Combining deep neural networks, a rule-based expert system and targeted manual coding for ICD-10 coding causes of death of French death certificates from 2018 to 2019.

OBJECTIVE: For ICD-10 coding causes of death in France in 2018 and 2019, predictions by deep neural networks (DNNs) are employed in addition to fully automatic batch coding by a rule-based expert system and to interactive coding by the coding team focused on certificates with a special public health interest and those for which DNNs have a low confidence index. METHODS: Supervised seq-to-seq DNNs are trained on previously coded data to ICD-10 code multiple causes and underlying causes of death. The DNNs are then used to target death certificates to be sent to the coding team and to predict multiple causes and underlying causes of death for part of the certificates. Hence, the coding campaign for 2018 and 2019 combines three modes of coding and a loop of interaction between the three. FINDINGS: In this campaign, 62% of the certificates are automatically batch coded by the expert system, 3% by the coding team, and the remainder by DNNs. Compared to a traditional campaign that would have relied on automatic batch coding and manual coding, the present campaign reaches an accuracy of 93.4% for ICD-10 coding of the underlying cause (95.6% at the European shortlist level). Some limitations (risks of under- or overestimation) appear for certain ICD categories, with the advantage of being quantifiable. CONCLUSION: The combination of the three coding methods illustrates how artificial intelligence, automated and human codings are mutually enriching. Quantified limitations on some chapters of ICD codes encourage an increase in the volume of certificates sent for manual coding from 2021 onward.

Development of a natural language processing model for deriving breast cancer quality indicators : A cross-sectional, multicenter study.

OBJECTIVES: Medico-administrative data are promising to automate the calculation of Healthcare Quality and Safety Indicators. Nevertheless, not all relevant indicators can be calculated with this data alone. Our feasibility study objective is to analyze 1) the availability of data sources; 2) the availability of each indicator elementary variables, and 3) to apply natural language processing to automatically retrieve such information. METHOD: We performed a multicenter cross-sectional observational feasibility study on the clinical data warehouse of Assistance Publique - Hôpitaux de Paris (AP-HP). We studied the management of breast cancer patients treated at AP-HP between January 2019 and June 2021, and the quality indicators published by the European Society of Breast Cancer Specialist, using claims data from the Programme de Médicalisation du Système d'Information (PMSI) and pathology reports. For each indicator, we calculated the number (%) of patients for whom all necessary data sources were available, and the number (%) of patients for whom all elementary variables were available in the sources, and for whom the related HQSI was computable. To extract useful data from the free text reports, we developed and validated dedicated rule-based algorithms, whose performance metrics were assessed with recall, precision, and f1-score. RESULTS: Out of 5785 female patients diagnosed with a breast cancer (60.9 years, IQR [50.0-71.9]), 5,147 (89.0%) had procedures related to breast cancer recorded in the PMSI, and 3732 (72.5%) had at least one surgery. Out of the 34 key indicators, 9 could be calculated with the PMSI alone, and 6 others became so using the data from pathology reports. Ten elementary variables were needed to calculate the 6 indicators combining the PMSI and pathology reports. The necessary sources were available for 58.8% to 94.6% of patients, depending on the indicators. The extraction algorithms developed had an average accuracy of 76.5% (min-max [32.7%-93.3%]), an average precision of 77.7% [10.0%-97.4%] and an average sensitivity of 71.6% [2.8% to 100.0%]. Once these algorithms applied, the variables needed to calculate the indicators were extracted for 2% to 88% of patients, depending on the indicators. DISCUSSION: The availability of medical reports in the electronic health records, of the elementary variables within the reports, and the performance of the extraction algorithms limit the population for which the indicators can be calculated. CONCLUSIONS: The automated calculation of quality indicators from electronic health records is a prospect that comes up against many practical obstacles.

Impact of the COVID-19 pandemic on clinical presentation, treatments, and outcomes of new breast cancer patients: A retrospective multicenter cohort study.

