rudyvdbrink/CitationDatabase huggingface dataset:
A simple linearization method unveils hidden enzymatic assay interferences.
Biophysical chemistry, 2019

Enzymes are among the most important drug targets in the pharmaceutical industry. The bioassays used to screen enzyme modulators can be affected by unaccounted interferences such as time-dependent inactivation and inhibition effects. Using procaspase-3, caspase-3, and α-thrombin as model enzymes, we show that some of these effects are not eliminated by merely ignoring the reaction phases that follow initial-rate measurements. We thus propose a linearization method (LM) for detecting spurious changes of enzymatic activity based on the representation of progress curves in modified coordinates. This method is highly sensitive to signal readout distortions, thereby allowing rigorous selection of valid kinetic data. The method allows the detection of assay interferences even when their occurrence is not suspected a priori. By knowing the assets and liabilities of the bioassay, enzymology results can be reported with enhanced reproducibility and accuracy. Critical analysis of full progress curves is expected to help discriminating experimental artifacts from true mechanisms of enzymatic inhibition.
European position paper on diagnostic tools in rhinology.
Rhinology, 2019

The accurate diagnosis of rhinologic disease depends on the clinical history, examination findings and, in many cases, further investigations. There are a wide variety of diagnostic tests available, the choice of which depends upon the condition being assessed. This position paper is intended to provide an up-to-date comprehensive description of the diagnostic tools available to rhinologists, allergists, general otolaryngologists and other physicians with an interest in sinonasal disease. The literature has been reviewed and evidence-based recommendations are included. The relevant history and examination techniques are described, including endoscopic assessment of the nose. General and disease-specific quality of life instruments are an important tool in assessing the impact of rhinologic disease and the response to treatment. Relevant blood tests are discussed, as well as the various methods of allergy testing. Techniques for collecting microbiological and tissue samples are described, as well as the use of more specialised tests such as nasal nitric oxide and those evaluating ciliary structure and function. Imaging techniques and their indications are included. Chemosensory (smell and taste) testing is explained, and the available techniques for objective measurement of nasal airflow and patency are reviewed. Prompt and accurate diagnosis allows appropriate management to be initiated; an understanding of the currently available diagnostic tools is a vital part of the assessment of rhinologic disease.
Microtubule organization is determined by the shape of epithelial cells.
Nature communications, 2016

Interphase microtubule organization is critical for cell function and tissue architecture. In general, physical mechanisms are sufficient to drive microtubule organization in single cells, whereas cells within tissues are thought to utilize signalling mechanisms. By improving the imaging and quantitation of microtubule alignment within developing Drosophila embryos, here we demonstrate that microtubule alignment underneath the apical surface of epithelial cells follows cell shape. During development, epidermal cell elongation and microtubule alignment occur simultaneously, but by perturbing cell shape, we discover that microtubule organization responds to cell shape, rather than the converse. A simple set of microtubule behaviour rules is sufficient for a computer model to mimic the observed responses to changes in cell surface geometry. Moreover, we show that microtubules colliding with cell boundaries zip-up or depolymerize in an angle-dependent manner, as predicted by the model. Finally, we show microtubule alignment responds to cell shape in diverse epithelia.
Skill learning induced plasticity of motor cortical representations is time and age-dependent.
Neurobiology of learning and memory, 2012

