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PubMed2026

ARISE: RNA-anchored shared-edge topology and hierarchical fusion for spatial multi-omics integration.

MOTIVATION: Spatial multi-omics technologies jointly profile transcriptomes, proteins and chromatin accessibility in situ, enabling integrative analysis of tissue organization across molecular layers. However, most existing graph-based integration methods rely on independently constructed modality-specific k-nearest-neighbor graphs. When auxiliary modalities are sparse or noisy, these graphs can become topologically discordant, propagate spurious edges, weaken cross-modal alignment, and reduce spatial domain resolution. RESULTS: We present Anchored RNA for Integrated Spatial Embedding (ARISE), an RNA expression anchored framework for spatial multi-omics integration. ARISE defines a shared-edge topology by intersecting RNA feature-similarity and spatial-proximity graphs, encodes auxiliary modalities on this common scaffold, and integrates them through inside-out hierarchical fusion. We further show theoretically that graph intersection minimizes false-positive edges within a broad class of k-of-r graph fusion rules, providing a principled basis for topology anchoring. Across various spatial multi-omics benchmarks spanning simulated and real datasets in bi-modal and tri-modal settings, ARISE improves spatial domain identification, cross-modal consistency, and preservation of tissue structure relative to existing methods. Furthermore, the learned representation supports biologically meaningful downstream analyses, including marker-based domain annotation, pathway enrichment, and cis-regulatory inference, indicating that ARISE yields a robust and interpretable framework for spatial multi-omics integration. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/XiangxiangWang-code/ARISE. The archived version used in this study is available at https://doi.org/10.6084/m9.figshare.32686137.v2.

Multiomics↗

PubMed2002

Repeated administration of the neurotensin analogue NT69L induces tolerance to its suppressant effect on conditioned avoidance behaviour.

Although acute neurotensin receptor stimulation exerts diverse behavioural effects that resemble those seen after administration of antipsychotic drugs, data on effects after repeated exposure to neurotensin receptor agonism is relatively sparse. Here, we demonstrate that repeated administration of the novel neurotensin-(8-13) analogue NT69L [(N-methyl-Arg), Lys, Pro, L-neo-Trp, tert-Leu, Leu] induce tolerance to its suppressant effect on conditioned avoidance behaviour in rats, a predictive assay for antipsychotic activity. In contrast, the inhibitory effect of haloperidol on this behaviour was sustained despite repeated administration of this classical antipsychotic drug. These findings indicate that repeated exposure to neurotensin receptor stimulation induces tolerance to the antipsychotic-like effects of neurotensin receptor agonists.

Animals↗

PubMed2002

Further evidence for the depressive effects of cytokines: anhedonia and neurochemical changes.

Although human studies have emphasized a role for IL-2 in depressive illness, limited attention has been devoted to the behavioral and neurochemical effects of this cytokine in animal studies. The present review assesses the behavioral effects of IL-2 in rodents, in counterpoint to the effects of interleukin-1beta (IL-1beta), necrosis factor-alpha (TNF-alpha) and endotoxin challenge. Unlike IL-1beta, systemic IL-2 provokes modest effects on hypothalamic-pituitary-adrenal (HPA) functioning, and does not provoke marked signs of illness or anxiety. In some respects, however, IL-2 elicits effects reminiscent of traditional stressors, including anhedonia (diminished pleasure gained from otherwise rewarding stimuli). Additionally, when chronically administered, IL-2 may impact on cognitive processes, including spatial working memory. While IL-2 may induce depressive-like symptoms, the available data are sparse, have hardly considered the impact of chronic cytokine treatment, only assessed behavior in a narrow range of tests, and it remains to be established whether the effects of IL-2 are modifiable by antidepressant treatments. Finally, as the effects of IL-2 on CNS processes vary in a biphasic fashion, and may also engender neurotoxic effects, further analyses are necessary to discern under what conditions this cytokine provokes depressive-like behavioral outcomes.

Adrenocorticotropic Hormone↗

PubMed1998

First- and second-order motion perception in Gabor micropattern stimuli: psychophysics and computational modelling.

