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At least 19 records

Electromechanical memcapacitor model offering biologically plausible spiking.

In this article, we introduce a new nanoscale electromechanical device - a leaky memcapacitor - and show that it may be useful for the hardware implementation of spiking neurons. The leaky memcapacitor is a movableplate capacitor that becomes quite conductive when the plates come close to each other. The equivalent circuit of the leaky memcapacitor involves a memcapacitive and memristive system connected in parallel. In the leaky memcapacitor, resistance and capacitance depend on the same internal state variable, which is the displacement of the movable plate. We have performed a comprehensive analysis showing that several types of spiking observed in biological neurons can be implemented with the leaky memcapacitor. Significant attention is paid to the dynamic properties of the model. As in leaky memcapacitors the capacitive, leaking resistive, and reset functionalities are implemented naturally within the same device structure, their use will simplify the creation of spiking neural networks.

Zhang, Zixi↗

Plausible Biological Mechanisms Underlying Sex Differences in Radiation-Induced Lung Cancer Risk

Some epidemiological studies suggest that women are at greater risk for radiation-induced lung cancer than men, but this observation is not consistent across all studies. A scientific committee formed by the National Council on Radiation Protection and Measurement evaluated evidence for a sex difference in lung cancer risk from radiation exposuresby reviewing animal studies and assessing the biological plausibility that such a difference might exist. The committee identified four mechanisms that could potentially result in greater radiogenic lung cancer risks for women. The first of these is that radiation exposure increases the relative risk for a molecular subtype of spontaneous lung cancer that occurs predominantly in women. The second is that is that sex chromosome or gene expression differences between men and women places women at greater risk. The third is that hormonal differences between men and women, particularly for estrogen levels, puts women at greater risk. The fourth mechanism is that sex differences in immune system function underlie a sex difference in radiation associated lung cancer risk.None of these mechanisms hasyet been proven to play a role in radiogenic lung cancer risk.

radiation↗

Backpropagation-based learning with local derivative approximation and memory replay in biologically plausible neural systems

When learning, the brain modifies individual synaptic connections to reach a desired behavior. Animal and human brains have been shown to be incredibly capable of learning complex and varied functions across a wide variety of tasks. In recent years, artificial neural networks, inspired by human and animal brains, have shown great capabilities in learning a wide variety of difficult tasks. However, artificial neural networks primarily teach themselves through the use of backpropagation, a learning method which has no clear analogue within the brain. Additionally, Artificial Neural Networks primarily use continuous activation functions, which differ significantly from the spiking neuronal behavior present in the brain. In this paper, we discuss and demonstrate a biologically plausible learning method that approximates backpropagation through two techniques on Spiking Neural Networks. First, we show that the local temporal derivatives that are necessary for backpropagation can be approximately recovered through reconstruction using spike timings. Second, we show that through learning during a sleep phase, inspired by neuroscience research into memory replay, the localized parallel feedback path can learn to approximate the derivative through the forward path weight matrix, thus solving the weight transport problem. Lastly, we demonstrate that the combination of these two methods can approach or exceed the accuracy of backpropagation-based methods for a variety of neuromorphic vision tasks while maintaining biological plausibility.

42 ENGINEERING↗

A Unidirectional Two-Compartment Neuron Circuit with On-chip STDP learning

Most neuromorphic chips implement the single-compartment point neuron model where synapse circuits connect directly to a leaky integrate and fire (LIF) soma circuit. However, when using a biologically plausible soma circuit (e.g., Hodgkin-Huxley neuron model), an interface circuitry, such as a current conveyor circuit, is needed to transmit synaptic current to the soma circuit. This is especially true for ultra-low power neuron circuits, where membrane capacitance is on the order of 20 fF. This need for an interface circuit arises because the parasitic capacitance and leakage current caused by fabrication mismatch and second-order effects of the output transistors in the synapse circuits can disturb the spiking dynamics of the soma circuit if connected without an interface. Using an interface circuit to isolate the soma’s membrane capacitor from synapses resolves this issue. We propose to use a unidirectional resistor (a transconductance circuit) to connect the synapse and soma circuits instead of conventional current conveyor circuits. Using a biologically plausible spike pattern detection model, we show that the on-chip spike-timing-dependent plasticity (STDP) learning performance of the proposed unidirectional two-compartment neuron circuit is similar to a single-compartment circuit (with a current conveyor as an interface) and additionally, it is more power-efficient and biologically plausible. The chip is fabricated in the Taiwan Semiconductor Manufacturing Company (TSMC) 250 nm technology node and comprises a single neuron circuit.

