rudyvdbrink/CitationDatabase huggingface dataset:
Dictionary learning for sparse representation and classification of neural spikes.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference, 2016

Spike sorting is the problem of identifying and clustering neurons spiking activity from recorded extracellular electro-physiological data. This is important for experimental neuroscience. Existing approaches to solve this problem consist of three steps: spike detection, feature extraction, and clustering. In our method, we use Fisher discriminant based dictionary learning to learn dictionary, whose sub-dictionaries are class specific, and estimate discriminative sparse coding coefficients by minimizing the within class scatter and maximizing the between class scatter. Both the reconstruction error and coding coefficients are used for clustering the testing data. The dictionary learn the proper features specific to this problem. The proposed method has high reconstruction power and high clustering accuracy of testing data.
Neurophysiological Evaluation of a Customizable μECoG-based Wireless Brain Implant.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference, 2018

The number of implantable bidirectional neural interfaces available for neuroscientific research applications is still limited, despite the rapidly increasing number of customized components. We previously reported on how to translate available components into "ready-to-use" wireless implantable systems utilizing components off-the-shelf (COTS). The aim of the present study was to verify the viability of a micro-electrocorticographic ($\mu $ECoG) device built by this approach. Functionality for both neural recording and stimulation was evaluated in an ovine animal model using acoustic stimuli and cortical electrical stimulation, respectively. We show that auditory evoked responses were reliably recorded in both time and frequency domain and present data that demonstrates the cortical electrical stimulation functionality. The successful recording of neuronal activity suggests that the device can compete with existing implantable systems as a neurotechnological research tool.
[Changes of the outcomes of epilepsy surgery within 10 years in the National Institute of Clinical Neurosciences, Hungary].
Orvosi hetilap, 2021

Összefoglaló. Bevezetés és célkitűzés: A terápiarezisztens fokális epilepsziák sebészeti kezelése elterjedten használt kezelési lehetőség. Célunk az epilepsziasebészet-hatékonyság változásának vizsgálata egy évtizednyi távlatból a budapesti centrumban. Módszerek: Az Országos Klinikai Idegtudományi Intézetben reszektív epilepsziasebészeti beavatkozásokon átesett fokális epilepsziás betegek adatai kerültek feldolgozásra. A vizsgált 10 év beteganyagát két periódusra osztottuk a műtét időpontja szerint (2006-2010 és 2011-2016). Vizsgálati szempontjaink: demográfiai adatok, az epilepszia kezdete és típusa, mágnesesrezonancia-lelet, preoperatív rohamfrekvencia, műtéttípus és szövettani lelet. Az epileptológiai kimenetelt az Engel-klasszifikáció alapján értékeltük. Eredmények: Epilepsziasebészeti beavatkozás 187 betegen történt, akik közül 137-nél került sor reszekciós műtétre. A betegek 65%-ában temporalis, 18%-ában frontalis, míg 7%-ában olyan multilobaris epilepszia igazolódott, mely a temporalis vagy a frontalis lebenyt érintette. Teljes rohammentességet (Engel I/A) az 1. évben 68%-ban, a 2. évben 64%-ban, míg az 5. évben 63%-ban mértünk. A két intervallum összehasonlításakor az 1 éves rohammentesség aránya 60%-ról (temporalis: 67%, extratemporalis: 50%) 73%-ra (temporalis: 79%, extratemporalis: 62%) javult a második periódusban. Az etiológia szempontjából a hippocampalis sclerosis aránya 28%-ról 14%-ra csökkent, a fokális corticalis dysplasiák aránya 22%-ról 31%-ra növekedett. Következtetés: A sebészeti kezelés fokális epilepsziák esetén - alapos előzetes kivizsgálást követően - általában biztonságos és a legnagyobb arányban sikeres beavatkozás. A legkedvezőbb kimenetel temporalis lokalizációban érhető el. A hatékonyság az évek során egyre javuló tendenciát mutatott az egyre nehezebb sebészeti esetek ellenére. Ez magyarázható a sebészeti technikák fejlődésével, illetve a jobb, műtét előtti elektrofiziológiai és képalkotó technikákkal, amelyek bevezetésével pontosabb lokalizáció adható. Orv Hetil. 2021; 162(6): 219-226.
Identification and Evaluation of Controlled Trials in Pediatric Cardiology: Crowdsourced Scoping Review and Creation of Accessible Searchable Database.
The Canadian journal of cardiology, 2020

