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Rule-based and machine learning algorithms identify patients with systemic sclerosis accurately in the electronic health record.
Jamian L, Wheless L, Crofford LJ, Barnado A
(2019) Arthritis Res Ther 21: 305
MeSH Terms: Adult, Aged, Aged, 80 and over, Algorithms, Databases, Factual, Electronic Health Records, Female, Humans, International Classification of Diseases, Machine Learning, Male, Middle Aged, Reproducibility of Results, Scleroderma, Systemic, Sensitivity and Specificity
Show Abstract · Added March 25, 2020
BACKGROUND - Systemic sclerosis (SSc) is a rare disease with studies limited by small sample sizes. Electronic health records (EHRs) represent a powerful tool to study patients with rare diseases such as SSc, but validated methods are needed. We developed and validated EHR-based algorithms that incorporate billing codes and clinical data to identify SSc patients in the EHR.
METHODS - We used a de-identified EHR with over 3 million subjects and identified 1899 potential SSc subjects with at least 1 count of the SSc ICD-9 (710.1) or ICD-10-CM (M34*) codes. We randomly selected 200 as a training set for chart review. A subject was a case if diagnosed with SSc by a rheumatologist, dermatologist, or pulmonologist. We selected the following algorithm components based on clinical knowledge and available data: SSc ICD-9 and ICD-10-CM codes, positive antinuclear antibody (ANA) (titer ≥ 1:80), and a keyword of Raynaud's phenomenon (RP). We performed both rule-based and machine learning techniques for algorithm development. Positive predictive values (PPVs), sensitivities, and F-scores (which account for PPVs and sensitivities) were calculated for the algorithms.
RESULTS - PPVs were low for algorithms using only 1 count of the SSc ICD-9 code. As code counts increased, the PPVs increased. PPVs were higher for algorithms using ICD-10-CM codes versus the ICD-9 code. Adding a positive ANA and RP keyword increased the PPVs of algorithms only using ICD billing codes. Algorithms using ≥ 3 or ≥ 4 counts of the SSc ICD-9 or ICD-10-CM codes and ANA positivity had the highest PPV at 100% but a low sensitivity at 50%. The algorithm with the highest F-score of 91% was ≥ 4 counts of the ICD-9 or ICD-10-CM codes with an internally validated PPV of 90%. A machine learning method using random forests yielded an algorithm with a PPV of 84%, sensitivity of 92%, and F-score of 88%. The most important feature was RP keyword.
CONCLUSIONS - Algorithms using only ICD-9 codes did not perform well to identify SSc patients. The highest performing algorithms incorporated clinical data with billing codes. EHR-based algorithms can identify SSc patients across a healthcare system, enabling researchers to examine important outcomes.
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15 MeSH Terms
Heart failure and atrial tachyarrhythmia on abiraterone: A pharmacovigilance study.
Bretagne M, Lebrun-Vignes B, Pariente A, Shaffer CM, Malouf GG, Dureau P, Potey C, Funck-Brentano C, Roden DM, Moslehi JJ, Salem JE
(2020) Arch Cardiovasc Dis 113: 9-21
MeSH Terms: Adverse Drug Reaction Reporting Systems, Aged, Aged, 80 and over, Androgen Antagonists, Androstenes, Antineoplastic Agents, Hormonal, Cardiotoxicity, Databases, Factual, Heart Failure, Humans, Male, Middle Aged, Pharmacovigilance, Phenylthiohydantoin, Prostatic Neoplasms, Retrospective Studies, Risk Assessment, Risk Factors, Tachycardia, Supraventricular, Time Factors
Show Abstract · Added November 12, 2019
BACKGROUND - Abiraterone and enzalutamide are recently-approved androgen deprivation therapies (ADTs) for metastatic prostate cancer, with unknown cardiac safety profiles. Abiraterone has a propensity to hypermineralocorticism on top of androgen deprivation, so might carry an additional risk for atrial tachyarrhythmia (AT) and heart failure (HF) compared with other ADTs.
AIM - To determine if abiraterone was associated with an increased proportion of AT and HF reports among all suspected adverse drug reactions (ADRs) reported in several pharmacovigilance databases compared with enzalutamide, other ADTs and all other drugs.