This paper examines the perception of first- and second-order motion in human vision. In an extension of previous work by Boulton and Baker [J.B. Boulton, C.L. Baker, Motion detection is dependent on spatial frequency not size, Vision Res., 31 (1991) 77-87; J.B. Boulton, C.L. Baker, Different parameters control motion perception above and below a critical density, Vision Res., 33 (1993) 1803-1811], the direction of two-frame apparent motion is measured for stimuli composed of Gabor or Gaussian micropatterns. Three conditions are investigated. Condition 1 is that used by Boulton and Baker, in which motion is defined by the displacement of Gabor micropatterns. In condition 2, motion is defined by the displacement of Gaussian micropatterns. In condition 3, the envelopes of Gabor micropatterns are displaced while their carriers remain static. Using sparsely distributed micropatterns, direction judgements in all three conditions are determined by the spacing of the micropatterns. With a dense stimulus, direction judgements vary as a function of displacement in qualitatively different ways for the three conditions. The psychophysical results are predicted by a two-channel computational model. In one channel, motion is calculated directly from stimulus luminance, while in the other it is preceded by a texture-grabbing operation. The relative activities of the two channels dictates which governs direction judgements for any given stimulus.

Computer Simulation↗

PubMed1998

The neuropathology of adult HIV infection.

Since the onset of the acquired immune deficiency syndrome (AIDS) epidemic fifteen years ago, much has been learned about the effects of the human immunodeficiency virus (HIV) in the nervous system. This review summarizes the pathology findings in the central nervous system (CNS). There is now abundant evidence that HIV can infect the CNS directly, leading to a characteristic HIV encephalitis (HIVE) which occurs in 10-50 p. 100 of AIDS autopsy series. Multinucleated giant cells are the pathognomonic feature of HIVE and are found predominantly in the central white matter and deep grey matter. Evidence of productive HIV infection in the CNS is confined to cells of the microglial/macrophage lineage, from which the giant cells are almost certainly derived. These cells are known to express both CD4 and beta-chemokine receptors, which act in conjunction to permit HIV entry. Restricted infection of astrocytes has also been identified by a variety of methods. HIVE is frequently associated with white matter damage ranging from inflammatory (microglia, macrophages and sparse lymphocytes) to degenerative (myelin loss and axonal damage) pathology. Although giant cells are seen less frequently in neocortical grey matter, significant neuronal loss has been established in a number of studies. Recent investigations using markers of apoptosis, (including TUNEL, Bcl-2 and BAX), have established the presence of DNA damage in some neurons and in other cell types. Axonal damage has also been confirmed by evidence of amyloid precursor protein expression. The CNS is also vulnerable to opportunistic infections and high grade B-cell lymphomas as a result of the immune suppression of advanced HIV infection. Cytomegalovirus (CMV) infection is reported in 10-30 p. 100 of AIDS cases at autopsy, toxoplasma in 10-25 p. 100, progressive multifocal leucoencephalopathy in about 5 p. 100 and lymphomas, usually primary, in up to 10 p. 100. A wide variety of other infections has also been reported. These may coexist with HIVE and may be difficult to diagnose in life. CMV gives rise to microglial nodular encephalitis, ventriculitis, necrotising encephalitis and myelo-radiculitis. Presymptomatic HIV positive patients do not show HIVE or opportunistic infections or lymphomas in the CNS. They frequently display a low-grade T-cell infiltrate in the leptomeninges and parenchyma, particularly around vessels. This lymphocytic infiltrate has been attributed to presumed early invasion of the CNS by HIV although the exact timing of entry is uncertain. It is possible that reported abnormalities in presymptomatic cases such as gliosis, microglial activation and rising proviral load may anticipate the onset of HIVE but most studies show that significant CNS damage and HIV-related pathology is confined to patients with AIDS. HIV-related pathology in the spinal cord includes not only HIV myelitis, opportunistic infections and lymphomas, but also vacuolar myelopathy (VM) which affects predominantly the dorsolateral white matter tracts. The cause of VM is not understood and has not been unequivocally linked with HIV infection. It is noted that none of these neuropathological features (including HIVE) correlates exactly with the clinical expression of AIDS-related dementia (ARD). The exact contribution of macrophage activation and cytokine release, astrocytic infection, neuronal loss and axonal damage to the neuropsychiatric syndromes of advanced HIV infection remain to be determined. While the current understanding of the pathogenesis of HIVE and ARD is beyond the scope of this review it is axiomatic that accurate documentation of neuropathology findings will help to resolve the outstanding dilemmas relating to HIV infection of the CNS. There is considerable optimism that progress in therapeutic regimes for HIV-infected patients will succeed in eliminating the virus from the blood and from lymphoid tissue. (ABSTRACT TRUNCATED)

AIDS-Related Opportunistic Infections↗

PubMed1996

Practitioner review: developmental language disorders: a clinical update.

