rudyvdbrink/CitationDatabase huggingface dataset:
Rare Multidrug-Resistant Pulmonary Nocardiosis in AIDS.
Cureus, 2017

Nocardiosis is an opportunistic infection in patients with depressed cell-mediated immunity. Inhalation is the primary route for exposure via dust particles. Patients with acquired immune deficiency syndrome (AIDS) are at increased risk of disseminated disease. A challenge in the diagnosis of pulmonary nocardiosis is that it can mimic other pulmonary diseases. Nocardia farcinica tends to be a more virulent, multidrug-resistant strain with an increased tendency to disseminate. This report describes a 64-year-old man with AIDS found to have pulmonary nocardiosis that did not respond to standard antibiotic therapy. Further evaluation revealed the virulent, multidrug-resistant Nocardia farcinica species. Targeted antibiotic therapy was initiated, after which the patient had an improvement in pulmonary symptoms. It is important to suspect pulmonary nocardiosis in immunocompromised patients who fail to respond to standard antimicrobial therapy. Susceptibilities should be obtained so that appropriate therapy can be promptly initiated as Nocardia farcinica is highly resistant to multiple antimicrobials.
Neurodevelopmental disorder in an Egyptian family with a biallelic ALKBH8 variant.
American journal of medical genetics. Part A, 2021

Alkylated DNA repair protein AlkB homolog 8 (ALKBH8) is a member of the AlkB family of dioxygenases. ALKBH8 is a methyltransferase of the highly variable wobble nucleoside position in the anticodon loop of tRNA and thus plays a critical role in tRNA modification by preserving codon recognition and preventing errors in amino acid incorporation during translation. Moreover, its activity catalyzes uridine modifications that are proposed to be critical for accurate protein translation. Previously, two distinct homozygous truncating variants in the final exon of ALKBH8 were described in two unrelated large Saudi Arabian kindreds with intellectual developmental disorder and autosomal recessive 71 (MRT71) syndrome (MIM# 618504). Here, we report a third family-of Egyptian descent-harboring a novel homozygous frame-shift variant in the last exon of ALKBH8. Two affected siblings in this family exhibit global developmental delay and intellectual disability as shared characteristic features of MRT71 syndrome, and we further characterize their observed dysmorphic features and brain MRI findings. This description of a third family with a truncating ALKBH8 variant from a distinct population broadens the phenotypic and genotypic spectrum of MRT71 syndrome, affirms that perturbations in tRNA biogenesis can contribute to neurogenetic disease traits, and firmly establishes ALKBH8 as a novel neurodevelopmental disease gene.
[A case of dermatomyositis positive for anti-nuclear matrix protein 2 antibody without dermatologic symptoms].
Rinsho shinkeigaku = Clinical neurology, 2021

We report a 47-year-old woman who presented with progressive myalgia, weakness in the proximal limbs, and dysphagia for a month and a half. No skin rash was observed on admission. Examination of MRI data suggested inflammatory changes in the proximal limbs and trunk muscles. Biopsy specimens from the left biceps muscle showed no perifascicular atrophy, but immunohistochemical staining revealed the presence of myxovirus resistance protein A (MxA) in myofibers, strongly suggesting dermatomyositis (DM). In addition, her serum was positive for anti-nuclear matrix protein 2 (anti-NXP-2) antibody, which is reportedly useful as a marker of DM without skin lesions. Her symptoms gradually improved upon intravenous methylprednisolone pulse therapy in conjunction with oral prednisolone, oral tacrolimus, and intravenous immunoglobulin therapy. Our findings suggest that in cases where inflammatory muscle disease is suspected, anti-NXP-2 antibody analyses should be considered for precise diagnosis, even if there are no dermatological symptoms.
Exploring characteristic features of attention-deficit/hyperactivity disorder: findings from multi-modal MRI and candidate genetic data.
Brain imaging and behavior, 2020