METHODS - In this observational retrospective pharmacovigilance study, we performed a disproportionality analysis of reports of suspected ADRs in men in the French pharmacovigilance database, the European pharmacovigilance database and the international pharmacovigilance database VigiBase, to evaluate the reporting odds ratios (RORs) of AT and HF for abiraterone compared with enzalutamide, other ADTs and all other drugs.
RESULTS - In the 5,759,781 ADR reports in men in VigiBase, 55,070 pertained to ADTs. The RORs for AT for abiraterone versus enzalutamide, other ADTs and all other drugs were 4.1 (95% confidence interval 3.1-5.3), 3.7 (3-4.5) and 3.2 (2.7-3.7), respectively (P<0.0001 for all). The corresponding RORs for HF were 2.5 (2-3), 1.5 (1.3-1.7) and 2 (1.7-2.3), respectively (P<0.0001 for all). These results were concordant with the French and European pharmacovigilance databases. Mean times to AT and HF onset were shorter with abiraterone (5.2±0.8 and 4.5±0.6 months, respectively) versus other ADTs (13.3±3.2 and 9.2±1.1 months, respectively) (both P<0.05). Cases on abiraterone versus other ADTs were more frequently associated with at least two ADR terms, including AT, HF, hypokalaemia, hypertension and oedema (13.6% vs 6%; P<0.0001). For abiraterone, age, but not dose, was associated with reporting of AT and HF versus any other ADR.
CONCLUSIONS - Compared with other ADTs, abiraterone was associated with higher reporting of AT and HF, associated with hypokalaemia, hypertension and oedema. These findings are consistent with the hypermineralocorticism induced by abiraterone, but not by other ADTs.
Copyright © 2019 Elsevier Masson SAS. All rights reserved.
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20 MeSH Terms
Increased reporting of fatal hepatitis associated with immune checkpoint inhibitors.
Vozy A, De Martin E, Johnson DB, Lebrun-Vignes B, Moslehi JJ, Salem JE
(2019) Eur J Cancer 123: 112-115
MeSH Terms: Adolescent, Adult, Aged, Aged, 80 and over, Antibodies, Monoclonal, Humanized, Antineoplastic Agents, Immunological, B7-H1 Antigen, CTLA-4 Antigen, Chemical and Drug Induced Liver Injury, Child, Databases, Factual, Female, Hepatitis, Autoimmune, Humans, Ipilimumab, Male, Massive Hepatic Necrosis, Middle Aged, Neoplasms, Nivolumab, Programmed Cell Death 1 Receptor, World Health Organization, Young Adult
Added November 12, 2019
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23 MeSH Terms
Cardiovascular Toxicities Associated With Ibrutinib.
Salem JE, Manouchehri A, Bretagne M, Lebrun-Vignes B, Groarke JD, Johnson DB, Yang T, Reddy NM, Funck-Brentano C, Brown JR, Roden DM, Moslehi JJ
(2019) J Am Coll Cardiol 74: 1667-1678
MeSH Terms: Adverse Drug Reaction Reporting Systems, Aged, Aged, 80 and over, Cardiovascular Diseases, Databases, Factual, Female, Humans, Male, Mortality, Pharmacovigilance, Pyrazoles, Pyrimidines, Retrospective Studies
Show Abstract · Added November 12, 2019
BACKGROUND - Ibrutinib has revolutionized treatment for several B-cell malignancies. However, a recent clinical trial where ibrutinib was used in a front-line setting showed increased mortality during treatment compared with conventional chemotherapy. Cardiovascular toxicities were suspected as the culprit but not directly assessed in the study.
OBJECTIVES - The purpose of this study was to identify and characterize cardiovascular adverse drug reactions (CV-ADR) associated with ibrutinib.
METHODS - This study utilized VigiBase (International pharmacovigilance database) and performed a disproportionality analysis using reporting odds ratios (ROR) and information component (IC) to determine whether CV-ADR and CV-ADR deaths were associated with ibrutinib. IC compares observed and expected values to find associations between drugs and adverse drug reactions using disproportionate Bayesian-reporting; IC (lower end of the IC 95% credibility interval) >0 is significant.
