rudyvdbrink/CitationDatabase huggingface dataset:
Aqueous humor proteome of primary open angle glaucoma: A combined dataset of mass spectrometry studies.
Data in brief, 2020

Analysis of the proteins of the aqueous humor can help to elucidate the complex pathogenesis of primary open angle glaucoma. Thanks to advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) it is now possible to identify hundreds of proteins in individual aqueous humor samples without the need to pool samples. We performed a systematic literature search to find publications that performed LC-MS/MS on aqueous humor samples of glaucoma patients and of non-glaucomatous controls. Of the seven publications that we found, we obtained the raw data of three publications. These three studies used glaucoma patients that were clinically similar (i.e. undergoing glaucoma filtration surgery) which prompted us to reanalyse and combine their data. Raw data of each study were analysed separately with the latest version of MaxQuant (version v1.6.11.0). Outcome files were exported to Microsoft Excel. Samples belonging to the same patient were averaged to obtain peptide expression values per individual. We compared the overlap of identified proteins using the VLOOKUP function of Excel and a publicly available Venn diagram software. For the peptide sequences that can belong to multiple proteins (usually of the same protein family), we initially included all possibly identified proteins. This ensured that we would not miss a potential overlap between the studies due to differences in identified peptide counts. Next, of those peptides of which we compared multiple proteins, only one unique protein was included in our analysis i.e. either the protein overlapping between studies or in case of no overlap, the protein that had the highest identified peptide count. This yielded 639 unique proteins detected in aqueous humor of either glaucoma patients or non-glaucomatous controls. In our manuscript entitled "The aqueous humor proteome of primary open angle glaucoma: An extensive review" [1], we further analysed this dataset. The dataset was exported to Perseus (version 1.6.5.0). We removed contaminants and filtered for proteins detected with high confidence, i.e. in more than 70% of the samples of at least one study. This yielded 248 proteins of which we compared the expression in glaucoma patients against control patients. Gene ontology enrichment analysis and pathway analysis was used to interpret the results. The unfiltered dataset reported in this data article and the approach reported here to reanalyse and combine raw data of different studies can be applied by other glaucoma researchers to gain more insight in the pathogenesis of glaucoma.
Methadone for the treatment of Prescription Opioids Dependence. A retrospective chart review.
Adicciones, 2016

Prescription opioids (PO) addiction is increasing to an epidemic level. Few studies exist regarding its treatment. Although buprenorphine has been the mainstay so far, other treatment options might be considered, such as methadone. We conducted a retrospective assessment of all patients admitted to a psychiatry ward for PO detoxification using methadone between 2010 and 2013. The assessment and description was carried out during a 3-month follow-up period after their discharge. Although this is a retrospective chart review, our exploration included sociodemographic and treatment variables in addition to the abstinence rates for the whole sample. Eleven patients were included, mostly women (81.8%), with a median age of 50 years. The median duration of dependence was 8 years. Dependence on other substances and psychiatric comorbidities were high. Eight patients were monitored during three months. Of these, 7 (87.5%) were abstinent after that period. The results suggest that methadone deserves further exploration as a potentially efficacious treatment option for PO dependence.
Periprosthetic fractures: the next fragility fracture epidemic? A national observational study.
BMJ open, 2020

Periprosthetic fractures have considerable clinical implications for patients and financial implications for healthcare systems. This study aims to determine the burden of periprosthetic fractures of the lower and upper limbs in England and identify any factors associated with differences in treatment and outcome.
NREM sleep in the rodent neocortex and hippocampus reflects excitable dynamics.
Nature communications, 2019

During non-rapid eye movement (NREM) sleep, neuronal populations in the mammalian forebrain alternate between periods of spiking and inactivity. Termed the slow oscillation in the neocortex and sharp wave-ripples in the hippocampus, these alternations are often considered separately but are both crucial for NREM functions. By directly comparing experimental observations of naturally-sleeping rats with a mean field model of an adapting, recurrent neuronal population, we find that the neocortical alternations reflect a dynamical regime in which a stable active state is interrupted by transient inactive states (slow waves) while the hippocampal alternations reflect a stable inactive state interrupted by transient active states (sharp waves). We propose that during NREM sleep in the rodent, hippocampal and neocortical populations are excitable: each in a stable state from which internal fluctuations or external perturbation can evoke the stereotyped population events that mediate NREM functions.
Cardiorespiratory Events in Infants Born Preterm during the Transitional Period.
The Journal of pediatrics, 2020

To investigate the features of cardiorespiratory events in infants born preterm during the transitional period, and to evaluate whether different neonatal characteristics may correlate with event type, duration, and severity.
Landscapes of becoming social: A systematic review of evidence for associations and pathways between interactions with nature and socioemotional development in children.
Environment international, 2021

