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438 records · Page 25

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DOE OSTI2024

Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model

The brain produces diverse functions, from perceiving sounds to producing arm reaches, through the collective activity of populations of many neurons. Determining if and how the features of these exogenous variables (e.g., sound frequency, reach angle) are reflected in population neural activity is important for understanding how the brain operates. Often, high-dimensional neural population activity is confined to low-dimensional latent spaces. However, many current methods fail to extract latent spaces that are clearly structured by exogenous variables. This has contributed to a debate about whether or not brains should be thought of as dynamical systems or representational systems. Here, we developed a new latent process Bayesian regression framework, the orthogonal stochastic linear mixing model (OSLMM) which introduces an orthogonality constraint amongst time-varying mixture coefficients, and provide Markov chain Monte Carlo inference procedures. We demonstrate superior performance of OSLMM on latent trajectory recovery in synthetic experiments and show superior computational efficiency and prediction performance on several real-world benchmark data sets. We primarily focus on demonstrating the utility of OSLMM in two neural data sets: μ ECoG recordings from rat auditory cortex during presentation of pure tones and multi-single unit recordings form monkey motor cortex during complex arm reaching. We show that OSLMM achieves superior or comparable predictive accuracy of neural data and decoding of external variables (e.g., reach velocity). Most importantly, in both experimental contexts, we demonstrate that OSLMM latent trajectories directly reflect features of the sounds and reaches, demonstrating that neural dynamics are structured by neural representations. Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale biological time-series datasets.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

Stabilization of gaze during circular locomotion in darkness. II. Contribution of velocity storage to compensatory eye and head nystagmus in the running monkey

1. Yaw eye in head (Eh) and head on body velocities (Hb) were measured in two monkeys that ran around the perimeter of a circular platform in darkness. The platform was stationary or could be counterrotated to reduce body velocity in space (Bs) while increasing gait velocity on the platform (Bp). The animals were also rotated while seated in a primate chair at eccentric locations to provide linear and angular accelerations similar to those experienced while running. 2. Both animals had head and eye nystagmus while running in darkness during which slow phase gaze velocity on the body (Gb) partially compensated for body velocity in space (Bs). The eyes, driven by the vestibuloocular reflex (VOR), supplied high-frequency characteristics, bringing Gb up to compensatory levels at the beginning and end of the slow phases. The head provided substantial gaze compensation during the slow phases, probably through the vestibulocollic reflex (VCR). Synchronous eye and head quick phases moved gaze in the direction of running. Head movements occurred consistently only when animals were running. This indicates that active body and limb motion may be essential for inducing the head-eye gaze synergy. 3. Gaze compensation was good when running in both directions in one animal and in one direction in the other animal. The animals had long VOR time constants in these directions. The VOR time constant was short to one side in one animal, and it had poor gaze compensation in this direction. Postlocomotory nystagmus was weaker after running in directions with a long VOR time constant than when the animals were passively rotated in darkness. We infer that velocity storage in the vestibular system had been activated to produce continuous Eh and Hb during running and to counteract postrotatory afterresponses. 4. Continuous compensatory gaze nystagmus was not produced by passive eccentric rotation with the head stabilized or free. This indicates that an aspect of active locomotion, most likely somatosensory feedback, was responsible for activating velocity storage. 5. Nystagmus was compared when an animal ran in darkness and in light. the beat frequency of eye and head nystagmus was lower, and the quick phases were larger in darkness. The duration of head and eye quick phases covaried. Eye quick phases were larger when animals ran in darkness than when they were passively rotated. The maximum velocity and duration of eye quick phases were the same in both conditions. 6. The platform was counterrotated under one monkey in darkness while it ran in the direction of its long vestibular time constant.(ABSTRACT TRUNCATED AT 400 WORDS).

NASA Discipline Neuroscience↗

DOE OSTI2023

Surface coverage dynamics for reversible dissociative adsorption on finite linear lattices

Dissociative adsorption onto a surface introduces dynamic correlations between neighboring sites not found in non-dissociative absorption. We study surface coverage dynamics where reversible dissociative adsorption of dimers occurs on a finite linear lattice. We derive analytic expressions for the equilibrium surface coverage as a function of the number of reactive sites, N, and the ratio of the adsorption and desorption rates. Using these results, we characterize the finite size effect on the equilibrium surface coverage. For comparable N’s, the finite size effect is significantly larger when N is even than when N is odd. Moreover, as N increases, the size effect decays more slowly in the even case than in the odd case. The finite-size effect becomes significant when adsorption and desorption rates are considerably different. These finite-size effects are related to the number of accessible configurations in a finite system where the odd-even dependence arises from the limited number of accessible configurations in the even case. We confirm our analytical results with kinetic Monte Carlo simulations. We also analyze the surface-diffusion case where adsorbed atoms can hop into neighboring sites. As expected, the odd-even dependence disappears because more configurations are accessible in the even case due to surface diffusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2024