RESULTS - This study identified 303 ibrutinib-associated cardiovascular deaths. Ibrutinib was associated with higher reporting of supraventricular arrhythmias (SVAs) (ROR: 23.1; 95% confidence interval: 21.6 to 24.7; p < 0.0001; IC: 3.97), central nervous system (CNS) hemorrhagic events (ROR: 3.7; 95% confidence interval: 3.4 to 4.1; p < 0.0001; IC: 1.63), heart failure (ROR: 3.5; 95% confidence interval: 3.1 to 3.8; p < 0.0001; IC: 1.46), ventricular arrhythmias (ROR: 4.7; 95% confidence interval: 3.7 to 5.9; p < 0.0001; IC: 0.96), conduction disorders (ROR: 3.5; 95% confidence interval: 2.7 to 4.6; p < 0.0001; IC: 0.76), CNS ischemic events (ROR: 2.2; 95% confidence interval: 2.0 to 2.5; p < 0.0001; IC: 0.73), and hypertension (ROR: 1.7; 95% confidence interval: 1.5 to 1.9; p < 0.0001; IC: 0.4). CV-ADR often occurred early after ibrutinib administration. Importantly, CV-ADR were associated with fatalities that ranged from ∼10% (SVAs and ventricular arrhythmias) to ∼20% (CNS events, heart failure, and conduction disorders). Ibrutinib-associated SVA portends poor prognosis when CNS events occur concomitantly, with 28.8% deaths (15 of 52 cases).
CONCLUSIONS - Severe and occasionally fatal cardiac events occur in patients exposed to ibrutinib. These events should be considered in patient care and in clinical trial designs. (Evaluation of Reporting of Cardio-vascular Adverse Events With Antineoplastic and Immunomodulating Agents [EROCA]; NCT03530215).
Copyright © 2019 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.
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13 MeSH Terms
Androgenic Effects on Ventricular Repolarization: A Translational Study From the International Pharmacovigilance Database to iPSC-Cardiomyocytes.
Salem JE, Yang T, Moslehi JJ, Waintraub X, Gandjbakhch E, Bachelot A, Hidden-Lucet F, Hulot JS, Knollmann BC, Lebrun-Vignes B, Funck-Brentano C, Glazer AM, Roden DM
(2019) Circulation 140: 1070-1080
MeSH Terms: Androgens, Antineoplastic Agents, Cell Differentiation, Cells, Cultured, Databases, Factual, Humans, Hypogonadism, Induced Pluripotent Stem Cells, International Cooperation, Long QT Syndrome, Male, Myocytes, Cardiac, Pharmacovigilance, Phenylthiohydantoin, Risk, Torsades de Pointes, Translational Medical Research
Show Abstract · Added November 12, 2019
BACKGROUND - Male hypogonadism, arising from a range of etiologies including androgen-deprivation therapies (ADTs), has been reported as a risk factor for acquired long-QT syndrome (aLQTS) and torsades de pointes (TdP). A full description of the clinical features of aLQTS associated with ADT and of underlying mechanisms is lacking.
METHODS - We searched the international pharmacovigilance database VigiBase for men (n=6 560 565 individual case safety reports) presenting with aLQTS, TdP, or sudden death associated with ADT. In cardiomyocytes derived from induced pluripotent stem cells from men, we studied electrophysiological effects of ADT and dihydrotestosterone.
RESULTS - Among subjects receiving ADT in VigiBase, we identified 184 cases of aLQTS (n=168) and/or TdP (n=68; 11% fatal), and 99 with sudden death. Of the 10 ADT drugs examined, 7 had a disproportional association (reporting odds ratio=1.4-4.7; <0.05) with aLQTS, TdP, or sudden death. The minimum and median times to sudden death were 0.25 and 92 days, respectively. The androgen receptor antagonist enzalutamide was associated with more deaths (5430/31 896 [17%]; <0.0001) than other ADT used for prostate cancer (4208/52 089 [8.1%]). In induced pluripotent stem cells, acute and chronic enzalutamide (25 µM) significantly prolonged action potential durations (action potential duration at 90% when paced at 0.5 Hz; 429.7±27.1 (control) versus 982.4±33.2 (acute, <0.001) and 1062.3±28.9 ms (chronic; <0.001), and generated afterdepolarizations and/or triggered activity in drug-treated cells (11/20 acutely and 8/15 chronically). Enzalutamide acutely and chronically inhibited delayed rectifier potassium current, and chronically enhanced late sodium current. Dihydrotestosterone (30 nM) reversed enzalutamide electrophysiological effects on induced pluripotent stem cells.