The current study examined whether machine learning features best distinguishing attention-deficit/hyperactivity disorder (ADHD) from typically developing children (TDC) can explain clinical phenotypes using multi-modal neuroimaging and genetic data. Cortical morphology, diffusivity scalars, resting-state functional connectivity and polygenic risk score (PS) from norepinephrine, dopamine and glutamate genes were extracted from 47 ADHD and 47 matched TDC. Using random forests, classification accuracy was measured for each uni- and multi-modal model. The optimal model was used to explain symptom severity or task performance and its robustness was validated in the independent dataset including 18 ADHD and 18 TDC. The model consisting of cortical thickness and volume features achieved the best accuracy of 85.1%. Morphological changes across insula, sensory/motor, and inferior frontal cortex were also found as key predictors. Those explained 18.0% of ADHD rating scale, while dynamic regional homogeneity within default network explained 6.4% of the omission errors in continuous performance test. Ensemble of PS to optimal model showed minor effect on accuracy. Validation analysis achieved accuracy of 69.4%. Current findings suggest that structural deformities relevant to salience detection, sensory processing, and response inhibition may be robust classifiers and symptom predictors of ADHD. Altered local functional connectivity across default network predicted attentional lapse. However, further investigation is needed to clarify roles of genetic predisposition.
Single Molecule Assay for Ultrasensitive Detection of Cathepsin B in Human Blood.
ACS omega, 2021

Cathepsin B (catB) is a lysosomal cysteine protease expressed in several cells and organs, where it plays a role in protein degradation and turnover. Extracellular, secreted catB has utility as a biomarker for a host of pathological or physiological states, including a myriad of cancers or neurological diseases and injuries. Analytical or diagnostic assessment may be limited by biological sample volume availability. Pathologically relevant changes in catB levels may occur at low-moderate concentrations that require accurate measurement to differentiate from basal levels. Furthermore, biological samples like plasma and serum, often occlude accurate catB measurements because of background and high variance, vastly limiting the ability to detect catB as a peripheral biomarker. Techniques for ultrasensitive protein detection that require low volumes of sample are necessary. To overcome these challenges, a digital enzyme-linked immunosorbent assay (ELISA) was developed for differential detection of catB within less than 5 μL of serum and plasma using the single molecule array (SiMoA) platform, which offers 1000-times more sensitivity and vastly reduced variance compared to colorimetric tests. In buffer, curve-fitting estimated the limit of detection (LoD) to be ∼1.56 and ∼8.47 pg/mL using two-step or three-step assay configurations, respectively. After correcting for endogenous levels, the estimated LoD was ∼4.7 pg/mL in the serum or plasma with the two-step assay. The lower limit of quantitation was ∼2.3 pg/mL in the buffer and ∼9.4 pg/mL in the serum or plasma, indicting the ability to measure small changes above endogenous levels within blood samples.
Steroid-responsive encephalopathy with a peculiar CSF biomarker profile in an 89-year-old man.
Oxford medical case reports, 2018

Being treatable, steroid-responsive encephalopathy associated with autoimmune thyroiditis (SREAT), or Hashimoto's encephalopathy, should be distinguished from untreatable conditions. Our patient was a previously healthy 89-year-old man, who presented with cognitive and balance deterioration over several months. His cerebrospinal fluid (CSF) examination was positive for protein 14-3-3 but no other test suggested Creutzfeldt-Jacob disease. His condition improved markedly, although not fully, with intravenous corticosteroids. In control CSF sampling, protein 14-3-3 was negative but a biomarker signature consistent with Alzheimer's disease was observed. SREAT should be considered also in the very elderly in case of subacute encephalopathy.
The effect of infliximab in patients with chronic low back pain and Modic changes (the BackToBasic study): study protocol of a randomized, double blind, placebo-controlled, multicenter trial.
BMC musculoskeletal disorders, 2020

Low back pain is common and a significant number of patients experience chronic low back pain. Current treatment options offer small to moderate effects. Patients with vertebral bone marrow lesions visualized as Modic changes on magnetic resonance imaging may represent a subgroup within the low back pain population. There is evidence for inflammatory mediators being involved in development of Modic changes; hence, suppression of inflammation could be a treatment strategy for these patients. This study examines the effect of anti-inflammatory treatment with the TNF-α inhibitor infliximab in patients with chronic low back pain and Modic changes.
Surgical Trapping With Revascularization of Concomitant Cervical and Petrous Internal Carotid Artery Aneurysms: 2-Dimensional Operative Video.
Operative neurosurgery (Hagerstown, Md.), 2019

