Development and Validation of a Natural Language Processing Algorithm to Pseudonymize Documents in the Context of a Clinical Data Warehouse

OBJECTIVE

 The objective of this study is to address the critical issue of deidentification of clinical reports to allow access to data for research purposes, while ensuring patient privacy. The study highlights the difficulties faced in sharing tools and resources in this domain and presents the experience of the Greater Paris University Hospitals (AP-HP for Assistance Publique-Hôpitaux de Paris) in implementing a systematic pseudonymization of text documents from its Clinical Data Warehouse.

METHODS

 We annotated a corpus of clinical documents according to 12 types of identifying entities and built a hybrid system, merging the results of a deep learning model as well as manual rules.

RESULTS AND DISCUSSION

 Our results show an overall performance of 0.99 of F1-score. We discuss implementation choices and present experiments to better understand the effort involved in such a task, including dataset size, document types, language models, or rule addition. We share guidelines and code under a 3-Clause BSD license.

How to Improve Cancer Patients ENrollment in Clinical Trials From rEal-Life Databases Using the Observational Medical Outcomes Partnership Oncology Extension: Results of the PENELOPE Initiative in Urologic Cancers

PURPOSE

To compare the computability of Observational Medical Outcomes Partnership (OMOP)-based queries related to prescreening of patients using two versions of the OMOP common data model (CDM; v5.3 and v5.4) and to assess the performance of the Greater Paris University Hospital (APHP) prescreening tool.

MATERIALS AND METHODS

We identified the prescreening information items being relevant for prescreening of patients with cancer. We randomly selected 15 academic and industry-sponsored urology phase I-IV clinical trials (CTs) launched at APHP between 2016 and 2021. The computability of the related prescreening criteria (PC) was defined by their translation rate in OMOP-compliant queries and by their execution rate on the APHP clinical data warehouse (CDW) containing data of 205,977 patients with cancer. The overall performance of the prescreening tool was assessed by the rate of true- and false-positive cases of three randomly selected CTs.

RESULTS

We defined a list of 15 minimal information items being relevant for patients' prescreening. We identified 83 PC of the 534 eligibility criteria from the 15 CTs. We translated 33 and 62 PC in queries on the basis of OMOP CDM v5.3 and v5.4, respectively (translation rates of 40% and 75%, respectively). Of the 33 PC translated in the v5.3 of the OMOP CDM, 19 could be executed on the APHP CDW (execution rate of 58%). Of 83 PC, the computability rate on the APHP CDW reached 23%. On the basis of three CTs, we identified 17, 32, and 63 patients as being potentially eligible for inclusion in those CTs, resulting in positive predictive values of 53%, 41%, and 21%, respectively.

CONCLUSION

We showed that PC could be formalized according to the OMOP CDM and that the oncology extension increased their translation rate through better representation of cancer natural history.

AP-HP Health Data Space (AHDS) to the Test of the Covid-19 Pandemic

Sharing observational and interventional health data within a common data space enables university hospitals to leverage such data for biomedical discovery and moving towards a learning health system.

OBJECTIVE

To describe the AP-HP Health Data Space (AHDS) and the IT services supporting piloting, research, innovation and patient care.

METHODS

Built on three pillars - governance and ethics, technology and valorization - the AHDS and its major component, the Clinical Data Warehouse (CDW) have been developed since 2015.

RESULTS

The AP-HP CDW has been made available at scale to AP-HP both healthcare professionals and public or private partners in January 2017. Supported by an institutional secured and high-performance cloud and an ecosystem of tools, mostly open source, the AHDS integrates a large amount of massive healthcare data collected during care and research activities. As of December 2021, the AHDS operates the electronic data capture for almost +840 clinical trials sponsored by AP-HP, the CDW is enabling the processing of health data from more than 11 million patients and generated +200 secondary data marts from IRB authorized research projects. During the Covid-19 pandemic, AHDS has had to evolve quickly to support administrative professionals and caregivers heavily involved in the reorganization of both patient care and biomedical research.

CONCLUSION

The AP-HP Data Space is a key facilitator for data-driven evidence generation and making the health system more efficient and personalized.

Deepwater formation in the North Pacific during the Last Glacial Termination

Between approximately 17,500 and 15,000 years ago, the Atlantic meridional overturning circulation weakened substantially in response to meltwater discharges from disintegrating Northern Hemispheric glacial ice sheets. The global effects of this reorganization of poleward heat flow in the North Atlantic extended to Antarctica and the North Pacific. Here we present evidence from North Pacific paleo surface proxy data, a compilation of marine radiocarbon age ventilation records, and global climate model simulations to suggest that during the early stages of the Last Glacial Termination, deep water extending to a depth of approximately 2500 to 3000 meters was formed in the North Pacific. A switch of deepwater formation between the North Atlantic and the North Pacific played a key role in regulating poleward oceanic heat transport during the Last Glacial Termination.

Chaos-assisted tunneling with cold atoms

In the context of quantum chaos, both theory and numerical analysis predict large fluctuations of the tunneling transition probabilities when irregular dynamics is present at the classical level. Here we consider the nondissipative quantum evolution of cold atoms trapped in a time-dependent modulated periodic potential generated by two laser beams. We give some precise guidelines for the observation of chaos-assisted tunneling between invariant phase space structures paired by time-reversal symmetry.

The posterior arm free flap

A new cutaneous free flap is described on the posterior side of the arm. This flap is supplied by an unnamed artery from the humeral artery or the deep humeral artery. It is drained by the accompanying venae comitantes. Its nerve supply is from the radial nerve. Its advantage is a flexible skin and a primary closure of the donor site if the flap does not exceed 7 cm in width. The principal disadvantage is its modest measurements. This flap has been employed in five cases for reconstruction of hand and foot. All flaps survived despite a necessary revision of an arterial anastomosis in one case and a partial necrosis in another case. Results are satisfactory, especially in restoration of weight-bearing areas of the foot.

[Covering distal amputations of the finger using homodigital neurovascular island flaps]

Large skin defects of the tips of the fingers are difficult to manage. The authors have used in fourteen cases a neurovascular homodigital island flap to cover the defect. Functional and esthetic results have been very encouraging.

[Surgical methods in non-traumatic perforations of the colon into the free peritoneum (36 cases)]

When operating as an emergency for a perforation of the colon should one carry out a by-pass operation, colostomy or restore intestinal continuity? 36 colonic perforations are reported here, as a complication of cancer in 50 p. 100 of cases, or sigmoiditis in 38 p. 100 of cases. The perforation was situated on the sigmoid in 77 p. 100 of cases. 13 by-pass operations were carried out with a 23 p. 100 mortality, 12 colectomies without anastomosis with a 50 p. 100 mortality, and 2 colectomies with restoration of continuity, 9 p. 100 mortality. The overall mortality was 27.7 p. 100 much less than reported by other authors but, nevertheless partly due to the severity of peritonitis due to the presence of feces and, partly due to the operation adopted. The present attitude of the authors depends on the merits of each case. A large incision is made and the peritoneum thoroughly cleaned. If the surgeon is experienced, colonic resection is advisable for perforated cnacer and certain cases of sigmoiditis. Restoration of continuity depends, above all, on the anatomical condition of the colon above the lesion. Hartmann's resections or by-pass operations thus still have indications.