rudyvdbrink/CitationDatabase huggingface dataset:
Comparing the effects of two different strains of mycobacteria, Mycobacterium vaccae NCTC 11659 and M. vaccae ATCC 15483, on stress-resilient behaviors and lipid-immune signaling in rats.
Brain, behavior, and immunity, 2021

Stress-related disorders, such as posttraumatic stress disorder (PTSD), are highly prevalent and often difficult to treat. In rodents, stress-related, anxiety-like defensive behavioral responses may be characterized by social avoidance, exacerbated inflammation, and altered metabolic states. We have previously shown that, in rodents, subcutaneous injections of a heat-killed preparation of the soil-derived bacterium Mycobacterium vaccae NCTC 11659 promotes stress resilience effects that are associated with immunoregulatory signaling in the periphery and the brain. In the current study, we sought to determine whether treatment with a heat-killed preparation of the closely related M. vaccae type strain, M. vaccae ATCC 15483, would also promote stress-resilience in adult male rats, likely due to biologically similar characteristics of the two strains. Here we show that immunization with either M. vaccae NCTC 11659 or M. vaccae ATCC 15483 prevents stress-induced increases in hippocampal interleukin 6 mRNA expression, consistent with previous studies showing that M. vaccae NCTC 11659 prevents stress-induced increases in peripheral IL-6 secretion, and prevents exaggeration of anxiety-like defensive behavioral responses assessed 24 h after exposure to inescapable tail shock stress (IS) in adult male rats. Analysis of mRNA expression, protein abundance, and flow cytometry data demonstrate overlapping but also unique effects of treatment with the two M. vaccae strains on immunological and metabolic signaling in the host. These data support the hypothesis that treatment with different M. vaccae strains may immunize the host against stress-induced dysregulation of physiology and behavior.
Two-Photon Voltage Imaging of Spontaneous Activity from Multiple Neurons Reveals Network Activity in Brain Tissue.
iScience, 2020

Recording the electrical activity of multiple neurons simultaneously would greatly facilitate studies on the function of neuronal circuits. The combination of the fast scanning by random-access multiphoton microscopy (RAMP) and the latest two-photon-compatible high-performance fluorescent genetically encoded voltage indicators (GEVIs) has enabled action potential detection in deep layers in in vivo brain. However, neuron connectivity analysis on optically recorded action potentials from multiple neurons in brain tissue has yet to be achieved. With high expression of a two-photon-compatible GEVI, ASAP3, via in utero electroporation and RAMP, we achieved voltage recording of spontaneous activities from multiple neurons in brain slice. We provide evidence for the developmental changes in intralaminar horizontal connections in somatosensory cortex layer 2/3 with a greater sensitivity than calcium imaging. This method thus enables investigation of neuronal network connectivity at the cellular resolution in brain tissue.
Different patterns of functional network reorganization across the variants of primary progressive aphasia: a graph-theoretic analysis.
Neurobiology of aging, 2020

Primary progressive aphasia (PPA) is a neurodegenerative syndrome with three main variants (nonfluent, logopenic, semantic) that are identified primarily based on language deficit profiles and are associated with neurotopographically distinct atrophic patterns. We used a graph-theoretic analytic approach to examine changes in functional network properties measured with resting-state fMRI in all three PPA variants compared with age-matched healthy controls. All three variants showed a more segregated network organization than controls. To better understand the changes underlying the increased segregation, we examined the distribution of functional "hubs". We found that while all variants lost hubs in the left superior frontal and parietal regions, new hubs were recruited in different areas across the variants. In particular, both logopenic and semantic variants recruited significant numbers of hubs in the right hemisphere. Importantly, these functional characteristics could not be fully explained by local volume changes. These findings indicate that patterns of functional connectivity can serve as further evidence to distinguish the PPA variants, and provide a basis for longitudinal studies and for investigating treatment effects. This study also highlights the utility of graph-theoretic approaches in understanding the brain's functional reorganization in response to neurodegenerative disease.
Tea Consumption and Risk of Cancer: An Umbrella Review and Meta-Analysis of Observational Studies.
Advances in nutrition (Bethesda, Md.), 2020