Gautam, Ashish [ORNL]↗

Sulfur Species in Zinc-Rich Condylar Zones of a Rat Temporomandibular Joint

We performed synchrotron-based micro-X-ray absorption near-edge spectroscopy (µ-XANES) coupled with micro-X-ray fluorescence (µ-XRF) for the identification of elements that included biometal zinc (Zn) and nonmetal sulfur (S) (and its species) in the condylar zones of a rat temporomandibular joint (TMJ). Zone-specific spatial localization of biometal Zn and nonmetal S from a materials viewpoint when correlated with hypoxia inducible factor-1α (HIF-1α) (a surrogate for tissue oxygenation) can provide insights into Zn-specific redox pathways at the vulnerable subchondral interface. Histologic localization of Zn, HIF-1α, and sulfur-rich proteoglycans (PGs) were mapped using an optical microscope. The µ-XRF maps coupled with site-specific micro-X-ray diffraction (µ-XRD) patterns were used to underline Zn-incorporated biological apatite in the subchondral bone and the bone of a rat TMJ condyle. Results demonstrated an association between Zn, PG, and HIF-1α histologic maps with µ-XRF, µ-XANES, and µ-XRD data and provided insights into plausible biological S species in Zn-enriched zones of a rat TMJ condyle. Spatially localized Zn and S underscore their roles in cell and tissue functions in a zone-specific manner. Elemental Zn with organic and inorganic S species at the cartilage-bone interface and the biomineral phase of Zn-enriched biological apatite from subchondral bone to condylar bone were ascertained using µ-XRF-XANES and µ-XRF-XRD. The coupled µ-XRF-XANES in situ complemented with µ-XRF-XRD in situ and immunohistochemistry provided valuable biological insights into zone-specific biological pathways in rat TMJ condyles. Based on these data, we present a workflow to reliably map and correlate S species within Zn-enriched regions of cartilage, bone, and their interface. We suggest the use of this correlative and complementary microspectroscopic spatial information for zone-specific localization of biometal Zn and nonmetal S to gain insights into plausible microanatomy-specific oxidative stress in the TMJ.

apatites↗

Chaotic neural dynamics facilitate probabilistic computations through sampling

Cortical neurons exhibit highly variable responses over trials and time. Theoretical works posit that this variability arises potentially from chaotic network dynamics of recurrently connected neurons. Here, we demonstrate that chaotic neural dynamics, formed through synaptic learning, allow networks to perform sensory cue integration in a sampling-based implementation. We show that the emergent chaotic dynamics provide neural substrates for generating samples not only of a static variable but also of a dynamical trajectory, where generic recurrent networks acquire these abilities with a biologically plausible learning rule through trial and error. Furthermore, the networks generalize their experience in the stimulus-evoked samples to the inference without partial or all sensory information, which suggests a computational role of spontaneous activity as a representation of the priors as well as a tractable biological computation for marginal distributions. These findings suggest that chaotic neural dynamics may serve for the brain function as a Bayesian generative model.

60 APPLIED LIFE SCIENCES↗

CRCNS22 Learning Rules in the Hippocampus and their Mapping to Neuromorphic Systems (Final Technical Report)