Non-specialists can identify three types of developmental language disorder. (1) mixed receptive/expressive disorders, which impair phonology, syntax, and semantics. Children who understand nothing are nonverbal, in others speech is sparse, nonfluent, poorly intelligible, and agrammatic; (2) expressive disorders with adequate comprehension affect phonologic production predominantly. Children with verbal dyspraxia, the most severe variant, may also be nonverbal but comprehend well; (3) higher order processing disorders affect semantics, pragmatics, and discourse. Semantics and pragmatics are invariably affected in preschool autistic children in whom isolated expressive deficits do not occur. Etiology of developmental language disorders is predominantly genetic. Structural brain lesions detectable by neuroimaging are exceptional. Severe receptive deficits require a sleep EEG to detect subclinical epilepsy. Early educational intervention is both critical and efficacious.

Autistic Disorder↗

PubMed2003

Representing spatial location and layout from sparse kinesthetic contacts.

Participants' fingers were guided to 2 locations on a table for 3 s, then back to the start. They reported distances and angles between the locations by (a) replacing 1 or 2 fingers, (b) translating the contacted configuration, or (c) estimating distance or angle alone. Distance error increased across these conditions. Angular error increased when the angular reference axis was rotated before the response. Replacing 1 finger was impaired by a change in posture from exposure to test. The results suggest a kinesthetic representation is used to replace the fingers, but to estimate distance and angle at new locations, a configural representation is computed. This presentation is oriented within an extrinsic reference frame and maintains shape more accurately than scale.

Adult↗

PubMed2000

Autotoxicity and Alzheimer disease.

I mmunological responses are considered to be either humoral, resulting from cloning of B lymphocytes, or cell mediated, resulting from cloning of T lymphocytes. Autoimmune diseases occur when the cloned products attack host tissue. Inflammation is considered a nonspecific response to injury, characterized by exudation of serum into damaged tissue, and identified by the cardinal signs of rubor, calor, dolor, and tumor. However, these classic mechanisms do not fit pathological observations of Alzheimer disease (AD)-affected brain tissue. Although many of the components prominently associated with peripheral immunological and inflammatory states are present in AD lesions, there are no identifiable B lymphocytes or antibodies, and T cells are sparse. Furthermore, the blood-brain barrier is intact, excluding exudation of exogenous serum proteins. Although "neuroinflammation" is the term commonly used to describe the pathological changes, it fails to define adequately the process that is taking place. The reaction is neither a nonspecific response to injury, as classically implied for inflammatory reactions, nor an autoimmune reaction, despite the directed attack against plaques and extracellular tangles. It is most appropriately defined as an innate immunoreaction. The fact that such a reaction can be mounted by brain, an organ frequently described as being immunologically privileged, suggests that a reevaluation is required of the dimensions of the innate immune system, including how it operates at the tissue level. The innate immune system is primitive, while the adaptive immune system, which is directed by peripheral immune organs, is an invention of vertebrates. Even in vertebrates, however, the innate immune system is the first line of defense. Much more needs to be learned about the operation of the innate immune system in health and disease. Arch Neurol. 2000.

Acute-Phase Proteins↗

PubMed1994

[Immunohistological study in Bruch's membrane of senescence accelerated mouse].

