rudyvdbrink/CitationDatabase huggingface dataset:
Deep learning for Koopman Operator Optimal Control.
ISA transactions, 2021

Nonlinear dynamics are ubiquitous in complex systems. Their applications range from robotics to computational neuroscience. In this work, the Koopman framework for globally linearizing nonlinear dynamics is introduced. Under this framework, the nonlinear observable states are lifted into a higher dimensional, linear regime. The challenge is to identify functions that facilitate the coordinate transformation to this raised linear space. This point is tackled using deep learning, where nonlinear dynamics are learned in a model-free manner, i.e., the underlying dynamics are uncovered using data rather than the nonlinear state-space equations. The main contributions include an implementation of the Linearly Recurrent Encoder Network (LREN) that is faster than the existing implementation and is significantly faster than the state-of-the-art deep learning-based approach. Also, a novel architecture termed Deep Encoder with Initial State Parameterization (DENIS) is proposed. By deriving an energy-budget control performance evaluation method, we demonstrate that DENIS also outperforms LREN in control performance. It is also on-par with and sometimes better than the iterative linear quadratic regulator (iLQR), which requires access to the state-space equations. Extensive experiments are done on DENIS to validate its performance. Also, another novel architecture termed Double Encoder for Input Nonaffine systems (DEINA) is described. Additionally, DEINA's potential ability to outperform existing Koopman frameworks for controlling nonaffine input systems is shown. We attribute this to using an auxiliary network to nonlinearly transform the inputs, thereby lifting the strong linear constraints imposed by the traditional Koopman approximation approach. Koopman model predictive control (KMPC) is implemented to verify that our models can also be successfully controlled under this popular approach. Overall, we demonstrate the deep learning-based Koopman framework shows promise for optimally controlling nonlinear dynamics.
Induction of Mutant 
The Journal of neuroscience : the official journal of the Society for Neuroscience, 2021

Sleep is regulated in a homeostatic manner. Sleep deprivation increases sleep need, which is compensated mainly by increased EEG δ power during non-rapid eye movement sleep (NREMS) and, to a lesser extent, by increased sleep amount. Although genetic factors determine the constitutive level of sleep need and sleep amount in mice and humans, the molecular entity behind sleep need remains unknown. Recently, we found that a gain-of-function
The Geometry of Abstraction in the Hippocampus and Prefrontal Cortex.
Cell, 2020

The curse of dimensionality plagues models of reinforcement learning and decision making. The process of abstraction solves this by constructing variables describing features shared by different instances, reducing dimensionality and enabling generalization in novel situations. Here, we characterized neural representations in monkeys performing a task described by different hidden and explicit variables. Abstraction was defined operationally using the generalization performance of neural decoders across task conditions not used for training, which requires a particular geometry of neural representations. Neural ensembles in prefrontal cortex, hippocampus, and simulated neural networks simultaneously represented multiple variables in a geometry reflecting abstraction but that still allowed a linear classifier to decode a large number of other variables (high shattering dimensionality). Furthermore, this geometry changed in relation to task events and performance. These findings elucidate how the brain and artificial systems represent variables in an abstract format while preserving the advantages conferred by high shattering dimensionality.
Dextran- Versus Crystalloid-Based Prime in Cardiac Surgery: A Prospective Randomized Pilot Study.
The Annals of thoracic surgery, 2020

The optimum priming fluid for the cardiopulmonary bypass (CPB) circuit is still debated. We compared a new hyperoncotic priming solution containing dextran 40, which has an electrolyte composition that mimics extracellular fluid, with a standard crystalloid-based prime.
NeuroConstruct-based implementation of structured-light stimulated retinal circuitry.
BMC neuroscience, 2020

Retinal circuitry provides a fundamental window to neural networks, featuring widely investigated visual phenomena ranging from direction selectivity to fast detection of approaching motion. As the divide between experimental and theoretical visual neuroscience is fading, neuronal modeling has proven to be important for retinal research. In neuronal modeling a delicate balance is maintained between bio-plausibility and model tractability, giving rise to myriad modeling frameworks. One biologically detailed framework for neuro modeling is NeuroConstruct, which facilitates the creation, visualization and analysis of neural networks in 3D.
Expression of nano-ferritin in neuronal cells encompassed by minimal Arc promoter system.
Biochemical and biophysical research communications, 2020