Petrous internal carotid artery (ICA) aneurysms are rare, complicated lesions to treat. The management paradigms include observation, endovascular exclusion, or surgical trapping with or without revascularization. The case described in this video involved a 67-yr-old woman with a known history of chronic lymphocytic leukemia, who presented after a mechanical ground-level fall. Clinically, she had a nasal deformity and resolving epistaxis consistent with mild facial trauma. Computed tomography (CT) revealed a comminuted nasal bone fracture and an incidental 3-cm right petrous ICA aneurysm. Subsequent vascular imaging demonstrated a concurrent 1.5-cm right cervical ICA dissecting pseudoaneurysm. Flow diversion with a Pipeline stent (Medtronic, Dublin, Ireland) was unsuccessful because the aneurysm's size precluded microcatheter selection of the ICA distal to the lesion. When the patient did not tolerate balloon test occlusion of the ICA, we proceeded with surgical trapping of both aneurysms and high-flow extracranial-to-intracranial bypass. The patient underwent a right frontotemporal craniotomy and an external carotid artery-to-frontal M2 middle cerebral artery bypass with a radial artery graft. Following a clinoidectomy, an aneurysm clip was applied to the paraclinoid ICA, and the cervical ICA was ligated just distal to the bifurcation, effectively trapping both aneurysms. The patient tolerated the procedure well. Postoperatively, she experienced symptomatic hypotension requiring vasopressor therapy and a transient partial oculomotor palsy that resolved during her hospital course. She was discharged home without neurological sequelae. Postoperative CT angiography demonstrated complete exclusion of the ICA aneurysms and a patent radial bypass graft after surgery and at 6-month follow-up. The patient provided consent for publication.
Experimental sleep disruption attenuates morphine analgesia: findings from a randomized trial and implications for the opioid abuse epidemic.
Scientific reports, 2020

Preclinical studies demonstrate that sleep disruption diminishes morphine analgesia and modulates reward processing. We sought to translate these preclinical findings to humans by examining whether sleep disruption alters morphine's analgesic and hedonic properties. We randomized 100 healthy adults to receive morphine versus placebo after two nights of undisturbed sleep (US) and two nights of forced awakening (FA) sleep disruption. Sleep conditions were counterbalanced, separated by a two-week washout. The morning after both sleep conditions, we tested cold pressor pain tolerance before and 40-min after double-blind injection of .08 mg/kg morphine or placebo. The primary outcome was the analgesia index, calculated as the change in cold pressor hand withdrawal latency (HWL) before and after drug injection. Secondary outcomes were ratings of feeling "high," drug "liking," and negative drug effects. We found a significant sleep condition by drug interaction on the analgesia index (95% CI - 0.57, - 0.001). After US, subjects receiving morphine demonstrated significantly longer HWL compared to placebo (95% CI 0.23, 0.65), but not after FA (95% CI - 0.05, 0.38). Morphine analgesia was diminished threefold under FA, relative to US. After FA, females (95% CI - 0.88, - 0.05), but not males (95% CI - 0.23, 0.72), reported decreased subjective "high" effects compared to US. After FA, females (95% CI 0.05, 0.27), but not males (95% CI - 0.10, 0.11), administered morphine reported increased negative drug effects compared to US. These data demonstrate that sleep disruption attenuates morphine analgesia in humans and suggest that sleep disturbed males may be at greatest risk for problematic opioid use.
A standardized framework for testing the performance of sleep-tracking technology: step-by-step guidelines and open-source code.
Sleep, 2021