Large scale biologically-realistic computational models are key to investigating the interplay between structure and function in nervous systems, thus paving the way to new clinical methods and neuro-inspired computing solutions. This project focuses on the hippocampus, in particular the CA3-CA1 regions, due to their role in associative learning and memory, pattern separation and completion, and spatial navigation. Investigations into the neuronal organization and learning rule(s) of this circuit can shed light into how declarative memories are formed, stored, recalled and forgotten and inform computational, experimental and clinical neuroscience work. Our project aims at developing a novel data-driven methodology supported by a broad heterogeneous base of neuroscience experimental knowledge and inspired from advances in computer science and engineering. Specifically, this work will benchmark existing and new learning rules within a full-scale spiking neural network simulation of the CA3-CA1 region. The model will be based on an open-source repository, called the Hippocampome, which contains neuronal morphologies, firing patterns, synapse probabilities, and most other required parameters for all known neuron types in the rodent hippocampal formation. The model will be first trained in a supervised fashion for associative memory tasks using backpropagation through time traditionally used in computer science, enhanced with a new technique called the surrogate gradient method. This optimization method will be used to obtain a global loss minimization, but it is not biologically inspired as it assumes the use of data not locally available to the synapses. However, we propose its use as a benchmarking tool, to compare the training performance of local biologically plausible and hardware-mappable learning rules at scale. New rules or combinations will be proposed and tested as needed, based on the obtained results. Progress in this area will also drive the development of novel hardware-mappable algorithms for continual lifelong learning and categorization of new events from few presented examples. This project goes beyond the existing state-of-the-art by looking at large scale realistic neuronal circuits as networks trainable via global optimization methods such as surrogate gradient descent. The objective function of the brain that supports learning is largely unknown, but it is likely that it operates through local learning rules. Studying network trajectories around local minima as proposed in this work represents a useful strategy for understanding whether a network is training by using a specific (set of) learning rule(s). Starting from a completely untrained network is a challenging test since it is difficult to determine how the learning rule affects the trajectory of the network. This interdisciplinary project will help understand what rule governs learning in these regions or if multiple learning rules are involved. The work will develop a robust methodology to measure if the network is converging to the target solution, oscillating around it, or diverging away.

59 BASIC BIOLOGICAL SCIENCES↗

Optoelectronic analogs of self-programming neural nets - Architecture and methodologies for implementing fast stochastic learning by simulated annealing

Self-organization and learning is a distinctive feature of neural nets and processors that sets them apart from conventional approaches to signal processing. It leads to self-programmability which alleviates the problem of programming complexity in artificial neural nets. In this paper architectures for partitioning an optoelectronic analog of a neural net into distinct layers with prescribed interconnectivity pattern to enable stochastic learning by simulated annealing in the context of a Boltzmann machine are presented. Stochastic learning is of interest because of its relevance to the role of noise in biological neural nets. Practical considerations and methodologies for appreciably accelerating stochastic learning in such a multilayered net are described. These include the use of parallel optical computing of the global energy of the net, the use of fast nonvolatile programmable spatial light modulators to realize fast plasticity, optical generation of random number arrays, and an adaptive noisy thresholding scheme that also makes stochastic learning more biologically plausible. The findings reported predict optoelectronic chips that can be used in the realization of optical learning machines.

Farhat, Nabil H.↗

Spike train generation and current-to-frequency conversion in silicon diodes

A device physics model is developed to analyze spontaneous neuron-like spike train generation in current driven silicon p(+)-n-n(+) devices in cryogenic environments. The model is shown to explain the very high dynamic range (0 to the 7th) current-to-frequency conversion and experimental features of the spike train frequency as a function of input current. The devices are interesting components for implementation of parallel asynchronous processing adjacent to cryogenically cooled focal planes because of their extremely low current and power requirements, their electronic simplicity, and their pulse coding capability, and could be used to form the hardware basis for neural networks which employ biologically plausible means of information coding.