Genetic engineering for neuronal cell activity labeling and neuronal cell activity modulation are invaluable for elucidating the underlying characteristics of the brain and neurons. In this study, ferritin fusion protein (FFP) was combined with Tet expression construct under a modified immediate-early gene (IEG) Arc/Arg3.1 promoter so-called SARE-ArcMin. This expression system is a neuronal activity-dependent expression module for nano-ferritin, a radio/magnetic wave-sensitive protein well-accepted as a potential recombinant neuronal actuator. The system was characterized in transcriptional and translational levels in human neuroblastoma SH-SY5Y cells. The mRNA and protein expression levels of nano-ferritin were significant in the activated neurons suggesting that the activity dependent expression patterns of the ferritin also acted as a neuronal cell activation indicator. The system sufficed the need for precise neuronal cell activity specific expression and demonstrated a platform that suggested the use of the nano-ferritin for the study of neuronal cells.
Providing Excellent Consumer Service Is Therapeutic: Insights from an Implicit Association Neuromarketing Study.
Behavioral sciences (Basel, Switzerland), 2019

This paper reports the results of a combined biometric and implicit affective priming study of the emotional consequences of being the provider or receiver of either positive or negative customer service experiences. The study was conducted in two stages. Study 1 captured the moment-by-moment implicit emotional and physiological responses associated with receiving and providing good customer service. Study 2 employed an affective priming task to evaluate the implicit associations with good and poor customer service in a large sample of 1200 respondents across three Western countries. Our results show that both giving and receiving good customer service was perceived as pleasurable (Study 1) and at the same time, was implicitly associated with positive feelings (Study 2). The authors discuss the implications of the research for service providers in terms of the impact of these interactions on employee wellbeing, staff retention rates and customer satisfaction.
Noise Damage Accelerates Auditory Aging and Tinnitus: A Canadian Population-Based Study.
Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology, 2020

Age-related hearing loss (ARHL) is the third most challenging disability in older adults. Noise is a known modifiable risk factor of ARHL, which can drive adverse health effects. Few large-scale studies, however, have shown how chronic noise exposure (CNE) impacts the progression of ARHL and tinnitus.
The neurochemistry of social reward during development: What have we learned from rodent models?
Journal of neurochemistry, 2021

Social rewards are fundamental to survival and overall health. Several studies suggest that adequate social stimuli during early life are critical for developing appropriate socioemotional and cognitive skills, whereas adverse social experiences negatively affect the proper development of brain and behavior, by increasing the susceptibility to develop neuropsychiatric conditions. Therefore, a better understanding of the neural mechanisms underlying social interactions, and their rewarding components in particular, is an important challenge of current neuroscience research. In this context, preclinical research has a crucial role: Animal models allow to investigate the neurobiological aspects of social reward in order to shed light on possible neurochemical alterations causing aberrant social reward processing in neuropsychiatric diseases, and they allow to test the validity and safety of innovative therapeutic strategies. Here, we discuss preclinical research that has investigated the rewarding properties of two forms of social interaction that occur in different phases of the lifespan of mammals, that is, mother-infant interaction and social interactions with peers, by focusing on the main neurotransmitter systems mediating their rewarding components. Together, the research performed so far helped to elucidate the mechanisms of social reward and its psychobiological components throughout development, thus increasing our understanding of the neurobiological substrates sustaining social functioning in health conditions and social dysfunction in major psychiatric disorders.
Dynamic Changes in Fibrinogen and Prognosis of Acute Ischemic Stroke Patients Treated with Intravenous Thrombolysis.
Neurotoxicity research, 2020