BACKGROUND: The SARS CoV-2 pandemic disrupted healthcare systems. We compared the cancer stage for new breast cancers (BCs) before and during the pandemic. METHODS: We performed a retrospective multicenter cohort study on the data warehouse of Greater Paris University Hospitals (AP-HP). We identified all female patients newly referred with a BC in 2019 and 2020. We assessed the timeline of their care trajectories, initial tumor stage, and treatment received: BC resection, exclusive systemic therapy, exclusive radiation therapy, or exclusive best supportive care (BSC). We calculated patients' 1-year overall survival (OS) and compared indicators in 2019 and 2020. RESULTS: In 2019 and 2020, 2055 and 1988, new BC patients underwent cancer treatment, and during the two lockdowns, the BC diagnoses varied by -18% and by +23% compared to 2019. De novo metastatic tumors (15% and 15%, p = 0.95), pTNM and ypTNM distributions of 1332 cases with upfront resection and of 296 cases with neoadjuvant therapy did not differ (p = 0.37, p = 0.3). The median times from first multidisciplinary meeting and from diagnosis to treatment of 19 days (interquartile 11-39 days) and 35 days (interquartile 22-65 days) did not differ. Access to plastic surgery (15% and 17%, p = 0.08) and to treatment categories did not vary: tumor resection (73% and 72%), exclusive systemic therapy (13% and 14%), exclusive radiation therapy (9% and 9%), exclusive BSC (5% and 5%) (p = 0.8). Among resected patients, the neoadjuvant therapy rate was lower in 2019 (16%) versus 2020 (20%) (p = 0.02). One-year OS rates were 99.3% versus 98.9% (HR = 0.96; 95% CI, 0.77-1.2), 72.6% versus 76.6% (HR = 1.28; 95% CI, 0.95-1.72), 96.6% versus 97.8% (HR = 1.09; 95% CI, 0.61-1.94), and 15.5% versus 15.1% (HR = 0.99; 95% CI, 0.72-1.37), in the treatment groups. CONCLUSIONS: Despite a decrease in the number of new BCs, there was no tumor stage shift, and OS did not vary.

No changes in clinical presentation, treatment strategies and survival of pancreatic cancer cases during the SARS-COV-2 outbreak: A retrospective multicenter cohort study on real-world data.

The SARS-COV-2 pandemic disrupted healthcare systems. We assessed its impact on the presentation, care trajectories and outcomes of new pancreatic cancers (PCs) in the Paris area. We performed a retrospective multicenter cohort study on the data warehouse of Greater Paris University Hospitals (AP-HP). We identified all patients newly referred with a PC between January 1, 2019, and June 30, 2021, and excluded endocrine tumors. Using claims data and health records, we analyzed the timeline of care trajectories, the initial tumor stage, the treatment categories: pancreatectomy, exclusive systemic therapy or exclusive best supportive care (BSC). We calculated patients' 1-year overall survival (OS) and compared indicators in 2019 and 2020 to 2021. We included 2335 patients. Referral fell by 29% during the first lockdown. The median time from biopsy and from first MDM to treatment were 25 days (16-50) and 21 days (11-40), respectively. Between 2019 and 2020 to 2021, the rate of metastatic tumors (36% vs 33%, P = .39), the pTNM distribution of the 464 cases with upfront tumor resection (P = .80), and the proportion of treatment categories did not vary: tumor resection (32% vs 33%), exclusive systemic therapy (49% vs 49%), exclusive BSC (19% vs 19%). The 1-year OS rates in 2019 vs 2020 to 2021 were 92% vs 89% (aHR = 1.42; 95% CI, 0.82-2.48), 52% vs 56% (aHR = 0.88; 95% CI, 0.73-1.08), 13% vs 10% (aHR = 1.00; 95% CI, 0.78-1.25), in the treatment categories, respectively. Despite an initial decrease in the number of new PCs, we did not observe any stage shift. OS did not vary significantly.

Impact of two waves of Sars-Cov2 outbreak on the number, clinical presentation, care trajectories and survival of patients newly referred for a colorectal cancer: A French multicentric cohort study from a large group of university hospitals.

The SARS-Cov2 may have impaired care trajectories, patient overall survival (OS), tumor stage at initial presentation for new colorectal cancer (CRC) cases. This study aimed at assessing those indicators before and after the beginning of the pandemic in France. In this retrospective cohort study, we collected prospectively the clinical data of the 11.4 million of patients referred to the Greater Paris University Hospitals (AP-HP). We identified new CRC cases between 1 January 2018 and 31 December 2020, and compared indicators for 2018-2019 to 2020. pTNM tumor stage was extracted from postoperative pathology reports for localized colon cancer, and metastatic status was extracted from CT-scan baseline text reports. Between 2018 and 2020, 3602 and 1083 new colon and rectal cancers were referred to the AP-HP, respectively. The 1-year OS rates reached 94%, 93% and 76% for new CRC patients undergoing a resection of the primary tumor, in 2018-2019, in 2020 without any Sars-Cov2 infection and in 2020 with a Sars-Cov2 infection, respectively (HR 3.78, 95% CI 2.1-7.1). For patients undergoing other kind of anticancer treatment, the percentages are 64%, 66% and 27% (HR 2.1, 95% CI 1.4-3.3). Tumor stage at initial presentation, emergency level of primary tumor resection, delays between the first multidisciplinary meeting and the first anticancer treatment did not differ over time. The SARS-Cov2 pandemic has been associated with less newly diagnosed CRC patients and worse 1-year OS rates attributable to the infection itself rather than to its impact on hospital care delivery or tumor stage at initial presentation.

