Maturation and current status of neuroscience: data from the 1976 Inventory of U.S. Neuroscientists.
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Demography↗
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SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis.
Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
Single-Cell Analysis↗
Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis.
Large single-cell RNA datasets have contributed to unprecedented biological insight. Often, these take the form of cell atlases and serve as a reference for automating cell labeling of newly sequenced samples. Yet, classification algorithms have lacked the capacity to accurately annotate cells, particularly in complex datasets. Here we present SIMS (Scalable, Interpretable Machine Learning for Single-Cell), an end-to-end data-efficient machine learning pipeline for discrete classification of single-cell data that can be applied to new datasets with minimal coding. We benchmarked SIMS against common single-cell label transfer tools and demonstrated that it performs as well or better than state of the art algorithms. We then use SIMS to classify cells in one of the most complex tissues: the brain. We show that SIMS classifies cells of the adult cerebral cortex and hippocampus at a remarkably high accuracy. This accuracy is maintained in trans-sample label transfers of the adult human cerebral cortex. We then apply SIMS to classify cells in the developing brain and demonstrate a high level of accuracy at predicting neuronal subtypes, even in periods of fate refinement, shedding light on genetic changes affecting specific cell types across development. Finally, we apply SIMS to single cell datasets of cortical organoids to predict cell identities and unveil genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. When cell types are obscured by stress signals, label transfer from primary tissue improves the accuracy of cortical organoid annotations, serving as a reliable ground truth. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
Brain organoids↗
The identification of a cis-acting element involved in cyclic 3',5'-adenosine monophosphate regulation of bovine vasopressin gene expression.
Cyclic adenosine 3',5'-monophosphate (cAMP) has been implicated as an intracellular messenger mediating osmotic regulation of expression of the gene encoding the neuropeptide vasopressin (VP) in the hypothalamus. We have used a heterologous transient transfection system to demonstrate that cAMP regulates the bovine VP gene promoter following transfection into CV1 cells. Mutational analysis identified a bovine VP cAMP-responsive element (BVP-CRE) 120-112 base-pairs upstream of the start of transcription. DNase I footprint analysis using nuclear protein extract from CV1 cells showed protection at the site of the BVP-CRE. Protection of the BVP-CRE was also observed using purified AP1 protein, while there was a weak interaction with the BVP-CRE using purified rat CREB protein. Nuclear proteins purified from the rat supraoptic nucleus bind to the BVP-CRE. As transgenic mouse studies have shown that the bovine VP gene is subject to appropriate physiological regulation in the mouse hypothalamus (Ang, H. L., Funkhouser, J., Carter, D. A., Ho, M. Y., and Murphy, D. (1991) Soc. Neurosci. Abstr. 513, 12), these data indicate a role for the BVP-CRE element in mediating VP gene expression in vivo. These data demonstrate that cAMP regulates bovine VP gene expression in vitro via a cis-acting element within the VP promoter, and this activation may be mediated by members of the AP1/ATF/CREB family of transcription factors.
Animals↗
[The spatial structure of the alpha rhythm in the healthy human being studied by EEG mapping].
EEG study was conducted in the state of relative rest in 15 healthy subjects with predominance of the alpha rhythm. Data processing was performed on neuromapper ("Neuroscience", Great Britain). Principal attention was paid to the dynamics of spatial-temporal relations of the alpha rhythm. Cyclic changes were shown of the alpha-rhythm amplitude, proceeding with change of high and low amplitudes during seconds, varying in time in various individuals. Three types of spatial distribution of the alpha rhythm over the cortex at the relative rest were obtained: 1) generalized distribution over the cortex with the wavy shift of the frequency fields; 2) formation of delimited local zones of the alpha rhythm, differing by the frequency from the rhythm in other cortical areas; 3) local zone of the low-frequency alpha rhythm in the visual projection zone (18 and 19 fields). Change of the distribution types of the alpha rhythm in the state of rest takes place in the seconds of time intervals, corresponding, according to the literature data, to the proceeding of elementary mental processes.
