rudyvdbrink/CitationDatabase huggingface dataset:
Development and Comparative Evaluation of Endolysosomal Proximity Labeling-Based Proteomic Methods in Human iPSC-Derived Neurons.
Analytical chemistry, 2020

Proximity-based in situ labeling techniques offer a unique way to capture both stable and transient protein-protein and protein-organelle interactions. Combining this technology with mass spectrometry (MS)-based proteomics allows us to obtain snapshots of molecular microenvironments with nanometer resolution, facilitating the discovery of complex and dynamic protein networks. However, a number of technical challenges still exist, such as interferences from endogenously biotinylated proteins and other highly abundant bystanders, how to select the proper controls to minimize false discoveries, and experimental variations among biological/technical replicates. Here, we developed a new method to capture the proteomic microenvironment of the neuronal endolysosomal network by knocking in (KI) an engineered ascorbate peroxidase (APEX) gene to the endogenous locus of lysosome-associated membrane protein 1 (LAMP1). We found that normalizing proximity labeling proteomics data to the endogenously biotinylated protein (PCCA) can greatly reduce variations and enable fair comparisons among different batches of APEX labeling and different APEX probes. We conducted a comparative evaluation between this KI-LAMP1-APEX method and our two overexpression LAMP1-APEX probes, achieving complementary coverage of both known and new lysosomal membrane and lysosomal-interacting proteins in human iPSC-derived neurons. To summarize, this study demonstrated new analytical tools to characterize lysosomal functions and microenvironment in human neurons and filled critical gaps in the field for designing and optimizing proximity labeling proteomic experiments.
Deep imaging in the brainstem reveals functional heterogeneity in V2a neurons controlling locomotion.
Science advances, 2020

V2a neurons are a genetically defined cell class that forms a major excitatory descending pathway from the brainstem reticular formation to the spinal cord. Their activation has been linked to the termination of locomotor activity based on broad optogenetic manipulations. However, because of the difficulties involved in accessing brainstem structures for in vivo cell type-specific recordings, V2a neuron function has never been directly observed during natural behaviors. Here, we imaged the activity of V2a neurons using micro-endoscopy in freely moving mice. We find that as many as half of the V2a neurons are excited at locomotion arrest and with low reliability. Other V2a neurons are inhibited at locomotor arrests and/or activated during other behaviors such as locomotion initiation or stationary grooming. Our results establish that V2a neurons not only drive stops as suggested by bulk optogenetics but also are stratified into subpopulations that likely contribute to diverse motor patterns.
Reduced Inhibitory Inputs On Basolateral Amygdala Principal Neurons Following Long-Term Alcohol Consumption.
Neuroscience, 2021

Recent studies have shown that manipulating basolateral amygdala (BLA) activity can affect alcohol consumption, particularly following chronic and/or long-term intake. Although the mechanisms underlying these effects remain unclear, the BLA is highly sensitive to emotional stimuli including stress and anxiety. Negative emotional states facilitate alcohol craving and relapse in patients with alcohol use disorders. Consequently, the aim of this study was to determine the effect of long-term (10 weeks) alcohol drinking on synaptic activity in BLA principal neurons. We utilized an intermittent drinking paradigm in rats, which facilitated escalating, binge-like alcohol intake over the 10 week drinking period. We then recorded spontaneous excitatory and inhibitory postsynaptic currents of BLA principal neurons from long-term alcohol drinking rats and aged-matched water drinking controls. Excitatory postsynaptic current properties from long-term alcohol drinking rats were unchanged compared to those from age-matched water drinking controls. Conversely, we observed significant reductions of inhibitory postsynaptic current amplitude and frequency in long-term ethanol drinking rats compared to age-matched water drinking controls. These results highlight substantive decreases in basal inhibitory synaptic activity of BLA principal neurons following long-term alcohol consumption. A loss of inhibitory control in the BLA could explain the high incidence of compulsive drinking and stress- or anxiety-induced relapse in patients with alcohol use disorders.
Differentiating robotic behavior and artificial intelligence from animal behavior and biological intelligence: Testing structural accuracy.
The Behavioral and brain sciences, 2001