Movement representations in the motor cortex can reorganize to support motor skill learning during young adulthood. However, little is known about how motor representations change during aging or whether their change is influenced by continued practice of a skill after it is learned. We used intracortical microstimulation to characterize the organization of the forelimb motor cortex in young and aged C57/BL6 mice after short (2-4 weeks) or long (8 weeks) durations of training on a skilled reaching task or control procedures. In young mice, a short duration of reach training increased the area of proximal forelimb movement representations at the expense of distal representations. Following a longer training duration, ratios of proximal to distal movements returned to baseline, even with ongoing practice and skill maintenance. However, lingering changes were evident in thresholds for eliciting distal forelimb movements, which declined over the longer training period. In aged mice, movement representations and movement thresholds failed to change after either duration of training. Furthermore, there was an age-related loss of digit representations and performance decrements on other sensorimotor tests. Nevertheless, in quantitative measures of reaching success, aged mice learned and performed the skilled reaching task at least as well as younger mice. These results indicate that experience-driven topographical reorganization of motor cortex varies with age, as well as time, and is partially dissociable from behavioral performance. They also support an enduring capacity to learn new manual skills during aging, even as more youthful forms of cortical plasticity and sensorimotor function are lost.
Links between psychotic and neurotic symptoms in the general population: an analysis of longitudinal British National Survey data using Directed Acyclic Graphs.
Psychological medicine, 2019

Non-psychotic affective symptoms are important components of psychotic syndromes. They are frequent and are now thought to influence the emergence of paranoia and hallucinations. Evidence supporting this model of psychosis comes from recent cross-fertilising epidemiological and intervention studies. Epidemiological studies identify plausible targets for intervention but must be interpreted cautiously. Nevertheless, causal inference can be strengthened substantially using modern statistical methods.
The role of the prefrontal cortex in freezing of gait in Parkinson's disease: insights from a deep repetitive transcranial magnetic stimulation exploratory study.
Experimental brain research, 2017

Freezing of Gait (FOG) is one of the most debilitating gait impairments in Parkinson's disease (PD), leading to increased fall risk and reduced health-related quality of life. The utility of parkinsonian medications is often limited in the case of FOG and it frequently becomes dopamine resistant. Recent studies have suggested that pre-frontal cortex (PFC) dysfunction contributes to FOG; however, most previous findings provide only indirect evidence. To better understand the role of the PFC, we aimed to investigate the impact of high frequency, deep, repetitive transcranial magnetic stimulation (drTMS) of the medial PFC on FOG and its mediators. Nine patients with advanced PD participated in a randomized, cross-over exploratory study. We applied drTMS over the medial PFC for 16 weeks, with real and sham conditions; each condition included an intensive (i.e., 3 times a week) phase and a maintenance (once a week) phase. Scores on a FOG-provoking test, the motor part of the Unified Parkinson's Disease Rating Scale, and gait variability significantly improved after real drTMS, but not after the sham condition. Self-report of FOG severity and cognitive scores did not improve. Due to discomfort and pain during treatment, two patients dropped out and the study was halted. These initial findings support the cause-and-effect role of the pre-frontal cortex in FOG among patients with PD. Due to the small sample size, findings should be interpreted cautiously. Further studies are needed to more fully assess the role of the medial PFC in the underlying mechanism of FOG and the possibility of using non-invasive brain stimulation to modify FOG.
Sensorized pacifier to evaluate non-nutritive sucking in newborns.
Medical engineering & physics, 2016

We developed a device for an objective measurement of non-nutritive sucking (NNS). NNS is newborns' spontaneous action that is a predictor of their neural system development and can be adopted as an intervention to train oral feeding skills in preterms. Two miniaturized digital pressure sensors were embedded into a commercial pacifier and the two signals were simultaneously acquired using the Inter-Integrated circuit (I²C) interface. This solution traced a complete pressures profile of the sucking pattern in order to better understand the functional aspects of the two NNS phases, the suction and the expression. Experimental tests with nine newborns confirmed that the sensorized pacifier is an adequate tool for measuring NNS burst-pause patterns. The identified parameters related to the suction/expression rhythmicity could be used as indicators of the NNS ability. This device might be used both for exploring the possible diagnostic data contained in NNS pattern and for monitoring the sucking skills of premature infants.
Brain-behaviour modes of covariation in healthy and clinically depressed young people.
Scientific reports, 2019