Adult↗
Deep FLASH-seq profiling of purified canine sensory neurons uncovers species-specific signatures relevant to pain and itch.
Naturally occurring pain and itch disorders in the domestic dog represent an important and underexploited opportunity for translational sensory neuroscience. These conditions largely mirror human disease, highlighting the need for detailed comparative understanding of canine somatosensory neurobiology. Here, we present a single-cell transcriptomic characterisation of the canine dorsal root ganglion (DRG), providing molecular insights into sensory neuron diversity in a species of direct veterinary and biomedical relevance. We develop a novel mechanical dissociation and fluorescence-activated cell sorting strategy enabling purification of intact whole neurons from adult canine DRG, followed by deep, full-length RNA sequencing using FLASH-seq. This approach yields high-quality transcriptional profiles with molecular depth analogous to deep neuronal profiling in human DRG, enabling resolution of neuronal identities and subtype-specific gene programs. Using these data, we identify canine sensory neuron clusters conforming to conserved principles of DRG molecular organization observed across species, including peptidergic and noncanonical peptidergic nociceptors, low-threshold mechanoreceptors, proprioceptors, and thermosensory populations. Cross-species comparisons with human and mouse DRG datasets reveal broad conservation of pain- and itch-relevant pathways and therapeutic targets, alongside biologically meaningful divergence. We further identify species-specific differences in subtype-restricted expression of the pharmacologically relevant receptors IL31RA and SSTR2 , which we validate using in situ hybridization and contextualize with human spatial transcriptomic data. Finally, we provide evidence that domestication-associated genes are nonrandomly enriched in specific sensory neurons, suggesting that evolutionary history may have shaped somatosensory function. These data represent a resource for comparative sensory neuroscience and inform translational interpretation of pain and itch therapeutics across species.
Animals↗
Individual Differences in Cognitive Aging Rodent Datasets (ID-CARD): A collaborative platform for behavioral analysis across the lifespan.
Understanding cognitive aging requires approaches that capture individual variability while enabling integration across studies. In rodent models, behavioral data are central to this effort, yet cross-laboratory differences in experimental design limit comparability and constrain secondary analysis. To address this gap, we developed the Individual Differences in Cognitive Aging Rodent Datasets (ID-CARD), a first-of-its-kind collaborative repository aggregating trial-level Morris water maze data from multiple laboratories. ID-CARD is designed to support large-scale, integrative analyses and to facilitate secondary use of existing behavioral data in alignment with emerging data-sharing and transparency initiatives. Rather than imposing retrospective harmonization of experimental protocols, we implemented a normalization and modeling framework that enables comparison of learning trajectories while preserving meaningful variation across studies. Behavioral data from > 5000 rats spanning common strains, both sexes, and multiple ages were normalized in training and performance domains and fit with a logarithmic function to derive an error accumulation rate coefficient (EARC) as a measure of spatial learning. Age was strongly associated with increased EARC, indicating attenuated learning, even after adjusting for non-spatial cue performance. Analyses of goodness of fit revealed systematic structure in learning dynamics, where age was associated with reduced learning-curve conformity after accounting for overall performance. Inter-individual variability in spatial learning also increased with age, with strain-specific interactions. These findings demonstrate that integrated analysis of heterogeneous behavioral datasets can yield robust, individual-level insights into cognitive aging. ID-CARD provides a scalable resource and analytic framework to advance discovery in behavioral neuroscience by enabling reuse, integration, and comparative analysis of existing data.
Cognitive aging↗
Dopaminergic mechanisms in the pathogenesis of schizophrenia.
