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161. Fast animal pose estimation using deep neural networks

Author(s):
Pereira, Talmo D.; Aldarondo, Diego E.; Willmore, Lindsay; Kislin, Mikhail; Wang, Samuel S.-H.; Murthy, Mala; Shaevitz, Joshua W.
Abstract:
Recent work quantifying postural dynamics has attempted to define the repertoire of behaviors performed by an animal. However, a major drawback to these techniques has been their reliance on dimensionality reduction of images which destroys information about which parts of the body are used in each behavior. To address this issue, we introduce a deep learning-based method for pose estimation, LEAP (LEAP Estimates Animal Pose). LEAP automatically predicts the positions of animal body parts using a deep convolutional neural network with as little as 10 frames of labeled data for training. This framework consists of a graphical interface for interactive labeling of body parts and software for training the network and fast prediction on new data (1 hr to train, 185 Hz predictions). We validate LEAP using videos of freely behaving fruit flies (Drosophila melanogaster) and track 32 distinct points on the body to fully describe the pose of the head, body, wings, and legs with an error rate of <3% of the animal's body length. We recapitulate a number of reported findings on insect gait dynamics and show LEAP's applicability as the first step in unsupervised behavioral classification. Finally, we extend the method to more challenging imaging situations (pairs of flies moving on a mesh-like background) and movies from freely moving mice (Mus musculus) where we track the full conformation of the head, body, and limbs.
Type:
Dataset
Issue Date:
30 May 2018

163. Modeling of a Laser-Induced Rydberg Spectroscopy diagnostic for Direct Measurement of the Local Electric Field in the Edge Region of NSTX/NSTX-U

Author(s):
Reymond, L.; Diallo, A.; Vekselman, V.
Abstract:
We discuss a novel diagnostic allowing direct measurements of the local electric field in the edge region in NSTX/NSTX-U. This laser based diagnostic's principle consists of depleting the naturally populated $n=3$ level to a Rydberg state --sensitive to electric fields-- that will result in a suppression of part of the $D_{\alpha}$ emission. We refer to this approach as Laser-Induced Rydberg Spectroscopy (LIRyS). It is shown that the local electric field can be measured through the Stark induced resonances observed as dips in the $D_\alpha$ emission. Using forward-modeling of simulated absorption spectra, we show precisions reaching \SI{\pm 2}{\kilo\volt\per\meter} in regions with a local electric field of \SI{15}{\kilo\volt\per\meter}.
Type:
Dataset
Issue Date:
July 2018

164. On the scattering correction of fast-ion D-alpha signal on NSTX-U

Author(s):
Hao, G.Z; Heidbrink, W.W.; Liu, D.; Stagner, L.; Podesta, M.; Bortolon, A.
Abstract:
Analysis of fast-ion D-alpha (FIDA) data on National Spherical Torus Experiment-Upgrade (NSTX-U) shows that the cold Dα line contaminates the FIDA baseline. The scattered light is comparable to the FIDA emission. A scattering correction is required to extract the FIDA signal. Two methods that relate the scattered light contamination to the intensity of the cold Dα line are employed. One method uses laboratory measurements with a calibration lamp; the other method uses data acquired during plasma operation and singular value decomposition analysis. After correction, both the FIDA spectra and spatial profile are in better agreement with theoretical predictions.
Type:
Dataset
Issue Date:
June 2018

165. Plasma boundary shape control and real-time equilibrium reconstruction on NSTX-U

Author(s):
Boyer, M.; Battaglia, D.; Mueller, D.; Eidietis, N.; Erickson, K.; Ferron, J.; Gates, D.; Gerhardt, S.; Johnson, R.; Kolemen, E.; Menard, J.; Myers, C.; Sabbagh, S.; Scotti, F.; Vail, P.
Abstract:
The upgrade to the National Spherical Torus eXperiment (NSTX-U) included two main improvements: a larger center-stack, enabling higher toroidal field and longer pulse duration, and the addition of three new tangentially aimed neutral beam sources, which increase available heating and current drive, and allow for flexibility in shaping power, torque, current, and particle deposition profiles. To best use these new capabilities and meet the high-performance operational goals of NSTX-U, major upgrades to the NSTX-U Control System (NCS) hardware and software have been made. Several control algorithms, including those used for real-time equilibrium reconstruction and shape control, have been upgraded to improve and extend plasma control capabilities. As part of the commissioning phase of first plasma operations, the shape control system was tuned to control the boundary in both inner-wall limited and diverted discharges. It has been used to accurately track the requested evolution of the boundary (including the size of the inner gap between the plasma and central solenoid, which is a challenge for the ST configuration), X-point locations, and strike point locations, enabling repeatable discharge evolutions for scenario development and diagnostic commissioning.
Type:
Dataset
Issue Date:
March 2018

