2013 - 31 January 2014

This article documents the public availability of (i) transcriptome sequence data, assembled and annotated contigs and unigenes, and BLAST hits from the Queensland fruit fly, Bactrocera tryoni; (ii) 75 single-nucleotide variants (SNVs) from 454 sequencing of reduced representation libraries for Phalangiidae harvestmen, Megabunus armatus, Megabunus vignai, Megabunus lesserti, and Rilaena triangularis; and (iii) expressed sequence tags from 454 sequencing of the lepidopterans Lymantria dispar and Lymantria monacha.

Rho GTPases mediate the mechanosensitive lineage commitment of neural stem cells

Adult neural stem cells (NSCs) play important roles in learning and memory and are negatively impacted by neurological disease. It is known that biochemical and genetic factors regulate self-renewal and differentiation, and it has recently been suggested that mechanical and solid-state cues, such as extracellular matrix (ECM) stiffness, can also regulate the functions of NSCs and other stem cell types. However, relatively little is known of the molecular mechanisms through which stem cells transduce mechanical inputs into fate decisions, the extent to which mechanical inputs instruct fate decisions versus select for or against lineage-committed blast populations, or the in vivo relevance of mechanotransductive signaling molecules in native stem cell niches. Here we demonstrate that ECM-derived mechanical signals act through Rho GTPases to activate the cellular contractility machinery in a key early window during differentiation to regulate NSC lineage commitment. Furthermore, culturing NSCs on increasingly stiff ECMs enhances RhoA and Cdc42 activation, increases NSC stiffness, and suppresses neurogenesis. Likewise, inhibiting RhoA and Cdc42 or downstream regulators of cellular contractility rescues NSCs from stiff matrix- and Rho GTPase-induced neurosuppression. Importantly, Rho GTPase expression and ECM stiffness do not alter proliferation or apoptosis rates indicating that an instructive rather than selective mechanism modulates lineage distributions. Finally, in the adult brain, RhoA activation in hippocampal progenitors suppresses neurogenesis, analogous to its effect in vitro. These results establish Rho GTPase-based mechanotransduction and cellular stiffness as biophysical regulators of NSC fate in vitro and RhoA as an important regulatory protein in the hippocampal stem cell niche.

Improving combustion stability in sugar factory boilers

Reliable operation of a sugar factory boiler station is essential for efficient and timely processing of the cane supply. Sugar factory boilers have to contend with changes in fuel quality caused by variations in performance of the extraction station, different cane varieties and associated agronomic factors along with fluctuations in factory steam demand. These variations can affect the stability of combustion in boiler furnaces leading to reductions in boiler steam output and large furnace pressure fluctuations that can cause serious damage. This paper investigates the causes of unstable combustion, discusses aspects of boiler design that make a boiler more susceptible to unstable combustion and uses modelling to evaluate different options for improving combustion stability.

Imaging of the asymmetric DC discharge: visualization to adjust plasma in the novel PECVD reactor

Normal asymmetric glow dc discharge in the thermal furnace converted into the efficient PECVD system was imaged to adjust the structure of the plasma column to the two possible localizations of the process zone. The visualization revealed the possibility to use short and long discharge configurations for the plasma-enabled growth and processing of various nanostructures in the modified setup. Images of the discharge in the two localizations are presented.

Property-performance control of multidimensional, hierarchical, single-crystalline ZnO nanoarchitectures

Diverse morphologies of multidimensional hierarchical single-crystalline ZnO nanoarchitectures including nanoflowers, nanobelts, and nanowires are obtained by use of a simple thermal evaporation and vapour-phase transport deposition technique by placing Au-coated silicon substrates in different positions inside a furnace at process temperatures as low as 550 °C. The nucleation and growth of ZnO nanostructures are governed by the vapour–solid mechanism, as opposed to the commonly reported vapour–liquid–solid mechanism, when gold is used in the process. The morphological, structural, compositional and optical properties of the synthesized ZnO nanostructures can be effectively tailored by means of the experimental parameters, and these properties are closely related to the local growth temperature and gas-phase supersaturation at the sample position. In particular, room-temperature photoluminescence measurements reveal an intense near-band-edge ultraviolet emission at about 386 nm for nanobelts and nanoflowers, which suggests that these nanostructures are of sufficient quality for applications in, for example, optoelectronic devices.

