rudyvdbrink/CitationDatabase huggingface dataset:
SimpylCellCounter: an automated solution for quantifying cells in brain tissue.
Scientific reports, 2020

Manual quantification of activated cells can provide valuable information about stimuli-induced changes within brain regions; however, this analysis remains time intensive. Therefore, we created SimpylCellCounter (SCC), an automated method to quantify cells that express cFos protein, an index of neuronal activity, in brain tissue and benchmarked it against two widely-used methods: OpenColonyFormingUnit (OCFU) and ImageJ Edge Detection Macro (IMJM). In Experiment 1, manually-obtained cell counts were compared to those detected via OCFU, IMJM and SCC. The absolute error in counts (manual versus automated method) was calculated and error types were categorized as false positives or negatives. In Experiment 2, performance analytics of OCFU, IMJM and SCC were compared. In Experiment 3, SCC analysis was conducted on images it was not trained on, to assess its general utility. We found SCC to be highly accurate and efficient in quantifying cells with circular morphologies that expressed cFos. Additionally, SCC utilized a new approach to count overlapping cells with a pretrained convolutional neural network classifier. The current study demonstrates that SCC is a novel, automated tool to quantify cells in brain tissue and complements current, open-sourced methods designed to detect cells in vitro.
Online Liver Imaging Course; Pivoting to Transform Radiology Education During the SARS-CoV-2 Pandemic.
Academic radiology, 2021

The SARS-CoV-2 pandemic has drastically disrupted radiology in-person education. The purpose of this study was to assess the implementation of a virtual teaching method using available technology and its role in the continuity of education of practicing radiologists and trainees during the pandemic.
Clivus chordoma in continuity with a large pontine cyst.
Skull base : official journal of North American Skull Base Society ... [et al.], 2009

Chordomas are tumors commonly of extradural origin associated with bone destruction; their central nervous system invasion has rarely been reported. The authors describe a rare case of a 37-year-old man presenting with a clivial chordoma invading the brainstem with a large pontine cyst. A median suboccipital approach was selected to remove the tumor.
Kappa Index Versus CSF Oligoclonal Bands in Predicting Multiple Sclerosis and Infectious/Inflammatory CNS Disorders.
Diagnostics (Basel, Switzerland), 2020

Cerebrospinal fluid (CSF) kappa free light chains (KFLC) are gaining increasing interest as markers of intrathecal immunoglobulin synthesis. The main aim of this study was to assess the diagnostic accuracy (AUC) of the kappa index (CSF/serum KFLC divided by the CSF/serum albumin ratio) compared to CSF oligoclonal IgG bands (OCB) in predicting Multiple Sclerosis (MS) or a central nervous system infectious/inflammatory disorder (CNSID).
Persistent pain induces mood problems and memory loss by the involvement of cytokines, growth factors, and supraspinal glial cells.
Brain, behavior, & immunity - health, 2020

Lesions of peripheral nerves lead to pain, hyperalgesia, and psychological comorbidities. However, the relationship between mood disorders and neuropathic pain is unclear, as well as the underlying mechanisms related to these disorders. Therefore, we investigated if nerve injury induces depression, anxiety, and cognitive impairment and if there were changes in cytokines, growth factors, and glial cell activation in cortical sites involved in processing pain and mood in animals with nerve injury. Nerve injury was induced by partial sciatic nerve ligation (PSNL) in male Swiss mice and compared to sham-operated animals. Nociceptive behavioral tests to mechanical and thermal (heat and cold) stimuli confirmed the development of hyperalgesia. We further examined mood disorders and memory behaviors. We show nerve injury induces a decrease in mechanical withdrawal thresholds and thermal latency to heat and cold. We also show that nerve injury causes depressive-like and anxiety-like behaviors as well as impairment in short-term memory in mice. There were increases in proinflammatory cytokines as well as Brain-Derived Neurotrophic Factor (BDNF) in the injured nerve. In the spinal cord, there were increases in both pro and anti-inflammatory cytokines, as well as of BDNF and Nerve Growth Factor (NGF). Further, in our data was a decrease in the density of microglia and astrocytes in the hippocampus and increased microglial density in the prefrontal cortex, areas associated with neuropathic pain conditions.
Global opioid agonist treatment: a review of clinical practices by country.
Addiction (Abingdon, England), 2020

