Similar Datasets
Project description:A Clock-Driven Neural Network Critical for Arousal
| PRJNA609641 | ENA
Project description:Purpose: highthroughput sequencing (scRNA-Seq) to study hypothalamic tanycytes and astrocytes with NrCAM KO
2021-12-29 | GSE192766 | GEO
Project description:We present an adaptive optical neural network based on a large-scale event-driven architecture. In addition to changing the synaptic weights (synaptic plasticity), the optical neural network's structure can also be reconfigured enabling various functionalities (structural plasticity). Key building blocks are wavelength-addressable artificial neurons with embedded phase-change materials that implement nonlinear activation functions and nonvolatile memory. Using multimode focusing, the activation function features both excitatory and inhibitory responses and shows a reversible switching contrast of 3.2 decibels. We train the neural network to distinguish between English and German text samples via an evolutionary algorithm. We investigate both the synaptic and structural plasticity during the training process. On the basis of this concept, we realize a large-scale network consisting of 736 subnetworks with 16 phase-change material neurons each. Overall, 8398 neurons are functional, highlighting the scalability of the photonic architecture.
| S-EPMC10588940 | biostudies-literature
Project description:Sleep arousals are transient periods of wakefulness punctuated into sleep. Excessive sleep arousals are associated with symptoms such as sympathetic activation, non-restorative sleep, and daytime sleepiness. Currently, sleep arousals are mainly annotated by human experts through looking at 30-second epochs (recorded pages) manually, which requires considerable time and effort. Here we present a deep learning approach for automatically segmenting sleep arousal regions based on polysomnographic recordings. Leveraging a specific architecture that 'translates' input polysomnographic signals to sleep arousal labels, this algorithm ranked first in the "You Snooze, You Win" PhysioNet Challenge. We created an augmentation strategy by randomly swapping similar physiological channels, which notably improved the prediction accuracy. Our algorithm enables fast and accurate delineation of sleep arousal events at the speed of 10 seconds per sleep recording. This computational tool would greatly empower the scoring process in clinical settings and accelerate studies on the impact of arousals.
| S-EPMC7782826 | biostudies-literature
Project description:Purpose: Alteration in light dark cycle leads to changes in daily behavior in mammals. We have previously demonstrated that different light:dark cycle lengths result in dynamic changes in DNA methylation within the suprachiasmatic nuclei (SCN) that globally alter transcription of both clock genes and non-clock genes. The goal of this study was to re-examine DNA methylation in the SCN separately for dorsal and ventral regions. Method: Six-week-old wild-type mice (C57BL/6Cr1) were entrained to light:dark cycles either 22, 24, or 26 hours in length (T22, T24, or T26) for six weeks. After 6 weeks, we recorded wheel-running behavior in constant darkness. After 3 days in DD, we used Clocklab software to predict time of activity onset for each mouse. Brains were isolated at the circadian time CT4 and then sliced immediately using vibratome, one coronal SCN slice of ~250μM was collected from the middle part of the SCN. Using ophthalmic knife vSCN and dSCN sub-regions were separated. To get enough DNA, a pool of vSCN and dSCN was prepared twice from 5 mice from each T-cycle. Genomic DNA was extracted from SCN slices by overnight Proteinase K digestion, followed by phenol-chloroform and ethanol precipitation. After RNase treatment, genomic DNA was sonicated to generate small fragments (average of 300bp), using a Covaris sonicator (BioRuptor). DNA immunoprecipitation was performed using Epiquik™ MeDIP Ultra Kit (EPIGENTEK™), following manufacturer's instructions. The methylated enriched DNA was then used for library preparation using Accel-NGS™ DNA Library Kits (Swift Biosciences), following manufacturer's instructions. Quality check, library preparation and sequencing were performed by Fasteris (CH). Results: 13-21 x 10^6 reads were obtained from each meDIP library. Quality control was performed on the fasta raw sequence data using FastQC.MeDIP-seq data were aligned to the mm9 mouse genome build using the Burrows-Wheeler Alignment tool (BWA) (Li and Durbin, 2009). Mapped reads were than analyzed using the MEDIPS package (Lienhard et al., 2014). Methylation score was calculated for each region of 500bp across the genome. CpG density-dependent normalization was incorporated. Pairwise correlation analysis of the genome wide coverage profile between MEDIP replicate samples was performed using the MEDIPS.correlation function. Pearson correlation coefficient r varied between 0.85 and 0.92, indicating good reproducibility of MEDIP-seq signal. Differential methylation analysis was performed using MEDIPS in 500bp widows excluding regions with less than 8 unique mapped reads. DMR were than identified by filtering for a widows associated with a p ≤0.001. DMR were than mapped using the web based chip-seq tool “ChIPseek” (Chen et al., 2014). Different sets of genes showed methylation changes in dorsal vs. ventral regions. Interestingly, far greater changes were observed in vSCN than in dSCN.