Immune checkpoint blockade toxicity among patients with cancer presenting to the emergency department.

OBJECTIVES: We sought to estimate the prevalence of patients with cancer presenting to the emergency department (ED) who are undergoing treatment with immune checkpoint blockade (ICB) therapy; report their chief complaints; describe and estimate the prevalence of immune-related adverse events (IRAEs). METHODS: Four abstractors reviewed the medical records of patients with cancer treated with ICB who presented to an ED in Paris, France between January 2012 and June 2017. Chief complaints, underlying malignancy and ICB characteristics, and the final diagnoses according to the emergency physician were recorded. Abstractors noted if an emergency physician identified that a patient was receiving an ICB and if the emergency physician considered the possibility of an IRAE. The gold standard as to whether an IRAE was the cause was the patients' referring oncologist's opinion that the ED symptoms were attributed to ICB and IRAE according to post-ED medical records. Descriptive statistics were reported. RESULTS: Among the 409 patients treated with ICB at our institution, 139 presented to the ED. Chief complaints were fatigue (25.2%), fever (23%), vomiting (13.7%), diarrhoea (13.7%), dyspnoea (12.2%), abdominal pain (11.5%), confusion (8.6%) and headache (7.9%). Symptoms were due to IRAEs in 20 (14.4%) cases. The most frequent IRAEs were colitis (40%), endocrine toxicity (30%), hepatitis (25%) and pulmonary toxicity (5%). Patients with IRAEs compared with those without them more frequently had melanoma; had received more distinct courses of ICB treatment, an increased number of ICB medications and ICB cycles; and had a shorter time course since the last infusion of ICB. Emergency physicians considered the possibility of an IRAE in 24 (17.3%) of cases and diagnosed IRAE in 10 (50%) of those with later confirmed IRAE. IRAE was more likely to be missed when the referring oncologist was not contacted or when the patient had respiratory symptoms, fatigue or fever. CONCLUSIONS: ICB exposes patients to potentially severe IRAEs. Emergency physicians must identify patients treated with ICB and consider their toxicity when patients present to the ED with symptoms compatible with IRAEs.

Incidence, risk factors and outcome of multi-drug resistant Acinetobacter baumannii nosocomial infections during an outbreak in a burn unit.

BACKGROUND: Multidrug-Resistant Acinetobacter baumannii (MR-AB) can cause outbreaks in burn units. We aimed to study the incidence, risk factors and outcome of MR-AB infections in a burn unit (BU). METHODS: A prospective study was conducted from April to November, 2014 during an outbreak in a BU in Paris. Weekly surveillance cultures were performed to determine MR-AB colonization. MR-AB nosocomial infections, discharge or death without MR-AB infection were considered as competing events. To identify risk factors for MR-AB infection, baseline characteristics and time-dependent variables were investigated in univariate analyses using Cox models. RESULTS: Eighty-six patients admissions were analyzed during the study period. Among them, 15 (17%) acquired MR-AB nosocomial infection. Median time to infection was 22days (interquartile range: 10-26 days). Cumulative incidence of MR-AB infections was 15% at 28days (95% CI=8-24). Risk factors for MR-AB infection in univariate analysis were SAPS II (Hazard Ratio (HR):1.08; 95% CI:1.05-1.12; P<0.0001) and ABSI (Abbreviated Burn Severity Index) scores (HR:1.32; 95% CI:1.12-1.56; P=0.001), MR-AB colonization (HR:10.2; 95%CI:2.05-50.3; P=0.004), invasive procedures (ventilation, arterial and/or venous catheter) (P=0.0001) and ≥2 skin grafts (HR:10.2; 95% CI:1.76-59.6; P=0.010). MR-AB infection was associated with an increased risk of death (HR: 7.11; 95%CI: 1.52-33.2; P=0.013) and longer hospital stay with a median estimated increase of 10days (IQR: 6; 14). CONCLUSIONS: Incidence of MR-AB nosocomial infection was high during this outbreak, and was associated with prolonged hospitalization and increased risk of death. High patient severity scores, prior MR-AB colonization, invasive procedures and repeated skin grafts were associated with an increased risk of nosocomial infection.

Factors associated with non-persistence to oral and inhaled antiviral therapies for seasonal influenza: a secondary analysis of a double-blind, multicentre, randomised clinical trial.