Global Sensitivity Analysis of Simulated Remote Sensing Polarimetric Observations Over Snow

This study presents a detailed theoretical assessment of the information content of passive polarimetric observations over snow scenes, using a global sensitivity analysis (GSA) method. Conventional sensitivity studies focus on varying a single parameter while keeping all other parameters fixed. In contrast, the GSA correctly addresses the covariance of state parameters across their entire parameter space, hence favoring a more correct interpretation of inversion algorithms and the optimal design of their state vectors. The forward simulations exploit a vector radiative transfer model to obtain the Stokes vector emerging at the top of the atmosphere for different solar zenith angles, when the bottom boundary consists of a vertically resolved snowpack of non-spherical grains. The presence of light-absorbing particulates (LAPs), either embedded in the snow or aloft in the atmosphere above in the form of aerosols, is also considered. The results are presented for a set of wavelengths spanning the visible (VIS), near-infrared (NIR), and shortwave infrared (SWIR) region of the spectrum. The GSA correctly captures the expected, high sensitivity of the reflectance to LAPs in the VIS–NIR and to grain size at different depths in the snowpack in the NIR–SWIR. With adequate viewing geometries, mono-angle measurements of total reflectance in the VIS–SWIR (akin to those of the Moderate Resolution Imaging Spectroradiometer, MODIS) resolve grain size in the top layer of the snowpack sufficiently well. The addition of multi-angle polarimetric observations in the VIS–NIR provides information on grain shape and microscale roughness. The simultaneous sensitivity in the VIS–NIR to both aerosols and snow-embedded impurities can be disentangled by extending the spectral range to the SWIR, which contains information on aerosol optical depth while remaining essentially unaffected when the same particulates are mixed with the snow. Multi-angle polarimetric observations can therefore (i) effectively partition LAPs between the atmosphere and the surface, which represents a notorious challenge for snow remote sensing based on measurements of total reflectance only and (ii) lead to better estimates of grain shape and roughness and, in turn, the asymmetry parameter, which is critical for the determination of albedo. The retrieval uncertainties are minimized when the degree of linear polarization is used in place of the polarized reflectance. The Sobol indices, which are the main metric for the GSA, were used to select the state parameters in retrievals performed on data simulated for multiple instrument configurations. Improvements in retrieval quality with the addition of measurements of polarization, multi-angle views, and different spectral channels reflect the information content, identified by the Sobol indices, relative to each configuration. The results encourage the development of new remote sensing algorithms that fully leverage multi-angle and polarimetric capabilities of modern remote sensors. They can also aid flight planning activities, since the optimal exploitation of the information content of multi-angle measurements depends on the viewing geometry. The better characterization of surface and atmospheric parameters in snow-covered regions advances research opportunities for scientists of the cryosphere and ultimately benefits albedo estimates in climate models.

remote sensing↗

DOE OSTI2022

An improved representation of the relationship between photosynthesis and stomatal conductance leads to more stable estimation of conductance parameters and improves the goodness-of-fit across diverse data sets

Stomata play a central role in surface-atmosphere exchange by controlling the flux of water and CO 2 between the leaf and the atmosphere. Representation of stomatal conductance (g sw ) is therefore an essential component of models that seek to simulate water and CO 2 exchange in plants and ecosystems. For given environmental conditions at the leaf surface (CO 2 concentration and vapor pressure deficit or relative humidity), models typically assume a linear relationship between g sw and photosynthetic CO 2 assimilation (A). However, measurement of leaf-level g sw response curves to changes in A are rare, particularly in the tropics, resulting in only limited data to evaluate this key assumption. Here, we measured the response of g sw and A to irradiance in six tropical species at different leaf phenological stages. We showed that the relationship between g sw and A was not linear, challenging the key assumption upon which optimality theory is based-that the marginal cost of water gain is constant. Our data showed that increasing A resulted in a small increase in g sw at low irradiance, but a much larger increase at high irradiance. We reformulated the popular Unified Stomatal Optimization (USO) model to account for this phenomenon and to enable consistent estimation of the key conductance parameters g 0 and g 1 . Our modification of the USO model improved the goodness-of-fit and reduced bias, enabling robust estimation of conductance parameters at any irradiance. In addition, our modification revealed previously undetectable relationships between the stomatal slope parameter g 1 and other leaf traits. We also observed nonlinear behavior between A and g sw in independent datasets that included data collected from attached and detached leaves, and from plants grown at elevated CO 2 concentration. We propose that this empirical modification of the USO model can improve the measurement of g sw parameters and the estimation of plant and ecosystem-scale water and CO 2 fluxes.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