Understanding how variations in dimensions of psychometrics, IQ and demographics relate to changes in brain connectivity during the critical developmental period of adolescence and early adulthood is a major challenge. This has particular relevance for mental health disorders where a failure to understand these links might hinder the development of better diagnostic approaches and therapeutics. Here, we investigated this question in 306 adolescents and young adults (14-24 y, 25 clinically depressed) using a multivariate statistical framework, based on canonical correlation analysis (CCA). By linking individual functional brain connectivity profiles to self-report questionnaires, IQ and demographic data we identified two distinct modes of covariation. The first mode mapped onto an externalization/internalization axis and showed a strong association with sex. The second mode mapped onto a well-being/distress axis independent of sex. Interestingly, both modes showed an association with age. Crucially, the changes in functional brain connectivity associated with changes in these phenotypes showed marked developmental effects. The findings point to a role for the default mode, frontoparietal and limbic networks in psychopathology and depression.
α-Synuclein is a Novel Microtubule Dynamase.
Scientific reports, 2016

α-Synuclein is a presynaptic protein associated to Parkinson's disease, which is unstructured when free in the cytoplasm and adopts α helical conformation when bound to vesicles. After decades of intense studies, α-Synuclein physiology is still difficult to clear up due to its interaction with multiple partners and its involvement in a pletora of neuronal functions. Here, we looked at the remarkably neglected interplay between α-Synuclein and microtubules, which potentially impacts on synaptic functionality. In order to identify the mechanisms underlying these actions, we investigated the interaction between purified α-Synuclein and tubulin. We demonstrated that α-Synuclein binds to microtubules and tubulin α2β2 tetramer; the latter interaction inducing the formation of helical segment(s) in the α-Synuclein polypeptide. This structural change seems to enable α-Synuclein to promote microtubule nucleation and to enhance microtubule growth rate and catastrophe frequency, both in vitro and in cell. We also showed that Parkinson's disease-linked α-Synuclein variants do not undergo tubulin-induced folding and cause tubulin aggregation rather than polymerization. Our data enable us to propose α-Synuclein as a novel, foldable, microtubule-dynamase, which influences microtubule organisation through its binding to tubulin and its regulating effects on microtubule nucleation and dynamics.
Association of amyloid angiopathy with microbleeds in logopenic progressive aphasia: an imaging-pathology study.
European journal of neurology, 2021

Cerebral microbleeds (MB) and superficial siderosis (SS) are frequent neuroimaging findings in patients with logopenic progressive aphasia (LPA), often with frontal lobe predilection. Cerebral amyloid angiopathy (CAA) is hypothesized to be the major pathologic determinant of MB/SS in these patients; however, neuroimaging-pathologic data are limited.
Domain-General Learning and Memory Substrates of Reading Acquisition.
Mind, brain and education : the official journal of the International Mind, Brain, and Education Society, 2020

Prior research has demonstrated that linguistic skills and knowledge contribute to successful reading acquisition. In contrast, little is known about the influence of domain-general learning abilities on reading. To investigate associations between general memory functions and reading during the early stages of learning to read, performance measures of word-level reading and of declarative and procedural learning were obtained in a cohort of 140 children, annually during their first 4 years of school. We hypothesized that differences in learning task performance would relate to reading ability in the early years, when children are first learning to read. We employed a series of linear mixed effects models to test the relationships between learning abilities and reading across time. Declarative learning performance predicted reading ability in first grade, while procedural learning performance predicted reading ability in second grade. Our findings suggest that reading acquisition may depend in part on general capacities for learning.
Time course of pharmacokinetic and hormonal effects of inhaled high-dose salvinorin A in humans.
Journal of psychopharmacology (Oxford, England), 2016

