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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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14 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Neurodata Without Borders ecosystem for neurophysiological data science

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB’s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task

A challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy re-use of this hard-to-obtain data for both teaching and research on the mechanisms of human memory.

Science & Technology - Other Topics↗
DOE OSTI2020

Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants

Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesion studies require removal of the skull as well as hazardous chemicals, dehydration, or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of hippocampal brain lesions.

3-D reconstruction↗
DOE OSTI2024

A Suppression-based STDP Rule Resilient to Jitter Noise in Spike Patterns for Neuromorphic Computing

Multi-spike models of synaptic plasticity, such as the triplet and suppression spike-timing-dependent plasticity (STDP) rules, exhibit better alignment with neurophysiological data in the brain compared to the pair-based STDP rule. Previous studies have empirically shown that the pair-based STDP rule can detect spatiotemporal spike patterns hidden in equally dense distractor spike trains in an unsupervised manner. However, it fails to detect spike patterns influenced by jitter noise. Given that spiking neural networks (SNNs) exhibit variability in generated spike trains in response to the same inputs, it becomes imperative to have learning rules capable of detecting spike patterns even in the presence of jitter noise. In this study, we introduce a simplified suppression-based STDP rule that demonstrates significantly enhanced tolerance to jitter in spike patterns compared to the pair-based STDP rule. Unlike the ideal suppression STDP rule, characterized by an exponential learning window and requiring high-resolution synapses, the simplified rule limits the synaptic efficacy update to a single bit at any given instant. Moreover, it employs 4-bit fixed-point synapses, facilitating straightforward implementation in neuromorphic hardware.

Gautam, Ashish [ORNL]↗
DOE OSTI2020

Neurodata Extensions Catalog (NDX Catalog) v1.0.0

The Neurodata Extensions Catalog (NDX Catalog) is a novel web archive and associated software tools that enable users to easily create, search for, test, review, and install extensions to the Neurodata Without Borders (NWB) data standard for neurophysiology. The Catalog consists of several software repositories that can be found at https://github.com/nwb-extensions.

Tritt, Andrew↗
DOE OSTI2024

AqNWB v0.1

This is a C ++ acquisition API for neurophysiological data in the NeurodataWithoutBorders (NWB) data standard.

Prince, Stephanie↗
DOE OSTI2022

Progress Toward a Multiomic Understanding of Traumatic Brain Injury: A Review

Traumatic brain injury (TBI) is not a single disease state but describes an array of conditions associated with insult or injury to the brain. While some individuals with TBI recover within a few days or months, others present with persistent symptoms that can cause disability, neuropsychological trauma, and even death. Understanding, diagnosing, and treating TBI is extremely complex for many reasons, including the variable biomechanics of head impact, differences in severity and location of injury, and individual patient characteristics. Because of these confounding factors, the development of reliable diagnostics and targeted treatments for brain injury remains elusive. We argue that the development of effective diagnostic and therapeutic strategies for TBI requires a deep understanding of human neurophysiology at the molecular level and that the framework of multiomics may provide some effective solutions for the diagnosis and treatment of this challenging condition. To this end, we present here a comprehensive review of TBI biomarker candidates from across the multiomic disciplines and compare them with known signatures associated with other neuropsychological conditions, including Alzheimer’s disease and Parkinson’s disease. We believe that this integrated view will facilitate a deeper understanding of the pathophysiology of TBI and its potential links to other neurological diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

A Computational Theory for the Emergence of Grammatical Categories in Cortical Dynamics

A general agreement in psycholinguistics claims that syntax and meaning are unified precisely and very quickly during online sentence processing. Although several theories have advanced arguments regarding the neurocomputational bases of this phenomenon, we argue that these theories could potentially benefit by including neurophysiological data concerning cortical dynamics constraints in brain tissue. In addition, some theories promote the integration of complex optimization methods in neural tissue. In this paper we attempt to fill these gaps introducing a computational model inspired in the dynamics of cortical tissue. In our modeling approach, proximal afferent dendrites produce stochastic cellular activations, while distal dendritic branches–on the other hand–contribute independently to somatic depolarization by means of dendritic spikes, and finally, prediction failures produce massive firing events preventing formation of sparse distributed representations. The model presented in this paper combines semantic and coarse-grained syntactic constraints for each word in a sentence context until grammatically related word function discrimination emerges spontaneously by the sole correlation of lexical information from different sources without applying complex optimization methods. By means of support vector machine techniques, we show that the sparse activation features returned by our approach are well suited—bootstrapping from the features returned by Word Embedding mechanisms—to accomplish grammatical function classification of individual words in a sentence. In this way we develop a biologically guided computational explanation for linguistically relevant unification processes in cortex which connects psycholinguistics to neurobiological accounts of language. We also claim that the computational hypotheses established in this research could foster future work on biologically-inspired learning algorithms for natural language processing applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Editorial: Functional microcircuits in the brain and in artificial intelligent systems

