Kinematics of dense gas in the L1495 filament

We study the kinematics of the dense gas of starless and protostellar cores traced by the N2D+(2-1), N2H+(1-0), DCO+(2-1), and H13CO+(1-0) transitions along the L1495 filament and the kinematic links between the cores and the surrounding molecular cloud. We measure velocity dispersions, local and total velocity gradients and estimate the specific angular momenta of 13 dense cores in the four transitions using the on-the-fly observations with the IRAM 30 m antenna. To study a possible connection to the filament gas, we use the fit results of the C18O(1-0) survey performed by Hacar et al. (2013). All cores show similar properties along the 10 pc-long filament. N2D+(2-1) shows the most centrally concentrated structure, followed by N2H+(1-0) and DCO+(2-1), which show similar spatial extent, and H13CO+(1-0). The non-thermal contribution to the velocity dispersion increases from higher to lower density tracers. The change of magnitude and direction of the total velocity gradients depending on the tracer used indicates that internal motions change at different depths within the cloud. N2D+ and N2H+ show smaller gradients than the lower density tracers DCO+ and H13CO+, implying a loss of specific angular momentum at small scales. At the level of cloud-core transition, the core's external envelope traced by DCO+ and H13CO+ is spinning up, consistent with conservation of angular momentum during core contraction. C18O traces the more extended cloud material whose kinematics is not affected by the presence of dense cores. The decrease in specific angular momentum towards the centres of the cores shows the importance of local magnetic fields to the small scale dynamics of the cores. The random distributions of angles between the total velocity gradient and large scale magnetic field suggests that the magnetic fields may become important only in the high density gas within dense cores.Comment: Accepted for publication in A&A. The abstract is shortene

Object-Centric Stereo Matching for 3D Object Detection

Safe autonomous driving requires reliable 3D object detection-determining the 6 DoF pose and dimensions of objects of interest. Using stereo cameras to solve this task is a cost-effective alternative to the widely used LiDAR sensor. The current state-of-the-art for stereo 3D object detection takes the existing PSMNet stereo matching network, with no modifications, and converts the estimated disparities into a 3D point cloud, and feeds this point cloud into a LiDAR-based 3D object detector. The issue with existing stereo matching networks is that they are designed for disparity estimation, not 3D object detection; the shape and accuracy of object point clouds are not the focus. Stereo matching networks commonly suffer from inaccurate depth estimates at object boundaries, which we define as streaking, because background and foreground points are jointly estimated. Existing networks also penalize disparity instead of the estimated position of object point clouds in their loss functions. We propose a novel 2D box association and object-centric stereo matching method that only estimates the disparities of the objects of interest to address these two issues. Our method achieves state-of-the-art results on the KITTI 3D and BEV benchmarks.Comment: Accepted in ICRA 202

Molecular dissection of translation initiation factor IF2. Evidence for two structural and functional domains.

By means of limited proteolysis of Bacillus stearothermophilus initiation factor IF2 and genetic manipulation of its structural gene, infB, we have been able to produce (or hyperproduce) and purify two polypeptide fragments corresponding to two structurally and functionally separate domains of the protein. The first is the G-domain (approximately 41 kDa), which makes up the central part of the molecule and contains the conserved structural elements found in all GTP/GDP-binding sites of G-proteins. This domain is resistant to proteolysis in the presence of GTP or GDP, retains the capacity to interact with the 50 S subunit, binds weakly to the 30 S subunit, and displays ribosome-dependent GTPase activity with an approximately 2-fold higher Km for GTP and the same Vmax as compared with intact IF2. The second is the C-domain (approximately 24 kDa), which corresponds to the COOH-terminal part of IF2 and constitutes an extraordinarily compact domain containing the fMet-tRNA binding site of IF2. In spite of its negligible affinity for the ribosomes, the C-domain weakly stimulates the ribosomal binding of fMet-tRNA, presumably by affecting the conformation of the initiator tRNA molecule