Tea is one of the most widely consumed beverages, but its association with cancer risk remains controversial and unclear. We performed an umbrella review to clarify and determine the associations between tea consumption and various types of cancer by summarizing and recalculating the existing meta-analyses. Meta-analyses of observational studies reporting associations between tea consumption and cancer risk were searched on PubMed and Embase. Associations found to be statistically significant were further classified into levels of evidence (convincing, suggestive, or weak), based on P value, between-study heterogeneity, prediction intervals, and small study effects. Sixty-four observational studies (case-control or cohort) corresponding to 154 effect sizes on the incidence of 25 types of cancer were included. Forty-three (27.9%) results in 15 different types of cancer were statistically significant. When combining all studies on the same type of cancer, 19 results in 11 different types of cancer showed significant associations with lower risk of gastrointestinal tract organ cancer (oral, gastric, colorectal, biliary tract, and liver cancer), breast cancer, and gynecological cancer (endometrial and ovarian cancer) as well as leukemia, lung cancer, and thyroid cancer. Only the reduced risk of oral cancer in tea-consuming populations (OR = 0.62; 95% CI: 0.55, 0.72; P value < 10-6) was supported by convincing evidence. Suggestive evidence was found for 6 results on biliary tract, breast, endometrial, liver, and oral cancer. To summarize, tea consumption was shown to have protective effects on some types of cancer, particularly oral cancer. More well-designed prospective studies are needed with consideration of other factors that can cause biases.
Therapeutic Factors in a Psychiatric Group Therapy: a Preliminary Validation of Therapeutic Factors Inventory-8, Italian Version.
The Psychiatric quarterly, 2021

Several studies support group therapy effectiveness due to the activation in patients of unique psychological mechanisms defined as non-specific therapeutic factors (Therapeutic Factors-TFs), which shape the setting and, at the same time, enhance the specific group therapeutic factors. The objectives of this study were to preliminarly validate Therapeutic Factors Inventory-8 (TFI-8) Italian version and identify group therapeutic factors. In a psychiatric residential facility, a weekly psychotherapeutic group was evaluated during 1 year. One scale on group process (TFI-8, Ferrara-Group Experience Scale) and three clinical scales (Brief Symptom Inventory-53, Sheehan Disability Scale, WHO Quality of Life-Bref) were administered to participating patients. Internal consistency, Exploratory Factor Analysis (EFA), convergent validity of TFI-8 were assessed. Correlations between TFI-8 and other scale scores and selected variables were pwerformed. Our sample consisted of 64 participants. TFI-8 showed good internal consistency (Chronbach's alpha = 0.84), concurrent validity with Fe-GES (Rho = 0.42, p = 0.0008). EFA highlighted a single Factor, accounting for 92% of variance. TFI-8 was not significantly related to clinical scale scores. TFI-8 Italian version proved to be a valid and reliable tool which allowed us to identify one therapeutic factor indicating relational attraction in group therapy, composed of three dimensions: infusion of hope, cohesion and social learning.
Enhancing transcranial direct current stimulation via motor imagery and kinesthetic illusion: crossing internal and external tools.
Journal of neuroengineering and rehabilitation, 2016

Transcranial direct current stimulation is a safe technique which is now part of the therapeutic armamentarium for the neuromodulation of motor functions and cognitive operations. It is currently considered that tDCS is an intervention that might promote functional recovery after a lesion in the central nervous system, thus reducing long-term disability and associated socio-economic burden.
Alprazolam for essential tremor.
The Cochrane database of systematic reviews, 2015