Existing research indicates that spending time in nature is associated with diverse aspects of children's health and wellbeing. Although fundamental to later life chances and health, no systematic reviews, to our knowledge, have focused specifically on the effects of interaction with nature on socioemotional functioning in childhood.
Coupling of gamma band activity to sleep spindle oscillations - a combined EEG/MEG study.
NeuroImage, 2021

Sleep spindles are crucial to memory consolidation. Cortical gamma oscillations (30-100 Hz) are considered to reflect processing of memory in local cortical networks. The temporal and regulatory relationship between spindles and gamma activity might therefore provide clues into how sleep strengthens cortical memory representations. Here, combining EEG with MEG recordings during sleep in healthy humans (n = 12), we investigated the temporal relationships of cortical gamma band activity, always measured by MEG, during fast (12-16 Hz) and slow (8-12 Hz) sleep spindles detected in the EEG or MEG. Time-frequency distributions did not show a consistent coupling of gamma to the spindle oscillation, although activity in the low gamma (30-40 Hz) and neighboring beta range (<30 Hz) was generally increased during spindles. However, more fine-grained analyses of cross-frequency interactions revealed that both low and high gamma power (30-100 Hz) was coupled to the phase of slow and fast EEG spindles, importantly, with this coupling at a fixed phase only for the oscillations within an individual spindle, but with variable phase across spindles. We did not observe any coupling of gamma activity for spindles detected solely in the MEG and not in parallel EEG recordings, raising the possibility that these are more local spindles of different quality. Similar to fast spindle activity, low gamma band power followed a ~0.025 Hz infraslow rhythm during sleep whose frequency, however, was significantly faster than that of spindle activity. Our findings suggest a general function of fast and slow spindles that by spanning larger cortical networks might serve to synchronize gamma band activity occurring in more local but distributed networks. Thereby, spindles might help linking local memory processing between distributed networks.
[Artificial intelligence and nursing care: reflections in psychiatry].
Soins; la revue de reference infirmiere, 2019

A key government priority, artificial intelligence (IA) in healthcare is a real opportunity for nursing professionals. Faced with the daily difficulties encountered, AI could bring a new perspective to nursing care in psychiatry and free up time for professionals which they can then spend with the patient. More training and a multi-disciplinary approach are required.
Neurodharma Self-Help: Personalized Science Communication as Brain Management.
The Journal of medical humanities, 2017

Over the past ten to fifteen years, medical interventions, therapeutic approaches and scientific studies involving mindfulness meditation have gained traction in areas such as clinical psychology, psychotherapy, and neuroscience. Simultaneously, mindfulness has had a very strong public appeal. This article examines some of the ways in which the medical and scientific meaning of mindfulness is communicated in public and to the public. In particular, it shows how experts in the field of mindfulness neuroscience seek to communicate to the public at large the imperative of brain fitness for the promotion of health, wellbeing and happiness. The study identifies claims being made in popular outlets that, by and large, bypass traditional mass media, such as self-help books, websites and online videos. By treating this material as a form of personalized science communication, this article contributes to the body of literature that understands science communication as a continuum and the boundary between science and popularized science as the outcome of human negotiations. The study finds that processes of personalization help to build bridges between scientific findings and their supposed application, that they infuse science with subjective meaning, and turn expert communication with the public into a moral vocation.
Proteomic and mitochondrial adaptations to early-life stress are distinct in juveniles and adults.
Neurobiology of stress, 2020

Exposure to early-life stress (ELS) increases risk for poor mental and physical health outcomes that emerge at different stages across the lifespan. Yet, how age interacts with ELS to impact the expression of specific phenotypes remains largely unknown. An established limited-bedding paradigm was used to induce ELS in mouse pups over the early postnatal period. Initial analyses focused on the hippocampus, based on documented sensitivity to ELS in humans and various animal models, and the large body of data reporting anatomical and physiological outcomes in this structure using this ELS paradigm. An unbiased discovery proteomics approach revealed distinct adaptations in the non-nuclear hippocampal proteome in male versus female offspring at two distinct developmental stages: juvenile and adult. Gene ontology and KEGG pathway analyses revealed significant enrichment in proteins associated with mitochondria and the oxidative phosphorylation (OXPHOS) pathway in response to ELS in female hippocampus only. To determine whether the protein adaptations to ELS reflected altered function, mitochondrial respiration (driven through complexes II-IV) and complex I activity were measured in isolated hippocampal mitochondria using a Seahorse X96 Flux analyzer and immunocapture ELISA, respectively. ELS had no effect on basal respiration in either sex at either age. In contrast, ELS increased OXPHOS capacity in juvenile males and females, and reduced OXPHOS capacity in adult females but not adult males. A similar pattern of ELS-induced changes was observed for complex I activity. These data suggest that initial adaptations in juvenile hippocampus due to ELS were not sustained in adults. Mitochondrial adaptations to ELS were also exhibited peripherally by liver. Overall, the temporal distinctions in mitochondrial responses to ELS show that ELS-generated adaptations and outcomes are complex over the lifespan. This may contribute to differences in the timing of appearance of mental and physical disturbances, as well as potential sex differences that influence only select outcomes.
Modulation of solute diffusivity in brain tissue as a novel mechanism of transcranial direct current stimulation (tDCS).
Scientific reports, 2020