Effect of soil properties on the response of pile to underground explosion

This paper develops and presents a fully coupled non-linear finite element procedure to treat the response of piles to ground shocks induced by underground explosions. The Arbitrary Lagrange Euler coupling formulation with proper state material parameters and equations are used in the study. Pile responses in four different soil types, viz, saturated soil, partially saturated soil and loose and dense dry soils are investigated and the results compared. Numerical results are validated by comparing with those from a standard design manual. Blast wave propagation in soils, horizontal pile deformations and damages in the pile are presented. The pile damage presented through plastic strain diagrams will enable the vulnerability assessment of the piles under the blast scenarios considered. The numerical results indicate that the blast performance of the piles embedded in saturated soil and loose dry soil are more severe than those in piles embedded in partially saturated soil and dense dry soil. Present findings should serve as a benchmark reference for future analysis and design.

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

Robotic explosive charging in mining and construction applications

Describes the development and testing of a robotic system for charging blast holes in underground mining. The automation system supports four main tactical functions: detection of blast holes; teleoperated arm pose control; automatic arm pose control; and human-in-the-loop visual servoing. We present the system architecture, and analyse the major components, Hole detection is crucial for automating the process, and we discuss theoretical and practical aspects in detail. The sensors used are laser range finders and cameras installed in the end effector. For automatic insertion, we consider image processing techniques to support visual servoing the tool to the hole. We also discuss issues surrounding the control of heavy-duty mining manipulators, in particular, friction, stiction, and actuator saturation.

Locality-sensitive hashing for protein classification

Determination of sequence similarity is a central issue in computational biology, a problem addressed primarily through BLAST, an alignment based heuristic which has underpinned much of the analysis and annotation of the genomic era. Despite their success, alignment-based approaches scale poorly with increasing data set size, and are not robust under structural sequence rearrangements. Successive waves of innovation in sequencing technologies – so-called Next Generation Sequencing (NGS) approaches – have led to an explosion in data availability, challenging existing methods and motivating novel approaches to sequence representation and similarity scoring, including adaptation of existing methods from other domains such as information retrieval. In this work, we investigate locality-sensitive hashing of sequences through binary document signatures, applying the method to a bacterial protein classification task. Here, the goal is to predict the gene family to which a given query protein belongs. Experiments carried out on a pair of small but biologically realistic datasets (the full protein repertoires of families of Chlamydia and Staphylococcus aureus genomes respectively) show that a measure of similarity obtained by locality sensitive hashing gives highly accurate results while offering a number of avenues which will lead to substantial performance improvements over BLAST..

Dynamic simulation of CFRP strengthened steel column under impact loading

Carbon fibre reinforced polymer (CFRP) strengthening of metallic structures under static loading has shown great potential in the recent years. However, steel structures are often experienced natural (e.g. earthquake, wind) as well as man-made (e.g. vehicular impact, blast) dynamic loading. Therefore, there is a growing interest among the researchers to investigate the capability of CFRP strengthened members under such dynamic conditions. This study focuses on the finite element (FE) numerical modelling and simulation of CFRP strengthened steel column under transverse impact loading to predict the behaviour and failure modes. Impact simulation process and the CFRP strengthened steel column are validated with the existing experimental results in literature. The validated FE model of CFRP strengthened steel column is then further used to investigate the effects of transverse impact loading on its structural performance. The results are presented in terms of transvers e impact force, lateral and axial displacement, and deformed shape to evaluate the effectiveness of CFRP strengthening technique. Comparisons between the bare steel and CFRP strengthened steel columns clearly indicate the performance enhancement of strengthened column under transverse impact loading.