We emphasize the feature of Webb's presentation that bears most directly on contemporary research with real animals. Many neuroscience modelers erroneously conclude that a model that performs like an animal must have achieved this goal through processes analogous with those used by the animal. A simulation failure justifies rejecting a model, but success does not justify acceptance. However, an important benefit of models, successful or otherwise, is to stimulate new research.
Stimulus complexity shapes response correlations in primary visual cortex.
Proceedings of the National Academy of Sciences of the United States of America, 2019

Spike count correlations (SCCs) are ubiquitous in sensory cortices, are characterized by rich structure, and arise from structured internal dynamics. However, most theories of visual perception treat contributions of neurons to the representation of stimuli independently and focus on mean responses. Here, we argue that, in a functional model of visual perception, featuring probabilistic inference over a hierarchy of features, inferences about high-level features modulate inferences about low-level features ultimately introducing structured internal dynamics and patterns in SCCs. Specifically, high-level inferences for complex stimuli establish the local context in which neurons in the primary visual cortex (V1) interpret stimuli. Since the local context differentially affects multiple neurons, this conjecture predicts specific modulations in the fine structure of SCCs as stimulus identity and, more importantly, stimulus complexity varies. We designed experiments with natural and synthetic stimuli to measure the fine structure of SCCs in V1 of awake behaving macaques and assessed their dependence on stimulus identity and stimulus statistics. We show that the fine structure of SCCs is specific to the identity of natural stimuli and changes in SCCs are independent of changes in response mean. Critically, we demonstrate that stimulus specificity of SCCs in V1 can be directly manipulated by altering the amount of high-order structure in synthetic stimuli. Finally, we show that simple phenomenological models of V1 activity cannot account for the observed SCC patterns and conclude that the stimulus dependence of SCCs is a natural consequence of structured internal dynamics in a hierarchical probabilistic model of natural images.
Brain activation during verbal fluency task in type II bipolar disorder patients: a near-infrared spectroscopy study.
Psychiatry research, 2021

Previous studies have shown that BD patients exhibited impairment when performing a verbal fluency task (VFT) and abnormal prefrontal cortex activation during this task. However, no study has specifically examined whether patients with type II BD demonstrate difficulty in performing VFT and impairments in relevant neural correlates or whether these are related to psychotic symptoms, the present study aimed to examine these issues.
Parameter comparison of white matter diffusion tensor imaging (DTI) in rhesus macaques (Macaca mulatta).
Dong wu xue yan jiu = Zoological research, 2014

In this study, we analyzed diffusion tensor imaging (DTI) results of brain white matter in rhesus macaques (Macaca mulatta) with four different parameter settings and found that the sequence A (b=1 000 s/mm(2), spatial resolution=1.25 mm×1.25 mm× 1.25 mm, numbers of direction=33, NSA=3) and B (b=800 s/mm(2), spatial resolution=1.25 mm×1.25 mm×1.25 mm, numbers of direction=33, NSA=3) could accurately track coarse fibers. The fractional anisotropy (FA) derived from sequence C (b=1 000s/mm(2), spatial resolution=0.55 mm×0.55 mm×2.5 mm, direction number=33, NSA=3) was too fuzzy to be used in tracking white matter fibers. By comparison, the high resolution and the FA with high contrast of gray matter and white matter derived from sequence D (b=800 s/mm(2), spatial resolution=1.0 mm×1.0 mm ×1.0 mm, numbers of direction=33, NSA=3) qualified in its application in tracking both thick and thin fibers, making it an optimal DTI setting for rhesus macaques.
Intermixed arteriovenous malformation and hemangioblastoma: case report and literature review.
CNS oncology, 2020