Cardiac disease in children is associated with significant morbidity and mortality as well as increased health resource utilisation. There is a perception that there is a paucity of high-quality studies, particularly randomized controlled trials (RCTs), in the field of pediatric cardiology. We sought to identify, examine, and map the range of RCTs conducted in children with cardiac conditions, including the development of a searchable open-access database. A literature search was conducted encompassing MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials from inception to 2018. All English-language RCTs enrolling children (age 0-21 years) with cardiac conditions were included. Data extraction and risk of bias assessments were performed in duplicate via crowdsourcing for each eligible study and entered into an online database. A total of 933 RCTs met eligibility criteria. Median trial recruitment was 49 patients (interquartile range 30-86) with 18.9% of studies (n = 176) including > 100 patients. A wide variety of populations and interventions were encompassed with congenital heart disease (79.8% of RCTs) and medications (63.3% of RCTs) often studied. Just over one-half of the trials (53.4%) clearly identified a primary outcome, and fewer than half (46.6%) fully documented a robust randomization process. Trials were summarised in a searchable online database (https://pediatrics.knack.com/cardiology-rct-database#cardiology-rcts/). Contrary to a commonly held perception, there are nearly 1,000 published RCTs in pediatric cardiology. The open-access database created as part of this project provides a resource that facilitates an efficient comprehensive review of the literature for clinicians and researchers caring for children with cardiac issues.
Multidisciplinary approach to enhancing provider well-being in a metropolitan medical group in the United States.
BMC family practice, 2020

Physician burnout refers to depersonalization, emotional exhaustion, and a sense of lower personal accomplishment. Affecting approximately 50% of physicians in the United States, physician burnout negatively impacts both the physician and patient. Over a 3-year-period, this prospective study evaluated the multidisciplinary approach to decreasing provider burnout and improving provider well-being in our metropolitan community.
A case of complete remission of advanced hepatocellular carcinoma with type III portal vein tumor thrombosis treated using transarterial chemoembolization with microspheres and radiation therapy.
Clinical journal of gastroenterology, 2020

Portal vein tumor thrombosis (PVTT) is an extremely locally advanced form of hepatocellular carcinoma. The natural median survival time of patients with hepatocellular carcinoma with PVTT is 2.7 to 4.0 months. A 63-year-old woman visited our clinic complaining of abdominal distention and appetite loss, which she had had for 3 weeks prior to admission. A contrast-enhanced computed tomography scan showed double hepatocellular carcinomas with Type III PVTT and massive ascites caused by arterio-portal shunts within the PVTT. The ascites could not be treated by concentrated ascites reinfusion therapy or diuretics. Transarterial embolization using microspheres followed by radiation therapy against PVTT and five courses of transarterial chemoembolization using microspheres and cisplatin led to the maintaining of complete remission of both ascites and tumors for over 12 months after treatment. Fluoroglucose accumulation of PVTT showed 11.2 as a maximum standard uptake value on positron emission tomography before treatment. No fluoroglucose accumulation within PVTT was observed for over 12 months following treatment. Transarterial chemoembolization using microspheres followed by radiation therapy against Type III PVTT may result in drastic anti-cancer effects and improvement of both serum albumin and intractable ascites after treatment of arterio-portal shunts within the PVTT causing portal hypertension.
Is "the brain" a helpful metaphor for neuroscience?
The Behavioral and brain sciences, 2019

Brette criticizes the notion of neural coding as used in neuroscience as a way to clarify the causal structure of the brain. This criticism will be positioned in a wider range of findings and ideas from other branches of neuroscience and biology. While supporting Brette's critique, these findings also suggest the need for more radical changes in neuroscience than Brette envisions.
Translational Intracerebral Hemorrhage Research: Has Current Neuroprotection Research ARRIVEd at a Standard for Experimental Design and Reporting?
Translational stroke research, 2020

