rudyvdbrink/CitationDatabase huggingface dataset:
LexOPS: An R package and user interface for the controlled generation of word stimuli.
Behavior research methods, 2020

LexOPS is an R package and user interface designed to facilitate the generation of word stimuli for use in research. Notably, the tool permits the generation of suitably controlled word lists for any user-specified factorial design and can be adapted for use with any language. It features an intuitive graphical user interface, including the visualization of both the distributions within and relationships among variables of interest. An inbuilt database of English words is also provided, including a range of lexical variables commonly used in psycholinguistic research. This article introduces LexOPS, outlining the features of the package and detailing the sources of the inbuilt dataset. We also report a validation analysis, showing that, in comparison to stimuli of existing studies, stimuli optimized with LexOPS generally demonstrate greater constraint and consistency in variable manipulation and control. Current instructions for installing and using LexOPS are available at https://JackEdTaylor.github.io/LexOPSdocs/ .
Endovascular Therapy for Acute Ischemic Stroke: A Comprehensive Review of Current Status.
Cardiovascular revascularization medicine : including molecular interventions, 2019

Stroke remains among the leading causes of disability and death worldwide. Fibrinolytic therapy is associated with poor patency and functional outcomes. Recently, multiple randomized trials have been published that have consolidated the role of endovascular therapy for ischemic stroke due to large vessel occlusion in the anterior cerebral circulation. This manuscript reviews the current understanding of the endovascular management of acute stroke including technical aspects and current evidence base.
Injectable Glycosaminoglycan-Based Cryogels from Well-Defined Microscale Templates for Local Growth Factor Delivery.
ACS chemical neuroscience, 2021

Glycosaminoglycan-based hydrogels hold great potential for applications in tissue engineering and regenerative medicine. By mimicking the natural extracellular matrix processes of growth factor binding and release, such hydrogels can be used as a sustained delivery device for growth factors. Since neural networks commonly follow well-defined, high-aspect-ratio paths through the central and peripheral nervous system, we sought to create a fiber-like, elongated growth factor delivery system. Cryogels, with networks formed at subzero temperatures, are well-suited for the creation of high-aspect-ratio biomaterials, because they have a macroporous structure making them mechanically robust (for ease of handling) yet soft and highly compressible (for interfacing with brain tissue). Unlike hydrogels, cryogels can be synthesized in advance of their use, stored with ease, and rehydrated quickly to their original shape. Herein, we use solvent-assisted microcontact molding to form sacrificial templates, in which we produced highly porous cryogel microscale scaffolds with a well-defined elongated shape via the photopolymerization of poly(ethylene glycol) diacrylate and maleimide-functionalized heparin. Dissolution of the template yielded cryogels that could load nerve growth factor (NGF) and release it over a period of 2 weeks, causing neurite outgrowth in PC12 cell cultures. This microscale template-assisted synthesis technique allows tight control over the cryogel scaffold dimensions for high reproducibility and ease of injection through fine gauge needles.
Epigenome-wide association study of Alzheimer's disease replicates 22 differentially methylated positions and 30 differentially methylated regions.
Clinical epigenetics, 2020

Growing evidence shows that epigenetic modifications play a role in Alzheimer's disease (AD). We performed an epigenome-wide association study (EWAS) to evaluate the DNA methylation differences using postmortem superior temporal gyrus (STG) and inferior frontal gyrus (IFG) samples.
Polycyclic aromatic hydrocarbons exposures and telomere length: A cross-sectional study on preschool children.
Environmental research, 2021