2016-10-28 | GSE89255 | GEO
Project description:Here we report meditative techniques, which modulate attentional control by arousal-driven influences and not by monitoring continuous thought processes as during mindfulness-related practices. We focus on Vajrayana (Tantric Buddhism) practices, during which a sequence of generation (self-visualization as a deity - Yidam) or completion with sign (inner heat -Tummo) stages necessarily precedes non-dual awareness (NDA) Tantric Mahamudra. We compared the electrocardiographic and electroencephalographic correlates of Mahamudra performed after rest (non-Tantric Mahamudra) with Mahamudra performed after Yidam (Tantric Mahamudra) in 16 highly experienced Vajrayana practitioners, 10 of whom also performed Tummo. Both Yidam and Tummo developed the state of PNS withdrawal (arousal) and phasic alertness, as reflected by HF HRV decreases and Alpha2 power increases, later neurophysiologically employed in Tantric Mahamudra. The latter led to the unique state of high cortical excitability, "non-selective" focused attention, and significantly reduced attentional control, quantified by power reductions in all frequency bands, except Theta. In contrast, similar to mindfulness-related practices, non-Tantric Mahamudra was performed in a state of PNS dominance (relaxation), tonic alertness, and active monitoring, as suggested by Alpha1 power increases and less pronounced decreases in other frequency bands. A neurobiological model of meditation is proposed, differentiating arousal-based and mindfulness-related practices.
| S-EPMC9559070 | biostudies-literature
Project description:One of the primary ways we interact with the world is using our hands. In macaques, the circuit spanning the anterior intraparietal area, the hand area of the ventral premotor cortex, and the primary motor cortex is necessary for transforming visual information into grasping movements. However, no comprehensive model exists that links all steps of processing from vision to action. We hypothesized that a recurrent neural network mimicking the modular structure of the anatomical circuit and trained to use visual features of objects to generate the required muscle dynamics used by primates to grasp objects would give insight into the computations of the grasping circuit. Internal activity of modular networks trained with these constraints strongly resembled neural activity recorded from the grasping circuit during grasping and paralleled the similarities between brain regions. Network activity during the different phases of the task could be explained by linear dynamics for maintaining a distributed movement plan across the network in the absence of visual stimulus and then generating the required muscle kinematics based on these initial conditions in a module-specific way. These modular models also outperformed alternative models at explaining neural data, despite the absence of neural data during training, suggesting that the inputs, outputs, and architectural constraints imposed were sufficient for recapitulating processing in the grasping circuit. Finally, targeted lesioning of modules produced deficits similar to those observed in lesion studies of the grasping circuit, providing a potential model for how brain regions may coordinate during the visually guided grasping of objects.
| S-EPMC7749336 | biostudies-literature
Project description:Systemic acute inflammatory signals can cause profound anorexia by disrupting the physiological appetite regulation in the hypothalamic milieu. Conversely, obesity related chronic inflammation of the hypothalamus can disturb anorexigenic signals and promote abnormal body weight control. The aim of the present study was to compare the global hypothalamic endophenotype in C57/Bl6 mice exposed to a high-fat diet or with acute illness mediated by LPS. Ten-week old male C57/Bl6 mice (n=18) were randomly divided into four groups; the control 1 group (n =3) was fed a normal diet whereas the high-fat diet (HFD) group (n =6) was fed a high-fat diet for eight weeks. The control 2 group (n=3) received an intraperitoneal injection of saline whereas the LPS group (n=6) received an intraperitoneal injection of LPS. Mice were sacrificed 18-hr post-injection. Both control 2 and LPS groups were fed a normal diet for eight weeks before the injection. The hypothalamic regions were removed and analysed using a 2D LC-MS methodology. The proteomic analysis profiled 9,235 proteins (q<0.05) across all biological states, of which 522 proteins were found modulated in the HFD group and another 579 in the LPS group. The proteomic profiles demonstrated that the systemic acute inflammation linked with anorexia induced a negative feedback loop of appetite control in the hypothalamus, suggesting an effort to re-establish homeostasis. By contrast, the chronic inflammation associated with obesity initiated a “perpetual cycle” of positive feedback enhancement of appetite regulation further exacerbating positive energy balance.
2018-01-29 | PXD002119 | Pride
Project description:To delineate sodium valproate (VPA) molecular effects underlying mitigation of skin fibrosis in RDEB mice, mass spectrometry-based expression proteomics was performed on protein extracts from back skin of 16 weeks-old VPA-treated RDEB mice, vehicle-treated RDEB mice and WT littermates.
2024-08-31 | PXD047998 | Pride
Project description:As the primary source of norepinephrine (NE) in the brain, the locus coeruleus (LC) regulates both arousal and stress responses1,2. However, how local neuromodulatory inputs contribute to LC function remains unresolved. Here we identify a network of transcriptionally and functionally diverse GABAergic neurons in the LC dendritic field that integrate distant inputs and modulate modes of LC firing to control arousal. We define peri-LC anatomy using viral tracing and combine single-cell RNA sequencing and spatial transcriptomics to molecularly define both LC and peri-LC cell types. We identify several cell types which underlie peri-LC functional diversity using a series of complementary approaches in behaving mice. Our findings indicate that LC and peri-LC neurons comprise transcriptionally and functionally heterogenous neuronal populations, alongside anatomically segregated features which coordinate specific influences on behavioral arousal and avoidance states. Defining the molecular, cellular and functional diversity in the LC provides a road map for understanding the neurobiological basis of arousal alongside hyperarousal-related neuropsychiatric phenotypes.
2024-03-01 | GSE244659 | GEO