166. Quantitative imaging of carbon dimer precursor for nanomaterial synthesis in the carbon arc

Author(s):
Vekselman, V.; Khrabry, A.; Kaganovich, I.; Stratton, B.; Selinsky, R. S.; Raitses, Y.
Abstract:
Delineating the dominant processes responsible for nanomaterial synthesis in a plasma environment requires measurements of the precursor species contributing to the growth of nanostructures. We performed comprehensive measurements of spatial and temporal profiles of carbon dimers in sub-atmospheric-pressure carbon arc by laser-induced fluorescence. Measured spatial profiles of carbon dimers coincide with the growth region of carbon nanotubes (Fang et al 2016 Carbon 107 273-80) and vary depending on the arc operation mode, which is determined by the discharge current and the ablation rate of the graphite anode. The carbon dimer density profile exhibits large spatial and time variations due to motion of the arc core. A comparison of the experimental data with the 2D simulation results of self-consistent arc modeling shows a good agreement. The model predicts well the main processes determining spatial profiles of carbon dimers.
Type:
Dataset
Issue Date:
January 2018

167. Reductions in Retrieval Competition Predict the Benefit of Repeated Testing

Author(s):
Rafidi, Nicole S; Hulbert, Justin C; Brooks, Paula P; Norman, Kenneth A
Abstract:
Repeated testing (as opposed to repeated study) leads to improved long-term memory retention, but the mechanism underlying this improvement remains controversial. In this work, we test the hypothesis that retrieval practice benefits subsequent recall by reducing competition from related memories. This hypothesis implies that the degree of reduction in competition between retrieval practice attempts should predict subsequent memory for the practiced items. To test this prediction, we collected electroencephalography (EEG) data across two sessions. In the first session, participants practiced selectively retrieving exemplars from superordinate semantic categories (high competition), as well as retrieving the names of the superordinate categories from exemplars (low competition). In the second session, participants repeatedly studied and were then tested on Swahili-English vocabulary. One week after session two, participants were again tested on the vocabulary. We trained a within-subject classifier on the data from session one to distinguish high and low competition states. We then used this classifier to measure competition across multiple retrieval practice attempts in the second session. The degree to which competition decreased for a given vocabulary word predicted whether that item was subsequently remembered in the third session. These results are consistent with the hypothesis that repeated testing improves retention by reducing competition.
Type:
Dataset
Issue Date:
April 2018

168. Regarding the optimization of O1-mode ECRH and the feasibility of EBW startup on NSTX-U

Author(s):
Lopez, N; Poli, F
Abstract:
Recently published scenarios for fully non-inductive startup and operation on the National Spherical Torus eXperiment Upgrade (NSTX-U) (Menard et al 2012 Nucl. Fusion 52 083015) show Electron Cyclotron Resonance Heating (ECRH) as an important component in preparing a target plasma for efficient High Harmonic Fast Wave and Neutral Beam heating. The modeling of the propagation and absorption of EC waves in the evolving plasma is required to define the most effective window of operation, and to optimize the launcher geometry for maximal heating and current drive during this window. Here, we extend a previous optimization of O1-mode ECRH on NSTX-U to account for the full time-dependent performance of the ECRH using simulations performed with TRANSP. We find that the evolution of the density profile has a prominent role in the optimization by defining the time window of operation, which in certain cases may be a more important metric to compare launcher performance than the average power absorption. This feature cannot be captured by analysis on static profiles, and should be accounted for when optimizing ECRH on any device that operates near the cutoff density. Additionally, the utility of the electron Bernstein wave (EBW) in driving current and generating closed flux surfaces in the early startup phase has been demonstrated on a number of devices. Using standalone GENRAY simulations, we find that efficient EBW current drive is possible on NSTX-U if the injection angle is shifted below the midplane and aimed towards the top half of the vacuum vessel. However, collisional damping of the EBW is projected to be significant, in some cases accounting for up to 97% of the absorbed EBW power
Type:
Dataset
Issue Date:
June 2018