Exposure to polycyclic aromatic hydrocarbons (PAHs) has been associated with shorter telomere length (TL), a marker of ageing at cellular level. However, the available evidence on this association among children is still scarce. We therefore aimed to assess, the relationship between urinary 1-hydroxipayrene (1-OHP), a marker of exposure to PAHs, and relative leukocyte TL (LTL) in children at preschool age. Our study was based on 200 children enrolled from 27 randomly-selected kindergartens in the city of Sabzevar, Iran (2017). 1-OHP levels in the participants' urine samples were measured using solid phase extraction (SPE) method and high-performance liquid chromatography (HPLC). Moreover, real-time PCR was used to measure the LTL in the participants' blood samples. Linear mixed effects models, controlled for relevant covariates, were applied to investigate the association of 1-OHP concentration and LTL. The median (interquartile range (IQR)) of relative LTL and urinary 1-OHP were 0.83 (0.7) and 257 (375.5) ng/L, respectively. In the fully adjusted model, an IQR increase in urinary 1-OHP was related to -0.05 (95% confidence interval (CI): 0.09, -0.01, P-value = 0.02) decrease in relative LTL. This association was similar among boys and girls; however, we observed indications for a stronger association for those children whose parents had university education. Our study suggested an inverse relationship between urinary 1-OHP and LTL in children at preschool age. However, further longitudinal research with repeated measures of PAHs and LTL are needed to confirm these findings.
Long-term benefit of enzyme replacement therapy with alglucosidase alfa in adults with Pompe disease: Prospective analysis from the French Pompe Registry.
Journal of inherited metabolic disease, 2020

Despite a wide clinical spectrum, the adult form of Pompe disease is the most common one, and represents more than 90% of diagnosed patients in France. Since the marketing of enzyme replacement therapy (alglucosidase alfa, Myozyme), all reports to date in adults demonstrated an improvement of the walking distance, and a trend toward stabilization of respiratory function, but the majority of these studies were less than 5 years of duration. We report here the findings from 158 treated patients included in the French Pompe Registry, who underwent regular clinical assessments based on commonly used standardized tests (6-minute walking test, MFM scale, sitting vital capacity, MIP and MEP). For longitudinal analyses, the linear mixed effects models were used to assess trends in primary endpoints over time under ERT. A two-phase model better described the changes in distance traveled in the 6-minute walk test and MFM. 6MWT showed an initial significant increase (1.4% ± 0.5/year) followed by a progressive decline (-2.3%/year), with a cut-off point at 2.2 years. A similar pattern was observed in total MFM score (6.6% ± 2.3/year followed by a - 1.1%/year decline after 0.5 years). A single-phase decline with a slope of -0.9 ± 0.1%/year (P < .001) was observed for FVC, and MEP remained stable over the all duration of follow-up. This study provides further evidence that ERT improves walking abilities and likely stabilizes respiratory function in adult patients with Pompe disease, with a ceiling effect for the 6MWT in the first 3 years of treatment.
Identification of α-chimaerin as a candidate gene for critical period neuronal plasticity in cat and mouse visual cortex.
BMC neuroscience, 2011

In cat visual cortex, critical period neuronal plasticity is minimal until approximately 3 postnatal weeks, peaks at 5 weeks, gradually declines to low levels at 20 weeks, and disappears by 1 year of age. Dark rearing slows the entire time course of this critical period, such that at 5 weeks of age, normal cats are more plastic than dark reared cats, whereas at 20 weeks, dark reared cats are more plastic. Thus, a stringent criterion for identifying genes that are important for plasticity in visual cortex is that they show differences in expression between normal and dark reared that are of opposite direction in young versus older animals.
RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.
Nucleic acids research, 2018

RepeatsDB-lite (http://protein.bio.unipd.it/repeatsdb-lite) is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are a widespread but poorly annotated class of non-globular proteins carrying heterogeneous functions. RepeatsDB-lite extends the prediction to all TR types and strongly improves the performance both in terms of computational time and accuracy over previous methods, with precision above 95% for solenoid structures. The algorithm exploits an improved TR unit library derived from the RepeatsDB database to perform an iterative structural search and assignment. The web interface provides tools for analyzing the evolutionary relationships between units and manually refine the prediction by changing unit positions and protein classification. An all-against-all structure-based sequence similarity matrix is calculated and visualized in real-time for every user edit. Reviewed predictions can be submitted to RepeatsDB for review and inclusion.
Effectiveness of osteopathic interventions in chronic non-specific low back pain: A systematic review and meta-analysis.
Complementary therapies in medicine, 2021