The dopamine hypothesis of schizophrenia has been the dominant theoretical construction guiding research and treatment of the schizophrenic disorders over the past generation. This hypothesis, in its simplest guise, posits the presence of a functional alteration in central dopaminergic systems in the brains of schizophrenic patients. Recent findings have resulted in a greater understanding of the complexity of the central dopaminergic systems and have led to revisions of the hypothesis of a simple functional hyperactivity of central dopaminergic systems. These recent data suggest that there may be regionally restricted changes in the function of the mesotelencephalic dopamine system, and that these changes may be in opposite directions. Such changes may be associated with dysfunctions of interactions between distinct dopaminergic terminal field regions, and may be subserved by functional derangements in other transmitter systems or reflect regionally restricted changes in expression or function of distinct dopamine receptors or catecholamine synthetic enzymes. A recent FASEB symposium reviewed new advances in molecular biology, biochemistry, pharmacology, anatomy, and systems neuroscience as they relate to schizophrenia, and discussed the implications of these data for guiding future research and treatment strategies.
Animals↗
Treatment of epilepsy: with special reference to developing countries.
1. Epilepsy, a common chronic neurological disorder, constitutes an important medical problem especially as in the developing countries there is a great dearth and shortage of health personnel, especially trained ones, in clinical neurosciences. The prevalence of epilepsy in developing countries is probably higher than in the Caucasians although accurate epidemiological data are lacking. 2. Epilepsy is discussed with special regard to the need for accurate diagnosis, and the difficulties encountered in developing countries. 3. Pharmacotherapy should be as simple as possible and suggestions are made on the essential drugs useful in the control of epilepsy with special reference to developing countries and in the context of economics and ready availability. Grand mal and focal epilepsies could be controlled by phenobarbitone, with phenytoin, sulthiame and carbamazepine kept as reserves or adjuncts. Minor (generalised) epilepsies could be controlled by ethosuximide, with clonazepam and sodium valproate (sodium dipropylacetate) as reserve drugs and adjuncts. For status epilepticus, diazepam is effective and readily available, with clonazepam and phenytoin as alternatives. 4. The problems in the management of epilepsy in the developing countries include lack of facilities and personnel to ensure accurate diagnosis and treatment, inadequate supply or non-availability of drugs, high defaulting rate of patients, the adverse and often pernicious social stigmatisation of the epileptic. 5. Possible solutions to some of these problems include integration of management (in simple terms) of convulsive disorders into the basic health system of delivery of health care in developing countries, aggressive pursuit of health education of the public by governmental and non-governmental agencies, active, intensive and sustained promotion of training of health personnel in clinical neurosciences and research aimed at producing long-acting anticonvulsants.
Africa↗
A porcine spectral assay library to quantify brain proteome by DIA-MS.
Neurological disorders are the leading cause of health loss worldwide. The growing number of patients suffering from such conditions calls for improved strategies for their prevention, diagnosis, and therapy. To better understand human pathologies, relevant models and methodologies must be made available. In this study, we focused on a biomedical model capable of recapitulating the complexity of human pathology, the pig (Sus scrofa). Brain tissue and cerebrospinal fluid samples from a transgenic minipig model of Huntington's disease were subjected to multiple extraction and fractionation steps. A proteomic mass spectrometry (MS) methodology then allowed the generation of a porcine spectral library for 8,321 proteins. Using data-independent acquisition (DIA), we demonstrated that our porcine spectral library substantially enhanced the quantitative potential of this untargeted MS approach, generating reproducible proteome-wide data. The porcine library also provides a comprehensive resource for the development of targeted MS assays, enabling the quantification of selected proteins with a key role not only in neuroscience.
Animals↗
Controlling influences of the autonomic nervous system.
Recent information about the localization of sympathetic nerves and catecholamine-containing cells suggests sites of action not usually described in the neuroscience textbooks. In this study, we focused on the autonomic controls that affect ganglia, heart, gut, and chemoreceptors. As a result of some speculation derived mainly from histochemical observations and partially from physiologic data, we concluded that at the organ level the interplay between a nerve terminal-receptor serves as a local control. Additional controls may function at the ganglion level where catecholamine-containing chromaffin cells may serve as interneurons. We suggest that all peripheral catecholamine-containing elements which function in a modulatory role are not vital to the survival of the individual but rather serve as "fine tune" adjustment that do not involve the central nervous system.