Age-related macular degeneration is one of the major causes of severe visual loss is elderly individuals. However, relatively little is known about its etiology. The disease may be associated with senescence. Ultrastructural and immunohistochemical studies on SAM (senescence accelerated mouse) eyes were carried out to learn details of aging changes in the retinal pigment epithelium (RPE) and Bruch's membrane. SAM P 1 mice aged 2, 10, 14 months were examined in this study. The eyes were analysed for type IV collagen and heparan sulfate proteoglycan (HSPG) by the avidin-biotin-peroxidase complexes (ABC) method and post-embeddig immunolocalization with colloidal gold. With the ABC method, the basement membranes of both the RPE and the choriocapillaris showed markedly positive staining when treated with anti-type IV collagen antibody and moderately positive staining when treated with anti-HSPG antibody. In ultrastructural immunolocalization, both basement membranes showed fairly heavy labeling in response to the antibodies to type IV collagen, and moderate labeling in response to the antibodies to HSPG. With aging, the thickness of the basement membrane of the choriocapillaris and gold particle labeling by the antibodies to type IV collagen increased. The gold particle labeling by the antibodies to HSPG increased slightly, but was distributed sparsely. These results showed the advancing process of senescence changes in Bruch's membrane.

Aging↗

PubMed2002

Cholinergic interneuron characteristics and nicotinic properties in the striatum.

The neostriatum (dorsal striatum) is composed of the caudate and putamen. The ventral striatum is the ventral conjunction of the caudate and putamen that merges into and includes the nucleus accumbens and striatal portions of the olfactory tubercle. About 2% of the striatal neurons are cholinergic. Most cholinergic neurons in the central nervous system make diffuse projections that sparsely innervate relatively broad areas. In the striatum, however, the cholinergic neurons are interneurons that provide very dense local innervation. The cholinergic interneurons provide an ongoing acetylcholine (ACh) signal by firing action potentials tonically at about 5 Hz. A high concentration of acetylcholinesterase in the striatum rapidly terminates the ACh signal, and thereby minimizes desensitization of nicotinic acetylcholine receptors. Among the many muscarinic and nicotinic striatal mechanisms, the ongoing nicotinic activity potently enhances dopamine release. This process is among those in the striatum that link the two extensive and dense local arbors of the cholinergic interneurons and dopaminergic afferent fibers. During a conditioned motor task, cholinergic interneurons respond with a pause in their tonic firing. It is reasonable to hypothesize that this pause in the cholinergic activity alters action potential dependent dopamine release. The correlated response of these two broad and dense neurotransmitter systems helps to coordinate the output of the striatum, and is likely to be an important process in sensorimotor planning and learning.

Acetylcholine↗

PubMed2006

Event-driven simulation scheme for spiking neural networks using lookup tables to characterize neuronal dynamics.

Nearly all neuronal information processing and interneuronal communication in the brain involves action potentials, or spikes, which drive the short-term synaptic dynamics of neurons, but also their long-term dynamics, via synaptic plasticity. In many brain structures, action potential activity is considered to be sparse. This sparseness of activity has been exploited to reduce the computational cost of large-scale network simulations, through the development of event-driven simulation schemes. However, existing event-driven simulations schemes use extremely simplified neuronal models. Here, we implement and evaluate critically an event-driven algorithm (ED-LUT) that uses precalculated look-up tables to characterize synaptic and neuronal dynamics. This approach enables the use of more complex (and realistic) neuronal models or data in representing the neurons, while retaining the advantage of high-speed simulation. We demonstrate the method's application for neurons containing exponential synaptic conductances, thereby implementing shunting inhibition, a phenomenon that is critical to cellular computation. We also introduce an improved two-stage event-queue algorithm, which allows the simulations to scale efficiently to highly connected networks with arbitrary propagation delays. Finally, the scheme readily accommodates implementation of synaptic plasticity mechanisms that depend on spike timing, enabling future simulations to explore issues of long-term learning and adaptation in large-scale networks.

Action Potentials↗

PubMed2000

Emergence of phase- and shift-invariant features by decomposition of natural images into independent feature subspaces.

Olshausen and Field (1996) applied the principle of independence maximization by sparse coding to extract features from natural images. This leads to the emergence of oriented linear filters that have simultaneous localization in space and in frequency, thus resembling Gabor functions and simple cell receptive fields. In this article, we show that the same principle of independence maximization can explain the emergence of phase- and shift-invariant features, similar to those found in complex cells. This new kind of emergence is obtained by maximizing the independence between norms of projections on linear subspaces (instead of the independence of simple linear filter outputs). The norms of the projections on such "independent feature subspaces" then indicate the values of invariant features.

Learning↗

PubMed1985

Characterization of hydroxyl radical-induced damage after sparsely and densely ionizing irradiation.