Salvinorin A is a kappa opioid agonist and the principal psychoactive constituent of the Salvia divinorum plant, which has been used for hallucinogenic effects. Previous research on salvinorin A pharmacokinetics likely underestimated plasma levels typically resulting from the doses administered due to inefficient vaporization and not collecting samples during peak drug effects. Six healthy adults inhaled a single high dose of vaporized salvinorin A (n = 4, 21 mcg/kg; n = 2, 18 mcg/kg). Participant- and monitor-rated effects were assessed every 2 min for 60 min post-inhalation. Blood samples were collected at 13 time points up to 90 min post-inhalation. Drug levels peaked at 2 min and then rapidly decreased. Drug levels were significantly, positively correlated with participant and monitor drug effect ratings. Significant elevations in prolactin were observed beginning 5 min post-inhalation and peaking at 15 min post-inhalation. Cortisol showed inconsistent increases across participants. Hormonal responses were not well correlated with drug levels. This is the first study to demonstrate a direct relationship between changes in plasma levels of salvinorin A and drug effects in humans. The results confirm the efficacy of an inhalation technique for salvinorin A.
Identification of a novel gene regulating amygdala-mediated fear extinction.
Molecular psychiatry, 2019

Recent years have seen advances in our understanding of the neural circuits associated with trauma-related disorders, and the development of relevant assays for these behaviors in rodents. Although inherited factors are known to influence individual differences in risk for these disorders, it has been difficult to identify specific genes that moderate circuit functions to affect trauma-related behaviors. Here, we exploited robust inbred mouse strain differences in Pavlovian fear extinction to uncover quantitative trait loci (QTL) associated with this trait. We found these strain differences to be resistant to developmental cross-fostering and associated with anatomical variation in basolateral amygdala (BLA) perineuronal nets, which are developmentally implicated in extinction. Next, by profiling extinction-driven BLA expression of QTL-linked genes, we nominated Ppid (peptidylprolyl isomerase D, a member of the tetratricopeptide repeat (TPR) protein family) as an extinction-related candidate gene. We then showed that Ppid was enriched in excitatory and inhibitory BLA neuronal populations, but at lower levels in the extinction-impaired mouse strain. Using a virus-based approach to directly regulate Ppid function, we demonstrated that downregulating BLA-Ppid impaired extinction, while upregulating BLA-Ppid facilitated extinction and altered in vivo neuronal extinction encoding. Next, we showed that Ppid colocalized with the glucocorticoid receptor (GR) in BLA neurons and found that the extinction-facilitating effects of Ppid upregulation were blocked by a GR antagonist. Collectively, our results identify Ppid as a novel gene involved in regulating extinction via functional actions in the BLA, with possible implications for understanding genetic and pathophysiological mechanisms underlying risk for trauma-related disorders.
Evolution of the binge drinking pattern in college students: neurophysiological correlates.
Alcohol (Fayetteville, N.Y.), 2014

It is well known that alcohol impairs response inhibition and that adolescence is a critical period of neuromaturation where cognitive processes such as inhibitory control are still developing. In recent years, growing evidence has shown the negative consequences of alcohol binge drinking on the adolescent and young human brain. However, the effects of cessation of binge drinking on brain function remain unexplored. The objective of the present study was to examine brain activity during response execution and inhibition in young binge drinkers in relation to the progression of their drinking habits over time. Event-related potentials (ERPs) elicited by a Go/NoGo task were recorded twice within a 2-year interval in 57 undergraduate students (25 controls, 22 binge drinkers, and 10 ex-binge drinkers) with no personal or family history of alcoholism or psychopathological disorders. The results showed that the amplitude of NoGo-P3 over the frontal region correlated with an earlier age of onset of regular drinking as well as with greater quantity and speed of alcohol consumption. Regression analysis showed that NoGo-P3 amplitude was significantly predicted by the speed of alcohol intake and the age of onset of regular drinking. The group comparisons showed that, after maintaining a binge drinking pattern for at least 2 years, binge drinkers displayed significantly larger NoGo-P3 amplitudes than controls, whereas ex-binge drinkers were in an intermediate position between the two other groups (with no significant differences with respect to controls or binge drinkers). These findings suggest that binge drinking in young people may impair the neural functioning related to inhibitory processes, and that the cessation of binge drinking may act as a brake on the neurophysiological impairments related to response inhibition.
Quantifying the performance of MEG source reconstruction using resting state data.
NeuroImage, 2018