Adrenal Medulla↗
Fetal signatures in the 3D genome of iPSC-derived neurons and their implications for disease modeling.
Induced pluripotent stem cells (iPSCs) have revolutionized neuroscience, providing an approach to generate patient-specific neurons for modeling of neurological diseases. However, it remains unclear how closely iPSC-derived neurons replicate the chromatin architecture of authentic brain neurons. Here, we uniformly processed newly generated Hi-C data from iPSC-derived neurons and neurons isolated from the human postmortem brain, together with previously published data sets comprising 228 human and 89 mouse Hi-C and snm3C-seq samples from different cell subtypes. These data were merged into 96 high-coverage contact maps used to examine chromatin features ranging from chromatin compartments and topologically associating domains (TADs) to chromatin loops, Polycomb-mediated contacts, and frequently interacting regions (FIREs). We find that iPSC-derived neurons largely retain the chromatin state of undifferentiated cells and resemble fetal rather than mature neurons. iPSC-derived neurons exhibit unusually strong compartmentalization, an enrichment of developmental genes at TAD borders, and a marked reduction of long-range repressive Polycomb-mediated contacts that typically silence early fetal programs. Although immature, iPSC-derived neurons offer advantages for modeling interactions between disease-associated SNPs and target genes, as many psychiatric disorders have neurodevelopmental origins. Integrating iPSC-derived and postmortem neuronal data sets therefore provides complementary insights into the chromatin landscape underlying disease-associated interactions. Our study offers a valuable Hi-C resource for the community and provides a detailed comparison of chromatin architecture throughout neuronal maturation, underscoring its importance for validating neuronal models and providing a robust framework for future studies.
Journal Article↗
The limbic system: a review of its empirical foundation.
The concept of the limbic system is highly influential in many areas of the neurosciences and in their applications to clinical medicine. The value of this concept has been questioned, denied, and defended several times in the past but a comprehensive critical evaluation has never been published. In this article we take several approaches to analyse empirical data of relevance to the limbic system. First we delineate its factual application in different areas. The limbic system has a very wide scope and divergent use. Secondly we extract criteria for its definition from research literature using the bibliographic database Medline. The limbic system has been defined variously on a number of different descriptive levels from morphology to behaviour. Thirdly we review its empirical foundations comparing evidence from different sources. The limbic system lacks an adequate empirical definition in spite of numerous efforts. Last we evaluate its construction as a scientific concept from empirical facts. The limbic system is a non-empirical explanatory concept for poorly understood brain functions. We conclude that the concept of the limbic system cannot be accepted on empirical grounds. However, it is a very attractive concept in the search for explanation of brain function. The non-empirical contents of the limbic system remains largely unexplored.
Animals↗
Immune dysregulation in depression and psychosis: summary of current evidence and future perspectives.
Despite compelling epidemiological, genetic and cellular evidence linking immune dysregulation to depression and schizophrenia (and other psychotic disorders), causality remains contested and no immune biomarker has yet demonstrated robust clinical utility. Emerging methodological approaches - from target trial emulation on observational data to functional genomics - offer a potential path towards precision immunopsychiatry and stratified immunomodulatory treatment.
Neuroimmunology↗
A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens.
High-resolution posture tracking of C. elegans has applications in genetics, neuroscience, and drug screening. While classic methods can reliably track isolated worms on uniform backgrounds, they fail when worms overlap, coil, or move in complex environments. Model-based tracking and deep learning approaches have addressed these issues to an extent, but there is still significant room for improvement in tracking crawling worms. Here we train a version of the DeepTangle algorithm developed for swimming worms using a combination of data derived from Tierpsy tracker and hand-annotated data for more difficult cases. DeepTangleCrawl (DTC) outperforms existing methods, reducing failure rates and producing more continuous, gap-free worm trajectories that are less likely to be interrupted by collisions between worms or self-intersecting postures (coils). We show that DTC enables the analysis of previously inaccessible behaviours and increases the signal-to-noise ratio in phenotypic screens, even for data that was specifically collected to be compatible with legacy trackers including low worm density and thin bacterial lawns. DTC broadens the applicability of high-throughput worm imaging to more complex behaviours that involve worm-worm interactions and more naturalistic environments including thicker bacterial lawns.