This study aimed to investigate the association between dynamic changes in fibrinogen and the prognosis of acute ischemic stroke (AIS) patients treated with intravenous thrombolysis (IVT). We measured fibrinogen levels at admission and 24 h after IVT in 364 consecutively recruited AIS patients. The primary outcome was the composite measure of death or major disability (modified Rankin Scale score 3-6) at 3 months. During the 3-month follow-up, 127 (34.89%) patients experienced death or major disability. After multivariate adjustment, a ≥ 2.5% increase in fibrinogen was associated with an increased risk of the primary outcome (odds ratio [OR], 2.26; 95% confidence interval [CI] 1.08-4.75; p trend = 0.030) when 2 extreme tertiles were compared. Each 1% increase in fibrinogen after IVT was associated with a 1% increase in the risk of the primary outcome (OR 1.01, 95% CI 1.00-1.03). Multivariable-adjusted spline regression revealed a linear dose-response relationship between fibrinogen changes after IVT and the primary outcome (p for linearity = 0.032). The addition of fibrinogen changes to conventional risk factors improved the re-classification (but not discrimination) of the primary outcome (net reclassification index 27.6%, p = 0.011). These findings indicated that an increase in fibrinogen after IVT was associated with an increased risk of death or major disability in AIS patients, suggesting that monitoring the dynamic profile of fibrinogen levels may help neurologists improve stroke outcomes in clinical settings.
Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma.
Cancer research, 2020

Medulloblastoma is among the most common malignant brain tumors in children. Recent studies have identified at least four subgroups of the disease that differ in terms of molecular characteristics and patient outcomes. Despite this heterogeneity, most patients with medulloblastoma receive similar therapies, including surgery, radiation, and intensive chemotherapy. Although these treatments prolong survival, many patients still die from the disease and survivors suffer severe long-term side effects from therapy. We hypothesize that each patient with medulloblastoma is sensitive to different therapies and that tailoring therapy based on the molecular and cellular characteristics of patients' tumors will improve outcomes. To test this, we assembled a panel of orthotopic patient-derived xenografts (PDX) and subjected them to DNA sequencing, gene expression profiling, and high-throughput drug screening. Analysis of DNA sequencing revealed that most medulloblastomas do not have actionable mutations that point to effective therapies. In contrast, gene expression and drug response data provided valuable information about potential therapies for every tumor. For example, drug screening demonstrated that actinomycin D, which is used for treatment of sarcoma but rarely for medulloblastoma, was active against PDXs representing Group 3 medulloblastoma, the most aggressive form of the disease. Functional analysis of tumor cells was successfully used in a clinical setting to identify more treatment options than sequencing alone. These studies suggest that it should be possible to move away from a one-size-fits-all approach and begin to treat each patient with therapies that are effective against their specific tumor. SIGNIFICANCE: These findings show that high-throughput drug screening identifies therapies for medulloblastoma that cannot be predicted by genomic or transcriptomic analysis.
Prevalence of temporomandibular disorder in adult patients with chronic pain.
Scandinavian journal of pain, 2021

Chronic pain patients often suffer in multiple locations. In health care, examinations of bodily pain usually do not include questions about temporomandibular disorders (TMD); hence TMD symptoms and potential comorbidities are not regularly assessed. Therefore, the primary aim was to evaluate the prevalence of TMD in patients referred to a pain rehabilitation clinic, and the secondary aim was to evaluate possible factors associated with TMD symptoms.
Modulation of arousal and sleep/wake architecture by M
Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology, 2020

Degeneration of basal forebrain cholinergic circuitry represents an early event in the development of Alzheimer's disease (AD). These alterations in central cholinergic function are associated with disruptions in arousal, sleep/wake architecture, and cognition. Changes in sleep/wake architecture are also present in normal aging and may represent a significant risk factor for AD. M
GABA in the medial prefrontal cortex regulates anxiety-like behavior during the postpartum period.
Behavioural brain research, 2021