We assessed how opioid agonist treatment (OAT) for opioid use disorder (OUD), specifically methadone and buprenorphine, including buprenorphine-naloxone, is delivered in routine clinical practice, with a focus on factors that affect access to and delivery of these services. The aims of this review were to summarize eligibility criteria for entry to OAT, doses in routine clinical practice, access to and eligibility for unsupervised dosing and urine drug screening practices in OAT programs globally.
Gene Chips: Applications to Neuroscience.
The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry, 2000

A convergence between molecular biological technique and the technology of miniaturization has produced the "gene chip" or microhybridization array. This device multiplies by several thousand fold the power of the northern blot for studying gene expression. Now, it is possible to survey simultaneously a large fraction of all genes in an experimental organism, and within a few years all of the approximately 140,000 human genes will be within reach of the technique. This capability is not only accelerating the rate of research into gene expression and function, it is changing the perspective of inquiry from single genes in isolation to networks of genes operating as a system. Many neurological diseases, from hydrocephalus to schizophrenia, have a genetic component, and individual responses to therapeutic drugs can vary with the genetic background of patients. In neurology and neurobiology, the ability to obtain "gene expression profiles" from nervous tissue promises to illuminate interactions between neuronal genes and the environment, development, disease, aging, and response to drugs and injury.
Concomitant LATE-NC in Alzheimer's disease is not associated with increased tau or amyloid-β pathological burden.
Neuropathology and applied neurobiology, 2020

Limbic-predominant age-related TDP-43 encephalopathy neuropathological change (LATE-NC) is present in approximately 50% of Alzheimer's disease (AD) cases and is associated with accelerated cognitive decline. Studies indicate a potential synergistic relationship between LATE-NC and hyperphosphorylated tau. It is unknown if LATE-NC is an independent driver of cognitive impairment or exerts its influence through synergistic relationships with tau. This cliniconeuropathological study investigated the impact of LATE-NC on quantified measures of AD-associated pathology and its impact on clinical measures.
Delayed Management of Zollinger-Ellison Syndrome in a Noncompliant Patient.
Cureus, 2020

We present a case of a 60-year-old male diagnosed with Zollinger-Ellison syndrome (ZES) after a protracted multicentric workup for chronic diarrhea and unexplained weight loss. ZES is intrinsically difficult to diagnose due to nonspecific symptoms, which are mimicked by other more frequent pathologies, such as peptic ulcer disease secondary to Helicobacter pylori or nonsteroidal anti-inflammatory drugs. The diagnostic challenge can be further complicated by patient noncompliance, resulting in delayed management and unnecessary health care. In our case report, the patient did not adhere to the care plan preceding endoscopy and failed to maintain communication with the treating doctor. As a result, crucial information was missing, and establishing the diagnosis of ZES took six months. Delay in appropriate management also contributed to poor disease course, heavy necrotic ulceration of the duodenum and proximal jejunum that was discovered on repeat endoscopy.
1q21.1 distal copy number variants are associated with cerebral and cognitive alterations in humans.
Translational psychiatry, 2021

