A regional atmosphere-ocean climate system model (CCLMv5.0clm7-NEMOv3.3-NEMOv3.6) over Europe including three marginal seas: On its stability and performance

The frequency of extreme events has changed, having a direct impact on human lives. Regional climate models help us to predict these regional climate changes. This work presents an atmosphere–ocean coupled regional climate system model (RCSM; with the atmospheric component COSMO-CLM and the ocean component NEMO) over the European domain, including three marginal seas: the Mediterranean, North, and Baltic Sea. To test the model, we evaluate a simulation of more than 100 years (1900–2009) with a spatial grid resolution of about 25 km. The simulation was nested into a coupled global simulation with the model MPI-ESM in a low-resolution configuration, whose ocean temperature and salinity were nudged to the ocean–ice component of the MPI-ESM forced with the NOAA 20th Century Reanalysis (20CR). The evaluation shows the robustness of the RCSM and discusses the added value by the coupled marginal seas over an atmosphere-only simulation. The coupled system is stable for the complete 20th century and provides a better representation of extreme temperatures compared to the atmosphere-only model. The produced long-term dataset will help us to better understand the processes leading to meteorological and climate extremes

Screw dislocation in zirconium: An ab initio study

Plasticity in zirconium is controlled by 1/3 screw dislocations gliding in the prism planes of the hexagonal close-packed structure. This prismatic and not basal glide is observed for a given set of transition metals like zirconium and is known to be related to the number of valence electrons in the d band. We use ab initio calculations based on the density functional theory to study the core structure of screw dislocations in zirconium. Dislocations are found to dissociate in the prism plane in two partial dislocations, each with a pure screw character. Ab initio calculations also show that the dissociation in the basal plane is unstable. We calculate then the Peierls barrier for a screw dislocation gliding in the prism plane and obtain a small barrier. The Peierls stress deduced from this barrier is lower than 21 MPa, which is in agreement with experimental data. The ability of an empirical potential relying on the embedded atom method (EAM) to model dislocations in zirconium is also tested against these ab initio calculations

Endovascular Management of Traumatic Iliac Vessel Disruption—Report of Two Cases

AbstractVascular injuries in a multi-trauma patient are associated with significant cardiovascular instability and organ injury. Injuries with active bleeding are best treated with a quick, safe and the least less invasive procedure available to the trauma surgeon. We report two cases of blunt trauma induced common and external iliac vessel injury, managed by endovascular treatment. In the second case, endovascular treatment prevented histological examination of the artery, which would have revealed an alternative diagnosis

Alanine scanning mutagenesis of a high-affinity nitrate transporter highlights the requirement for glycine and asparagine residues in the two nitrate signature motifs

Common to all of the nitrate nitrite porter family are two conserved motifs in transmembrane helices 5 and 11 termed NS (nitrate signature) 1 and NS2. Although perfectly conserved substrate-interacting arginine residues have been described in transmembrane helices 2 and 8, the role of NSs has not been investigated. In the present study, a combination of structural modelling of NrtA (nitrate transporter from Aspergillus nidulans) with alanine scanning mutagenesis of residues within and around the NSs has been used to shed light on the probable role of conserved residues in the NSs. Models show that Asn 168 in NS1 and Asn 459 in NS2 are positioned approximately midway within the protein at the central pivot point in close proximity to the substrate-binding residues Arg 368 and Arg 87 respectively, which lie offset from the pivot point towards the cytoplasmic face. The Asn 168 /Arg 368 and Asn 459 /Arg 87 residue pairs are relatively widely separated on opposite sides of the probable substrate translocation pore. The results of the present study demonstrate the critical structural contribution of several glycine residues in each NS at sites of close helix packing. Given the relative locations of Asn 168 /Arg 368 and Asn 459 /Arg 87 pairs, the validity of the models and possible role of the NSs together with the substrate-binding arginine residues are discusse

Generalization Error in Deep Learning

Deep learning models have lately shown great performance in various fields such as computer vision, speech recognition, speech translation, and natural language processing. However, alongside their state-of-the-art performance, it is still generally unclear what is the source of their generalization ability. Thus, an important question is what makes deep neural networks able to generalize well from the training set to new data. In this article, we provide an overview of the existing theory and bounds for the characterization of the generalization error of deep neural networks, combining both classical and more recent theoretical and empirical results

A microbial platform for renewable propane synthesis based on a fermentative butanol pathway

