Special features of RAD Sequencing data:implications for genotyping

Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools

Warm and fertile sub-humid conditions enhance litterfall to sustain high soil respiration fluxes in a mediterranean cork oak forest

Soil respiration is a major component of the global carbon budget and Mediterranean ecosystems have usually been studied in locations with shallow soils, mild temperatures, and a prolonged dry season. This study investigates seasonal soil respiration rates and underlying mechanisms under wetter, warmer, and more fertile conditions in a Mediterranean cork oak forest of Northern Tunisia (Africa), acknowledged as one of the most productive forests in the Mediterranean basin. We applied a soil respiration model based on soil temperature and relative water content and investigated how ecosystem functioning under these favorable conditions affected soil carbon storage through carbon inputs to the soil litter. Annual soil respiration rates varied between 1774 gC m(-2) year(-1) and 2227 gC m(-2) year(-1), which is on the highest range of observations under Mediterranean climate conditions. We attributed this high soil carbon flux as a response to favorable temperatures and soil water content, but this could be sustained only by a small carbon allocation to roots (root/shoot ratio = 0.31-0.41) leading to a large allocation to leaves with a multiannual leaf production, enhanced annual twig elongation (11.5-28.5 cm) with a reduced leaf life span (<1 year) maintaining a low LAI (1.68-1.88) and generating a high litterfall (386-636 gC m(-2) year(-1)). Thus, the favorable climatic and edaphic conditions experienced by these Mediterranean cork oak forests drove high soil respiration fluxes which balanced the high carbon assimilation leading to a relatively small overall contribution (10.96-14.79 kgC m(-2)) to soil carbon storage

Determination of the interfacial heat transfer coefficient for a hot aluminium stamping process

The interfacial heat transfer coefficient (IHTC) is an important thermophysical parameter in hot stamping processes and must be identified not only to retain the full mechanical strength of formed components, but also to optimise the production rate. In this work, a novel experimental facility was developed and applied to measure the temperature evolutions of the specimens and tools in stamping processes. Simulated temperature evolutions obtained using the FE software PAM-STAMP were then fit to this data. The IHTC values between AA7075 and three different tool materials were characterized at different contact pressures under both dry and lubricated conditions. In addition, a mechanism based IHTC model was developed and validated as a function of contact pressure, tool material and lubricant thickness to predict the IHTC values under different conditions

Digitally-enhanced lubricant evaluation scheme for hot stamping applications

Digitally-enhanced technologies are set to transform every aspect of manufacturing. Networks of sensors that compute at the edge (streamlining information flow from devices and providing real-time local data analysis), and emerging Cloud Finite Element Analysis technologies yield data at unprecedented scales, both in terms of volume and precision, providing information on complex processes and systems that had previously been impractical. Cloud Finite Element Analysis technologies enable proactive data collection in a supply chain of, for example the metal forming industry, throughout the life cycle of a product or process, which presents revolutionary opportunities for the development and evaluation of digitally-enhanced lubricants, which requires a coherent research agenda involving the merging of tribological knowledge, manufacturing and data science. In the present study, data obtained from a vast number of experimentally verified finite element simulation results is used for a metal forming process to develop a digitally-enhanced lubricant evaluation approach, by precisely representing the tribological boundary conditions at the workpiece/tooling interface, i.e., complex loading conditions of contact pressures, sliding speeds and temperatures. The presented approach combines the implementation of digital characteristics of the target forming process, data-guided lubricant testing and mechanism-based accurate theoretical modelling, enabling the development of data-centric lubricant limit diagrams and intuitive and quantitative evaluation of the lubricant performance

Immunogenic Human Papillomavirus Pseudovirus-Mediated Suicide-Gene Therapy for Bladder Cancer.

Bladder cancer is the second most common urological malignancy in the world. In 70% of cases it is initially diagnosed as non-muscle-invasive bladder cancer (NMIBC) and it is amenable to local treatments, with intravesical (IVES) Bacillus-Calmette-Guerin (BCG) immunotherapy being routinely used after transurethral resection of the lesion. However, this treatment is associated with significant side-effects and treatment failures, highlighting the necessity of novel strategies. One potent approach is the suicide-gene mediated therapy/prodrug combination, provided tumor-specificity can be ensured and anti-tumor immune responses induced. Using the mouse syngeneic orthotopic MB49-bladder tumor model, here we show that IVES human papillomavirus non-replicative pseudovirions (PsV) can pseudoinfect tumors with a ten-fold higher efficacy than normal bladders. In addition, PsV carrying the suicide-gene herpes-simplex virus thymidine kinase (PsV-TK) combined to Ganciclovir (GCV) led to immunogenic cell-death of tumor cells in vitro and to MB49-specific CD8 T-cells in vivo. This was associated with reduction in bladder-tumor growth and increased mice survival. Altogether, our data show that IVES PsV-TK/GCV may be a promising alternative or combinatory treatment for NMIBC

Interactive mechanism and friction modelling of transient tribological phenomena in metal forming processes: A review

The accurate representation of tribological boundary conditions at the tool-workpiece interface is crucial for analysis and optimization of formability, material flow, and surface quality of components during metal forming processes. It has been found that these tribological conditions vary spatially and historically with process parameters and contact conditions. These time-dependent tribological behaviours are also known as transient tribological phenomena, which are widely observed during forming processes and many other manufacturing application scenarios. However, constant friction values are usually assigned to represent complex and dynamic interfacial conditions, which would introduce deviations in the relevant predictions. In this paper, transient tribological phenomena and the contemporary understanding of the interaction between friction and wear are reviewed, and it has been found that these phenomena are induced by the transitions of friction mechanisms and highly dependent on complex loading conditions at the interface. Friction modelling techniques for transient behaviours for metal forming applications are also reviewed. To accurately describe the evolutionary friction values and corresponding wear during forming, the advanced interactive friction modelling has been established for different application scenarios, including lubricated condition, dry sliding condition (metal-on-metal contact), and coated system

Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oysters (Crassostrea gigas) revealed by genome-wide SNP data.

Cultivated bivalves are important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium-density single nucleotide polymorphism (SNP) array to investigate the genetic structure of this species in Europe, where it was introduced during the 1960s and has since become a prolific invader of coastal ecosystems across the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from 23 localities spanning a latitudinal cline from Portugal to Norway and including the source populations of Japan and Canada. We confirmed the results of previous studies by finding clear support for a southern and a northern group, with the former being indistinguishable from the source populations indicating the absence of a pronounced founder effect. We furthermore conducted a large-scale comparison of oysters sampled from the wild and from hatcheries to reveal substantial genetic differences including significantly higher levels of inbreeding in some but not all of the sampled hatchery cohorts. These findings were confirmed by a smaller but representative SNP dataset generated using restriction site-associated DNA sequencing. We therefore conclude that genomic approaches can generate increasingly detailed insights into the genetics of wild and hatchery produced Pacific oysters