Chronic low back pain (CLBP) is a frequent cause of disability and it represents a medical, social and economic burden globally. Therefore, we assessed effectiveness of osteopathic interventions in the management of NS-CLBP for pain and functional status.
Rare Bilateral Caudate Infarction in a Patient with a Common Circle of Willis Variant.
The Canadian journal of neurological sciences. Le journal canadien des sciences neurologiques, 2019

A 62-year-old male presented to hospital with acute aphasia. His past medical history was significant for a previous left middle cerebral artery stroke, from which he fully recovered, hypertension, dyslipidemia, coronary artery disease, one episode of atrial fibrillation postoperatively, and thalidomide exposure in utero. Although initially he was thought to be aphasic, on further examination, he demonstrated significant abulia. His level of consciousness was normal, and neurological examination was otherwise unremarkable. A CT angiogram of the head and neck was performed. The patient was not a candidate for acute therapy, as he had established stroke on imaging, and the time of onset was unclear.
Animal Models of CMT2A: State-of-art and Therapeutic Implications.
Molecular neurobiology, 2020

Charcot-Marie-Tooth disease type 2A (CMT2A), arising from mitofusin 2 (MFN2) gene mutations, is the most common inherited axonal neuropathy affecting motor and sensory neurons. The cellular and molecular mechanisms by which MFN2 mutations determine neuronal degeneration are largely unclear. No effective treatment exists for CMT2A, which has a high degree of genetic/phenotypic heterogeneity. The identification of mutations in MFN2 has allowed the generation of diverse transgenic animal models, but to date, their ability to recapitulate the CMT2A phenotype is limited, precluding elucidation of its pathogenesis and discovery of therapeutic strategies. This review will critically present recent progress in in vivo CMT2A disease modeling, discoveries, drawbacks and limitations, current challenges, and key reflections to advance the field towards developing effective therapies for these patients.
Video data for the cognitive mapping process of NeuroBayesSLAM system.
Data in brief, 2020

Simultaneous localization and mapping (SLAM), which addresses the problem of constructing a spatial map of an unknown environment while simultaneously determining the mobile robot's position relative to this map, is regarded as one of the key technologies in mobile robot navigation. This data article presents four raw video files, demonstrating the mapping and localization processes of NeuroBayesSLAM, a neurobiologically inspired SLAM system, on two publicly available datasets, namely the St Lucia suburb dataset and the iRat Australia dataset. The cognitive mapping process was recorded by a free screen recorder software on ubuntu Linux system. Neural activities of the head-direction cells and the grid cells, the local view templates of visual scenes, and experience map were included. These data envision the possibility of transferring the multisensory integration mechanism found in the spatial memory circuits of the mammalian brain to develop intelligent cognitive mapping systems for indoor and large outdoor environments as in the research article "NeuroBayesSLAM: Neurobiologically Inspired Bayesian Integration of Multisensory Information for Robot Navigation" Zeng et al., 2020.
Estimation and testing problems in auditory neuroscience via clustering.
Biometrics, 2017

The processing of auditory information in neurons is an important area in neuroscience. We consider statistical analysis for an electrophysiological experiment related to this area. The recorded synaptic current responses from the experiment are observed as clusters, where the number of clusters is related to an important characteristic of the auditory system. This number is difficult to estimate visually because the clusters are blurred by biological variability. Using singular value decomposition and a Gaussian mixture model, we develop an estimator for the number of clusters. Additionally, we provide a method for hypothesis testing and sample size determination in the two-sample problem. We illustrate our approach with both simulated and experimental data.
Reversal of Visual Feedback Modulates Somatosensory Plasticity.
Neuroscience, 2021