Low-frequency 1q21.1 distal deletion and duplication copy number variant (CNV) carriers are predisposed to multiple neurodevelopmental disorders, including schizophrenia, autism and intellectual disability. Human carriers display a high prevalence of micro- and macrocephaly in deletion and duplication carriers, respectively. The underlying brain structural diversity remains largely unknown. We systematically called CNVs in 38 cohorts from the large-scale ENIGMA-CNV collaboration and the UK Biobank and identified 28 1q21.1 distal deletion and 22 duplication carriers and 37,088 non-carriers (48% male) derived from 15 distinct magnetic resonance imaging scanner sites. With standardized methods, we compared subcortical and cortical brain measures (all) and cognitive performance (UK Biobank only) between carrier groups also testing for mediation of brain structure on cognition. We identified positive dosage effects of copy number on intracranial volume (ICV) and total cortical surface area, with the largest effects in frontal and cingulate cortices, and negative dosage effects on caudate and hippocampal volumes. The carriers displayed distinct cognitive deficit profiles in cognitive tasks from the UK Biobank with intermediate decreases in duplication carriers and somewhat larger in deletion carriers-the latter potentially mediated by ICV or cortical surface area. These results shed light on pathobiological mechanisms of neurodevelopmental disorders, by demonstrating gene dose effect on specific brain structures and effect on cognitive function.
Alpha-synuclein: between synaptic function and dysfunction.
Histology and histopathology, 2003

Alpha-synuclein belongs to a family of vertebrate proteins, encoded by three different genes: alpha, ss, and gamma. The protein has become of interest to the neuroscience community in the last few years after the discovery that a mutation in the alpha-synuclein gene is associated with familial autosomal-dominant early-onset forms of Parkinson Disease. However, it is not yet clear how the protein is involved in the disease. Several studies have suggested that alpha-synuclein plays a role in neurotransmitter release and synaptic plasticity. This hypothesis might help elucidate how alpha-synuclein malfunctioning contributes to the development of a series of disorders known as synucleinopathies.
Early maternal separation and chronic variable stress as adults differentially affect Fos expression in the anterodorsal thalami nuclei.
The International journal of neuroscience, 2008

The present study examined the participation of the anterodorsal thalamic nuclei (ADTN) in mediating the long-term effects of early maternal separation on the stress/hypothalamic-pituitary-adrenal axis response of adult animals. The study measured Fos and glucocorticoid receptor immunoreactivity (GR-ir) in the ADTN of maternally separated female rats subsequently exposed to variable chronic stress. Maternal separation increased the number of neurons immunoreactive to Fos in the ADTN of chronically stressed adult rats. GR-ir was absent in the ADTN. Linking these results with previous endocrine evidence led the authors to propose a dual role of these nuclei. Maternal separation and chronic stress enhance the neuronal activity of the ADTN, nevertheless it is not regulated, at least directly, via GR.
Developing Guidelines for the Reversal of Anticoagulant and Antithrombotic Agents in the Setting of Intracranial Hemorrhage.
The Journal of neuroscience nursing : journal of the American Association of Neuroscience Nurses, 2016

The use of anticoagulants and antithrombotic agents in the population is increasing as the population ages with a concomitant rise in chronic diseases such as atrial fibrillation. The incidence of intracranial hemorrhage (ICH) with these agents is small but clinically significant. The purpose of this article is to illustrate how a single institution developed anticoagulation-associated ICH treatment guidelines.
How the humble insect brain became a powerful experimental model system.
Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology, 2017

In the 21st century, neurobiological studies focused on the insect brain are revealing unprecedented insight into the molecular, cellular, developmental, and circuit aspects of brain organization and function, notably in the genetic model system of Drosophila melanogaster. Underlying this accelerating progress in understanding the insect brain is a century-long history of ground breaking experimental investigation, methodological advance, and conceptual insight catalyzed by the integration of two emerging research fields, neuroscience and genetics. This review traces some of the key early steps in this remarkable historical scientific adventure of exploring the brain of "these apparently humble representatives of life".
Feasibility and preliminary effectiveness of an online training and support program for caregivers of people with dementia in India: a randomized controlled trial.
International journal of geriatric psychiatry, 2021

Internet-based interventions involving elements of cognitive behavior therapy, psychoeducation, relaxation and skills training for caregivers of people with dementia have been found to be promising in Western countries. Given these outcomes, the adapted version of a multi-component online caregiver skills training and support program of the World Health Organization, called iSupport, was tested for feasibility and preliminary effectiveness in India.
Neuroanatomical, neurochemical, and neurodevelopmental basis of obsessive-compulsive symptoms in schizophrenia.
Indian journal of psychological medicine, 2009