169. Regional hydroclimatic variability due to contemporary deforestation in southern Amazonia and associated boundary layer characteristics

Author(s):
Khanna, Jaya; Medvigy, David; Fisch, Gilberto; Neves, Theomar Trindade de Araújo Tiburtino
Abstract:
Amazonian deforestation causes systematic changes in regional dry season precipitation. Some of these changes at contemporary large scales (a few hundreds of kilometers) of deforestation have been associated with a ‘dynamical mesoscale circulation’, induced by the replacement of rough forest with smooth pasture. In terms of decadal averages, this dynamical mechanism yields increased precipitation in downwind regions and decreased precipitation in upwind regions of deforested areas. Daily, seasonal, and interannual variations in this phenomenon may exist, but have not yet been identified or explained. This study uses observations and numerical simulations to develop relationships between the dynamical mechanism and the local- and continental-scale atmospheric conditions across a range of time scales. It is found that the strength of the dynamical mechanism is primarily controlled by the regional-scale thermal and dynamical conditions of the boundary layer, and not by the continental- and global-scale atmospheric state. Lifting condensation level and wind speed within the boundary layer have large and positive correlations with the strength of the dynamical mechanism. The strength of these relationships depends on time scale and is strongest over the seasonal cycle. Overall, the dynamical mechanism is found to be strongest during times when the atmosphere is relatively stable. Hence, for contemporary large scales of deforestation this phenomenon is found to be the prevalent convective triggering mechanism during the dry and parts of transition seasons (especially during the dry-to-wet transition), significantly affecting the hydroclimate during this period.
Type:
Dataset and Software
Issue Date:
2018

170. Scenario Development During Commissioning Operations on the National Spherical Torus Experiment Upgrade

Author(s):
Battaglia, D.J.; Boyer, M.D.; Gerhardt, S.; Mueller, D.; Myers, C.E.; Guttenfelder, W.; Menard, J.E.; Sabbagh, S.A.; Scotti, F.; Bedoya, F.; Bell, R.E.; Berkery, J.W.; Diallo, A.; Ferraro, N.; Jaworski, M.A.; Kaye, S.M.; LeBlanc, B.P.; Ono, M.; Park, J.-K.; Podesta, M.; Raman, R.; Soukhanovskii, V.A.
Abstract:
The National Spherical Torus Experiment Upgrade (NSTX-U) will advance the physics basis required for achieving steady-state, high-beta, and high-confinement conditions in a tokamak by accessing high toroidal field (1 T) and plasma current (1.0 - 2.0 MA) in a low aspect ratio geometry (A = 1.6 - 1.8) with flexible auxiliary heating systems (12 MW NBI, 6 MW HHFW). This paper describes progress in the development of L- and H-mode discharge scenarios and the commissioning of operational tools in the first ten weeks of operation that enable the scientific mission of NSTX-U. Vacuum field calculations completed prior to operations supported the rapid development and optimization of inductive breakdown at different values of ohmic solenoid current. The toroidal magnetic field (B_T0 = 0.65 T) exceeded the maximum values achieved on NSTX and novel long-pulse L-mode discharges with regular sawtooth activity exceeded the longest pulses produced on NSTX (tpulse > 1.8s). The increased flux of the central solenoid facilitated the development of stationary L-mode discharges over a range of density and plasma current (Ip). H-mode discharges achieved similar levels of stored energy, confinement (H98y,2 > 1) and stability (beta_N/beta_N-nowall > 1) compared to NSTX discharges for Ip < 1 MA. High-performance H-mode scenarios require an L-H transition early in the Ip ramp-up phase in order to obtain low internal inductance (li) throughout the discharge, which is conducive to maintaining vertical stability at high elongation (kappa > 2.2) and achieving long periods of MHD quiescent operations. The rapid progress in developing L- and H-mode scenarios in support of the scientific program was enabled by advances in real-time plasma control, efficient error field identification and correction, effective conditioning of the graphite wall and excellent diagnostic availability.
Type:
Dataset
Issue Date:
April 2018