We report the third presentation of an intermixed arteriovenous malformation and hemangioblastoma. The rare occurrence of the diagnostic histologic features of both a neoplasm and vascular malformation in a single lesion is more common in gliomas, as angioglioma, and is termed an 'intermixed' lesion. We review the literature concerning the developmental biology of each lesion, and potential interplay in the formation of an intermixed vascular neoplasm and vascular malformation. The roles of cellular origin, genetic susceptibility, favourable microenvironment, altered local gene expression and key regulatory pathways are reviewed. Our review supports angiography and genetic profiling in intermixed lesions to inform management strategies. Consideration should be given to multimodality therapeutic interventions as required, including microsurgical resection, stereotactic radiosurgery and further research to exploit emerging molecular targets.
Neonatal spectral EEG is prognostic of cognitive abilities at school age in premature infants without overt brain damage.
European journal of pediatrics, 2021

Prematurity is a prototype of biological risk that could affect the late neurocognitive outcome; however, the condition itself remains a non-specific marker. This longitudinal 6-year study aimed to evaluate the prognostic role of neonatal spectral EEG in premature infants without neurological complications. The study cohort was 26 children born 23-34 gestational ages; all neonates underwent multichannel EEG recordings at 35 weeks post-conception. EEG data were transformed into the frequency domain and divided into delta (0.5-4 Hz), theta (5-7 Hz), alpha (8-13 Hz), and beta (14-20 Hz) frequency bands. At 6 years, a neuropsychological and behavioral evaluation was performed. Correlations between spectral bands and neuropsychological assessments were performed with a conservative and robust Bayesian correlation model using weakly informative priors. The correlation of neuropsychological tasks to spectral frequency bands highlighted a significant association with visual and auditory attention tests. The performance on the same tests appears to be mainly impaired.Conclusions: We found that spectral EEG frequencies are independent predictors of performance in attention tasks. We hypothesized that spectral EEG might reflect early circuitries' imbalance in the reticular ascending system and cumulative effect on ongoing development, pointing to the importance of early prognostic instruments. What is Known: • Prematurity is a non-specific marker of late neurocognitive risk. • Precise prognostic instruments are lacking, mostly in patients with low-grade conditions. What is New: • Longitudinal long-term studies are scarce but crucial for the inferential attributive process. • Spectral EEG frequencies are independent predictors of performance in attention tasks.
Genetic polymorphisms of the serotonin transporter are not related with depression in temporal lobe epilepsy caused by hippocampal sclerosis.
Epilepsy & behavior : E&B, 2021

Mood disorders are the most frequent psychiatric disorders in patients with temporal lobe epilepsy caused by hippocampal sclerosis (TLE-HS). The pathophysiological mechanisms in common between TLE and mood disorders include abnormalities in the serotonergic pathway. We aimed to evaluate the association between serotonin transporter genetic polymorphisms - 5-HTTLPR and 5-HTTVNTR - and the presence of mood disorders in patients with TLE-HS.
Usher Parsons (1788-1868) and His 19th-Century Understanding and Surgical Treatment of Spinal Curvatures.
World neurosurgery, 2017

Usher Parsons was a prominent surgeon in the 19th century. However, his contributions to the understanding and treatment of spinal curvatures have been largely forgotten. Herein, we review Parsons' theories, understanding, and treatment strategies for treating abnormal spinal curvatures. This glimpse into history offers insight into the thought processes and surgical strategies that were available in the early 19th century. It is pioneers in this field, such as Usher Parsons, on which our current understanding of spinal curvatures and its treatment is built.
Effects of dopamine D1- and D2-like receptors in the CA1 region of the hippocampus on expression and extinction of morphine-induced conditioned place preference in rats.
Behavioural brain research, 2021

