Construction of Cohorts of Similar Patients From Automatic Extraction of Medical Concepts: Phenotype Extraction Study

Background Reliable and interpretable automatic extraction of clinical phenotypes from large electronic medical record databases remains a challenge, especially in a language other than English. Objective We aimed to provide an automated end-to-end extraction of cohorts of similar patients from electronic health records for systemic diseases. Methods Our multistep algorithm includes a named-entity recognition step, a multilabel classification using medical subject headings ontology, and the computation of patient similarity. A selection of cohorts of similar patients on a priori annotated phenotypes was performed. Six phenotypes were selected for their clinical significance: P1, osteoporosis; P2, nephritis in systemic erythematosus lupus; P3, interstitial lung disease in systemic sclerosis; P4, lung infection; P5, obstetric antiphospholipid syndrome; and P6, Takayasu arteritis. We used a training set of 151 clinical notes and an independent validation set of 256 clinical notes, with annotated phenotypes, both extracted from the Assistance Publique-Hôpitaux de Paris data warehouse. We evaluated the precision of the 3 patients closest to the index patient for each phenotype with precision-at-3 and recall and average precision. Results For P1-P4, the precision-at-3 ranged from 0.85 (95% CI 0.75-0.95) to 0.99 (95% CI 0.98-1), the recall ranged from 0.53 (95% CI 0.50-0.55) to 0.83 (95% CI 0.81-0.84), and the average precision ranged from 0.58 (95% CI 0.54-0.62) to 0.88 (95% CI 0.85-0.90). P5-P6 phenotypes could not be analyzed due to the limited number of phenotypes. Conclusions Using a method close to clinical reasoning, we built a scalable and interpretable end-to-end algorithm for extracting cohorts of similar patients

Construction of Cohorts of Similar Patients From Automatic Extraction of Medical Concepts: Phenotype Extraction Study

International audienceBackground. Reliable and interpretable automatic extraction of clinical phenotypes from large electronic medical record databases remains a challenge, especially in a language other than English.Objective.We aimed to provide an automated end-to-end extraction of cohorts of similar patients from electronic health records for systemic diseases.Methods. Our multistep algorithm includes a named-entity recognition step, a multilabel classification using medical subject headings ontology, and the computation of patient similarity. A selection of cohorts of similar patients on a priori annotated phenotypes was performed. Six phenotypes were selected for their clinical significance: P1, osteoporosis; P2, nephritis in systemic erythematosus lupus; P3, interstitial lung disease in systemic sclerosis; P4, lung infection; P5, obstetric antiphospholipid syndrome; and P6, Takayasu arteritis. We used a training set of 151 clinical notes and an independent validation set of 256 clinical notes, with annotated phenotypes, both extracted from the Assistance Publique-Hôpitaux de Paris data warehouse. We evaluated the precision of the 3 patients closest to the index patient for each phenotype with precision-at-3 and recall and average precision.Results. For P1-P4, the precision-at-3 ranged from 0.85 (95% CI 0.75-0.95) to 0.99 (95% CI 0.98-1), the recall ranged from 0.53 (95% CI 0.50-0.55) to 0.83 (95% CI 0.81-0.84), and the average precision ranged from 0.58 (95% CI 0.54-0.62) to 0.88 (95% CI 0.85-0.90). P5-P6 phenotypes could not be analyzed due to the limited number of phenotypes.Conclusions. Using a method close to clinical reasoning, we built a scalable and interpretable end-to-end algorithm for extracting cohorts of similar patients

Acute Myocarditis Revealing Adult-Onset Still’s Disease

International audienceA 34-year-old man presented with fever, palpitations, maculopapular rash, pharyngitis, left cheilitis, and bilateral gonalgia. High-sensitivity troponin I concentration was 4,900 ng/l. Transthoracic echocardiogram revealed reduced global longitudinal strain. Cardiac magnetic resonance imaging showed acute myocarditis. Adult-onset Still’s disease was diagnosed, and treatment with intravenous corticosteroids and tocilizumab was initiated. (Level of Difficulty: Beginner.