The breadth of brain disorders and functions reported responsive to transcranial direct current stimulation (tDCS) suggests a generalizable mechanism of action. Prior efforts characterized its cellular targets including neuron, glia and endothelial cells. We propose tDCS also modulates the substance transport in brain tissue. High resolution multiphoton microscopy imaged the spread across rat brain tissue of fluorescently-labeled solutes injected through the carotid artery after tDCS. The effective solute diffusion coefficient of brain tissue (D
Drug repurposing and cytokine management in response to COVID-19: A review.
International immunopharmacology, 2020

Coronavirus disease 2019 (COVID-19), the infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an aggressive disease that attacks the respiratory tract and has a higher fatality rate than seasonal influenza. The COVID-19 pandemic is a global health crisis, and no specific therapy or drug has been formally recommended for use against SARS-CoV-2 infection. In this context, it is a rational strategy to investigate the repurposing of existing drugs to use in the treatment of COVID-19 patients. In the meantime, the medical community is trialing several therapies that target various antiviral and immunomodulating mechanisms to use against the infection. There is no doubt that antiviral and supportive treatments are important in the treatment of COVID-19 patients, but anti-inflammatory therapy also plays a pivotal role in the management COVID-19 patients due to its ability to prevent further injury and organ damage or failure. In this review, we identified drugs that could modulate cytokines levels and play a part in the management of COVID-19. Several drugs that possess an anti-inflammatory profile in others illnesses have been studied in respect of their potential utility in the treatment of the hyperinflammation induced by SAR-COV-2 infection. We highlight a number of antivirals, anti-rheumatic, anti-inflammatory, antineoplastic and antiparasitic drugs that have been found to mitigate cytokine production and consequently attenuate the "cytokine storm" induced by SARS-CoV-2. Reduced hyperinflammation can attenuate multiple organ failure, and even reduce the mortality associated with severe COVID-19. In this context, despite their current unproven clinical efficacy in relation to the current pandemic, the repurposing of drugs with anti-inflammatory activity to use in the treatment of COVID-19 has become a topic of great interest.
A model to study orienting responses in zebrafish, and applications towards the emotion-cognition interaction.
Animal cognition, 2020

Orienting responses (ORs) are whole-organism reflexes that are elicited by innocuous stimuli, and which decrease in magnitude after stimulus repetition. ORs represent relatively simple responses that can be used to study attentional processes, and are modulated by the organism's state, including arousal and activation levels, as well as by emotional processes. Here we describe a simple method to study ORs in zebrafish, a model organism increasingly being used in behavioural neuroscience. After presentation of a static visual stimulus, an OR is elicited, characterized by approaching the stimulus and orienting towards it. After repeated stimulation, OR decreases, suggesting habituation. These responses are qualitatively altered by exposure to a fear-eliciting alarm substance (i.e., derived from the skin of a conspecific), since exposed animals avoid the visual stimulus and orient either away from the stimulus or towards it, but at a distance. The protocol can be used to study orienting responses, as well as the impact of fear and arousal on these reflexes.
Neonatal developmental and epileptic encephalopathy due to autosomal recessive variants in SLC13A5 gene.
Epilepsia, 2020

Autosomal recessive pathogenic variants of the SLC13A5 gene are associated with severe neonatal epilepsy, developmental delay, and tooth hypoplasia/hypodontia. We report on 14 additional patients and compare their phenotypic features to previously published patients to identify the clinical hallmarks of this disorder.
A Molecular Code for Imprinting Drug-Cue Associations.
Neuron, 2017

Previous studies suggest that nuclear histone deacetylase HDAC5 has a dynamic relationship with drug-induced behavioral neuroadaptations. The new work by Taniguchi et al. (2017) suggests that targets of nuclear HDAC5 mediate the behavioral effects of rewarding drugs via regulation of cocaine-associated stimuli.
Author Correction: Stay alert, don't get hurt.
Nature neuroscience, 2018

In the version of this article initially published, paragraph 8 mentioned intra-accumbens administration of SB334867. This should have read systemic (intraperitoneal) administration. The error has been corrected in the HTML and PDF versions of the article.
Inflammation to Infertility: Panoramic View on Endometriosis.
Cureus, 2020