Effect of nano-silica on the mechanical and transport properties of lightweight concrete

This paper investigated the influence of nano-silica (NS) on the mechanical and transport properties of lightweight concrete (LWC). The resistance of LWC to water and chloride ions penetration was enhanced despite strength marginally increased. Water penetration depth, moisture sorptivity, chloride migration and diffusion coefficient was reduced by 23% and 49%, 23% and 10%, 5% and 0%, 22% and 12% compared to the two reference LWC mixes (pure cement and 60% slag blended cement), respectively with 1% NS. Such improvements were attributed to more compact microstructures because the micropore system was refined and the interface between aggregates and paste was enhanced.

Analysis, characterisation and expression of gill-expressed carbonic anhydrase genes in the freshwater crayfish Cherax quadricarinatus

Changes in water quality parameters such as pH and salinity can have a significant effect on productivity of aquaculture species. Similarly, relative osmotic pressure influences various physiological processes and regulates expression of a number of osmoregulatory genes. Among those, carbonic anhydrase (CA) plays a key role in systemic acid–base balance and ion regulation. Redclaw crayfish (Cherax quadricarinatus) are unique in their ability to thrive in environments with naturally varied pH levels, suggesting unique adaptation to pH stress. To date, however, no studies have focused on identification and characterisation of CA or other osmoregulatory genes in C. quadricarinatus. Here, we analysed the redclaw gill transcriptome and characterized CA genes along with a number of other key osmoregulatory genes that were identified in the transcriptome. We also examined patterns of gene expression of these CA genes when exposed to three pH treatments. In total, 72,382,710 paired end Illumina reads were assembled into 36,128 contigs with an average length of 800 bp. Approximately 37% of contigs received significant BLAST hits and 22% were assigned gene ontology terms. Three full length CA isoforms; cytoplasmic CA (ChqCAc), glycosyl-phosphatidylinositol-linked CA (ChqCAg), and β-CA (ChqCA-beta) as well as two partial CA gene sequences were identified. Both partial CA genes showed high similarity to ChqCAg and appeared to be duplicated from the ChqCAg. Full length coding sequences of Na+/K+-ATPase, V-type H+-ATPase, sarcoplasmic Ca+-ATPase, arginine kinase, calreticulin and Cl− channel protein 2 were also identified. Only the ChqCAc gene showed significant differences in expression across the three pH treatments. These data provide valuable information on the gill expressed CA genes and their expression patterns in freshwater crayfish. Overall our data suggest an important role for the ChqCAc gene in response to changes in pH and in systemic acid–base balance in freshwater crayfish.

VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Damage assessment of basaltic rock mass due to repeated blasting in a railway tunnelling project - A case study

The demand for tunnelling and underground space creation is rapidly growing due to the requirement of civil infrastructure projects and urbanisation. Blasting remains the most inexpensive method of underground excavations in hard rock. Unfortunately, there are no specific safety guidelines available for the blasted tunnels with regards to the threshold limits of vibrations caused by repeated blasting activity in the close proximity. This paper presents the results of a comprehensive study conducted to find out the effect of repeated blast loading on the damage experienced by jointed basaltic rock mass during tunnelling works. Conducting of multiple rounds of blasts for various civil excavations in a railway tunnel imparted repeated loading on rock mass of sidewall and roof of the tunnel. The blast induced damage was assessed by using vibration attenuation equations of charge weight scaling law and measured by borehole extensometers and borehole camera. Ground vibrations of each blasting round were also monitored by triaxial geophones installed near the borehole extensometers. The peak particle velocity (V-max) observations and plastic deformations from borehole extensometers were used to develop a site specific damage model. The study reveals that repeated dynamic loading imparted on the exposed tunnel from subsequent blasts, in the vicinity, resulted in rock mass damage at lesser vibration levels than the critical peak particle velocity (V-cr). It was found that, the repeated blast loading resulted in the near-field damage due to high frequency waves and far-field damage due to low frequency waves. The far field damage, after 45-50 occurrences of blast loading, was up to 55% of the near-field damage in basaltic rock mass. The findings of the study clearly indicate that the phenomena of repeated blasting with respect to number of cycles of loading should be taken into consideration for proper assessment of blast induced damage in underground excavations.