Intrications organo-psychiatriques : le concept de troubles psychiatriques complexes, quels examens complémentaires ?

International audienceThe purpose of this article is to describe complex psychiatric disorders, to recall “minimal classical” explorations in psychiatry, to describe the concept of “complex psychiatric disorders” and to propose a systematized method of exploration.Some organic diseases are well known for their links with psychiatric disorders (manic syndrome and hyperthyroidism, depressive syndrome and corticotropic insufficiency, anxiety disorder and heart disease, etc.).Many other neurological, autoimmune, metabolic, paraneoplastic or endocrine pathologies can have essentially psycho-behavioral manifestations before being neurological or systemic.A large number of factors (nutritional, toxic, immunological, etc.), often ignored, influence the links between organicity and psychiatric pathologies.It is necessary to optimize the medical management of these patients in whom the psychiatric diagnosis masks a curable organo-psychiatric cause.Cet article a pour objectifs de décrire des troubles psychiatriques complexes, de rappeler les explorations « classiques minimales » en psychiatrie, de décrire le concept de « troubles psychiatriques complexes » et de proposer une méthode d’exploration systématisée.Certaines pathologies organiques sont bien connues pour leurs liens avec les troubles psychiatriques (syndrome maniaque et hyperthyroïdie, syndrome dépressif et insuffisance corticotrope, trouble anxieux et maladie cardiaque, etc.).De nombreuses autres pathologies neurologiques, auto-immunes, métaboliques, paranéoplasiques ou endocriniennes peuvent avoir des manifestations essentiellement psycho-comportementales avant d’être neurologiques ou systémiques.Un grand nombre de facteurs (nutritionnels, toxiques, immunologiques, etc.), souvent ignorés, exercent une influence sur les liens existants entre organicité et pathologies psychiatriques.Il est nécessaire d’optimiser la prise en charge médicale de ces patients chez qui le diagnostic psychiatrique masque une cause organo-psychiatrique curable

Systemic Pulmonary Events Associated with Myelodysplastic Syndromes: A Retrospective Multicentre Study

International audienceAlthough pulmonary events are considered to be frequently associated with malignant haemopathies, they have been sparsely studied in the specific context of myelodysplastic syndromes (MDS). We aimed to describe their different types, their relative proportions and their relative effects on overall survival (OS). We conducted a multicentre retrospective cohort study. Patients with MDS (diagnosed according to the 2016 WHO classification) and pulmonary events were included. The inclusion period was 1 January 2007 to 31 December 2017 and patients were monitored until August 2019. Fifty-five hospitalized patients were included in the analysis. They had 113 separate pulmonary events. Thirteen patients (23.6%) had a systemic autoimmune disease associated with MDS. Median age at diagnosis of MDS was 77 years. Median time to onset of pulmonary events was 13 months. Pulmonary events comprised: 70 infectious diseases (62%); 27 interstitial lung diseases (23.9%), including 13 non-specific interstitial pneumonias and seven secondary organizing pneumonias or respiratory bronchiolitis–interstitial lung diseases; 10 pleural effusions (8.8%), including four cases of chronic organizing pleuritis with exudative effusion; and six pulmonary hypertensions (5.3%). The median OS of the cohort was 29 months after MDS diagnosis but OS was only 10 months after a pulmonary event. The OS was similar to that of the general myelodysplastic population. However, the occurrence of a pulmonary event appeared to be either an accelerating factor of death or an indicator for the worsening of the underlying MDS in our study. More than a third of pulmonary events were non-infectious and could be systemic manifestations of MDS

Circulating follicular helper T cells are increased in systemic sclerosis and promote plasmablast differentiation through the IL-21 pathway which can be inhibited by ruxolitinib