Coon, D. D.↗

Non-Protein Amino Acids Identified in Carbon-Rich Hayabusa Particles

Amino acid abundances in acid-hydrolyzed hot water extracts of gold foils containing five Category 3 (carbon-rich) Hayabusa particles were studied using liquid chromatography with tandem fluorescence and accurate mass detection. Initial particle analyses using field emission scanning electron microscopy with energy-dispersive X-ray spectrometry indicated that the particles were composed mainly of carbon. Prior to amino acid analysis, infrared and Raman microspectroscopy showed some grains possessed primitive organic carbon. Although trace terrestrial contamination, namely L-protein amino acids, was observed in all Hayabusa extracts, several terrestrially uncommon non-protein amino acids were also identified. Some Hayabusa particles contained racemic (D≈L) mixtures of the non-protein amino acids β-aminoisobutyric acid (β-AIB) and β-amino-n-butyric acid (β-ABA) at low abundances ranging from 0.09 to 0.31 nmol g −1 . Larger abundances of the non-protein amino acid β-alanine (9.2 nmol g −1 , ≈4.5 times greater than background levels) were measured in an extract of three Hayabusa particles. This β-alanine abundance was ≈6 times higher than that measured in an extract of a CM2 Murchison grain processed in parallel. The comparatively high β-alanine abundance is surprising as asteroid Itokawa is similar to amino acid-poor LL ordinary chondrites. Elevated β-alanine abundances and racemic β-AIB and β-ABA in Hayabusa grains suggested these compounds have non-biological and plausibly non-terrestrial origins. These results are the first evidence of plausibly extraterrestrial amino acids in asteroid material from a sample-return mission and demonstrate the capabilities of the analytical protocols used to study asteroid Ryugu and Bennu samples returned by the JAXA Hayabusa2 and NASA OSIRIS-REx missions, respectively.

Eric T. Parker↗

Computing motion using resistive networks

Recent developments in the theory of early vision are described which lead from the formulation of the motion problem as an ill-posed one to its solution by minimizing certain 'cost' functions. These cost or energy functions can be mapped onto simple analog and digital resistive networks. It is shown how the optical flow can be computed by injecting currents into resistive networks and recording the resulting stationary voltage distribution at each node. These networks can be implemented in cMOS VLSI circuits and represent plausible candidates for biological vision systems.

Koch, Christof↗

Effects of radiobiological uncertainty on vehicle and habitat shield design for missions to the moon and Mars

Some consequences of uncertainties in radiobiological risk due to galactic cosmic ray (GCR) exposure are analyzed for their effect on engineering designs for the first lunar outpost and a mission to explore Mars. This report presents the plausible effect of biological uncertainties, the design changes necessary to reduce the uncertainties to acceptable levels for a safe mission, and an evaluation of the mission redesign cost. Estimates of the amount of shield mass required to compensate for radiobiological uncertainty are given for a simplified vehicle and habitat. The additional amount of shield mass required to provide a safety factor for uncertainty compensation is calculated from the expected response to GCR exposure. The amount of shield mass greatly increases in the estimated range of biological uncertainty, thus, escalating the estimated cost of the mission. The estimates are used as a quantitative example for the cost-effectiveness of research in radiation biophysics and radiation physics.

Wilson, John W.↗

Automatic variable selection in ecological niche modeling: A case study using Cassin’s Sparrow (Peucaea cassinii)

MERRA/Max provides a feature selection approach to dimensionality reduction that enables direct use of global climate model outputs in ecological niche modeling. The system accomplishes this reduction through a Monte Carlo optimization in which many independent MaxEnt runs, operating on a species occurrence file and a small set of randomly selected variables in a large collection of variables, converge on an estimate of the top contributing predictors in the larger collection. These top predictors can be viewed as potential candidates in the variable selection step of the ecological niche modeling process. MERRA/Max’s Monte Carlo algorithm operates on files stored in the underlying filesystem, making it scalable to large data sets. Its software components can run as parallel processes in a high-performance cloud computing environment to yield near real-time performance. In tests using Cassin’s Sparrow (Peucaea cassinii) as the target species, MERRA/Max selected a set of predictors from Worldclim’s Bioclim collection of 19 environmental variables that have been shown to be important determinants of the species’ bioclimatic niche. It also selected biologically and ecologically plausible predictors from a more diverse set of 86 environmental variables derived from NASA’s Modern-Era Retrospective Analysis for Research and Applications Version 2 (MERRA-2) reanalysis, an output product of the Goddard Earth Observing System Version 5 (GEOS-5) modeling system. We believe these results point to a technological approach that could expand the use global climate model outputs in ecological niche modeling, foster exploratory experimentation with otherwise difficult-to-use climate data sets, streamline the modeling process, and, eventually, enable automated bioclimatic modeling as a practical, readily accessible, low-cost, commercial cloud service.

John L. Schnase↗

Dormancy and Recovery Testing for Biological Wastewater Processors

Resource recovery and recycling waste streams to usable water via biological water processors is a plausible component of an integrated water purification system. Biological processing as a pretreatment can reduce the load of organic carbon and nitrogen compounds entering physiochemical systems downstream. Aerated hollow fiber membrane bioreactors, have been proposed and studied for a number of years as an approach for treating wastewater streams for space exploration.