OBJECTIVES: We aimed to evaluate and compare non-adherence to oral and inhaled antiviral therapies prescribed of a randomised clinical trial in outpatients with influenza A infection. DESIGN: A parallel, three-arm, double-blinded trial randomly allocated antiviral therapies twice daily for 5 days: (1) oral oseltamivir plus inhaled zanamivir (arm OZ); (2) oseltamivir plus inhaled placebo (arm Opz); or (3) oral placebo plus inhaled zanamivir (arm poZ). Analysis of non-adherence was a secondary objective of the trial. SETTINGS: Outpatients were enrolled by 145 general practitioners throughout France during the 2008-2009 seasonal influenza epidemics. PARTICIPANTS: A total of 541 adults presenting with influenza-like illness for less than 36 hours. PRIMARY OUTCOMES: Non-persistence, the time between inclusion and the last dose treated as a failure time, was used as the primary endpoint. RESULTS: The proportions of patients who persisted on treatment until the end of prescription were estimated at 85.73% (±3.28%) for the oral route and 82.73% (±3.44%) for the inhaled route. Based on multivariable models, non-persistence was associated with a PCR confirmation of influenza for both the oral (HR=0.54, p=0.010) and inhaled (HR=0.59, p=0.018) drugs and antibiotic coprescriptions (HR=2.07, p=0.007; and HR=1.88, p=0.017, respectively) and active combination treatment (HR=1.71, p=0.035; and HR=1.58, p=0.035, respectively). The hazard of non-persistence of the inhaled therapy was increased compared with that of the oral therapy (HR=1.23, p=0.043). CONCLUSION: In addition to the clinical and virological profiles of influenza infection, non-persistence may have been influenced by an active combination and the route of administration. RCT REGISTRATION NUMBER: NCT00799760. This is a post-result analysis.

Correlates of general practitioners' recommendations to patients regarding vaccination for the 2009-2010 pandemic influenza (A/H1N1) in France: implications for future vaccination campaigns.

BACKGROUND: General practitioners' (GPs) recommendations to their patients regarding influenza vaccination is a key determinant of patient uptake of influenza vaccination. OBJECTIVES: To study factors associated with GPs' recommendations regarding pandemic vaccination (pvaccination) to adults ≤65 years of age (hereafter referred to as adults) at risk and not at risk of severe complications of the 2009-2010 A/H1N1 influenza. PATIENTS/METHODS: National cross-sectional survey of 1431 French GPs. Pvaccination recommendations by GPs to adults were studied according to three categories: recommended pvaccination to at-risk adults only; recommended pvaccination to all adults; recommended against pvaccination or did not provide any advice to any adult. RESULTS: GPs were more likely to recommend pvaccination to at-risk than not-at-risk adults (73.4% vs 40.1%, p<0.01). GPs who consulted official sources of information rather than news media during the pandemic were more likely to recommend pvaccination to at-risk adults only (OR=1.78; CI 95%=1.27-2.48) and to all adults (OR=2.03; CI 95%=1.42-2.92) than other GPs. GPs' unfavorable perceptions of the risk/efficacy balance of the pandemic vaccine (pvaccine) together with their perceptions of the low severity of the disease were negatively associated with recommending pvaccination. Hospitalization of GPs' patients because of the influenza was specifically associated with pvaccine recommendation to all adults (OR=2.81; CI 95%=1.98-3.99) but not with pvaccine recommendation to at-risk adults only. CONCLUSION: In the pandemic context, GPs' perceptions of disease severity and the risk/efficacy balance of the pvaccine were the major determinants of French GPs recommending pvaccination or not. To increase the general public's acceptability of vaccination policies, GPs should be adequately informed about the course of the epidemics and the safety of the vaccine.

Pandemic influenza (A/H1N1) vaccine uptake among French private general practitioners: a cross sectional study in 2010.