The postpartum period is commonly accompanied by emotional changes, which for many new mothers includes a reduction in anxiety. Previous research in rodents has shown that the postpartum attenuation in anxiety is dependent on offspring contact and has further implicated enhanced GABAergic neurotransmission as an underlying mechanism. However, the specific brain regions where GABA acts to regulate the offspring-induced reduction in postpartum anxiety requires further investigation. Here, we test the hypothesis that offspring interactions suppress anxiety-like behavior in postpartum female rats via GABA signaling in the medial prefrontal cortex (mPFC). Our results show a postpartum reduction in anxiety-like behavior, an effect which was abolished by localized infusion of the GABA
Finding gaps and building bridges in movement disorders.
Expert review of neurotherapeutics, 2012

Movement disorders are one of the most rapidly growing fields of neurology from both the clinical and neurobiological perspectives. Despite many recent advances in genetic, pathogenetic, clinical and therapeutic fields, several shortcomings remain in the diagnostic and therapeutic realms, with a plethora of challenges threatening further advances. Aimed at recognizing and bridging these knowledge gaps, the 2nd International Conference on Knowledge Gaps in Parkinson's Disease and Other Movement Disorders was held last February in Santa Margherita Ligure, Italy, with the support of the Movement Disorder Society and the Italian Association for Parkinson's Disease and Extrapyramidal Disorders. The 3-day symposium, which was attended by approximately 300 clinicians and researchers from around the world, gathered around 27 leading young and senior clinical scientists, each of whom addressed the field's main knowledge gaps and brainstormed on how to bridge or minimize their impact. This meeting report summarizes the topics that gathered the most attention from the speakers and the audience.
Fast Retrograde Access to Projection Neuron Circuits Underlying Vocal Learning in Songbirds.
Cell reports, 2020

Understanding the structure and function of neural circuits underlying speech and language is a vital step toward better treatments for diseases of these systems. Songbirds, among the few animal orders that share with humans the ability to learn vocalizations from a conspecific, have provided many insights into the neural mechanisms of vocal development. However, research into vocal learning circuits has been hindered by a lack of tools for rapid genetic targeting of specific neuron populations to meet the quick pace of developmental learning. Here, we present a viral tool that enables fast and efficient retrograde access to projection neuron populations. In zebra finches, Bengalese finches, canaries, and mice, we demonstrate fast retrograde labeling of cortical or dopaminergic neurons. We further demonstrate the suitability of our construct for detailed morphological analysis, for in vivo imaging of calcium activity, and for multi-color brainbow labeling.
CARD19, the protein formerly known as BinCARD, is a mitochondrial protein that does not regulate Bcl10-dependent NF-κB activation after TCR engagement.
Cellular immunology, 2020

After T cell receptor (TCR) engagement, the CARD11-Bcl10-Malt1 (CBM) complex oligomerizes to transduce NF-κB activating signals. Bcl10 is then degraded to limit NF-κB activation. The cDNA AK057716 (BinCARD-1) was reported to encode a novel CARD protein that interacts with Bcl10 and modestly inhibits NF-κB activation. In a later study, a second isoform, BinCARD-2, was identified. Here, we report that the cDNA AK057716 (BinCARD-1) is an incompletely spliced derivative of the gene product of C9orf89, whereas CARD19 (BinCARD-2) represents the properly spliced isoform, with conservation across diverse species. Immunoblotting revealed expression of CARD19 in T cells, but no evidence of BinCARD-1 expression, and microscopy demonstrated that endogenous CARD19 localizes to mitochondria. Although we confirmed that both BinCARD-1 and CARD19 can inhibit NF-κB activation and promote Bcl10 degradation when transiently overexpressed in HEK293T cells, loss of endogenous CARD19 expression had little effect on Bcl10-dependent NF-κB activation, activation of Malt1 protease function, or Bcl10 degradation after TCR engagement in primary murine CD8 T cells. Together, these data indicate that the only detectable translated product of C9orf89 is the mitochondrial protein CARD19, which does not play a discernible role in TCR-dependent, Bcl10-mediated signal transduction to Malt1 or NF-κB.
Night shift work is associated with an increased risk of asthma.
Thorax, 2021