Sleep-tracking devices, particularly within the consumer sleep technology (CST) space, are increasingly used in both research and clinical settings, providing new opportunities for large-scale data collection in highly ecological conditions. Due to the fast pace of the CST industry combined with the lack of a standardized framework to evaluate the performance of sleep trackers, their accuracy and reliability in measuring sleep remains largely unknown. Here, we provide a step-by-step analytical framework for evaluating the performance of sleep trackers (including standard actigraphy), as compared with gold-standard polysomnography (PSG) or other reference methods. The analytical guidelines are based on recent recommendations for evaluating and using CST from our group and others (de Zambotti and colleagues; Depner and colleagues), and include raw data organization as well as critical analytical procedures, including discrepancy analysis, Bland-Altman plots, and epoch-by-epoch analysis. Analytical steps are accompanied by open-source R functions (depicted at https://sri-human-sleep.github.io/sleep-trackers-performance/AnalyticalPipeline_v1.0.0.html). In addition, an empirical sample dataset is used to describe and discuss the main outcomes of the proposed pipeline. The guidelines and the accompanying functions are aimed at standardizing the testing of CSTs performance, to not only increase the replicability of validation studies, but also to provide ready-to-use tools to researchers and clinicians. All in all, this work can help to increase the efficiency, interpretation, and quality of validation studies, and to improve the informed adoption of CST in research and clinical settings.
An fMRI Compatible Smart Device for Measuring Palmar Grasping Actions in Newborns.
Sensors (Basel, Switzerland), 2020

Grasping is one of the first dominant motor behaviors that enable interaction of a newborn infant with its surroundings. Although atypical grasping patterns are considered predictive of neuromotor disorders and injuries, their clinical assessment suffers from examiner subjectivity, and the neuropathophysiology is poorly understood. Therefore, the combination of technology with functional magnetic resonance imaging (fMRI) may help to precisely map the brain activity associated with grasping and thus provide important insights into how functional outcomes can be improved following cerebral injury. This work introduces an MR-compatible device (i.e., smart graspable device (SGD)) for detecting grasping actions in newborn infants. Electromagnetic interference immunity (EMI) is achieved using a fiber Bragg grating sensor. Its biocompatibility and absence of electrical signals propagating through the fiber make the safety profile of the SGD particularly favorable for use with fragile infants. Firstly, the SGD design, fabrication, and metrological characterization are described, followed by preliminary assessments on a preterm newborn infant and an adult during an fMRI experiment. The results demonstrate that the combination of the SGD and fMRI can safely and precisely identify the brain activity associated with grasping behavior, which may enable early diagnosis of motor impairment and help guide tailored rehabilitation programs.
Confidence in subjective pain is predicted by reaction time during decision making.
Scientific reports, 2020

Self-report is the gold standard for measuring pain. However, decisions about pain can vary substantially within and between individuals. We measured whether self-reported pain is accompanied by metacognition and variations in confidence, similar to perceptual decision-making in other modalities. Eighty healthy volunteers underwent acute thermal pain and provided pain ratings followed by confidence judgments on continuous visual analogue scales. We investigated whether eye fixations and reaction time during pain rating might serve as implicit markers of confidence. Confidence varied across trials and increased confidence was associated with faster pain rating reaction times. The association between confidence and fixations varied across individuals as a function of the reliability of individuals' association between temperature and pain. Taken together, this work indicates that individuals can provide metacognitive judgments of pain and extends research on confidence in perceptual decision-making to pain.
Comparing GBMI and non-GBMI Female Prisoners in Michigan.
The journal of the American Academy of Psychiatry and the Law, 2018

The guilty but mentally ill (GBMI) verdict was first adopted in Michigan in part to provide treatment for offenders suffering from mental illness. Currently, little is known of its impact among women prisoners. Therefore, the primary aim of this study was to explore if GBMI women (
Diabetes causes marked inhibition of mitochondrial metabolism in pancreatic β-cells.
Nature communications, 2019

Diabetes is a global health problem caused primarily by the inability of pancreatic β-cells to secrete adequate levels of insulin. The molecular mechanisms underlying the progressive failure of β-cells to respond to glucose in type-2 diabetes remain unresolved. Using a combination of transcriptomics and proteomics, we find significant dysregulation of major metabolic pathways in islets of diabetic βV59M mice, a non-obese, eulipidaemic diabetes model. Multiple genes/proteins involved in glycolysis/gluconeogenesis are upregulated, whereas those involved in oxidative phosphorylation are downregulated. In isolated islets, glucose-induced increases in NADH and ATP are impaired and both oxidative and glycolytic glucose metabolism are reduced. INS-1 β-cells cultured chronically at high glucose show similar changes in protein expression and reduced glucose-stimulated oxygen consumption: targeted metabolomics reveals impaired metabolism. These data indicate hyperglycaemia induces metabolic changes in β-cells that markedly reduce mitochondrial metabolism and ATP synthesis. We propose this underlies the progressive failure of β-cells in diabetes.
Intractable Hiccups as the Primary Symptom of a Perimedullary Arteriovenous Fistula at the Craniocervical Junction.
World neurosurgery, 2020