Understanding and Utilizing PBL Height Data from Multiple Observing Systems in the GEOS System

The accuracy of PBL height simulation is a key issue in many applications including forecasting near surface meteorology and air quality, however, it is a very challenging problem due to the lack of not only comprehensive, global Planetary Boundary Layer (PBL) observations but also a strategy and infrastructure to utilize PBL height data from a variety of sensors. Following the designation of PBL as an incubation class observable in the 2017 Decadal Survey, the PBL Incubation Study Team Report [14] made clear that “a future global PBL observing system requires modeling and data assimilation as essential components.” There is an urgent need for global modeling development in order to utilize Program of Record (POR) observations, assess their impacts, and identify gaps to be filled by future PBL missions. Our overall objective is to develop PBL data assimilation capabilities in the NASA Global Earth Observing System (GEOS), focusing on PBL height from multiple observing systems, to support the assessment and use of future PBL observations. The NASA GEOS system is composed of the GEOS global atmospheric general circulation model (AGCM) and the atmospheric data assimilation system (ADAS). The PBL parameterizations include the “Lock” K-profile scheme driven by surface and cloud-top buoyancy fluxes ([4]), and the “Louis” local scheme for stable conditions based on the Richardson number ([5]). Above the mixed layer defined by the Lock surface plume, shallow cumulus convection is represented by the mass flux scheme of [9]. Additional parameterizations are summarized in [1]. The ADAS employs the hybrid 4D Ensemble- Variational (EnVar) configuration ([15]), with the ensemble providing flow-dependent background error covariance information. The resultant analysis increments are fed back to the forecast model through the 4D incremental analysis update (IAU) approach ([11]). In this study, PBL height data are being or have been generated from radiosondes, GNSS RO, satellite (CATS, CALIPSO and ICESat-2) and ground-based (MPLNET) lidars, and wind profiler. Investigations have been conducted to specify quality marks for PBL height retrievals for the data assimilation purpose. These PBL height data have different strengths and weaknesses ([2], [3], [6], [7], [8], [10]), and the satellite PBL height data provide better global coverage and complement in-situ PBL height data. Radiosondes offer high accuracy and in situ measurement of temperature and humidity profiles, but with poor spatio-temporal sampling. The in-situ observing systems like MPLNET and wind profiler provide long history of PBL height records at each station. The GNSS RO based PBL height is retrieved based on the sharp gradients in refractivity profile that represent the fine vertical structure of temperature and moisture changes above the PBL. However, not all RO refractivity profiles reach the surface depending on location and regime, and RO refractivity retrievals can be negatively biased below 2km. The PBL height data from satellite lidars provide high resolution along track PBL height retrievals, but over land they are affected by previous day convective PBL aerosol and strongly associated with mixing layer and retrievals cannot be made below thick, attenuating clouds. A successful assimilation of PBL height data requires a thorough understanding of the observing method and the retrieval algorithm for each observing system in order to use the PBL height data from multiple observing systems properly. Due to the sensitivity of PBL height data to the observing method and choice of algorithm, it is important to use a model definition appropriate for each observation type to compute differences between PBL height data and model PBL height (OmFs). The GEOS model currently includes two PBL height definitions suitable for direct comparison with observed PBL height, and additional definitions are being added in this study. Evaluation of different model PBL height definitions is underway. Meanwhile, efforts have been made in the GEOS data assimilation system to develop PBL height data assimilation capability. PBL height data can be assimilated using two different approaches. The traditional approach is to construct an observation operator and its tangent linear and adjoint, which link control variables to PBL height data from each observing system. This observation operator can be very complicated, e.g., the lidar-based PBL height observation operator includes the backscatter lidar forward observation operator, the algorithm to derive PBL height from attenuated total backscatter, interpolation, and calculations handling the mismatch between observed and model scales. The other approach is to augment PBL height to the control variable vector, and it is adopted in this study. The latter approach was also used in previous studies, e.g., the assimilation of PBL height data from radiosonde and aircraft in the Real Time Mesoscale Analysis (RTMA) system for a dispersion modelling study ([13]); the PBL height assimilation study using lidar PBL height data at Greensburg, Kansas for a field campaign ([12]). The PBL height assimilation from multiple observing systems in this study allows us to take advantage of the diverse PBL height data that provide much better global coverage collectively under different meteorological conditions and with different temporal and spatial scales. As all the PBL heights are tightly coupled with the PBL thermodynamic variables, the strong correlations, which are provided by the 4D ensemble forecast, enable PBL height data from various sources to interact and combine coherently and provide additional information for PBL temperature and moisture fields. The results of comparisons among PBL height data from different sources and the evaluation of the model PBL height definitions with the PBL height data will be presented, and the PBL height data synergy strategies and preliminary results will also be discussed at the conference.

Y. Zhu↗