One major aim of preclinical intracerebral hemorrhage (ICH) research is to develop and test potential neuroprotectants. Published guidelines for experimental design and reporting stress the importance of clearly and completely reporting results and methodological details to ensure reproducibility and maximize information availability. The current review has two objectives: first, to characterize current ICH neuroprotection research and, second, to analyze aspects of translational design in preclinical ICH studies. Translational design is the adoption and reporting of experimental design characteristics that are thought to be clinically relevant and critical to reproducibility in animal studies (e.g., conducting and reporting experiments according to the STAIR and ARRIVE guidelines, respectively). Given that ICH has no current neuroprotective treatments and an ongoing reproducibility crisis in preclinical research, translational design should be considered by investigators. We conducted a systematic review of ICH research from 2015 to 2019 using the PubMed database. Our search returned 281 published manuscripts studying putative neuroprotectants in animal models. Contemporary ICH research predominantly uses young, healthy male rodents. The collagenase model is the most commonly used. Reporting of group sizes, blinding, and randomization are almost unanimous, but group size calculations, mortality and exclusion criteria, and animal model characteristics are infrequently reported. Overall, current ICH neuroprotection research somewhat aligns with experimental design and reporting guidelines. However, there are areas for improvement. Because failure to consider translational design is associated with inflation of effect sizes (and possibly hindered reproducibility), we suggest that researchers, editors, and publishers collaboratively consider enhanced adherence to published guidelines.
Improvement of Cardiac Function in Rats With Myocardial Infarction by Low-Intensity to Moderate-Intensity Endurance Exercise Is Associated With Normalization of Klotho and SIRT1.
Journal of cardiovascular pharmacology, 2021

Exercise training (Ex) has beneficial effects on cardiovascular diseases by increasing Klotho and SIRT1. This study aimed to investigate whether the beneficial impact of Ex on myocardial infarction (MI) is mediated through Klotho and SIRT1. Fifty-six Wistar rats were divided into 4 main groups of Sham, MI, Ex, and MI + Ex. MI was induced by the closure of the left anterior descending. Animals were trained by endurance exercise for 4 weeks. In the end, hemodynamic and heart contractility indices were assessed. The levels of Klotho and SIRT1 in the serum and heart were measured by enzyme-linked immunosorbent assay and Western blot, respectively. The ADAM17 level in the heart and kidneys was assessed by enzyme-linked immunosorbent assay. The infarct size and fibrosis area were assessed by triphenyltetrazolium chloride and Masson trichrome staining, respectively. Ex recovered the reduction of dp/dt max and dp/dt min and decreased myocardial infarct size and fibrotic area in the MI group. Ex normalized the increase in heart rate, systolic blood pressure, left ventricular systolic pressure, and left ventricular end diastolic pressure in the MI group. Ex also normalized the reduction of the levels of Klotho and SIRT1 in serum and heart in the MI group. The changes of Klotho and SIRT1 in serum were positively correlated. Ex also restored ADAM17 levels in the MI group. Ex improved cardiac function in the MI group and is associated with reduction of the infarct size and normalization of Klotho and SIRT1 levels. Regarding unidirectional changes in Klotho and SIRT1, these proteins may play a role in beneficial effects of Ex on MI recovery.
Nonsarcoid granulomatous myopathy: two cases and a review of literature.
The International journal of neuroscience, 2013

Granulomatous myopathy is an uncommon skeletal muscles disorder. It can develop in association with other granuloma-forming diseases and is then considered a secondary myopathy or, less frequently, a primary disorder for which no etiology is identified. Studies of granulomatous myopathies have focused on examining the differences between primary and secondary diseases. Herein, we describe two cases of nonsarcoid granulomatous myopathies, for which diagnostic work-up did not reveal an underlying granuloma-causing pathology. The patients exhibited similar histopathological characteristics in skeletal muscle biopsies. However, they had different clinical presentations and therapeutic responses. Specifically, one patient had distal muscle weakness with a poor response to immunosuppressive treatment, whereas the other had a more proximal muscle weakness distribution and a very good response to treatment with corticosteroids and azathioprine, resulting in remission. More studies are warranted to further characterize the clinical course and effect of different treatment modalities on nonsarcoid granulomatous myopathy.
Suboptimalities for sure: Arguments from evolutionary theory.
The Behavioral and brain sciences, 2018

