Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.

The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3'-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3'-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation

Adsorption and dissociation of molecular oxygen on the (0001) surface of double hexagonal close packed americium

In our continuing attempts to understand theoretically various surface properties such as corrosion and potential catalytic activity of actinide surfaces in the presence of environmental gases, we report here the first ab initio study of molecular adsorption on the double hexagonal packed (dhcp) americium (0001) surface. Dissociative adsorption is found to be energetically more favorable compared to molecular adsorption. The most stable configuration corresponds to a horizontal approach molecular dissociation with the oxygen atoms occupying neighboring h3 sites, with chemisorption energies at the NSOC and SOC theoretical levels being 9.395 eV and 9.886 eV, respectively. The corresponding distances of the oxygen molecule from the surface and oxygen-oxygen distance were found to be 0.953 Ang. and 3.731 Ang., respectively. Overall our calculations indicate that chemisorption energies in cases with SOC are slightly more stable than the cases with NSOC in the 0.089-0.493 eV range. The work functions and net magnetic moments respectively increased and decreased in all cases compared with the corresponding quantities of the bare dhcp Am (0001) surface. The adsorbate-substrate interactions have been analyzed in detail using the partial charges inside the muffin-tin spheres, difference charge density distributions, and the local density of states. The effects, if any, of chemisorption on the Am 5f electron localization-delocalization characteristics in the vicinity of the Fermi level are also discussed.Comment: 6 tables, 10 figure

Towards Infield Navigation: leveraging simulated data for crop row detection

Agricultural datasets for crop row detection are often bound by their limited number of images. This restricts the researchers from developing deep learning based models for precision agricultural tasks involving crop row detection. We suggest the utilization of small real-world datasets along with additional data generated by simulations to yield similar crop row detection performance as that of a model trained with a large real world dataset. Our method could reach the performance of a deep learning based crop row detection model trained with real-world data by using 60% less labelled real-world data. Our model performed well against field variations such as shadows, sunlight and grow stages. We introduce an automated pipeline to generate labelled images for crop row detection in simulation domain. An extensive comparison is done to analyze the contribution of simulated data towards reaching robust crop row detection in various real-world field scenarios.Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible. arXiv admin note: substantial text overlap with arXiv:2109.0824

Leaving the Lines Behind: Vision-Based Crop Row Exit for Agricultural Robot Navigation

Usage of purely vision based solutions for row switching is not well explored in existing vision based crop row navigation frameworks. This method only uses RGB images for local feature matching based visual feedback to exit crop row. Depth images were used at crop row end to estimate the navigation distance within headland. The algorithm was tested on diverse headland areas with soil and vegetation. The proposed method could reach the end of the crop row and then navigate into the headland completely leaving behind the crop row with an error margin of 50 cm.Comment: Best Paper Award at TIG-IV workshop at ICRA 2023 https://sites.google.com/view/icra23tig4ws/call-for-contribution

Stress and productivity patterns of interrupted, synergistic, and antagonistic office activities.

We describe a controlled experiment, aiming to study productivity and stress effects of email interruptions and activity interactions in the modern office. The measurement set includes multimodal data for n = 63 knowledge workers who volunteered for this experiment and were randomly assigned into four groups: (G1/G2) Batch email interruptions with/without exogenous stress. (G3/G4) Continual email interruptions with/without exogenous stress. To provide context, the experiment's email treatments were surrounded by typical office tasks. The captured variables include physiological indicators of stress, measures of report writing quality and keystroke dynamics, as well as psychometric scores and biographic information detailing participants' profiles. Investigations powered by this dataset are expected to lead to personalized recommendations for handling email interruptions and a deeper understanding of synergistic and antagonistic office activities. Given the centrality of email in the modern office, and the importance of office work to people's lives and the economy, the present data have a valuable role to play

Effect of the oxygen flow on the properties of ITO thin films deposited by ion beam assisted deposition (IBAD)

ITO films were deposited onto glass substrates by ion beam assisted deposition method. The oxygen ions were produced using a Kaufman ion source. The oxygen flow was varied from 20 until 60 sccm and the effect of the oxygen flow on properties of ITO films has been studied. The structural properties of the film were characterized by X-ray diffraction and atomic force microscopy. The optical properties were characterized by optical transmission measurements and the optical constants (refractive index n and extinction coefficient k) and film thickness have been obtained by fitting the transmittance using a semi-quantum model. The electrical properties were characterized by Hall effect measurements. It has been found that the ITO film with low electrical resistivity and high transmittance can be obtained with 40 sccm oxygen flow (the working pressure is about 2.3 × 10−2 Pa at this oxygen flow).Fundação para a Ciência e a Tecnologia (FCT) - SFRH-BSAB-514

Effects of CO2 enrichment on photosynthesis, growth, and nitrogen metabolism of the seagrass Zostera noltii

Seagrass ecosystems are expected to benefit from the global increase in CO2 in the ocean because the photosynthetic rate of these plants may be C-i-limited at the current CO2 level. As well, it is expected that lower external pH will facilitate the nitrate uptake of seagrasses if nitrate is cotransported with H+ across the membrane as in terrestrial plants. Here, we investigate the effects of CO2 enrichment on both carbon and nitrogen metabolism of the seagrass Zostera noltii in a mesocosm experiment where plants were exposed for 5 months to two experimental CO2 concentrations (360 and 700 ppm). Both the maximum photosynthetic rate (Pm) and photosynthetic efficiency (alpha) were higher (1.3- and 4.1-fold, respectively) in plants exposed to CO2-enriched conditions. On the other hand, no significant effects of CO2 enrichment on leaf growth rates were observed, probably due to nitrogen limitation as revealed by the low nitrogen content of leaves. The leaf ammonium uptake rate and glutamine synthetase activity were not significantly affected by increased CO2 concentrations. On the other hand, the leaf nitrate uptake rate of plants exposed to CO2-enriched conditions was fourfold lower than the uptake of plants exposed to current CO2 level, suggesting that in the seagrass Z. noltii nitrate is not cotransported with H+ as in terrestrial plants. In contrast, the activity of nitrate reductase was threefold higher in plant leaves grown at high-CO2 concentrations. Our results suggest that the global effects of CO2 on seagrass production may be spatially heterogeneous and depend on the specific nitrogen availability of each system. Under a CO2 increase scenario, the natural levels of nutrients will probably become limiting for Z. noltii. This potential limitation becomes more relevant because the expected positive effect of CO2 increase on nitrate uptake rate was not confirmed.Fundacao para a Ciencia e a Tecnologia [SFRH/BD/21487/2005]; POCI; FSE; COST; EC; EUinfo:eu-repo/semantics/publishedVersio