The prevalence of the obsessive-compulsive symptoms in schizophrenia (OCSS) appears to be higher than that expected on the basis of comorbidity rates. Review of brain abnormalities in schizophrenia and obsessive-compulsive disorder (OCD) reveals involvement of similar regions namely the frontal lobe, the basal ganglia, the thalamus, and the cerebellum, in both the disorders. Neurodevelopmental etiopathogenesis has been proposed to explain schizophrenia as well as OCD. Significant overlap in neurotransmitter dysfunction (serotonin, glutamate, and dopamine) has been documented between schizophrenia and OCD. The New-onset obsessive-compulsive (OC) symptoms have been reported with the use of atypical antipsychotics in the schizophrenia patients In this background, OCSS is an emerging area of recent interests. This article attempts to review the literature on the neurobiology of OCSS. Neuroimaging, neuropsychological, and neuromotor abnormalities in OCSS discussed in the context of neurodevelopmental etiopathogenesis suggest glutamate abnormalities in OCSS. Atypical antipsychotic induced OCSS points towards the possible roles of glutamate and serotonin. Dopamine may be responsible for the beneficial role of antipsychotics in the treatment of OCD. In summary, we propose that glutamate, serotonin, and dopamine abnormalities may be the probable basis for OCSS.
The technical reasoning hypothesis does not rule out the potential key roles of imitation and working memory for CTC.
The Behavioral and brain sciences, 2020

To support their claim for technical reasoning skills rather than imitation as the key for cumulative technological culture (CTC), Osiurak and Reynaud argue that chimpanzees can imitate mechanical actions, but do not have CTC. They also state that an increase in working memory in human evolution could not have been a key driver of CTC. We discuss why we disagree with these claims.
Delayed administration of the human anti-RGMa monoclonal antibody elezanumab promotes functional recovery including spontaneous voiding after spinal cord injury in rats.
Neurobiology of disease, 2020

Spinal cord injury (SCI) often results in permanent functional loss due to a series of degenerative events including cell death, axonal damage, and the upregulation of inhibitory proteins that impede regeneration. Repulsive Guidance Molecule A (RGMa) is a potent inhibitor of axonal growth that is rapidly upregulated following injury in both the rodent and human central nervous system (CNS). Previously, we showed that monoclonal antibodies that specifically block inhibitory RGMa signaling promote neuroprotective and regenerative effects when administered acutely in a clinically relevant rat model of thoracic SCI. However, it is unknown whether systemic administration of RGMa blocking antibodies are effective for SCI after delayed administration. Here, we administered elezanumab, a human monoclonal antibody targeting RGMa, intravenously either acutely or at 3 h or 24 h following thoracic clip impact-compression SCI. Rats treated with elezanumab acutely and at 3 h post-injury showed improvements in overground locomotion and fine motor function and gait. Rats treated 24 h post-SCI trended towards better recovery demonstrating significantly greater stride length and swing speed. Treated rats also showed greater tissue preservation with reduced lesion areas. As seen with acute treatment, delayed administration of elezanumab at 3 h post-SCI also increased perilesional neuronal sparing and serotonergic and corticospinal axonal plasticity. In addition, all elezanumab treated rats showed earlier spontaneous voiding ability and less post-trauma bladder wall hypertrophy. Together, our data demonstrate the therapeutic efficacy of delayed systemic administration of elezanumab in a rat model of SCI, and uncovers a new role for RGMa inhibition in bladder recovery following SCI.
U-shape short-range extrinsic connectivity organisation around the human central sulcus.
Brain structure & function, 2021