Rahnev &amp; Denison (R&amp;D) addressed the issue of (sub)optimalities in perception but only made a passing reference to evolutionary thinking. In our commentary, we concur with the authors' claim that evolution does not work toward optimalities, but argue that an evolutionary perspective on perception questions the Bayesian approach that the authors adopted.
Effect of interpopulation spike-timing-dependent plasticity on synchronized rhythms in neuronal networks with inhibitory and excitatory populations.
Cognitive neurodynamics, 2020

We consider a two-population network consisting of both inhibitory (I) interneurons and excitatory (E) pyramidal cells. This I-E neuronal network has adaptive dynamic I to E and E to I interpopulation synaptic strengths, governed by interpopulation spike-timing-dependent plasticity (STDP). In previous works without STDPs, fast sparsely synchronized rhythms, related to diverse cognitive functions, were found to appear in a range of noise intensity
A Randomized Controlled Trial of Intranasal Neuropeptide Y in Patients With Major Depressive Disorder.
The international journal of neuropsychopharmacology, 2020

Since about one-third of patients with major depressive disorder (MDD) do not respond adequately to available antidepressants, there is a need for treatments based on novel mechanisms of action. Neuropeptide Y (NPY), a normal brain constituent, is reduced in cerebrospinal fluid of patients with MDD and post-traumatic stress disorder and in corresponding rodent models. Moreover, NPY administered centrally or intranasally rescues pathophysiology in these models. Consequently, we conducted the first, to our knowledge, controlled trial of NPY as a treatment for MDD.
An effort toward molecular biology of food deprivation induced food hoarding in gonadectomized NMRI mouse model: focus on neural oxidative status.
BMC neuroscience, 2018

Environmental uncertainty, such as food deprivation, may alter internal milieu of nervous system through various mechanisms. In combination with circumstances of stress or aging, high consumption of unsaturated fatty acids and oxygen can make neural tissues sensitive to oxidative stress (OS). For adult rats, diminished level of gonadal steroid hormones accelerates OS and may result in special behavioral manifestations. This study was aimed to partially answer the question whether OS mediates trade-off between food hoarding and food intake (fat hoarding) in environmental uncertainty (e.g., fluctuations in food resource) within gonadectomized mouse model in the presence of food deprivation-induced food hoarding behavior.
Referenceless one-dimensional Nyquist ghost correction in multicoil single-shot spatiotemporally encoded MRI.
Magnetic resonance imaging, 2017

Single-shot spatiotemporally encoded (SPEN) MRI is a novel fast imaging method capable of retaining the time efficiency of single-shot echo planar imaging (EPI) but with distortion artifacts significantly reduced. Akin to EPI, the phase inconsistencies between mismatched even and odd echoes also result in the so-called Nyquist ghosts. However, the characteristic of the SPEN signals provides the possibility of obtaining ghost-free images directly from even and odd echoes respectively, without acquiring additional reference scans. In this paper, a theoretical analysis of the Nyquist ghosts manifested in single-shot SPEN MRI is presented, a one-dimensional correction scheme is put forward capable of maintaining definition of image features without blurring when the phase inconsistency along SPEN encoding direction is negligible, and a technique is introduced for convenient and robust correction of data from multi-channel receiver coils. The effectiveness of the proposed processing pipeline is validated by a series of experiments conducted on simulation data, in vivo rats and healthy human brains. The robustness of the method is further verified by implementing distortion correction on ghost corrected data.
Social safety learning: Shared safety abolishes the recovery of learned threat.
Behaviour research and therapy, 2020