Hiccups are a well-known short-term phenomenon in daily life. If they persist or become intractable, they may be a primary symptom of a disease. Recent studies identified the medulla oblongata as the neuroanatomic center of the hiccup reflex arc. In previous cases, an isolated lesion at the dorsal side of the medulla oblongata induced intractable hiccups.
Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective.
International journal of biological macromolecules, 2020

The current pandemic of 2019 novel coronavirus disease (COVID-19) caused by a novel virus strain, 2019-nCoV/SARS-CoV-2 have posed a serious threat to global public health and economy. It is largely unknown how the human immune system responds to this infection. A better understanding of the immune response to SARS-CoV-2 will be important to develop therapeutics against COVID-19. Here, we have used transcriptomic profile of human alveolar adenocarcinoma cells (A549) infected with SARS-CoV-2 and employed a network biology approach to generate human-virus interactome. Network topological analysis discovers 15 SARS-CoV-2 targets, which belongs to a subset of interferon (IFN) stimulated genes (ISGs). These ISGs (IFIT1, IFITM1, IRF7, ISG15, MX1, and OAS2) can be considered as potential candidates for drug targets in the treatments of COVID-19. We have identified significant interaction between ISGs and TLR3 agonists, like poly I: C, and imiquimod, and suggests that TLR3 agonists can be considered as a potential drug for drug repurposing in COVID-19. Our network centric analysis suggests that moderating the innate immune response is a valuable approach to target COVID-19.
A whole-brain modeling approach to identify individual and group variations in functional connectivity.
Brain and behavior, 2021

Resting-state functional connectivity is an important and widely used measure of individual and group differences. Yet, extant statistical methods are limited to linking covariates with variations in functional connectivity across subjects, especially at the voxel-wise level of the whole brain. This paper introduces a modeling approach that regresses whole-brain functional connectivity on covariates. Our approach is a mesoscale approach that enables identification of brain subnetworks. These subnetworks are composite of spatially independent components discovered by a dimension reduction approach (such as whole-brain group ICA) and covariate-related projections determined by the covariate-assisted principal regression, a recently introduced covariance matrix regression method. We demonstrate the efficacy of this approach using a resting-state fMRI dataset of a medium-sized cohort of subjects obtained from the Human Connectome Project. The results suggest that the approach may improve statistical power in detecting interaction effects of gender and alcohol on whole-brain functional connectivity, and in identifying the brain areas contributing significantly to the covariate-related differences in functional connectivity.
Relationship between allostatic load and clinical outcomes in youth at ultra-high risk for psychosis in the NEURAPRO study.
Schizophrenia research, 2020

Individuals at ultra-high risk (UHR) for psychosis have an elevated risk of developing psychosis and other psychiatric outcomes. Risk biomarkers can assist in delineating individual risk and allow better prediction of longer-term outcomes. The aim of the present study was to examine if allostatic load (AL), a multisystem index of neuroendocrine, cardiovascular, immune and metabolic dysregulation, is associated with clinical outcomes in youth at UHR for psychosis. AL was measured in 106 participants of the NEURAPRO study (n = 70 female, n = 36 male; mean age 17.21, SD 2.37), a multicentre randomized-controlled trial of long-chain omega-3 polyunsaturated fatty acids versus placebo in people at UHR for psychosis. Psychiatric symptoms and social and occupational functioning were assessed at baseline and 6 and 12 months after study intake. Multivariate linear and logistic regression models were used to test the relationship between AL and clinical outcomes. High AL at baseline was associated with poor social and occupational functioning at 6 months (β = -0.224, p = 0.025) and with more severe manic symptoms at 6 months (β = 0.207, p = 0.026), taking into account relevant covariates including age and smoking status. No significant associations were observed at the 12-month follow-up assessment or with any other clinical outcome measures. Our data provide initial evidence for a link between AL and impaired functioning in individuals at UHR for psychosis. Further studies are needed to evaluate AL as a potential predictor of early treatment response.