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2. 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
3. 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
4. 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
5. Electron-density-sensitive Line Ratios of Fe XIII--XVI from Laboratory Sources Compared to CHIANTI
- Author(s):
- Weller, M.E.; Beiersdorfer, P.; Soukhanovskii, V.A.; Scotti, F.; LeBlanc, B.P.
- Abstract:
- We present electron-density-sensitive line ratios for Fe XIII–XVI measured in the spectral wavelength range of 200–440 Å and an electron density range of (1–4)×10^13 cm^−3. The results provide a test at the high-density limit of density-sensitive line ratios useful for astrophysical studies. The measurements were performed on the National Spherical Torus Experiment-Upgrade, where electron densities were measured independently by the laser Thomson scattering diagnostic. Spectra were collected with a flat-field grazing-incidence spectrometer, which provided a spectral resolution of up to 0.3 Å, i.e., high resolution across the broad wavelength range. The response of the instrument was relatively calibrated using spectroscopic techniques in order to improve accuracy. The line ratios are compared to other laboratory sources and the latest version of CHIANTI (8.0.2), and an agreement within 30% is found.
- Type:
- Dataset
- Issue Date:
- February 2018
6. Two-dimensional full-wave simulations of waves in space and tokamak plasmas
- Author(s):
- Kim, E.-W.; Bertelli, N.; Johnson, J.R.; Valeo, E.; Hosea, J.; Perkins, R.
- Abstract:
- We illustrate the capabilities of a recently developed two-dimensional full wave code (FW2D) in space and tokamak plasmas by adopting various values of density, magnetic field configuration and strength as well as boundary shape. As example, we first showed fast compressional wave propagation in the inner magnetosphere is dramatically modified by a plasmaspheric plume at Earth's magnetosphere. The results show that wave energy is trapped in the plume showing a leaky eigenmode-like structure with plume, which is similar to the detected magnetosonic waves. We also performed simulations of high harmonic fast waves in the scrape-off layer (SOL) plasmas of the National Spherical Torus eXperiment (NSTX)/NSTX-Upgrade. Comparison the results with previous full-wave simulations show that although the FW2D code uses a cold plasma approximation, the electric field and the fraction of the power losses in the SOL plasmas show excellent consistency and agreement with the previous full wave simulations performed by the AORSA code.
- Type:
- Dataset
- Issue Date:
- October 2018
7. 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
8. 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
9. ELM frequency enhancement and discharge modification through lithium granule injection into EAST H-modes
- Author(s):
- Lunsford; Hsu, J.S.; Sun, Z.; Maingi, R.; Mansfield, D.K.; Xu, W.; Zuo, G.Z.; Huang, M.; Diallo, A.; Osborne, T.; Tritz, K.; Canik, J.; Meng, X.C.; Gong, X.Z.; Wan, B.N.; Li, J.G.; EAST Team
- Abstract:
- The injection of impurity granules into fusion research discharges can serve as a catalyst for ELM events. For sufficiently low ELM frequencies, and granule sizes above a threshold, this can result in full control of the ELM cycle, referred to as ELM pacing. For this research, we extend the investigation to conditions where the natural ELM frequency is too high for ELM pacing to be realized. Utilizing multiple sizes of lithium granules and classifying their effects by granule size, we demonstrate that ELM mitigation through frequency multiplication can be used at ELM triggering rates that nominally make ELM pacing unrealizable. We find that above a size threshold, injected granules promptly trigger ELMs and commensurately enhance the ELM frequency . Below this threshold size, injection of an individual granule does not always lead to the prompt triggering of an ELM; however, collective ablation in the edge pedestal region does enhance the ELM frequency. Specifically, Li granules too small to individually trigger ELMs were injected into EAST H-mode discharges at frequencies up to 2.3 kHz; collectively the granules were observed to enhance the natural ELM frequency up to 620 Hz, resulting in a ~2.4x multiplication of the natural ELM frequency and a 50% decrease of the ELM size.
- Type:
- Dataset
- Issue Date:
- October 2018
10. Effects of Axial Boundary Conductivity on a Free Stewartson-Shercliff Layer
- Author(s):
- Caspary, Kyle J.; Choi, Dahan; Ebrahimi, Fatima; Gilson, Erik P.; Goodman, Jeremy; Ji, Hantao
- Abstract:
- The effects of axial boundary conductivity on the formation and stability of a magnetized free Stewartson-Shercliff layer (SSL) in a short Taylor-Couette device are reported. As the axial field increases with insulating endcaps, hydrodynamic Kelvin-Helmholtz-type instabilities set in at the SSLs of the conducting fluid, resulting in a much reduced flow shear. With conducting endcaps, SSLs respond to an axial field weaker by the square root of the conductivity ratio of endcaps to fluid. Flow shear continuously builds up as the axial field increases despite the local violation of the Rayleigh criterion, leading to a large number of hydrodynamically unstable modes. Numerical simulations of both the mean flow and the instabilities are in agreement with the experimental results.
- Type:
- Dataset
- Issue Date:
- 2018
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