BACKGROUND: In July, 2009, French health authorities, like those in many other countries, decided to embark on a mass vaccination campaign against the pandemic A(H1N1) influenza. Private general practitioners (GPs) were not involved in this campaign. We studied GPs' pandemic vaccine (pvaccine) uptake, quantified the relative contribution of its potential explanatory factors and studied whether their own vaccination choice was correlated with their recommendations to patients about pvaccination. METHODOLOGY/PRINCIPAL FINDINGS: In this cross-sectional telephone survey, professional investigators interviewed an existing panel of randomly selected private GPs (N = 1431; response rate at inclusion in the panel: 36.8%; participation rate in the survey: 100%). The main outcome variable was GPs' own pvaccine uptake. We used an averaging multi-model approach to quantify the relative contribution of factors associated with their vaccination. The pvaccine uptake rate was 61% (95%CI = 58.3-63.3). Four independent factors contributed the most to this rate (partial Nagelkerke's R(2)): history of previous vaccination against seasonal influenza (14.5%), perception of risks and efficacy of the pvaccine (10.8%), opinions regarding the organization of the vaccination campaign (7.1%), and perception of the pandemic's severity (5.2%). Overall, 71.3% (95%CI = 69.0-73.6) of the participants recommended pvaccination to young adults at risk and 40.1% (95%CI = 37.6-42.7) to other young adults. GPs' own pvaccination was strongly predictive of their recommendation to both young adults at risk (OR = 9.6; 95%CI = 7.2-12.6) and those not at risk (OR = 8.5; 95%CI = 6.4-11.4). CONCLUSIONS/SIGNIFICANCE: These results suggest that around 60% of French private GPs followed French authorities' recommendations about vaccination of health care professionals against the A(H1N1) influenza. They pinpoint priority levers for improving preparedness for future influenza pandemics. Besides encouraging GPs' own uptake of regular vaccination against seasonal influenza, providing GPs with clear information about the risks and efficacy of any new pvaccine and involving them in the organization of any future vaccine campaign may improve their pvaccine uptake.

Arthroscopic Measurement of Cartilage Lesions of the Knee Condyle: Principles and Experimental Validation of a New Method.

PURPOSE: To present a new method of arthroscopic measurement of the surface and location of condylar lesions. METHODS: We propose measuring the height of the condylar lesion by using the lesion's arc (Δ°) obtained from the difference between the angle of flexion at the beginning of the lesion and the angle of flexion at the end of the lesion. The first goal of the study was to determine the intra and inter reliability of the lesion's arc. Experiment 1: 20 deep lesions were evaluated using the lesional arc by two arthroscopists. Experiment 2: In a second series of 20 lesions, the flexion angles of the knees were recorded using a goniometer. All 10 knees (5 in each series) were then disarticulated and the true lesion arc was checked with a goniometer to assess the validity of the scopic measurements. The second goal was to obtain the height of the lesion from the lesion's arc. The lesion arc Δ° of the condylar is converted into height (millimeters) on the basis of a table obtained from 5 standard profiles of the lateral X-ray of the knee. RESULTS: Experiment 1: The intra observer reliability was good but the inter observer reliability was poor. Experiment 2: The intra and inter observers' reliability were good. On the anatomic control after disarticulating the knee, the confidence interval was narrower when using the goniometer. CONCLUSIONS: We propose a simple, reliable method to measure the height of a condylar lesion with the lesion's arc during arthroscopy.

Low acceptability of A/H1N1 pandemic vaccination in French adult population: did public health policy fuel public dissonance?

BACKGROUND: In July 2009, French public health authorities embarked in a mass vaccination campaign against A/H1N1 2009 pandemic-influenza. We explored the attitudes and behaviors of the general population toward pandemic vaccination. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a cross-sectional online survey among 2,253 French representative adults aged 18 to 64 from November 17 to 25, 2009 (completion rate: 93.8%). The main outcome was the acceptability of A/H1N1 vaccination as defined by previous receipt or intention to get vaccinated ("Yes, certainly", "Yes, probably"). Overall 17.0% (CI 95%, 15.5% to 18.7%) of respondents accepted A/H1N1 vaccination. Independent factors associated with acceptability included: male sex (p = .0001); older age (p = .002); highest or lowest level of education (p = .016); non-clerical occupation (p = .011); having only one child (p = .008); and having received seasonal flu vaccination in prior 3 years (p<.0001). Acceptability was also significantly higher among pregnant women (37.9%) and other at risk groups with chronic diseases (34.8%) (p = .002). Only 35.5% of respondents perceived A/H1N1 influenza illness as a severe disease and 12.7% had experienced A/H1N1 cases in their close relationships with higher acceptability (p<.0001 and p = .006, respectively). In comparison to 26.0% respondents who did not consult their primary care physician, acceptability was significantly higher among 8.0% respondents who were formally advised to get vaccinated, and lower among 63.7% respondents who were not advised to get vaccinated (respectively: 15.8%, 59.5% and 11.7%- p<.0001). Among respondents who refused vaccination, 71.2% expressed concerns about vaccine safety. CONCLUSIONS/SIGNIFICANCE: Our survey occurred one week before the peak of the pandemic in France. We found that alarming public health messages aiming at increasing the perception of risk severity were counteracted by daily personal experience which did not confirm the threat, while vaccine safety was a major issue. This dissonance may have been amplified by having not involved primary care physicians in the mass vaccination campaign.