Ribosomal selection of mRNAs with degenerate initiation triplets

To assess the influence of degenerate initiation triplets on mRNA recruitment by ribosomes, five mRNAs identical but for their start codon (AUG, GUG, UUG, AUU and AUA) were offered to a limiting amount of ribosomes, alone or in competition with an identical AUGmRNA bearing a mutation conferring different electrophoretic mobility to the product. Translational efficiency and competitiveness of test mRNAs toward this AUGmRNA were determined quantifying the relative amounts of the electrophoretically separated wt and mutated products synthesized in vitro and found to be influenced to different extents by the nature of their initiation triplet and by parameters such as temperature and nutrient availability in the medium. The behaviors of AUAmRNA, UUGmRNA and AUGmRNA were the same between 20 and 40°C whereas the GUG and AUUmRNAs were less active and competed poorly with the AUGmRNA, especially at low temperature. Nutrient limitation and preferential inhibition by ppGpp severely affected activity and competitiveness of all mRNAs bearing non-AUG starts, the UUGmRNA being the least affected. Overall, our data indicate that beyond these effects exclusively due to the degenerate start codons within an optimized translational initiation region, an important role is played by the context in which the rare start codons are present

Strategies for Oligoribonucleotide Synthesis According to the Phosphoramidite Method

Advances in oligoribonucleotide synthesis have lagged behind those in oligodeoxyribonucleotide synthesis because of the difficulty in identifying orthogonal protecting groups for the 2′‐ and 5′‐hydroxyls. Adaptation of the phosphoramidite method for DNA synthesis to RNA synthesis has greatly improved our understanding of RNA. It allows site‐specific introduction of modified nucleosides to any position in an RNA molecule, as well as introduction of variations at multiple sites in the molecule. This overview discusses issues that are relevant to RNA synthesis by the phosphoramidite approach, including supports used, activation of the ribonucleoside phosphoramidites, and protection of the nucleobase, phosphate, and 2′‐ and 5′‐hydroxyls.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143793/1/cpnc0305.pd

Dietary nitrate increases arginine availability and protects mitochondrial complex I and energetics in the hypoxic rat heart

This is the final version. It was first published by Wiley in The Journal of Physiology at http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2014.275263/abstract.Hypoxic exposure is associated with impaired cardiac energetics in humans and altered mitochondrial function, with suppressed complex I-supported respiration, in rat heart. This response might limit reactive oxygen species (ROS) generation, but at the cost of impaired electron transport chain (ETC) activity. Dietary nitrate supplementation improves mitochondrial efficiency and can promote tissue oxygenation by enhancing blood flow. We therefore hypothesised that ETC dysfunction, impaired energetics and oxidative damage in the hearts of rats exposed to chronic hypoxia could be alleviated by sustained administration of a moderate dose of dietary nitrate. Male Wistar rats (n=40) were given water supplemented with 0.7 mmol/L NaCl (as control) or 0.7 mmol/L NaNO3, elevating plasma nitrate levels by 80%, and were exposed to 13% O2 (hypoxia) or normoxia (n=10 per group) for 14 days. Respiration rates, ETC protein levels, mitochondrial density, ATP content and protein carbonylation were measured in cardiac muscle. Complex I respiration rates and protein levels were 33% lower in hypoxic/NaCl rats compared with normoxic/NaCl controls. Protein carbonylation was 65% higher in hearts of hypoxic rats compared with controls, indicating increased oxidative stress, whilst ATP levels were 62% lower. Respiration rates, complex I protein and activity, protein carbonylation and ATP levels were all fully protected in the hearts of nitrate-supplemented hypoxic rats. Both in normoxia and hypoxia, dietary nitrate suppressed cardiac arginase expression and activity and markedly elevated cardiac L-arginine concentrations, unmasking a novel mechanism of action by which nitrate enhances tissue NO bioavailability. Dietary nitrate therefore alleviates metabolic abnormalities in the hypoxic heart, improving myocardial energetics