Dormancy↗

Isotopic, petrologic and biogeochemical investigations of banded iron-formations

It is recognized that the first occurrence of banded iron-formations (BIFs) clearly predates biological oxygenation of the atmosphere-hydrosphere system and that their last occurrences extend beyond plausible dates of pervasive biological oxygenation. For this reason, and because enormous quantities of oxidizing power have been sequestered in them, it is widely thought that these massive, but enigmatic, sediments must encode information about the mechanism and timing of the rise of atmospheric O2. By coupling isotopic analyses of iron-formation carbonates with biogeochemical and petrologic investigations, we are studying (1) the mechanism of initial sedimentation of iron; (2) the role of iron in microbially mediated diagenetic processes in fresh iron-formation sediments; and (3) the logical integration of mechanisms of deposition with observed levels of banding. Thus far, it has been shown that (1) carbonates in BIFs of the Hamersley Group of Western Australia are isotopically inhomogenous; (2) the nature and pattern of isotopic ordering is not consistent with a metamorphic origin for the overall depletion of C-13 observed in the carbonates; (3) if biological, the origin of the C-13 depleted carbonate could be either respiratory or fermentative; (4) iron may have been precipitate d as Fe(3+), then reduced to Fe(2+) within the sediment; and (5) sedimentary biogeochemical systems may have been at least partially closed to mass transport of carbonate species.

Hayes, J. M.↗

Two-stage model of radon-induced malignant lung tumors in rats: effects of cell killing

A two-stage stochastic model of carcinogenesis is used to analyze lung tumor incidence in 3750 rats exposed to varying regimens of radon carried on a constant-concentration uranium ore dust aerosol. New to this analysis is the parameterization of the model such that cell killing by the alpha particles could be included. The model contains parameters characterizing the rate of the first mutation, the net proliferation rate of initiated cells, the ratio of the rates of cell loss (cell killing plus differentiation) and cell division, and the lag time between the appearance of the first malignant cell and the tumor. Data analysis was by standard maximum likelihood estimation techniques. Results indicate that the rate of the first mutation is dependent on radon and consistent with in vitro rates measured experimentally, and that the rate of the second mutation is not dependent on radon. An initial sharp rise in the net proliferation rate of initiated cell was found with increasing exposure rate (denoted model I), which leads to an unrealistically high cell-killing coefficient. A second model (model II) was studied, in which the initial rise was attributed to promotion via a step function, implying that it is due not to radon but to the uranium ore dust. This model resulted in values for the cell-killing coefficient consistent with those found for in vitro cells. An "inverse dose-rate" effect is seen, i.e. an increase in the lifetime probability of tumor with a decrease in exposure rate. This is attributed in large part to promotion of intermediate lesions. Since model II is preferable on biological grounds (it yields a plausible cell-killing coefficient), such as uranium ore dust. This analysis presents evidence that a two-stage model describes the data adequately and generates hypotheses regarding the mechanism of radon-induced carcinogenesis.

NASA Program Radiation Health↗

Analysis and interpretation of Viking labeled release experimental results

The Viking Labeled Release (LR) life detection experiment on the surface of Mars produced data consistent with a biological interpretation. In considering the plausibility of this interpretation, terrestrial life forms were identified which could serve as models for Martian microbial life. Prominent among these models are lichens which are known to survive for years in a state of cryptobiosis, to grow in hostile polar environments, to exist on atmospheric nitrogen as sole nitrogen source, and to survive without liquid water by absorbing water directly from the atmosphere. Another model is derived from the endolithic bacteria found in the dry Antarctic valleys; preliminary experiments conducted with samples of these bacteria indicate that they produce positive LR responses approximating the Mars results. However, because of the hositility of the Martian environment to life, and the failure to find organics on the surface of Mars, a number of nonbiological explanations were advanced to account for the Viking LR data. A reaction of the LR nutrient with putative surface hydrogen peroxide is the leading candidate. Other possibilities raised include reactions caused by or with ultraviolet irradiation, gamma-Fe2O3, metalloperoxides or superoxides.

Levin, G. V.↗