International audienceApproximately 1 to 3% of women have recurrent early miscarriages, defined as ≥3 pregnancy losses before 14 weeks of gestation. The immune deregulation and tolerance rupture could be the origin of these miscarriages in at least 30% of these women. Chronic intervillositis of unknown etiology (CIUE) is a rare placental lesion characterized by intrauterine deaths, growth restriction and high recurrence rate. In cases with recurrent obstetrical adverse events and intrauterine deaths, we previously reported the benefit of hydroxychloroquine combination to prednisone. Even few data raised the potential value of TNF antagonists in early recurrent miscarriages, these cases show its potential value in the setting of recurrent refractory chronic intervillositis and unexplained miscarriages

18F-FDG positron emission tomography scanning in systemic sclerosis-associated interstitial lung disease: a pilot study

International audienceBackground: Interstitial lung disease is a common complication of systemic sclerosis (SSc-ILD), and it remains difficult to accurately predict its course. Progressing ILD could be more metabolically active, suggesting that the 18F-FDG tracer could be a tool in the managing of SSc-ILD.Methods: In our center, SSc patients and controls (non-Hodgkin lymphoma cured after first-line regimen) who had received a PET/CT were screened retrospectively. The FDG uptake (visual intensity, pattern, SUVmax) was systematically recorded in > 30 regions of interest (ROIs) linked to SSc in a blind reviewing by 2 independent nuclear medicine physicians using a standardized form.Results: Among the 545 SSc patients followed up in our center, 36, including 22 SSc-ILDs, had a PET/CT, whose indication was cancer screening in most cases. The mean ± SD age was 57.9 ± 13.0 years with 20/36 females. Fourteen patients had a disease duration of less than 2 years. A third had anti-centromere antibodies and 27.8% had anti-topoisomerase antibodies. Pulmonary FDG uptakes were higher in SSc patients than in controls (n = 89), especially in those with ILD compared with those without ILD. Pulmonary FDG uptakes were positively correlated with the ILD severity (fibrosis extent, %FVC, and %DLCO). No significant difference was found in the FDG uptakes from extrathoracic ROIs. Progressing SSc-ILDs within the 2 years after PET/CT (n = 9) had significant higher pulmonary FDG uptakes at baseline than stable SSc-ILDs (n = 13).Conclusion: PET/CT could be a useful tool in the assessment of the severity and the prediction of pulmonary function outcome of SSc-ILD

Emerging RNA-Dependent RNA Polymerase Mutation in a Remdesivir-Treated B-cell Immunodeficient Patient With Protracted Coronavirus Disease 2019

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly discovered virus for which remdesivir is the only antiviral available. We report the occurrence of a mutation in RdRP (D484Y) following treatment with remdesivir in a 76-year-old female with post-rituximab B-cell immunodeficiency and persistent SARS-CoV-2 viremia. A cure was achieved after supplementation with convalescent plasma

IgG1 Subclass Restriction and Biochemical Peculiarities of Monoclonal Immunoglobulins in Scleromyxedema

International audienceBackground: Scleromyxedema (SME) is a rare mucinosis associated with monoclonal gammopathy. Several biochemical peculiarities of monoclonal immunoglobulins (Ig) in SME patients were reported in case reports or short series, such as IgGλ over-representation, cationic migration, and partial deletion. Methods: Monoclonal immunoglobulins (Ig) from the serum of 12 consecutive patients diagnosed with scleromyxedema (SME) were analyzed using electrophoretic and immunoblotting techniques. Results: All monoclonal Ig from 12 SME were of IgG1 subclass, with an overrepresentation of the lambda-type light chain and a cationic mobility on standard zone electrophoresis, as compared with 21 cases of monoclonal gammopathy of undetermined significance (MGUS) of IgG1 subclass. Reactivity with specific monoclonal antibodies demonstrated no evident deletion of the heavy chain constant domains, which was also confirmed by analysis of Ig heavy chain molecular weight on a purified monoclonal component from one case. Conclusions: Significant isotype restriction of both heavy and light chains, and peculiar biochemical properties suggest that monoclonal Ig might be involved in pathophysiological events of SME