A dynamical model for generating synthetic data to quantify active tactile sensing behavior in the rat.
Ontology highlight
ABSTRACT:
SUBMITTER: Zweifel NO
PROVIDER: S-EPMC8271597 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In this article, we present an open source neuroinformatics platform for exploring, analyzing, and validating distilled graphical representations of high-dimensional neuroimaging data extracted using topological data analysis (TDA). TDA techniques like Mapper have been recently applied to examine the brain's dynamical organization during ongoing cognition without averaging data in space, in time, or across participants at the outset. Such TDA-based approaches mark an important deviation from standard neuroimaging analyses by distilling complex high-dimensional neuroimaging data into simple-yet neurophysiologically valid and behaviorally relevant-representations that can be interactively explored at the single-participant level. To facilitate wider use of such techniques within neuroimaging and general neuroscience communities, our work provides several tools for visualizing, interacting with, and grounding TDA-generated graphical representations in neurophysiology. Through Python-based Jupyter notebooks and open datasets, we provide a platform to assess and visualize different intermittent stages of Mapper and examine the influence of Mapper parameters on the generated representations. We hope this platform could enable researchers and clinicians alike to explore topological representations of neuroimaging data and generate biological insights underlying complex mental disorders.
| S-EPMC6663215 | biostudies-literature
Project description:The rodent vibrissal-trigeminal system is one of the most widely used models for the study of somatosensation and tactile perception, but to date the field has been unable to quantify the complete set of mechanical input signals generated during natural whisking behavior. In this report we show that during whisking behavior of awake rats (Rattus norvegicus), the whisker will often bend out of its plane of rotation, generating sizeable mechanical (tactile) signals out of the plane. We then develop a model of whisker bending that allows us to compute the three-dimensional tactile signals at the vibrissal base during active whisking behavior. Considerable information can be lost if whisking motions are considered only in two dimensions, and we offer some suggestions for experimentalists concerned with monitoring the direction of bending. These data represent the first quantification of the physical signals transmitted to the mechanoreceptors in the follicle during active whisking behavior.
| S-EPMC4455487 | biostudies-literature
Project description:Getting access to administrative health data for research purposes is a difficult and time-consuming process due to increasingly demanding privacy regulations. An alternative method for sharing administrative health data would be to share synthetic datasets where the records do not correspond to real individuals, but the patterns and relationships seen in the data are reproduced. This paper assesses the feasibility of generating synthetic administrative health data using a recurrent deep learning model. Our data comes from 120,000 individuals from Alberta Health's administrative health database. We assess how similar our synthetic data is to the real data using utility assessments that assess the structure and general patterns in the data as well as by recreating a specific analysis in the real data commonly applied to this type of administrative health data. We also assess the privacy risks associated with the use of this synthetic dataset. Generic utility assessments that used Hellinger distance to quantify the difference in distributions between real and synthetic datasets for event types (0.027), attributes (mean 0.0417), Markov transition matrices (order 1 mean absolute difference: 0.0896, sd: 0.159; order 2: mean Hellinger distance 0.2195, sd: 0.2724), the Hellinger distance between the joint distributions was 0.352, and the similarity of random cohorts generated from real and synthetic data had a mean Hellinger distance of 0.3 and mean Euclidean distance of 0.064, indicating small differences between the distributions in the real data and the synthetic data. By applying a realistic analysis to both real and synthetic datasets, Cox regression hazard ratios achieved a mean confidence interval overlap of 68% for adjusted hazard ratios among 5 key outcomes of interest, indicating synthetic data produces similar analytic results to real data. The privacy assessment concluded that the attribution disclosure risk associated with this synthetic dataset was substantially less than the typical 0.09 acceptable risk threshold. Based on these metrics our results show that our synthetic data is suitably similar to the real data and could be shared for research purposes thereby alleviating concerns associated with the sharing of real data in some circumstances.
| S-EPMC10034254 | biostudies-literature
Project description:As a surrogate for human tactile cognition, an artificial tactile perception and cognition system are proposed to produce smooth/soft and rough tactile sensations by its user's tactile feeling; and named this system as "tactile avatar". A piezoelectric tactile sensor is developed to record dynamically various physical information such as pressure, temperature, hardness, sliding velocity, and surface topography. For artificial tactile cognition, the tactile feeling of humans to various tactile materials ranging from smooth/soft to rough are assessed and found variation among participants. Because tactile responses vary among humans, a deep learning structure is designed to allow personalization through training based on individualized histograms of human tactile cognition and recording physical tactile information. The decision error in each avatar system is less than 2% when 42 materials are used to measure the tactile data with 100 trials for each material under 1.2N of contact force with 4cm s-1 of sliding velocity. As a tactile avatar, the machine categorizes newly experienced materials based on the tactile knowledge obtained from training data. The tactile sensation showed a high correlation with the specific user's tendency. This approach can be applied to electronic devices with tactile emotional exchange capabilities, as well as advanced digital experiences.