Reversed visual feedback during unimanual training increases transfer of skills to the opposite untrained hand and modulates plasticity in motor areas of the brain. However, it is unclear if unimanual training with reversed visual feedback also affects somatosensory areas. Here we manipulated visual input during unimanual training using left-right optical reversing spectacles and tested whether unimanual training with reversed vision modulates somatosensory cortical excitability to facilitate motor performance. Thirty participants practiced a unimanual ball-rotation task using the right hand with either left-right reversed vision (incongruent visual and somatosensory feedback) or direct vision (congruent feedback) of the moving hand. We estimated cortical excitability in primary somatosensory cortex (S1) before and after unimanual training by measuring somatosensory evoked potentials (SEPs). This was done by electrically stimulating the median nerve in the wrist while participants rested, and recording potentials over both hemispheres using electroencephalography. Performance of the ball-rotation task improved for both the right (trained) and left (untrained) hand after training across both direct and reversed vision conditions. Participants with direct vision of the right hand during training showed SEPs amplitudes increased bilaterally. In contrast, participants in the reversed visual condition showed attenuated SEPs following training. The results suggest that cortical suppression of S1 activity supports skilled motor performance after unimanual training with reversed vision, presumably by sensory gating of afferent signals from the movement. This finding provides insight into the mechanisms by which visual input interacts with the sensorimotor system and induces neuroplastic changes in S1 to support skilled motor performance.
Autistic-like behaviours and associated brain structural plasticity are modulated by oxytocin in maternally separated rats.
Behavioural brain research, 2020

Early psycho-social experiences influence the developing brain and possible onset of various neurodevelopmental disorders, such as Autism Spectrum Disorder (ASD). ASD is characterized by a variety of brain abnormalities, including alteration of oxytocin receptors in the brain. Recently, early life adverse experiences, such as maternal separation (MS), have been shown to constitute risk factors for ASD in preclinical studies. Therefore, the main aims of the current study were to i) explore the association between onset of autistic-like behaviours and molecular/structural changes in the brain following MS, and ii) evaluate the possible beneficial effects of oxytocin treatment on the same parameters.
Event-related potential correlates of gist and verbatim encoding.
International journal of psychophysiology : official journal of the International Organization of Psychophysiology, 2010

The neural correlates of gist and verbatim encoding of episodes sharing semantically related components were investigated. At study, participants were presented with lists of word pairs formed by pairing one of two associated words with different associates of an unstudied theme word. At test, participants discriminated Old pairs from rearranged pairs generated by re-pairing study pairs belonging to the same study list (Intra pairs) or different study lists (Inter pairs). ERPs were recorded for each study pair. For the study pairs that later served as Old pairs, the ERPs were more positive when these pairs were subsequently correctly identified than when they were incorrectly rejected. For the study pairs containing words that subsequently appeared in Intra pairs, the ERPs were also more positive when the Intra pair was correctly rejected than when it was incorrectly accepted. However, the topographies of the subsequent memory effects for accepted Old pairs and rejected Intra pairs were different. We argue that specific information is more important for rejecting Intra pairs than accepting Old pairs. The different topographies of these two subsequent memory effects therefore reflect qualitatively distinct encoding operations for specific and non-specific information.
Kinematic analysis of sensorimotor behavior during variable ladder rung walking in short-tailed opossums (
STAR protocols, 2021

This protocol presents a workflow for detecting differences in kinematics between experimental conditions. It is tailored for short-tailed opossums but can be applied to any species capable of completing the ladder rung task. There are four phases of this protocol: (1) data collection, (2) pose tracking, (3) analysis of single trials, and (4) cross-condition comparisons. This pipeline implements aspects of machine learning and signal processing, allowing for rapid data analysis that provides insight into how animals perform this task. For complete details on the use and execution of this protocol, please refer to Englund et al. (2020).
Modeling of Frontotemporal Dementia Using iPSC Technology.
International journal of molecular sciences, 2020

Frontotemporal dementia (FTD) is caused by the progressive degeneration of the frontal and temporal lobes of the brain. Behavioral variant FTD (bvFTD) is the most common clinical subtype of FTD and pathological subtypes of bvFTD are known as FTD-tau, transactive response (TAR) DNA-binding protein 43 (TDP-43), and fused in sarcoma (FUS). Pathological mechanisms of bvFTD are largely unknown. In this study, we investigated the expression of pathological markers, such as p-Tau, TDP-43, and FUS, in the induced pluripotent stem-cell-derived neurons (iPSN) from two sporadic bvFTD patients and one normal subject. We also used an FTD-patient-derived iPSC-line-carrying microtubule-associated protein tau
Calorie restriction promotes remyelination in a Cuprizone-Induced demyelination mouse model of multiple sclerosis.
Metabolic brain disease, 2020