Background Propane (C3H8) is a volatile hydrocarbon with highly favourable physicochemical properties as a fuel, in addition to existing global markets and infrastructure for storage, distribution and utilization in a wide range of applications. Consequently, propane is an attractive target product in research aimed at developing new renewable alternatives to complement currently used petroleum-derived fuels. This study focuses on the construction and evaluation of alternative microbial biosynthetic pathways for the production of renewable propane. The new pathways utilize CoA intermediates that are derived from clostridial-like fermentative butanol pathways and are therefore distinct from the first microbial propane pathways recently engineered in Escherichia coli. Results We report the assembly and evaluation of four different synthetic pathways for the production of propane and butanol, designated a) atoB-adhE2 route, b) atoB-TPC7 route, c) nphT7-adhE2 route and d) nphT7-TPC7 route. The highest butanol titres were achieved with the atoB-adhE2 (473 ± 3 mg/L) and atoB-TPC7 (163 ± 2 mg/L) routes. When aldehyde deformylating oxygenase (ADO) was co-expressed with these pathways, the engineered hosts also produced propane. The atoB-TPC7-ADO pathway was the most effective in producing propane (220 ± 3 μg/L). By (i) deleting competing pathways, (ii) including a previously designed ADOA134F variant with an enhanced specificity towards short-chain substrates and (iii) including a ferredoxin-based electron supply system, the propane titre was increased (3.40 ± 0.19 mg/L). Conclusions This study expands the metabolic toolbox for renewable propane production and provides new insight and understanding for the development of next-generation biofuel platforms. In developing an alternative CoA-dependent fermentative butanol pathway, which includes an engineered ADO variant (ADOA134F), the study addresses known limitations, including the low bio-availability of butyraldehyde precursors and poor activity of ADO with butyraldehyde

Prediction of Signed Protein Kinase Regulatory Circuits.

Complex networks of regulatory relationships between protein kinases comprise a major component of intracellular signaling. Although many kinase-kinase regulatory relationships have been described in detail, these tend to be limited to well-studied kinases whereas the majority of possible relationships remains unexplored. Here, we implement a data-driven, supervised machine learning method to predict human kinase-kinase regulatory relationships and whether they have activating or inhibiting effects. We incorporate high-throughput data, kinase specificity profiles, and structural information to produce our predictions. The results successfully recapitulate previously annotated regulatory relationships and can reconstruct known signaling pathways from the ground up. The full network of predictions is relatively sparse, with the vast majority of relationships assigned low probabilities. However, it nevertheless suggests denser modes of inter-kinase regulation than normally considered in intracellular signaling research. A record of this paper's transparent peer review process is included in the Supplemental Information

Central nervous system demyelination associated with etanercept in a 51 years old woman

There are few case reports documenting a new onset of demyelinating processes in patients receiving anti-tumour necrosis factor alpha therapy (anti-TNF alpha) for chronic inflammatory arthropathies. Whether anti-TNF alpha therapy induces new onset demyelination or just exacerbates pre-existing latent multiple sclerosis is not fully understood. We are reporting a 51-year-old woman without a prior history of multiple sclerosis, who developed demyelinating brain lesions three months after starting Etanercept. Her symptoms partially resolved on cessation of the drug. Our case was unusual compared to some previous case reports, as the patient's age at presentation was beyond that for idiopathic multiple sclerosis. This may strengthen the hypothesis of a causal relationship between new onset demyelination and Etanercept; however, exacerbation of pre-existing demyelinating process by Etanercept in this patient still cannot be totally excluded. We recommend doing magnetic resonance imaging (MRI) of the brain before starting patients on anti-TNF alpha therapy to exclude latent demyelination. In addition, new onset demyelination following anti-TNF alpha therapy should be reported and studied thoroughly as this may yield a significant advancement in our understanding of the pathogenesis of multiple sclerosis. Long-term follow-up of these cases is also important to determine the long-term prognosis and the rate of relapse of demyelinating process in this group of patients

Bridging the gaps among research, policy and practice in ten low- and middle-income countries: Development and testing of a questionnaire for researchers

<p>Abstract</p> <p>Background</p> <p>A questionnaire could assist researchers, policymakers, and healthcare providers to describe and monitor changes in efforts to bridge the gaps among research, policy and practice. No questionnaire focused on researchers' engagement in bridging activities related to high-priority topics (or the potential correlates of their engagement) has been developed and tested in a range of low- and middle-income countries (LMICs).</p> <p>Methods</p> <p>Country teams from ten LMICs (China, Ghana, India, Iran, Kazakhstan, Laos, Mexico, Pakistan, Senegal, and Tanzania) participated in the development and testing of a questionnaire. To assess reliability we calculated the internal consistency of items within each of the ten conceptual domains related to bridging activities (specifically Cronbach's alpha). To assess face and content validity we convened several teleconferences and a workshop. To assess construct validity we calculated the correlation between scales and counts (i.e., criterion measures) for the three countries that employed both and we calculated the correlation between different but theoretically related (i.e., convergent) measures for all countries.</p> <p>Results</p> <p>Internal consistency (Cronbach's alpha) for sets of related items was very high, ranging from 0.89 (0.86-0.91) to 0.96 (0.95-0.97), suggesting some item redundancy. Both face and content validity were determined to be high. Assessments of construct validity using criterion-related measures showed statistically significant associations for related measures (with gammas ranging from 0.36 to 0.73). Assessments using convergent measures also showed significant associations (with gammas ranging from 0.30 to 0.50).</p> <p>Conclusions</p> <p>While no direct comparison can be made to a comparable questionnaire, our findings do suggest a number of strengths of the questionnaire but also the need to reduce item redundancy and to test its capacity to monitor changes over time.</p