| S-EPMC8024994 | biostudies-literature
Project description:IntroductionFederated Learning (FL) is a decentralised approach to training statistical models, where training is performed across multiple clients, producing one global model. Since the training data remains with each local client and is not shared or exchanged with other clients the use of FL may reduce privacy and security risks (compared to methods where multiple data sources are pooled) and can also address data access and heterogeneity problems. Synthetic data is artificially generated data that has the same structure and statistical properties as the original but that does not contain any of the original data records, therefore minimising disclosure risk. Using FL to produce synthetic data (which we refer to as "federated synthesis") has the potential to combine data from multiple clients without compromising privacy, allowing access to data that may otherwise be inaccessible in its raw format.ObjectivesThe objective was to review current research and practices for using FL to generate synthetic data and determine the extent to which research has been undertaken, the methods and evaluation practices used, and any research gaps.MethodsA scoping review was conducted to systematically map and describe the published literature on the use of FL to generate synthetic data. Relevant studies were identified through online databases and the findings are described, grouped, and summarised. Information extracted included article characteristics, documenting the type of data that is synthesised, the model architecture and the methods (if any) used to evaluate utility and privacy risk.ResultsA total of 69 articles were included in the scoping review; all were published between 2018 and 2023 with two thirds (46) in 2022. 30% (21) were focussed on synthetic data generation as the main model output (with 6 of these generating tabular data), whereas 59% (41) focussed on data augmentation. Of the 21 performing federated synthesis, all used deep learning methods (predominantly Generative Adversarial Networks) to generate the synthetic data.ConclusionsFederated synthesis is in its early days but shows promise as a method that can construct a global synthetic dataset without sharing any of the local client data. As a field in its infancy there are areas to explore in terms of the privacy risk associated with the various methods proposed, and more generally in how we measure those risks.
| S-EPMC10898505 | biostudies-literature
Project description:Neural computation involves diverse types of GABAergic inhibitory interneurons that are integrated with excitatory (E) neurons into precisely structured circuits. To understand how each neuron type shapes sensory representations, we measured firing patterns of defined types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Touch excited fast-spiking (FS) interneurons at short latency, followed by activation of E neurons and somatostatin-expressing (SST) interneurons. Touch only weakly modulated vasoactive intestinal polypeptide-expressing (VIP) interneurons. Voluntary whisker movement activated FS neurons in the ventral posteromedial nucleus (VPM) target layers, a subset of SST neurons and a majority of VIP neurons. Together, FS neurons track thalamic input, mediating feedforward inhibition. SST neurons monitor local excitation, providing feedback inhibition. VIP neurons are activated by non-sensory inputs, disinhibiting E and FS neurons. Our data reveal rules of recruitment for interneuron types during behavior, providing foundations for understanding computation in cortical microcircuits.
| S-EPMC6813892 | biostudies-literature
Project description:The posterior parietal cortex (PPC) in rodents is reciprocally connected to primary somatosensory and vibrissal motor cortices. The PPC neuronal circuitry could thus encode and potentially integrate incoming somatosensory information and whisker motor output. However, the information encoded across PPC layers during refined sensorimotor behavior remains largely unknown. To uncover the sensorimotor features represented in PPC during voluntary whisking and object touch, we performed loose-patch single-unit recordings and extracellular recordings of ensemble activity, covering all layers of PPC in anesthetized and awake, behaving male rats. First, using single-cell receptive field mapping, we revealed the presence of coarse somatotopy along the mediolateral axis in PPC. Second, we found that spiking activity was modulated during exploratory whisking in layers 2-4 and layer 6, but not in layer 5 of awake, behaving rats. Population spiking activity preceded actual movement, and whisker trajectory endpoints could be decoded by population spiking, suggesting that PPC is involved in movement planning. Finally, population spiking activity further increased in response to active whisker touch but only in PPC layers 2-4. Thus, we find layer-specific processing, which emphasizes the computational role of PPC during whisker sensorimotor behavior.SIGNIFICANCE STATEMENT The posterior parietal cortex (PPC) is thought to merge information on motor output and sensory input to orchestrate interaction with the environment, but the function of different PPC microcircuit components is poorly understood. We recorded neuronal activity in rat PPC during sensorimotor behavior involving motor and sensory pathways. We uncovered that PPC layers have dedicated function: motor and sensory information is merged in layers 2-4; layer 6 predominantly represents motor information. Collectively, PPC activity predicts future motor output, thus entailing a motor plan. Our results are important for understanding how PPC computationally processes motor output and sensory input. This understanding may facilitate decoding of brain activity when using brain-machine interfaces to overcome loss of function after, for instance, spinal cord injury.