Essential tremor (ET) is one of the most common movement disorders. Treatment is based primarily on pharmacological agents. On this basis, although primidone and propranolol are well-established treatments in clinical practice, they could be ineffective in 25% to 55% of patients and can produce serious adverse events (AEs) in a large percentage of individuals. For these reasons, evaluating treatment alternatives for ET may be a worthwhile pursuit. Alprazolam has been suggested as a potentially useful agent for treatment of individuals with ET, but its efficacy and safety are uncertain.
Lectin complement pathway initiators after subarachnoid hemorrhage - an observational study.
Journal of neuroinflammation, 2020

This exploratory study investigated the time-course of lectin complement pathway (LCP) initiators in cerebrospinal fluid (CSF) and plasma in patients with subarachnoid hemorrhage (SAH), as well as their relationship to delayed cerebral ischemia (DCI) and functional outcome.
The Chemokine CXCL14-like Immunoreactivity Co-exists with Somatostatin, but not NPY in the Rat Dorsal Horn and Has Intimate Association with GABAergic Neurons in the Lateral Spinal Nucleus.
Acta histochemica et cytochemica, 2020

Recent studies have proposed that the chemokine CXCL14 not only has a chemotactic activity, but also functions as a neuromodulator and/or neurotransmitter. In this study, we investigated the distribution of CXCL14 immunoreactive structures in the rat spinal cord and clarified the association of these structures with somatostatin, glutamic acid decarboxylase (GAD; a marker for GABAergic neurons), and neuropeptide Y (NPY). CXCL14 immunoreactive fibers and puncta were observed in lamina II, which modulates somatosensation including nociception, and the lateral spinal nucleus of the spinal dorsal horn at cervical, thoracic, and lumber spinal cord levels. These CXCL14 immunoreactive structures were also immuno-positive for somatostatin, but were immuno-negative for GAD and NPY. In the cervical lateral spinal nucleus, CXCL14 immunoreactive puncta, which were also immuno-positive for somatostatin, existed along the proximal dendrites of some of GABAergic neurons. Together, these results suggest that CXCL14 contributes to the modulation of somatosensation in concert with somatostatin. Neurons targeted by the CXCL14 fiber system include GABAergic neurons located in the lateral spinal nucleus suggesting that CXCL14 with somatostatin can influence the GABAergic neuron function.
Normal human macula densa morphology and cell turnover: A histological, ultrastructural, and immunohistochemical investigation.
Anatomical record (Hoboken, N.J. : 2007), 2020

The aim was to analyze the morphology of normal human macula densa (MD), evaluate the cells that may be responsible for its turnover, and collect quantitative data. Of four samples of normal human renal tissue, two were embedded in resin to measure the longitudinal extension and examine the ultrastructure of the MD, the other two were embedded in paraffin to study apoptosis and cell proliferation. The MD is composed of a monolayer tissue about 40 μm long, which includes 35-40 cells arranged in overlapping rows. Ultrastructurally, MD cells show two polarized portions: an apical end, with sensory features, and a basolateral aspect, with paracrine function. MD cells are connected apically by tight junctions, with/without adherens junctions, which form a barrier between the distal tubule lumen and the interstitium. Cells in degeneration, often associated with macrophages, and undifferentiated cells were found in the MD and adjacent distal tubule. A filamentous mat previously described in proximal tubule scattered tubular cells (STCs) was detected in the basal cytoplasm in undifferentiated cells. The tissue was consistently negative for the proliferation marker Ki67 and for the apoptotic markers caspase-3 and caspase-9. This work confirms our earlier morphological findings and provides new data: (a) MD cells display both apical adherens and tight junctions, the latter forming a tubulo-mesangial barrier; (b) the MD is a monolayer made up of about 40 cells arranged in rows; (c) the simultaneous presence of degenerating (8-13%) and undifferentiated (4-13%) cells reminiscent of STCs suggests a non-negligible cell turnover.
Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium.
Cell stem cell, 2020