Humans, like other social animals, learn about threats and safety in the environment through social cues. Yet, the processes that contribute to the efficacy of social safety learning during threat transmission remain unknown. Here, we developed a novel dyadic model of associative threat and extinction learning. In three separate social groups, we manipulated whether safety information during extinction was acquired via direct exposure to the conditioned stimulus (CS) in the presence of another individual (Direct exposure), via observation of other's safety behavior (Vicarious exposure), or via the combination of both (Shared exposure).These groups were contrasted against a fourth group receiving direct CS exposure alone (Asocial exposure). Based on skin conductance responses, we observed that all social groups outperformed asocial learning in inhibiting the recovery of threat, but only Shared exposure abolished threat recovery. These results suggest that social safety learning is optimized by a combination of direct exposure and vicariously transmitted safety signals. This work might help develop exposure therapies used to treat symptoms of threat and anxiety-related disorders to counteract maladaptive fears in humans.
A system for automatic recording and analysis of motor activity in rats.
Behavior research methods, 2013

We describe the design and evaluation of an electronic system for the automatic recording of motor activity in rats. The device continually locates the position of a rat inside a transparent acrylic cube (50 cm/side) with infrared sensors arranged on its walls so as to correspond to the x-, y-, and z-axes. The system is governed by two microcontrollers. The raw data are saved in a text file within a secure digital memory card, and offline analyses are performed with a library of programs that automatically compute several parameters based on the sequence of coordinates and the time of occurrence of each movement. Four analyses can be made at specified time intervals: traveled distance (cm), movement speed (cm/s), time spent in vertical exploration (s), and thigmotaxis (%). In addition, three analyses are made for the total duration of the experiment: time spent at each x-y coordinate pair (min), time spent on vertical exploration at each x-y coordinate pair (s), and frequency distribution of vertical exploration episodes of distinct durations. User profiles of frequently analyzed parameters may be created and saved for future experimental analyses, thus obtaining a full set of analyses for a group of rats in a short time. The performance of the developed system was assessed by recording the spontaneous motor activity of six rats, while their behaviors were simultaneously videotaped for manual analysis by two trained observers. A high and significant correlation was found between the values measured by the electronic system and by the observers.
Insights into microbiome research 5: Mapping is first but function must come next.
Multiple sclerosis (Houndmills, Basingstoke, England), 2019

Several efforts identifying differential bacterial prevalence in the gut of multiple sclerosis (MS) patients have been reported and many more are underway. While these are critical first steps in determining the involvement of gut microbes in MS pathogenesis, functional assays (both in vitro and in vivo) are needed to explore the mechanisms underlying the observed changes and ultimately implementing interventional strategies to counter severity, progression or even reduce the chance that it develops in the first place.
Antipsychotic Dose in Acute Schizophrenia: A Meta-analysis.
Schizophrenia bulletin, 2020

Little is known regarding optimal antipsychotic doses in the acute phase of schizophrenia. The aim of the present study was to employ the concept of minimum effective dose (MED) in examining efficacy and tolerability within this population. MED was identified for each antipsychotic through a previous systematic review. We then identified double-blind placebo-controlled randomized trials that involved fixed-dose antipsychotic monotherapy in acute schizophrenia and compared the identified MED vs higher doses of the same oral antipsychotic. Studies were selected from a recent meta-analysis examining dose-response relationship of second-generation antipsychotics and haloperidol. We extracted the data on study discontinuation, psychopathology, extrapyramidal symptoms, and treatment-emergent adverse events. For each antipsychotic, we conducted a meta-analysis to compare outcomes between MED and 2-fold MED, and MED and 3-fold MED. A total of 26 studies involving 5618 patients were included in the meta-analysis. In terms of study discontinuation, significant differences were found in study discontinuation due to lack of efficacy between MED and higher doses, in favor of 2-fold and 3-fold MEDs. Regarding psychopathology, both 2-fold and 3-fold MEDs were superior to MED for total and positive symptom scores. As for side effects, 2-fold MED proved inferior to MED for parkinsonism scores and diarrhea, whereas 3-fold MED was inferior for akathisia, somnolence, and vomiting. Findings suggest that clinicians can dose an antipsychotic at 2-fold or 3-fold MED for patients with acute schizophrenia but should closely monitor side effects.