| S-EPMC6759035 | biostudies-literature
Project description:Synthetic constructs in biotechnology, biocomputing, and modern gene therapy interventions are often based on plasmids or transfected circuits which implement some form of "on-off" switch. For example, the expression of a protein used for therapeutic purposes might be triggered by the recognition of a specific combination of inducers (e.g., antigens), and memory of this event should be maintained across a cell population until a specific stimulus commands a coordinated shut-off. The robustness of such a design is hampered by molecular ("intrinsic") or environmental ("extrinsic") noise, which may lead to spontaneous changes of state in a subset of the population and is reflected in the bimodality of protein expression, as measured for example using flow cytometry. In this context, a "majority-vote" correction circuit, which brings deviant cells back into the required state, is highly desirable, and quorum-sensing has been suggested as a way for cells to broadcast their states to the population as a whole so as to facilitate consensus. In this paper, we propose what we believe is the first such a design that has mathematically guaranteed properties of stability and auto-correction under certain conditions. Our approach is guided by concepts and theory from the field of "monotone" dynamical systems developed by M. Hirsch, H. Smith, and others. We benchmark our design by comparing it to an existing design which has been the subject of experimental and theoretical studies, illustrating its superiority in stability and self-correction of synchronization errors. Our stability analysis, based on dynamical systems theory, guarantees global convergence to steady states, ruling out unpredictable ("chaotic") behaviors and even sustained oscillations in the limit of convergence. These results are valid no matter what are the values of parameters, and are based only on the wiring diagram. The theory is complemented by extensive computational bifurcation analysis, performed for a biochemically-detailed and biologically-relevant model that we developed. Another novel feature of our approach is that our theorems on exponential stability of steady states for homogeneous or mixed populations are valid independently of the number N of cells in the population, which is usually very large (N ≫ 1) and unknown. We prove that the exponential stability depends on relative proportions of each type of state only. While monotone systems theory has been used previously for systems biology analysis, the current work illustrates its power for synthetic biology design, and thus has wider significance well beyond the application to the important problem of coordination of toggle switches.
| S-EPMC4851387 | biostudies-literature
Project description:Human-robot interaction technology has contributed to improving sociality for humanoid robots. At scales far from human scales, a microrobot can interact with an environment in a small world. Microsensors have been applied to measurement of forces by flying or walking insects. Meanwhile, most previous works focused on the measurement of the behavior of insects. Here, we propose microrobot-insect interactions by soft microfingers integrated with artificial muscle actuators and tactile sensors, which has been developed for a haptic teleoperation robot system. A soft pneumatic balloon actuator acts as the artificial muscle, and a flexible strain sensor using a liquid metal provides tactile sensing. Force interaction between a pill bug and the microfinger could be accomplished. The microfinger (12 mm × 3 mm × 490 μm) can move and touch an insect, and it can detect reaction force from an insect. The measured reaction force from the legs of a pill bug as a representative insect was less than 10 mN. This paper presents a microfinger as an end effector for the active sensing of reaction force from a small insect. We anticipate that our results will lead to further evaluation of small living things as well as technology development for human-environment interaction.
| S-EPMC9550801 | biostudies-literature
Project description:Epilepsy is one of the most common neurological disorders worldwide. Recent findings suggest that the brain is a complex system composed of a network of neurons, and seizure is considered an emergent property resulting from its interactions. Based on this perspective, network physiology has emerged as a promising approach to explore how brain areas coordinate, synchronize and integrate their dynamics, both under perfect health and critical illness conditions. Therefore, the objective of this paper is to present an application of (Dynamic) Bayesian Networks (DBN) to model Local Field Potentials (LFP) data on rats induced to epileptic seizures based on the number of arcs found using threshold analytics. Results showed that DBN analysis captured the dynamic nature of brain connectivity across ictogenesis and a significant correlation with neurobiology derived from pioneering studies employing techniques of pharmacological manipulation, lesion, and modern optogenetics. The arcs evaluated under the proposed approach achieved consistent results based on previous literature, in addition to demonstrating robustness regarding functional connectivity analysis. Moreover, it provided fascinating and novel insights, such as discontinuity between forelimb clonus and generalized tonic-clonic seizure (GTCS) dynamics. Thus, DBN coupled with threshold analytics may be an excellent tool for investigating brain circuitry and their dynamical interplay, both in homeostasis and dysfunction conditions.
| S-EPMC9399918 | biostudies-literature