Neurological complications are common in patients with COVID-19. Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal pathogen of COVID-19, has been detected in some patient brains, its ability to infect brain cells and impact their function is not well understood. Here, we investigated the susceptibility of human induced pluripotent stem cell (hiPSC)-derived monolayer brain cells and region-specific brain organoids to SARS-CoV-2 infection. We found that neurons and astrocytes were sparsely infected, but choroid plexus epithelial cells underwent robust infection. We optimized a protocol to generate choroid plexus organoids from hiPSCs and showed that productive SARS-CoV-2 infection of these organoids is associated with increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. Together, our findings provide evidence for selective SARS-CoV-2 neurotropism and support the use of hiPSC-derived brain organoids as a platform to investigate SARS-CoV-2 infection susceptibility of brain cells, mechanisms of virus-induced brain dysfunction, and treatment strategies.
Generalization of conditioned fear along a dimension of increasing positive valence.
Neuropsychologia, 2020

The amount of fear evoked by potential threats is oftentimes proportional to the overlap in shared features with known threats. An adaptive learning system should therefore extract relevant features from threat stimuli to successfully detect other novel threats in the environment. But what if the most relevant feature of a threat stimulus is emotionally positive? Here, we used Pavlovian fear conditioning to ask whether people extract positive emotional features of a fear conditioned stimulus (CS) to selectively generalize to other stimuli that contain positive features. In a between subjects design, we first paired a picture of a face expressing either a slight amount of happiness or fear with an electrical shock to the wrist. We then tested fear generalization to modified face stimuli of the same identity expressing more or less happiness or fear. Both groups exhibited biased physiological arousal (a peak shift) to a face stimulus with the most exaggerated emotional expression, regardless of valence. Fear generalization diminished to unreinforced happy faces over the course of testing, whereas arousal was maintained to unreinforced fearful faces throughout testing. Finally, subjects fear conditioned to a slightly happy face were accurate at retrospectively identifying the correct CS, whereas subjects fear conditioned to a fearful face retrospectively misidentified a more fearful face as the threat CS. These findings suggest that positive emotional features extracted from a known threat can guide biased fear generalization, but that generalization is maintained by a dimension of increasing fear which also produces retrospective biases in threat intensity estimation.
Metabolomic study of altered energy metabolism during global forebrain ischemia and ischemic precoditioning in blood plasma in homocysteine treated rats.
Journal of physiology and pharmacology : an official journal of the Polish Physiological Society, 2018

Elevated homocysteine (Hcy) level is a well known risk factor for cardiovascular and neuropsychiatric diseases. In this study, we investigated metabolic changes in blood plasma in Hcy-treated rats. In combination with Hcy injections to induce hyperhomocysteinemia-like state, we used an animal model of global cerebral ischemia to investigate metabolic changes after 24 h reperfusion in rats. We also focused on the endogenous phenomenon known as ischemic tolerance induced by the preischemic treatment. The experiments were carried out on blood plasma samples as they are easily available and metabolically reflect the overall changes in injured organism. We observed significant changes in plasma metabolite levels of: pyruvate, citrate, acetate implicating alterations in energy metabolism, and increase in triacylglycerols, arginine and lysine, in Hcy-treated rats compared with naive animals. Ischemic insult with 24 reperfusion in Hcy-treated rats led to increase in plasma lactate, and decrease in plasma glucose, pyruvate, citrate and acetate. Complementary, an increase in ketone body 3-hydroxybutyrate was observed. The plasma metabolites: alanine, lactate, valine, glucose, leucine, isoleucine, acetate, citrate and 3-hydroxybutyrate were considered to reflect the response induced by ischemic preconditioning in Hcy rats, where the extent of postischemic damage was not as high as in the non-preconditioned rats. Our results provide evidence that nuclear magnetic resonance (NMR) spectra analysis can identify a specific group of metabolites present in plasma with the capability of discriminating between individual groups of animals. Regarding the effect of elevated Hcy level on plasma metabolome, we showed, that acetate, pyruvate and glucose had the excellent discriminatory power between Hcy-treated and naive rats plasma. Concerning ischemic insult in Hcy-treated animals, we also document the ideal discrimination of ischemic from non-ischemic rats by various groups of metabolites, that can be considered as a potential plasma biomarkers.
The Wiring Logic of an Identified Serotonergic Neuron That Spans Sensory Networks.
The Journal of neuroscience : the official journal of the Society for Neuroscience, 2020