In magnetoencephalography (MEG) research there are a variety of inversion methods to transform sensor data into estimates of brain activity. Each new inversion scheme is generally justified against a specific simulated or task scenario. The choice of this scenario will however have a large impact on how well the scheme performs. We describe a method with minimal selection bias to quantify algorithm performance using human resting state data. These recordings provide a generic, heterogeneous, and plentiful functional substrate against which to test different MEG recording and reconstruction approaches. We used a Hidden Markov model to spatio-temporally partition data into self-similar dynamic states. To test the anatomical precision that could be achieved, we then inverted these data onto libraries of systematically distorted subject-specific cortical meshes and compared the quality of the fit using cross validation and a Free energy metric. This revealed which inversion scheme was able to identify the least distorted (most accurate) anatomical models, and allowed us to quantify an upper bound on the mean anatomical distortion accordingly. We used two resting state datasets, one recorded with head-casts and one without. In the head-cast data, the Empirical Bayesian Beamformer (EBB) algorithm showed the best mean anatomical discrimination (3.7 mm) compared with Minimum Norm/LORETA (6.0 mm) and Multiple Sparse Priors (9.4 mm). This pattern was replicated in the second (conventional dataset) although with a marginally poorer (non-significant) prediction of the missing (cross-validated) data. Our findings suggest that the abundant resting state data now commonly available could be used to refine and validate MEG source reconstruction methods and/or recording paradigms.
Reciprocal Spatiotemporally Controlled Apoptosis Regulates Wolffian Duct Cloaca Fusion.
Journal of the American Society of Nephrology : JASN, 2018

The epithelial Wolffian duct (WD) inserts into the cloaca (primitive bladder) before metanephric kidney development, thereby establishing the initial plumbing for eventual joining of the ureters and bladder. Defects in this process cause common anomalies in the spectrum of congenital anomalies of the kidney and urinary tract (CAKUT). However, developmental, cellular, and molecular mechanisms of WD-cloaca fusion are poorly understood. Through systematic analysis of early WD tip development in mice, we discovered that a novel process of spatiotemporally regulated apoptosis in WD and cloaca was necessary for WD-cloaca fusion. Aberrant RET tyrosine kinase signaling through tyrosine (Y) 1062, to which PI3K- or ERK-activating proteins dock, or Y1015, to which PLC
Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs.
Nature biotechnology, 2019

Fluorescent RNAs (FRs), aptamers that bind and activate fluorescent dyes, have been used to image abundant cellular RNA species. However, limitations such as low brightness and limited availability of dye/aptamer combinations with different spectral characteristics have limited use of these tools in live mammalian cells and in vivo. Here, we develop Peppers, a series of monomeric, bright and stable FRs with a broad range of emission maxima spanning from cyan to red. Peppers allow simple and robust imaging of diverse RNA species in live cells with minimal perturbation of the target RNA's transcription, localization and translation. Quantification of the levels of proteins and their messenger RNAs in single cells suggests that translation is governed by normal enzyme kinetics but with marked heterogeneity. We further show that Peppers can be used for imaging genomic loci with CRISPR display, for real-time tracking of protein-RNA tethering, and for super-resolution imaging. We believe these FRs will be useful tools for live imaging of cellular RNAs.
Variation in genes encoding the neuroactive steroid synthetic enzymes 5α-reductase type 1 and 3α-reductase type 2 is associated with alcohol dependence.
Alcoholism, clinical and experimental research, 2011

Studies of alcohol effects in rodents and in vitro implicate endogenous neuroactive steroids as key mediators of alcohol effects at GABA(A) receptors. We used a case-control sample to test the association with alcohol dependence (AD) of single nucleotide polymorphisms in the genes encoding two key enzymes required for the generation of endogenous neuroactive steroids: 5α-reductase, type I (5α-R), and 3α-hydroxysteroid dehydrogenase, type 2 (3α-HSD), both of which are expressed in human brain.