The central sulcus is probably one of the most studied folds in the human brain, owing to its clear relationship with primary sensory-motor functional areas. However, due to the difficulty of estimating the trajectories of the U-shape fibres from diffusion MRI, the short structural connectivity of this sulcus remains relatively unknown. In this context, we studied the spatial organization of these U-shape fibres along the central sulcus. Based on high quality diffusion MRI data of 100 right-handed subjects and state-of-the-art pre-processing pipeline, we first define a connectivity space that provides a comprehensive and continuous description of the short-range anatomical connectivity around the central sulcus at both the individual and group levels. We then infer the presence of five major U-shape fibre bundles at the group level in both hemispheres by applying unsupervised clustering in the connectivity space. We propose a quantitative investigation of their position and number of streamlines as a function of hemisphere, sex and functional scores such as handedness and manual dexterity. Main findings of this study are twofold: a description of U-shape short-range connectivity along the central sulcus at group level and the evidence of a significant relationship between the position of three hand related U-shape fibre bundles and the handedness score of subjects.
Joint Bayesian Estimation of Voxel Activation and Inter-regional Connectivity in fMRI Experiments.
Psychometrika, 2020

Brain activation and connectivity analyses in task-based functional magnetic resonance imaging (fMRI) experiments with multiple subjects are currently at the forefront of data-driven neuroscience. In such experiments, interest often lies in understanding activation of brain voxels due to external stimuli and strong association or connectivity between the measurements on a set of pre-specified groups of brain voxels, also known as regions of interest (ROI). This article proposes a joint Bayesian additive mixed modeling framework that simultaneously assesses brain activation and connectivity patterns from multiple subjects. In particular, fMRI measurements from each individual obtained in the form of a multi-dimensional array/tensor at each time are regressed on functions of the stimuli. We impose a low-rank parallel factorization decomposition on the tensor regression coefficients corresponding to the stimuli to achieve parsimony. Multiway stick-breaking shrinkage priors are employed to infer activation patterns and associated uncertainties in each voxel. Further, the model introduces region-specific random effects which are jointly modeled with a Bayesian Gaussian graphical prior to account for the connectivity among pairs of ROIs. Empirical investigations under various simulation studies demonstrate the effectiveness of the method as a tool to simultaneously assess brain activation and connectivity. The method is then applied to a multi-subject fMRI dataset from a balloon-analog risk-taking experiment, showing the effectiveness of the model in providing interpretable joint inference on voxel-level activations and inter-regional connectivity associated with how the brain processes risk. The proposed method is also validated through simulation studies and comparisons to other methods used within the neuroscience community.
In vivo microstimulation with cathodic and anodic asymmetric waveforms modulates spatiotemporal calcium dynamics in cortical neuropil and pyramidal neurons of male mice.
Journal of neuroscience research, 2020

Electrical stimulation has been critical in the development of an understanding of brain function and disease. Despite its widespread use and obvious clinical potential, the mechanisms governing stimulation in the cortex remain largely unexplored in the context of pulse parameters. Modeling studies have suggested that modulation of stimulation pulse waveform may be able to control the probability of neuronal activation to selectively stimulate either cell bodies or passing fibers depending on the leading polarity. Thus, asymmetric waveforms with equal charge per phase (i.e., increasing the leading phase duration and proportionately decreasing the amplitude) may be able to activate a more spatially localized or distributed population of neurons if the leading phase is cathodic or anodic, respectively. Here, we use two-photon and mesoscale calcium imaging of GCaMP6s expressed in excitatory pyramidal neurons of male mice to investigate the role of pulse polarity and waveform asymmetry on the spatiotemporal properties of direct neuronal activation with 10-Hz electrical stimulation. We demonstrate that increasing cathodic asymmetry effectively reduces neuronal activation and results in a more spatially localized subpopulation of activated neurons without sacrificing the density of activated neurons around the electrode. Conversely, increasing anodic asymmetry increases the spatial spread of activation and highly resembles spatiotemporal calcium activity induced by conventional symmetric cathodic stimulation. These results suggest that stimulation polarity and asymmetry can be used to modulate the spatiotemporal dynamics of neuronal activity thus increasing the effective parameter space of electrical stimulation to restore sensation and study circuit dynamics.