Shift work causes misalignment between internal circadian time and the external light/dark cycle and is associated with metabolic disorders and cancer. Approximately 20% of the working population in industrialised countries work permanent or rotating night shifts, exposing this large population to the risk of circadian misalignment-driven disease. Analysis of the impact of shift work on chronic inflammatory diseases is lacking. We investigated the association between shift work and asthma.
Inferior temporal tau is associated with accelerated prospective cortical thinning in clinically normal older adults.
NeuroImage, 2020

Neurofibrillary tau tangles are a hallmark pathology of Alzheimer's disease (AD) and are more closely associated with AD-related cortical atrophy and symptom severity than amyloid-beta (Aβ). However, studies regarding the effect of tau on longitudinal cortical thinning, particularly in healthy aging and preclinical AD, have been limited in number due to the relatively recent introduction of in vivo PET tracers for imaging tau pathology. Here, we investigate [18F]-flortaucipir (FTP, a marker of paired helical filament tau) PET as a predictor of atrophy in healthy aging and preclinical AD. We examine longitudinal structural MRI brain imaging data, retrospectively and prospectively relative to FTP imaging, using piecewise linear mixed-effect models with time centered at each participant's FTP-PET session. Participants include 111 individuals from the Harvard Aging Brain Study who underwent at least three MRI sessions over an average of 4.46 years and one FTP-PET at the approximate midpoint of the observation period. Our primary analyses focus on inferior temporal (IT) FTP standardized uptake value ratios and longitudinal FreeSurfer defined cortical regions of interest. Relationships were also explored using other regional FTP measures (entorhinal, composite, and local), within high and low Pittsburgh compound-B (PiB) PET groups, and with longitudinal subcortical volume. Strong associations between IT FTP and cortical thinning were found, most notably in temporal, midline, and prefrontal regions, with stronger effects generally observed in the prospective as compared to retrospective time frame. Significant differences between prospective and retrospective rates of thinning were found in the inferior and middle temporal gyri, cingulate areas, as well as pars orbitalis such that higher IT FTP was associated with greater prospective rates of thinning. Within the high PiB group, significant differences between prospective and retrospective rates of thinning were similarly observed. However, no consistent pattern of tau-related change in cortical thickness within the low PiB group was discerned. These results provide support for the hypothesis that tau pathology is a driver of future atrophy as well as provide additional evidence for tau-PET as an effective AD biomarker for interventional clinical trials.
Evaluation of the effect of Cooled HaEmodialysis on Cognitive function in patients suffering with end-stage KidnEy Disease (E-CHECKED): feasibility randomised control trial protocol.
Trials, 2020

Cognitive impairment is common in haemodialysis (HD) patients and is associated independently with depression and mortality. This association is poorly understood, and no intervention is proven to slow cognitive decline. There is evidence that cooler dialysis fluid (dialysate) may slow white matter changes in the brain, but no study has investigated the effect of cooler dialysate on cognition. This study addresses whether cooler dialysate can prevent the decline in cognition and improve quality of life (QOL) in HD patients.
Beyond action observation: Neurobehavioral mechanisms of memory for visually perceived bodies and actions.
Neuroscience and biobehavioral reviews, 2020

Examining the processing of others' body-related information in the perceivers' brain (action observation) is a key topic in cognitive neuroscience. However, what happens beyond the perceptual stage, when the body is not within view and it is transformed into an associative form that can be stored, updated, and later recalled, remains poorly understood. Here we examine neurobehavioural evidence on the memory processing of visually perceived bodily stimuli (dynamic actions and images of bodies). The reviewed studies indicate that encoding and maintaining bodily stimuli in memory recruits the sensorimotor system. This process arises when bodily stimuli are either recalled through action recognition or reproduction. Interestingly, the memory capacity for these stimuli is rather limited: only 2 or 3 bodily stimuli can be simultaneously held in memory. Moreover, this process is disrupted by increasing concurrent bodily operations; i.e., moving one's body, seeing or memorising additional bodies. Overall, the evidence suggests that the neural circuitry allowing us to move and feel ourselves supports the encoding, retention, and memory recall of others' visually perceived bodies.