CONCLUSIONS - QT prolongation and TdP are a risk in men receiving enzalutamide and other ADTs.
CLINICAL TRIAL REGISTRATION - URL: https://www.clinicaltrials.gov. Unique identifier: NCT03193138.
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17 MeSH Terms
Immune checkpoint inhibitor-associated hypophysitis-World Health Organisation VigiBase report analysis.
Guerrero E, Johnson DB, Bachelot A, Lebrun-Vignes B, Moslehi JJ, Salem JE
(2019) Eur J Cancer 113: 10-13
MeSH Terms: Adult, Aged, Aged, 80 and over, Antibodies, Monoclonal, Antibodies, Monoclonal, Humanized, Antineoplastic Agents, Immunological, B7-H1 Antigen, CTLA-4 Antigen, Databases, Factual, Female, Humans, Hypophysitis, Ipilimumab, Male, Middle Aged, Nivolumab, Pharmacovigilance, Programmed Cell Death 1 Receptor, World Health Organization, Young Adult
Added November 12, 2019
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20 MeSH Terms
Hematologic Complications of Immune Checkpoint Inhibitors.
Davis EJ, Salem JE, Young A, Green JR, Ferrell PB, Ancell KK, Lebrun-Vignes B, Moslehi JJ, Johnson DB
(2019) Oncologist 24: 584-588
MeSH Terms: Adult, Adverse Drug Reaction Reporting Systems, Aged, Aged, 80 and over, Antibodies, Monoclonal, Humanized, Antineoplastic Agents, Immunological, B7-H1 Antigen, Databases, Factual, Female, Hematologic Diseases, Humans, Incidence, Ipilimumab, Male, Middle Aged, Neoplasms, Pharmacovigilance, Programmed Cell Death 1 Receptor, Risk Factors
Show Abstract · Added November 12, 2019
Immune checkpoint inhibitors have improved outcomes for patients with numerous hematological and solid cancers. Hematologic toxicities have been described, but the spectrum, timing, and clinical presentation of these complications are not well understood. We used the World Health Organization's pharmacovigilance database of individual-case-safety-reports (ICSRs) of adverse drug reactions, VigiBase, to identify cases of hematologic toxicities complicating immune checkpoint inhibitor therapy. We identified 168 ICSRs of immune thrombocytopenic purpura (ITP), hemolytic anemia (HA), hemophagocytic lymphohistiocytosis, aplastic anemia, and pure red cell aplasia in 164 ICSRs. ITP ( = 68) and HA ( = 57) were the most common of these toxicities and occurred concomitantly in four patients. These events occurred early on treatment (median 40 days) and were associated with fatal outcome in 12% of cases. Ipilimumab-based therapy (monotherapy or combination with anti-programmed death-1 [PD-1]) was associated with earlier onset (median 23 vs. 47.5 days,  = .006) than anti-PD-1/programmed death ligand-1 monotherapy. Reporting of hematologic toxicities has increased over the past 2 years (98 cases between January 2017 and March 2018 vs. 70 cases before 2017), possibly because of increased use of checkpoint inhibitors and improved recognition of toxicities. Future studies should evaluate incidence of hematologic toxicities, elucidate risk factors, and determine the most effective treatment algorithms. KEY POINTS: Immune-mediated hematologic toxicities are a potential side effect of immune checkpoint inhibitors (ICIs).Providers should monitor complete blood counts during treatment with ICIs.Corticosteroids are the mainstay of treatment for immune-mediated hematologic toxicities.Further research is needed to define patient-specific risk factors and optimal management strategies for hematologic toxicities.
© AlphaMed Press 2019.
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19 MeSH Terms
Identifying lupus patients in electronic health records: Development and validation of machine learning algorithms and application of rule-based algorithms.
