GPU accelerated real-time multi-functional spectral-domain optical coherence tomography system at 1300 nm.

We present a GPU accelerated multi-functional spectral domain optical coherence tomography system at 1300 nm. The system is capable of real-time processing and display of every intensity image, comprised of 512 pixels by 2048 A-lines acquired at 20 frames per second. The update rate for all four images with size of 512 pixels by 2048 A-lines simultaneously (intensity, phase retardation, flow and en face view) is approximately 10 frames per second. Additionally, we report for the first time the characterization of phase retardation and diattenuation by a sample comprised of a stacked set of polarizing film and wave plate. The calculated optic axis orientation, phase retardation and diattenuation match well with expected values. The speed of each facet of the multi-functional OCT CPU-GPU hybrid acquisition system, intensity, phase retardation, and flow, were separately demonstrated by imaging a horseshoe crab lateral compound eye, a non-uniformly heated chicken muscle, and a microfluidic device. A mouse brain with thin skull preparation was imaged in vivo and demonstrated the capability of the system for live multi-functional OCT visualization

Reroute Prediction Service

The cost of delays was estimated as 33 billion US dollars only in 2019 for the US National Airspace System, a peak value following a growth trend in past years. Aiming to address this huge inefficiency, we designed and developed a novel Data Analytics and Machine Learning system, which aims at reducing delays by proactively supporting re-routing decisions. Given a time interval up to a few days in the future, the system predicts if a reroute advisory for a certain Air Route Traffic Control Center or for a certain advisory identifier will be issued, which may impact the pertinent routes. To deliver such predictions, the system uses historical reroute data, collected from the System Wide Information Management (SWIM) data services provided by the FAA, and weather data, provided by the US National Centers for Environmental Prediction (NCEP). The data is huge in volume, and has many items streamed at high velocity, uncorrelated and noisy. The system continuously processes the incoming raw data and makes it available for the next step where an interim data store is created and adaptively maintained for efficient query processing. The resulting data is fed into an array of ML algorithms, which compete for higher accuracy. The best performing algorithm is used in the final prediction, generating the final results. Mean accuracy values higher than 90% were obtained in our experiments with this system. Our algorithm divides the area of interest in units of aggregation and uses temporal series of the aggregate measures of weather forecast parameters in each geographical unit, in order to detect correlations with reroutes and where they will most likely occur. Aiming at practical application, the system is formed by a number of microservices, which are deployed in the cloud, making the system distributed, scalable and highly available.Comment: Submitted to the 2023 IEEE/AIAA Digital Aviation Systems Conference (DASC

Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function

Protein kinases use ATP as a phosphoryl donor for the posttranslational modification of signaling targets. It is generally thought that the binding of this nucleotide induces conformational changes leading to closed, more compact forms of the kinase domain that ideally orient active-site residues for efficient catalysis. The kinase domain is oftentimes flanked by additional ligand binding domains that up- or down-regulate catalytic function. C-terminal Src kinase (Csk) is a multidomain tyrosine kinase that is up-regulated by N-terminal SH2 and SH3 domains. Although the X-ray structure of Csk suggests the enzyme is compact, X-ray scattering studies indicate that the enzyme possesses both compact and open conformational forms in solution. Here, we investigated whether interactions with the ATP analog AMP-PNP and ADP can shift the conformational ensemble of Csk in solution using a combination of small angle x-ray scattering and molecular dynamics simulations. We find that binding of AMP-PNP shifts the ensemble towards more extended rather than more compact conformations. Binding of ADP further shifts the ensemble towards extended conformations, including highly extended conformations not adopted by the apo protein, nor by the AMP-PNP bound protein. These ensembles indicate that any compaction of the kinase domain induced by nucleotide binding does not extend to the overall multi-domain architecture. Instead, assembly of an ATP-bound kinase domain generates further extended forms of Csk that may have relevance for kinase scaffolding and Src regulation in the cell

Mitochondrial superoxide generation induces a parkinsonian phenotype in zebrafish and huntingtin aggregation in human cells.