Serotonergic neurons project widely throughout the brain to modulate diverse physiological and behavioral processes. However, a single-cell resolution understanding of the connectivity of serotonergic neurons is currently lacking. Using a whole-brain EM dataset of a female
Computational and neurophysiological principles underlying auditory perceptual decisions.
Current opinion in physiology, 2020

A fundamental scientific goal in auditory neuroscience is identifying what mechanisms allow the brain to transform an unlabeled mixture of auditory stimuli into distinct perceptual representations. This transformation is accomplished by a complex interaction of multiple neurocomputational processes, including Gestalt grouping mechanisms, categorization, attention, and perceptual decision-making. Despite a great deal of scientific energy devoted to understanding these principles of hearing, we still do not understand either how auditory perception arises from neural activity or the causal relationship between neural activity and auditory perception. Here, we review the contributions of cortical and subcortical regions to auditory perceptual decisions with an emphasis on those studies that simultaneously measure behavior and neural activity. We also put forth challenges to the field that must be faced if we are to further our understanding of the relationship between neural activity and auditory perception.
Individual differences among deep neural network models.
Nature communications, 2020

Deep neural networks (DNNs) excel at visual recognition tasks and are increasingly used as a modeling framework for neural computations in the primate brain. Just like individual brains, each DNN has a unique connectivity and representational profile. Here, we investigate individual differences among DNN instances that arise from varying only the random initialization of the network weights. Using tools typically employed in systems neuroscience, we show that this minimal change in initial conditions prior to training leads to substantial differences in intermediate and higher-level network representations despite similar network-level classification performance. We locate the origins of the effects in an under-constrained alignment of category exemplars, rather than misaligned category centroids. These results call into question the common practice of using single networks to derive insights into neural information processing and rather suggest that computational neuroscientists working with DNNs may need to base their inferences on groups of multiple network instances.
Rat mPFC and M2 Play a Waiting Game (at Different Timescales).
Neuron, 2017

In this issue of Neuron, Murakami et al. (2017) relate neural activity in frontal cortex to stochastic and deterministic components of waiting behavior in rats; they find that mPFC biases waiting time, while M2 is ultimately responsible for trial-to-trial variability in decisions about how long to wait.
The role of anterior prefrontal cortex in prospective memory: an exploratory FDG-PET study in early Alzheimer's disease.
Neurobiology of aging, 2020

From previous studies in healthy volunteers the prefrontal regions are deeply involved in prospective memory (PM), although little is known about the functional neural basis of PM in prodromal Alzheimer's disease (AD). To this end, we retrospectively recruited 18 patients with mild cognitive impairment caused by AD and 23 matched healthy control subjects who had undergone
Quadrature demodulation in line-scan focal modulation microscopy for imaging three-dimensional zebrafish neural structure.
Journal of biophotonics, 2020

Visualizing biological processes in neuroscience requires in vivo functional imaging at single-neuron resolution, high image acquisition speed and strong optical sectioning ability. However, due to light scattering of in tissue, very often conventional wide-field fluorescence microscopes are unable to resolve cells in the presence of a strong out-of-focus background. Line-scan focal modulation microscopy enables high temporal resolution and good optical sectioning ability at the same time. Here we demonstrate a quadrature demodulation method to extract the focal information with an extended frequency bandwidth and therefore higher spatial resolution. The performance of the demodulation scheme in line-scan focal modulation microscope has been evaluated by performing imaging experiments with fluorescence beads and zebrafish neural structure. Reduced background, reduced artifacts and more detailed morphological information are evident in the obtained images.