Jorge A, Castro VM, Barnado A, Gainer V, Hong C, Cai T, Cai T, Carroll R, Denny JC, Crofford L, Costenbader KH, Liao KP, Karlson EW, Feldman CH
(2019) Semin Arthritis Rheum 49: 84-90
MeSH Terms: Adult, Aged, Algorithms, Databases, Factual, Electronic Health Records, Female, Humans, Lupus Erythematosus, Systemic, Machine Learning, Male, Middle Aged, Natural Language Processing, Sensitivity and Specificity
Show Abstract · Added March 25, 2020
OBJECTIVE - To utilize electronic health records (EHRs) to study SLE, algorithms are needed to accurately identify these patients. We used machine learning to generate data-driven SLE EHR algorithms and assessed performance of existing rule-based algorithms.
METHODS - We randomly selected subjects with ≥ 1 SLE ICD-9/10 codes from our EHR and identified gold standard definite and probable SLE cases by chart review, based on 1997 ACR or 2012 SLICC Classification Criteria. From a training set, we extracted coded and narrative concepts using natural language processing and generated algorithms using penalized logistic regression to classify definite or definite/probable SLE. We assessed predictive characteristics in internal and external cohort validations. We also tested performance characteristics of published rule-based algorithms with pre-specified permutations of ICD-9 codes, laboratory tests and medications in our EHR.
RESULTS - At a specificity of 97%, our machine learning coded algorithm for definite SLE had 90% positive predictive value (PPV) and 64% sensitivity and for definite/probable SLE, 92% PPV and 47% sensitivity. In the external validation, at 97% specificity, the definite/probable algorithm had 94% PPV and 60% sensitivity. Adding NLP concepts did not improve performance metrics. The PPVs of published rule-based algorithms ranged from 45-79% in our EHR.
CONCLUSION - Our machine learning SLE algorithms performed well in internal and external validation. Rule-based SLE algorithms did not transport as well to our EHR. Unique EHR characteristics, clinical practices and research goals regarding the desired sensitivity and specificity of the case definition must be considered when applying algorithms to identify SLE patients.
Copyright © 2019 Elsevier Inc. All rights reserved.
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13 MeSH Terms
Cardiovascular toxicities associated with immune checkpoint inhibitors: an observational, retrospective, pharmacovigilance study.
Salem JE, Manouchehri A, Moey M, Lebrun-Vignes B, Bastarache L, Pariente A, Gobert A, Spano JP, Balko JM, Bonaca MP, Roden DM, Johnson DB, Moslehi JJ
(2018) Lancet Oncol 19: 1579-1589
MeSH Terms: Adult, Adverse Drug Reaction Reporting Systems, Aged, Aged, 80 and over, Antineoplastic Agents, Immunological, Bayes Theorem, Cardiotoxicity, Cardiovascular Diseases, Databases, Factual, Female, Humans, Immunotherapy, Male, Middle Aged, Pharmacovigilance, Retrospective Studies, Risk Assessment, Risk Factors, Time Factors
Show Abstract · Added December 13, 2018
BACKGROUND - Immune checkpoint inhibitors (ICIs) have substantially improved clinical outcomes in multiple cancer types and are increasingly being used in early disease settings and in combinations of different immunotherapies. However, ICIs can also cause severe or fatal immune-related adverse-events (irAEs). We aimed to identify and characterise cardiovascular irAEs that are significantly associated with ICIs.
METHODS - In this observational, retrospective, pharmacovigilance study, we used VigiBase, WHO's global database of individual case safety reports, to compare cardiovascular adverse event reporting in patients who received ICIs (ICI subgroup) with this reporting in the full database. This study included all cardiovascular irAEs classified by group queries according to the Medical Dictionary for Regulatory Activities, between inception on Nov 14, 1967, and Jan 2, 2018. We evaluated the association between ICIs and cardiovascular adverse events using the reporting odds ratio (ROR) and the information component (IC). IC is an indicator value for disproportionate Bayesian reporting that compares observed and expected values to find associations between drugs and adverse events. IC is the lower end of the IC 95% credibility interval, and an IC value of more than zero is deemed significant. This study is registered with ClinicalTrials.gov, number NCT03387540.