The extent of hydroxyl radical mediated cell inactivation was measured for a variety of particle beams ranging from 8.5 Me V/u neon ions to 570 Me V/u argon ions. In general, the fraction of the total radiosensitivity caused by OH decreases from close to 60 per cent at low ionization density or low linear energy transfer (low LET) to close to 25 per cent at high LET for aerobically irradiated mammalian cells. The extent of OH induced cell lethality can be explained in terms of LET infinity only for low energy or low atomic number particles where fragmentations and complicated track structures do not contaminate the characteristic particle LET. For example, at a calculated LET infinity of 100 ke V/micron, the OH mediated fraction of the total radiation damage is about 25 per cent for low energy carbon but close to 40 per cent for high energy carbon ions. For low energy charged nuclei of approximately the same energy, as the 5.4-13.4 MeV/u He, Li, C and Ne ions in this report, there is a predictable diminution of the OH mediated effect with increasing LET infinity; however, the biological effect cannot be predicted accurately from calculated LET infinity values for high energy particle irradiation, nor indeed from a variety of low energy charged particles of quite different energies (incident velocities). This illustrates the unsuitability of using LET as a unifying parameter, except under specific circumstances. As more is learned about the energy deposition for energized charged particles in terms of track structure (core and penumbra), it may be possible to characterize the radiobiological data with a better physical parameter than LET infinity.

Animals↗

PubMed2006

Hyperammonemia increases sensitivity to LPS.

Metabolic and cognitive alterations occur during hyperammonemia. Here, we report that chronic hyperammonemia also leads to increased sensitivity to LPS. Sparse-fur mice were challenged i.p. with LPS or saline control and then tested for motivation to investigate a novel juvenile over 24 h. Cytokine, ammonia, and urea concentration were quantified at the peak of sickness (2 h post injection). Chronic hyperammonemic Otc(spf-ash) mice displayed more pronounced and prolonged sickness behavior in response to LPS (P=0.02). LPS significantly (P<0.0001) increased plasma concentrations of TNFalpha, IL-1 beta, IL-6, IL-15, IL-9, IL-2, IL-1 alpha, IL-1 beta, Rantes, MIP1 alpha, MIP1 beta, MCP-1, KC, GM-CSF, G-CSF, Eotaxin, IL-13, and IL-12 in both wild type and Otc(spf-ash) mice. No significant genotype/treatment interactions (P>0.1) were detected for any cytokine. Adult Otc(spf-ash) mice (168+/-41 microM) had four times higher plasma ammonia compared to wild type mice (40 +/- 6 microM) (P=0.002). Two hours after LPS injection, plasma ammonia concentrations tended (P=0.08) to decrease in both wild type and Otc(spf-ash) mice. Learning and memory behaviors were assessed in mice under basal conditions to determine the impact of chronic hyperammonemia on cognition. Otc(spf-ash) mice performed significantly poorer in the two trial Y-maze (P=0.02) and the Morris water maze (P=0.001) than their littermate wild type controls. Taken together, these data indicate that chronic hyperammonemia results in impaired cognition and creates a state of LPS hypersensitivity.

Animals↗

PubMed1998

Structural and functional evolution of the basal ganglia in vertebrates.

While a basal ganglia with striatal and pallidal subdivisions is 1 clearly present in many extant anamniote species, this basal ganglia is cell sparse and receives only a relatively modest tegmental dopaminergic input and little if any cortical input. The major basal ganglia influence on motor functions in anamniotes appears to be exerted via output circuits to the tectum. In contrast, in modern mammals, birds, and reptiles (i.e., modern amniotes), the striatal and pallidal parts of the basal ganglia are very neuron-rich, both consist of the same basic populations of neurons in all amniotes, and the striatum receives abundant tegmental dopaminergic and cortical input. The functional circuitry of the basal ganglia also seems very similar in all amniotes, since the major basal ganglia influences on motor functions appear to be exerted via output circuits to both cerebral cortex and tectum in sauropsids (i.e., birds and reptiles) and mammals. The basal ganglia, output circuits to the cortex, however, appear to be considerably more developed in mammals than in birds and reptiles. The basal ganglia, thus, appears to have undergone a major elaboration during the evolutionary transition from amphibians to reptiles. This elaboration may have enabled amniotes to learn and/or execute a more sophisticated repertoire of behaviors and movements, and this ability may have been an important element of the successful adaptation of amniotes to a fully terrestrial habitat. The mammalian lineage appears, however, to have diverged somewhat from the sauropsid lineage with respect to the emergence of the cerebral cortex as the major target of the basal ganglia circuitry devoted to executing the basal ganglia-mediated control of movement.