Fundamental principles underlying higher-order cognitive functions remain elusive, but recent breakthroughs in neurophysiology and deep learning offer new perspectives. First, experimental studies have uncovered neural circuit motifs consisting of various neuron types; see Brain Initiative Cell Census Network (https://www.nature.com/collections/cicghheddj). For example, inhibitory neuron types expressing exclusive genes have specific targets and distinct functions (Pfeffer et al., 2013). Furthermore, diverse neuron types in cortex and their connectomes were identified in cortical columns (Jiang et al., 2015); see also Barth et al. (2016) for a debate on neuron types. Second, artificial neural networks were originally inspired by structures of the brain (McCulloch and Pitts, 1943) and could be trained to perform complex functions similar to human perception/cognition by deep learning (DL) (Lecun et al., 2015).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Peripheral Nerve Magnetoneurography With Optically Pumped Magnetometers

Electrodiagnosis is routinely integrated into clinical neurophysiology practice for peripheral nerve disease diagnoses, such as neuropathy, demyelinating disorders, nerve entrapment/impingement, plexopathy, or radiculopathy. Measured with conventional surface electrodes, the propagation of peripheral nerve action potentials along a nerve is the result of ionic current flow which, according to Ampere’s Law, generates a small magnetic field that is also detected as an “action current” by magnetometers, such as superconducting quantum interference device (SQUID) Magnetoencephalography (MEG) systems. Optically pumped magnetometers (OPMs) are an emerging class of quantum magnetic sensors with a demonstrated sensitivity at the 1 fT/√Hz level, capable of cortical action current detection. But OPMs were ostensibly constrained to low bandwidth therefore precluding their use in peripheral nerve electrodiagnosis. With careful OPM bandwidth characterization, we hypothesized OPMs may also detect compound action current signatures consistent with both Sensory Nerve Action Potential (SNAP) and the Hoffmann Reflex (H-Reflex). In as much, our work confirms OPMs enabled with expanded bandwidth can detect the magnetic signature of both the SNAP and H-Reflex. Taken together, OPMs now show potential as an emerging electrodiagnostic tool.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules

Quantitative structure–odor relationships are critically important for studies related to the function of olfaction. Current literature data sets contain expert-labeled molecules but lack feature data. This paper introduces QuantumScents, a quantum mechanics augmented derivative of the Leffingwell data set. QuantumScents contains 3.5k structurally and chemically diverse molecules ranging from 2 to 30 heavy atoms (CNOS) and their corresponding 3D coordinates, total PBE0 energy, molecular dipole moment, and per-atom Hirshfeld charges, dipoles, and ratios. The authors demonstrate that Hirshfeld charges and ratios contain sufficient information to perform molecular classification by training a Message Passing Neural Network with chemprop (Heid, E.; et al. ChemRxiv, 2023, DOI: 10.26434/chemrxiv-2023-3zcfl) to predict scent labels. Finally, the QuantumScents data set is freely available on Zenodo along with the authors’ code, example models, and data set generation workflow (https://zenodo.org/doi/10.5281/zenodo.8239853).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Cell specific photoswitchable agonist for reversible control of endogenous dopamine receptors

Dopamine controls diverse behaviors and their dysregulation contributes to many disorders. Our ability to understand and manipulate the function of dopamine is limited by the heterogenous nature of dopaminergic projections, the diversity of neurons that are regulated by dopamine, the varying distribution of the five dopamine receptors (DARs), and the complex dynamics of dopamine release. In order to improve our ability to specifically modulate distinct DARs, here we develop a photo-pharmacological strategy using a Membrane anchored Photoswitchable orthogonal remotely tethered agonist for the Dopamine receptor (MP-D). Our design selectively targets D1R/D5R receptor subtypes, most potently D1R (MP-D1 ago ), as shown in HEK293T cells. In vivo, we targeted dorsal striatal medium spiny neurons where the photo-activation of MP-D1 ago increased movement initiation, although further work is required to assess the effects of MP-D1 ago on neuronal function. Our method combines ligand and cell type-specificity with temporally precise and reversible activation of D1R to control specific aspects of movement. Our results provide a template for analyzing dopamine receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Stimulus edges induce orientation tuning in superior colliculus

Orientation columns exist in the primary visual cortex (V1) of cat and primates but not mouse. Intriguingly, some recent studies reported the presence of orientation and direction columns in the mouse superficial superior colliculus (sSC), while others reported a lack of columnar organization therein. Using in vivo calcium imaging of sSC in the awake mouse brain, we found that the presence of columns is highly stimulus dependent. Specifically, we observed orientation and direction columns formed by sSC neurons retinotopically mapped to the edge of grating stimuli. For both excitatory and inhibitory neurons in sSC, orientation selectivity can be induced by the edge with their preferred orientation perpendicular to the edge orientation. Furthermore, we found that this edge-induced orientation selectivity is associated with saliency encoding. These findings indicate that the tuning properties of sSC neurons are not fixed by circuit architecture but rather dependent on the spatiotemporal properties of the stimulus.

59 BASIC BIOLOGICAL SCIENCES↗