Caenorhabditis elegans↗
Metabotropic glutamate receptor agonists potentiate a slow afterdepolarization in CNS neurons.
We have previously reported that, in the rat dorsolateral septal nucleus (DLSN), metabotropic glutamate receptor (met-GluR) agonists evoked a slow depolarization accompanied by an increase in membrane conductance and burst firing. We have speculated that the burst firing elicited by met-GluR agonists may be due to activation or enhancement of a non-specific cation current, which exists in some DLSN neurons. Now we report that a slow afterdepolarization (sADP) mediated by a non-specific cation current was potentiated by both 1S,3R-ACPD and quisqualate. In addition, met-GluR agonists unmask a sADP in DLSN neurons which did not show a sADP under control conditions. Our data suggest that a non-specific cation current can be potentiated by activation of the met-GluR.
6-Cyano-7-nitroquinoxaline-2,3-dione↗
The cellular associates of late life changes in white matter microstructure.
The microstructural architecture of white matter supporting information flow across local circuits and large-scale networks changes throughout the lifespan. However, the genetic and cellular factors underlying age-related variations in white matter microstructure have yet to be established. Here, we examined the genetic associates of individual differences in diffusion-based measures of white matter in a population-based cohort (N=29,862) from the UK Biobank. Estimates of heritability from Genome-Wide Association Study (GWAS) data revealed that genetic factors are linked to population variability in 96.1% of 432 tract microstructural measures. The presence of shared genetic influences was observed to be greater within, relative to between, broad tract classes (commissural, association, projection, and complex cerebellar). Age associations with microstructural changes were estimated across diffusivity measures, with association class tracts showing the greatest vulnerability to age-related decline in older adults. Analyses of imputed cellular associates of age-related changes in white matter revealed a preferential relationship with cell gene markers of oligodendrocytes and other glial cell types, with sparse relationships observed for inhibitory and excitatory cells. These data indicate that white matter tract microstructure is shaped by genetic factors and suggest a role for glial cell-related transcripts in late-life changes in the structural wiring properties of the human brain.
Aging↗
The role of inhibitory amino acids in control of respiratory motor output in an arterially perfused rat.
The respiratory effects of drugs affecting GABAergic and glycinergic transmission were examined in order to assess the role of synaptic inhibition in breathing rhythmogenesis. Experiments were performed in the arterially perfused in situ brainstem-spinal cord preparation from adult rats (Hayashi et al., 1991, J. Neurosci. Meth. 36:63-70). Administration to the perfusate of agonists of GABAA, GABAB, and glycine receptors reduced both the frequency and amplitude of the activity recorded from the phrenic and hypoglossal nerves. Similar effects were observed following the infusion of aminooxyacetic acid (a blocker of GABA-transaminase). Picrotoxin (0.1-2 microM), bicuculline (0.05-0.2 microM), strychnine (0.1-1 microM) and phaclofen (0.1-0.2 mM) usually increased the frequency and amplitude of inspiratory bursts. Perfusion with low Cl- (8 mM) solution elicited tonic discharge followed by reversible arrest of the respiratory activity. It is concluded that synaptic inhibition is involved in the respiratory rhythm generation process in the mature mammalian brain. As data from the literature indicate that interference with central inhibitory processes does not largely affect the rhythm generation process in newborn rats, a possibility is discussed that the brainstem respiratory generator undergoes a developmental change from a 'pacemaker' driven circuit at the neonatal stage to a network requiring post-synaptic inhibition in the mature brain.
Amino Acids↗