Endometriosis is a disease caused by the implantation of endometrial glands and stroma outside the uterine cavity. It affects 10% of the reproductive-age women this means that 190 million women are affected worldwide. The definitive diagnosis requires surgical exploration or a laparoscopy which is of a high expense. The pathogenesis of the disease is heterogeneous and poorly understood despite the progress in the research field. Infertility is one of the main symptoms of Endometriosis. The mechanism behind this remains unclear. Literature suggests that Endometriosis reduces implantation capacity, increases the risk of pregnancy loss, and causes anatomical obstruction imposed by endometriotic lesions. The disease has a high burden to it by decreasing the quality of women's life and imposing negative consequences for their productivity, social life, and emotional wellbeing. Since inflammation is considered the hallmark of endometriosis, it is worth looking at the mechanism of how inflammation is linked to infertility in endometriosis patients. In this study, we summarized the recent finding of how inflammation can affect oocyte, endometrium, hormones, and sperm.
Repurposing developmental mechanisms in the adult nervous system.
Current opinion in genetics & development, 2020

Molecules and cellular processes important for nervous system development can be repurposed in adulthood for the regulation of adult neurogenesis, synaptic plasticity, and neural regeneration following injury or degeneration. Efforts to recapitulate neural development in order to ameliorate injury or disease are promising, but these often fall short of functional restoration due in part to our incomplete understanding of how these damaged circuits initially developed. Despite these limitations, such strategies provide hope that harnessing developmental mechanisms can restore nervous system functions following damage or disease.
Forebrain dopamine depletion impairs motor behavior in lamprey.
The European journal of neuroscience, 2008

The structure of the basal ganglia appears to be conserved throughout vertebrate evolution, with characteristic cellular and transmitter components in each area, and the same types of afferent input. As described in rodents and primates, depletion of the striatal dopamine results in characteristic motor deficits. To explore if this role of the basal ganglia in modulating motor function was present early in vertebrate evolution, we investigated here the effects of striatal dopamine depletion in the lamprey, a cyclostome, which diverged from the main vertebrate line around 560 million years ago. The lamprey striatum contains the same cellular elements as found in mammals, and receives the same types of input, including a prominent dopamine innervation. We show here that MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; 100 mg/kg i.p.), a neurotoxin, depletes forebrain and striatal dopamine levels in lamprey to 15% of control values, and has profound effects on motor performance. Twenty-four and 48 h after MPTP injection, lampreys demonstrated marked reductions in spontaneous swimming and the duration of each swimming episode. Impairments in the ability to initiate movements were shown by a decreased rate of initiation. Furthermore, the initiation and maintenance of locomotion induced by olfactory mucosa stimulation was severely impaired, as was the coordination of different motor tasks. These deficits were ameliorated by the dopamine agonist apomorphine. The motor deficits arising after striatal dopamine depletion are thus qualitatively similar in cyclostomes and mammals. The role of the dopamine innervation of the striatum thus appears to be conserved throughout vertebrate evolution.
Social Observation Task in a Linear Maze for Rats.
Bio-protocol, 2017

Animals often learn through observing their conspecifics. However, the mechanisms of them obtaining useful knowledge during observation are beginning to be understood. This protocol describes a novel social observation task to test the 'local enhancement theory', which proposes that presence of social subjects in an environment facilitates one's understanding of the environments. By combining behavior test and
Predicting outcomes after acute reperfusion therapy for basilar artery occlusion.
European journal of neurology, 2020

Basilar artery occlusion (BAO) leads to high rates of morbidity and mortality, despite successful recanalization. The discordance between flow restoration and long-term functional status clouds clinical decision-making regarding further aggressive care. We sought to develop and validate a practical, prognostic tool for the prediction of 3-month favorable outcome after acute reperfusion therapy for BAO.
Perinatal encephalopathy, the syndrome of intracranial hypertension and associated diagnostic labels in the Commonwealth of Independent States: a systematic review.
Archives of disease in childhood, 2020

The WHO reports excessive rates of ill-defined neurological diagnoses and ineffective and potentially harmful drug treatments in children in the Commonwealth of Independent States (CIS). Collectively termed perinatal encephalopathy and the syndrome of intracranial hypertension (PE-SIH), these diagnoses are important contributors to perceived childhood morbidity and disability in the CIS. A systematic compilation of information on PE-SIH is lacking.
The use of intraoperative suprasellar pneumocisternogram for resection of large pituitary tumors.
Clinical neurology and neurosurgery, 2010

Adequate removal of large pituitary tumors with significant suprasellar extension remains a challenge through the trans-sphenoidal corridor because of this route's limited working window. The application of intracisternal air and intraoperative fluoroscopy is explored as a form of intraoperative imaging to maximize tumor resection and to confirm adequate suprasellar tumor decompression. The authors confirmed adequate decompression of suprasellar space using this technique of fluoroscopy with the present intrathecal air for 10 of 12 patients with giant, non-functioning pituitary tumors. Intraoperative cerebrospinal fluid fistulae prevented the use of intrathecal air in the remaining two patients.