Over the past few decades several attempts have been made to introduce a potential and promising therapy for Multiple sclerosis (MS). Calorie restriction (CR) is a dietary manipulation to reduce calorie intake which has been shown to improve neuroprotection and attenuate neurodegenerative disorders. Here, we evaluated the effect of 33% CR regimen for 4 weeks on the remyelination capacity of Cuprizone (CPZ) induced demyelination in a mouse model of MS. Results showed that CR induced a significant increase in motor coordination and balance performance in CPZ mice. Also, luxol fast blue (LFB) staining showed that CR regimen significantly improved the remyelination in the corpus callosum of CPZ + CR mice compared to the CPZ group. In addition, CR regimen significantly increased the transcript expression levels of BDNF, Sox2, and Sirt1 in the corpus callosum of CPZ mice, while decreasing the p53 levels. Moreover, CR regimen significantly decreased the apoptosis rate. Furthermore, astrogliosis (GFAP + astrocytes) and microgliosis (Iba-1 + microglia) were significantly decreased by CR regimen while oligodendrogenesis (Olig2+) and Sirt1 + cell expression were significantly increased in the corpus callosum of CPZ + CR mice compared to the CPZ group. In conclusion, CR regimen can promote remyelination potential in a CPZ-demyelinating mouse model of MS by increasing oligodendrocyte generation while decreasing their apoptosis.
Migraine-like headache with autonomic symptoms in midbrain malformation.
Headache, 2014

We report a case of midbrain malformation characterized by right deviation of the medulla oblongata associated with elongation and ectasia of the basilar and left vertebral arteries in a patient with a long history of migraine-like headache with autonomic symptoms.
Development and preliminary validation of the Chronic Pain Acceptance Questionnaire for Clinicians.
Scandinavian journal of pain, 2020

Background and Aims Higher chronic pain acceptance is associated with lower pain and disability. Clinician beliefs are associated with patients' beliefs. This study therefore aimed to develop the Chronic Pain Acceptance Questionnaire for Clinicians (CPAQ-C) to measure clinicians' beliefs regarding the importance of levels of acceptance in patients with chronic pain, and to examine the questionnaire's psychometric properties. Methods Phase one: the CPAQ-C was adapted from the Chronic Pain Acceptance Questionnaire. Data on 162 completed questionnaires were analysed using Rasch analysis. Phase Two: the cohort completed the Healthcare Providers Pain and Impairment Relationship Scale, and the association (Pearson's correlation co-efficient) between these questionnaires examined to assist CPAQ-C validation. Twenty-four participants completed the CPAQ-C one-week later. Test re-test reliability was examined using intraclass correlation co-efficient (2,1) and standard error of measurement. Phase Three: to examine responsiveness 17 clinicians attending a workshop on Acceptance and Commitment Therapy completed the CPAQ-C before and immediately after the workshop, and six-months later. The Skillings Mack test was used to determine whether CPAQ-C scores differed across different timepoints. Results Rasch analysis supported two subscales: activity engagement and pain willingness. Five poorly functioning items were excluded. There was good correlation between the CPAQ-C and Healthcare Providers Pain and Impairment Relationship Scale (-.54). The CPAQ-C demonstrated good reliability (ICC (2,1): .81; standard error of measurement: 4.76). There was significant improvement in CPAQ-C scores following the workshop (p=<.001). Conclusions The CPAQ-C appears a valid, reliable and responsive measure of clinicians' beliefs regarding the importance of levels of acceptance in patients with chronic pain. Implications Where the CPAQ-C reveals that clinicians have low perceived levels of importance regarding acceptance in patients with chronic pain those clinicians may benefit from specific education, however, this requires further examination.
Axons Navigate Noise with 190RhoGAP.
Neuron, 2019

In this issue of Neuron, Bonanomi et al. (2019) investigate how navigating axons ignore irrelevant guidance signals. They show that the binding of p190RhoGAP to DCC suppresses inappropriate responses to Netrin-1, allowing motor axons to exit the embryonic spinal cord.