A large dataset of software mentions in the biomedical literature

<p>We describe the CZ Software Mentions, a new dataset of software mentions in biomedical papers. Plain-text mentions are extracted with a trained SciBERT model from several sources: the NIH PubMed Central collection and papers provided by various publishers to the Chan Zuckerberg Initiative. The dataset provides sources, context and metadata, and, for a number of mentions, the disambiguated software entities and links. We extract 1.12 million unique string software mentions from 2.4 million papers in the NIH PMC-OA Commercial subset, 481k unique mentions from the NIH PMC-OA Non-Commercial subset and 934k unique mentions from 3 million papers in the Publishers' collection. We propose a clustering-based disambiguation algorithm to map plain-text software mentions into distinct software entities and apply it on the NIH PubMed Central Commercial collection. Through this methodology, we disambiguate 1.12 million unique strings into 97600 unique software entities, covering 78% of all software-paper links. We link 185,000 of the mentions to repositories, covering about 55% of all software-paper links. We describe in detail the process of building the datasets, disambiguating and linking the software mentions. We make all data and code publicly available to help assess the impact of software (in particular scientific open source projects) on science.</p&gt

Global impact of COVID-19 on newborn screening programmes

Introduction The global COVID-19 pandemic has presented extraordinary disruption to healthcare services and exposed them to numerous challenges. Newborn screening (NBS) programmes were also affected; however, scarce data exist on the impact of COVID-19 on NBS. Methods We conducted an international survey to assess the global impact of COVID-19 on NBS, with the main aim of gathering the experiences of the COVID-19 pandemic from a large and representative number of NBS centres worldwide. Results The results of our study showed that COVID-19 impacted the NBS programmes, at least partially, in 29 out of 38 responding countries. Majority of the screening centres experienced a broad spectrum of difficulties and most were affected more in the second wave of the pandemic. Delays and unreliability with the postal service as well as flight cancellations caused delays in samples arriving to screening centres and with the provision of laboratory equipment and reagents. The availability of laboratory staff was sometimes reduced due to infection, quarantine or reassignment within the healthcare facility. Sample collection at home, second-tier tests and follow-up were also affected. Social restrictions and interruptions in public transport added to these difficulties. Only a limited number of centres managed to retain a fully functioning NBS programme. Conclusion As the pandemic might continue or could recur in future years, it would be useful to develop guidelines to protect these valuable services

Efficacy and safety of empagliflozin in glycogen storage disease type Ib: Data from an international questionnaire.

PURPOSE This paper aims to report collective information on safety and efficacy of empagliflozin drug repurposing in individuals with glycogen storage disease type Ib (GSD Ib). METHODS This is an international retrospective questionnaire study on the safety and efficacy of empagliflozin use for management of neutropenia/neutrophil dysfunction in patients with GSD Ib, conducted among the respective health care providers from 24 countries across the globe. RESULTS Clinical data from 112 individuals with GSD Ib were evaluated, representing a total of 94 treatment years. The median age at start of empagliflozin treatment was 10.5 years (range = 0-38 years). Empagliflozin showed positive effects on all neutrophil dysfunction-related symptoms, including oral and urogenital mucosal lesions, recurrent infections, skin abscesses, inflammatory bowel disease, and anemia. Before initiating empagliflozin, most patients with GSD Ib were on G-CSF (94/112; 84%). At the time of the survey, 49 of 89 (55%) patients previously treated with G-CSF had completely stopped G-CSF, and another 15 (17%) were able to reduce the dose. The most common adverse event during empagliflozin treatment was hypoglycemia, occurring in 18% of individuals. CONCLUSION Empagliflozin has a favorable effect on neutropenia/neutrophil dysfunction-related symptoms and safety profile in individuals with GSD Ib