Considering the extent of drug use and its relapse rate worldwide, in the present study, we explored the role of intra-CA1 administration of D1-like and D2-like receptor antagonists on the expression and extinction of morphine-induced CPP. To induce morphine CPP, adult male Wistar rats received a daily subcutaneous injection of morphine (5 mg/kg) during a 3-day conditioning phase. Different doses of SCH23390 (0.25, 1 or 4 μg/0.5 μl saline), as a selective D1-like receptor antagonist, and sulpiride (0.25, 1, or 4 μg/0.5 μl DMSO), as a selective D2-like receptor antagonist, were bilaterally microinjected into the CA1 region in the expression and extinction phases 1 h before CPP evaluation. Conditioning scores and locomotor activities were recorded during the tests. Results indicated that the injection of the antagonists into the CA1 region dose-dependently attenuated the expression of the morphine-induced CPP and sulpiride revealed prominent behavioral results compared to SCH23390 in the expression phases. Furthermore, microinjections of SCH23390 and sulpiride shortened the extinction phase of the morphine-induced CPP without changing the locomotor activity. The results indicated the involvement of D1- and D2-like receptors within the CA1 region in the expression and extinction of rewarding properties of morphine.
Blood flow, capillary transit times, and tissue oxygenation: the centennial of capillary recruitment.
Journal of applied physiology (Bethesda, Md. : 1985), 2020

The transport of oxygen between blood and tissue is limited by blood's capillary transit time, understood as the time available for diffusion exchange before blood returns to the heart. If all capillaries contribute equally to tissue oxygenation at all times, this physical limitation would render vasodilation and increased blood flow insufficient means to meet increased metabolic demands in the heart, muscle, and other organs. In 1920, Danish physiologist August Krogh was awarded the Nobel Prize in Physiology or Medicine for his mathematical and quantitative, experimental demonstration of a solution to this conceptual problem: capillary recruitment, the active opening of previously closed capillaries to meet metabolic demands. Today, capillary recruitment is still mentioned in textbooks. When we suspect symptoms might represent hypoxia of a vascular origin, however, we search for relevant, flow-limiting conditions in our patients and rarely ascribe hypoxia or hypoxemia to short capillary transit times. This review describes how natural changes in capillary transit-time heterogeneity (CTH) and capillary hematocrit (HCT) across open capillaries during blood flow increases can account for a match of oxygen availability to metabolic demands in normal tissue. CTH and HCT depend on a number of factors: on blood properties, including plasma viscosity, the number, size, and deformability of blood cells, and blood cell interactions with capillary endothelium; on anatomical factors including glycocalyx, endothelial cells, basement membrane, and pericytes that affect the capillary diameter; and on any external compression. The review describes how risk factor- and disease-related changes in CTH and HCT interfere with flow-metabolism coupling and tissue oxygenation and discusses whether such
Ferroptosis and its potential role in the physiopathology of Parkinson's Disease.
Progress in neurobiology, 2021

Parkinson's Disease (PD) is a common and progressive neurodegenerative disorder characterised by motor impairments as well as non-motor symptoms. While dopamine-based therapies are effective in fighting the symptoms in the early stages of the disease, a lack of neuroprotective drugs means that the disease continues to progress. Along with the traditionally recognised pathological hallmarks of dopaminergic neuronal death and intracellular α-synuclein (α-syn) depositions, iron accumulation, elevated oxidative stress and lipid peroxidation damage are further conspicuous features of PD pathophysiology. However, the underlying mechanisms linking these pathological hallmarks with neurodegeneration still remain unclear. Ferroptosis, a regulated iron dependent cell death pathway involving a lethal accumulation of lipid peroxides, shares several features with PD pathophysiology. Interestingly, α-syn has been functionally linked with the metabolism of both iron and lipid, suggesting a possible interplay between dysregulated α-syn and other PD pathological hallmarks related to ferroptosis. This review will address the importance for understanding these disease mechanisms that could be targeted therapeutically. Anti-ferroptosis molecules are neuroprotective in PD animal models and the anti-ferroptotic iron chelator, deferiprone, slowed disease progression and improved motor function in two independent clinical trials for PD. An ongoing larger multi-centre phase 2 clinical trial will confirm the therapeutic potential of deferiprone and the relevance of ferroptosis in PD. This review addresses the known pathological features of PD in relation to the ferroptosis pathway with therapeutic implications of targeting this cell death pathway.
Methamphetamine induces cardiomyopathy by Sigmar1 inhibition-dependent impairment of mitochondrial dynamics and function.
Communications biology, 2020