FINDINGS - We identified 31 321 adverse events reported in patients who received ICIs and 16 343 451 adverse events reported in patients treated with any drugs (full database) in VigiBase. Compared with the full database, ICI treatment was associated with higher reporting of myocarditis (5515 reports for the full database vs 122 for ICIs, ROR 11·21 [95% CI 9·36-13·43]; IC 3·20), pericardial diseases (12 800 vs 95, 3·80 [3·08-4·62]; IC 1·63), and vasculitis (33 289 vs 82, 1·56 [1·25-1·94]; IC 0·03), including temporal arteritis (696 vs 18, 12·99 [8·12-20·77]; IC 2·59) and polymyalgia rheumatica (1709 vs 16, 5·13 [3·13-8·40]; IC 1·33). Pericardial diseases were reported more often in patients with lung cancer (49 [56%] of 87 patients), whereas myocarditis (42 [41%] of 103 patients) and vasculitis (42 [60%] of 70 patients) were more commonly reported in patients with melanoma (χ test for overall subgroup comparison, p<0·0001). Vision was impaired in five (28%) of 18 patients with temporal arteritis. Cardiovascular irAEs were severe in the majority of cases (>80%), with death occurring in 61 (50%) of 122 myocarditis cases, 20 (21%) of 95 pericardial disease cases, and five (6%) of 82 vasculitis cases (χ test for overall comparison between pericardial diseases, myocarditis, and vasculitis, p<0·0001).
INTERPRETATION - Treatment with ICIs can lead to severe and disabling inflammatory cardiovascular irAEs soon after commencement of therapy. In addition to life-threatening myocarditis, these toxicities include pericardial diseases and temporal arteritis with a risk of blindness. These events should be considered in patient care and in combination clinical trial designs (ie, combinations of different immunotherapies as well as immunotherapies and chemotherapy).
FUNDING - The Cancer Institut Thématique Multi-Organisme of the French National Alliance for Life and Health Sciences (AVIESAN) Plan Cancer 2014-2019; US National Cancer Institute, National Institutes of Health; the James C. Bradford Jr. Melanoma Fund; and the Melanoma Research Foundation.
Copyright © 2018 Elsevier Ltd. All rights reserved.
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19 MeSH Terms
Incidence of Epilepsy and Associated Risk Factors in Perinatal Ischemic Stroke Survivors.
Rattani A, Lim J, Mistry AM, Prablek MA, Roth SG, Jordan LC, Shannon CN, Naftel RP
(2019) Pediatr Neurol 90: 44-55
MeSH Terms: Brain Ischemia, Cerebral Palsy, Databases, Factual, Epilepsy, Female, Hippocampus, Humans, Incidence, Infant, Newborn, Male, Risk Factors, Stroke, Survivors
Show Abstract · Added March 24, 2020
INTRODUCTION - Epilepsy is a serious and often lifelong consequence of perinatal arterial ischemic stroke (PAIS). Variable incidences and risk factors for long-term epilepsy in PAIS have been reported. To determine the incidence of epilepsy in PAIS survivors and report factors associated with the risk of developing epilepsy, a meta-analysis and systematic review of prior publications was performed.
METHODS - We examined studies on perinatal or neonatal patients (≤28 days of life) with arterial ischemic strokes in which the development of epilepsy was reported. EMBASE and MEDLINE/PubMed databases were systematically searched in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses.
RESULTS - A meta-analysis of 10 studies revealed a summary incidence of epilepsy in PAIS patients of 27.2% (95% confidence interval 16.6% to 41.4%) over a mean study duration of 10.4 years (range 1.5 to 17). More recent studies generally reported a lower epilepsy incidence. A systematic review identified seven possible risk factors for epilepsy in PAIS patients: hippocampal volume reduction, infarct on prenatal ultrasound, a modified Alberta Stroke Program Early Computed Tomography score ≥9, family history of seizures, cerebral palsy, and initial presentation with cognitive impairment or seizures.
CONCLUSIONS - About a third of children with PAIS will develop epilepsy. While seven possible risk factors have been reported, further research is warranted to confirm the strength of their association with the development of epilepsy.
Copyright © 2019 Elsevier Ltd. All rights reserved.
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