Superoxide generation by mitochondria respiratory complexes is a major source of reactive oxygen species (ROS) which are capable of initiating redox signaling and oxidative damage. Current understanding of the role of mitochondrial ROS in health and disease has been limited by the lack of experimental strategies to selectively induce mitochondrial superoxide production. The recently-developed mitochondria-targeted redox cycler MitoParaquat (MitoPQ) overcomes this limitation, and has proven effective in vitro and in Drosophila. Here we present an in vivo study of MitoPQ in the vertebrate zebrafish model in the context of Parkinson's disease (PD), and in a human cell model of Huntington's disease (HD). We show that MitoPQ is 100-fold more potent than non-targeted paraquat in both cells and in zebrafish in vivo. Treatment with MitoPQ induced a parkinsonian phenotype in zebrafish larvae, with decreased sensorimotor reflexes, spontaneous movement and brain tyrosine hydroxylase (TH) levels, without detectable effects on heart rate or atrioventricular coordination. Motor phenotypes and TH levels were partly rescued with antioxidant or monoaminergic potentiation strategies. In a HD cell model, MitoPQ promoted mutant huntingtin aggregation without increasing cell death, contrasting with the complex I inhibitor rotenone that increased death in cells expressing either wild-type or mutant huntingtin. These results show that MitoPQ is a valuable tool for cellular and in vivo studies of the role of mitochondrial superoxide generation in redox biology, and as a trigger or co-stressor to model metabolic and neurodegenerative disease phenotypes

Size and frequency of natural forest disturbances and Amazon carbon balance

Forest inventory studies in the Amazon indicate a large terrestrial carbon sink. However, field plots may fail to represent forest mortality processes at landscape-scales of tropical forests. Here we characterize the frequency distribution of disturbance events in natural forests from 0.01 ha to 2,651 ha size throughout Amazonia using a novel combination of forest inventory, airborne lidar and satellite remote sensing data. We find that small-scale mortality events are responsible for aboveground biomass losses of B1.28 Pg C y 1 over the entire Amazon region. We also find that intermediate-scale disturbances account for losses of B0.01 Pg C y 1 , and that the largest-scale disturbances as a result of blow-downs only account for losses of B0.003 Pg C y 1 . Simulation of growth and mortality indicates that even when all carbon losses from intermediate and large-scale disturbances are considered, these are outweighed by the net biomass accumulation by tree growth, supporting the inference of an Amazon carbon sink

Estimates of forest canopy height and aboveground biomass using ICESat

Exchange of carbon between forests and the atmosphere is a vital component of the global carbon cycle. Satellite laser altimetry has a unique capability for estimating forest canopy height, which has a direct and increasingly well understood relationship to aboveground carbon storage. While the Geoscience Laser Altimeter System (GLAS) onboard the Ice, Cloud and land Elevation Satellite (ICESat) has collected an unparalleled dataset of lidar waveforms over terrestrial targets, processing of ICESat data to estimate forest height is complicated by the pulse broadening associated with large-footprint, waveform-sampling lidar. We combined ICESat waveforms and ancillary topography from the Shuttle Radar Topography Mission to estimate maximum forest height in three ecosystems; tropical broadleaf forests in Brazil, temperate broadleaf forests in Tennessee, and temperate needleleaf forests in Oregon. Final models for each site explained between 59% and 68% of variance in field-measured forest canopy height (RMSE between 4.85 and 12.66 m). In addition, ICESat-derived heights for the Brazilian plots were correlated with field-estimates of aboveground biomass (r(2) = 73%, RMSE = 58.3 Mgha(-1))

Short-range potentials from QCD at order g2g^2

We systematically compute the effective short-range potentials arising from second order QCD-diagrams related to bound states of quarks, antiquarks, and gluons. Our formalism relies on the assumption that the exchanged gluons are massless, while the constituent gluons as well as the lightest quarks acquire a nonvanishing constituent mass because of confinement. The potentials we obtain include the first relativistic corrections, thus spin-spin terms, spin-orbit terms, etc. Such effective potentials are expected to be relevant for the building of accurate potential models describing usual hadrons as well as exotic ones like glueballs and $q\bar q g$ hybrids. In particular, we compute for the first time an effective quark-gluon potential, and show the existence of a quadrupolar interaction term in this case. We also discuss the influence of a possible nonzero mass for the exchanged gluons.Comment: 33 pages, 4 tables and 12 figures ; typos correcte