Animals↗

PubMed1994

Dynamics of the CA3 pyramidal neuron autoassociative memory network in the hippocampus.

A theory for the dynamics of sparse associative memory has been applied to the CA3 pyramidal recurrent network in the hippocampus. The CA3 region is modelled as a network of pyramidal neurons randomly connected through their recurrent collaterals. Both the elliptical spread of the axonal systems and the exponential decrease in connectivity with distance are taken into account in estimating the connection probabilities. Pyramidal neurons also receive connections from inhibitory interneurons which occur in large numbers throughout the network; these in turn receive inputs from other inhibitory interneurons and from pyramidal neurons. These inhibitory neurons are modelled as rapidly acting linear devices which produce outputs proportional to their inputs; they perform an important regulatory function in the setting of the membrane potentials of the pyramidal neurons. The probability of a neuron firing in a stored memory, which determines the average number of neurons active when a memory is recalled, can be set at will. Memories are stored at the recurrent collateral synapses using a two-valued Hebbian. Allowance is made in the theory both for the spatial correlations between the learned strengths of the recurrent collateral synapses and temporal correlations between the state of the network and these synaptic strengths. The recall of a memory begins with the firing of a set of CA3 pyramidal neurons that overlap with the memory to be recalled as well as the firing of a set of pyramidal neurons not in the memory to be recalled; the firing of both sets of neurons is probably induced by synapses formed on CA3 neurons by perforant pathway axons. The firing of different sets of pyramidal neurons then evolves by discrete synchronous steps. The CA3 recurrent network is shown to retrieve memories under specific conditions of the setting of the membrane potential of the pyramidal neurons by inhibitory interneurons. The adjustable parameters in the theory have been assigned values in accord with the known physiology of the CA3 region. Certain levels of overlap between the input and the memory to be retrieved must also be satisfied for almost complete retrieval. The number of memories which can be stored and retrieved without degradation is primarily a function of the number of active neurons when a memory is recalled and the degree of connectivity in the network. The inhomogeneity in the connectivity of the pyramidal cells improves both capacity and overlap of the final state with the memory.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed2004

Evidence for patchwork approximation of shape primitives.

Investigators have proposed that qualitative shapes are the primitive information of spatial vision: They preserve an approximately one-to-one mapping between surfaces, images, and perception. Given their importance, we examined how the visual system recovers these primitives from sparse disparity fields that do not provide sufficient information for their recovery. We hypothesized that the visual system interpolates sparse disparities with planes, resulting in a patchwork approximation of the implicitly defined shapes. We presented observers with stereo displays simulating planar or smooth curved surfaces having different curvatures. The observers' task was to detect whether dots deviated from these surfaces or to discriminate planar from curved or planar from scrambled surfaces. Consistent with our hypothesis, increasing curvature had detrimental effects on observers' performance (Experiments 1-3). Importantly, this patchwork approximation leads to the recovery of the proposed shape primitives, since observers were more accurate at discriminating planar-from-curved than planar-from-scrambled surfaces with matched disparity range (Experiment 4).

Computer Graphics↗

PubMed2005

Examining rhythm and melody processing in young children using FMRI.

While it is often reported that musical experience can have positive effects on cognitive development in young children, the neural basis of such potential effects remains relatively unexplored. Employing functional magnetic resonance imaging (fMRI) for such research presents as many challenges as possibilities, not least of which is the fact that young children can find it difficult to remain still and attentive for long periods of time. Here we describe an fMRI scanning protocol designed specifically for young children using short scanning runs, a sparse temporal sampling data acquisition technique, simple rhythmic and melodic discrimination tasks with a button-press response, and a child-oriented preparation session. Children were recruited as part of a large-scale longitudinal study examining the effects of musical training on cognitive development and the structure and function of the growing brain. Results from an initial analysis of 33 children and from the first five children to be re-scanned after musical training indicate that our scanning protocol is successful and that activation differences can be detected both between conditions and over time.

Child↗