Methamphetamine-associated cardiomyopathy is the leading cause of death linked with illicit drug use. Here we show that Sigmar1 is a therapeutic target for methamphetamine-associated cardiomyopathy and defined the molecular mechanisms using autopsy samples of human hearts, and a mouse model of "binge and crash" methamphetamine administration. Sigmar1 expression is significantly decreased in the hearts of human methamphetamine users and those of "binge and crash" methamphetamine-treated mice. The hearts of methamphetamine users also show signs of cardiomyopathy, including cellular injury, fibrosis, and enlargement of the heart. In addition, mice expose to "binge and crash" methamphetamine develop cardiac hypertrophy, fibrotic remodeling, and mitochondrial dysfunction leading to contractile dysfunction. Methamphetamine treatment inhibits Sigmar1, resulting in inactivation of the cAMP response element-binding protein (CREB), decreased expression of mitochondrial fission 1 protein (FIS1), and ultimately alteration of mitochondrial dynamics and function. Therefore, Sigmar1 is a viable therapeutic agent for protection against methamphetamine-associated cardiomyopathy.
Proposal for human visual pathway in the extrastriate cortex by fiber tracking method using diffusion-weighted MRI.
NeuroImage, 2020

The extrastriate cortex in the human visual cortex is divided into two distinct clusters: the "what-information" processing area and the "where-information" processing area. It is widely accepted that the "what-information" cluster is processed through the ventral stream to the temporal cortex, and the "where-information" cluster through the dorsal stream to the parietal cortex. In human neuroanatomy, fiber bundles for the ventral stream (such as the inferior longitudinal fasciculus) are well defined, whereas fibers for the dorsal stream are poorly understood. In this study, we attempted to trace the dorsal stream fibers using a fiber tracking method using 7.0T diffusion-weighted MRI. We used data from a healthy male subject as well as from an unbiasedly selected nine-subject dataset in the Human Connectome Project. The surface of the visual area, including V1, V2, V3, V4, MT, was determined from the Brainnetome atlas (Fan et al., 2016), which is the connectivity-based parcellation framework of the human brain. The resulting visual pathway indicated that the putative pathway for the classical dorsal stream is unlikely to exist. Instead, we demonstrated that fiber connections exist between the angular gyrus with MT in the visual cortex, and between the angular gyrus and IT in the temporal cortex. Through that, we composed a two-pathway model for where-information processing that passes through the angular gyrus. Finally, we proposed a modified human visual pathway model based on our fiber tracking results in this report. The modified where-information pathway will provide a new aspect for the study of human visual processing.
Repetitive Blast Promotes Chronic Aversion to Neutral Cues Encountered in the Peri-Blast Environment.
Journal of neurotrauma, 2021

Repetitive mild traumatic brain injury (mTBI) has been called the "signature injury" of military service members in the Iraq and Afghanistan wars and is highly comorbid with post-traumatic stress disorder (PTSD). Correct attribution of adverse blast-induced mTBI and/or PTSD remains challenging. Pre-clinical research using animal models can provide important insight into the mechanisms by which blast produces injury and dysfunction-but only to the degree by which such models reflect the human experience. Avoidance of trauma reminders is a hallmark of PTSD. Here, we sought to understand whether a mouse model of blast reproduces this phenomenon, in addition to blast-induced physical injuries. Drawing on well-established work from the chronic stress and Pavlovian conditioning literature, we hypothesized that even while one is anesthetized during blast exposure, environmental cues encountered in the peri-blast environment could be conditioned to evoke aversion/dysphoria and re-experiencing of traumatic stress. Using a pneumatic shock tube that recapitulates battlefield-relevant open-field blast forces, we provide direct evidence that stress is inherent to repetitive blast exposure, resulting in chronic aversive/dysphoric-like responses to previous blast-paired cues. The results in this report demonstrate that, although both single and repetitive blast exposures produce acute stress responses (weight loss, corticosterone increase), only repetitive blast exposure also results in co-occurring aversive/dysphoric-like stress responses. These results extend appreciation of the highly complex nature of repetitive blast exposure; and lend further support for the potential translational relevance of animal modeling approaches currently used by multiple laboratories aimed at elucidating the mechanisms (both molecular and behavioral) of repetitive blast exposure.