Project description:ObjectiveHealthcare data such as clinical notes are primarily recorded in an unstructured manner. If adequately translated into structured data, they can be utilized for health economics and set the groundwork for better individualized patient care. To structure clinical notes, deep-learning methods, particularly transformer-based models like Bidirectional Encoder Representations from Transformers (BERT), have recently received much attention. Currently, biomedical applications are primarily focused on the English language. While general-purpose German-language models such as GermanBERT and GottBERT have been published, adaptations for biomedical data are unavailable. This study evaluated the suitability of existing and novel transformer-based models for the German biomedical and clinical domain.Materials and methodsWe used 8 transformer-based models and pre-trained 3 new models on a newly generated biomedical corpus, and systematically compared them with each other. We annotated a new dataset of clinical notes and used it with 4 other corpora (BRONCO150, CLEF eHealth 2019 Task 1, GGPONC, and JSynCC) to perform named entity recognition (NER) and document classification tasks.ResultsGeneral-purpose language models can be used effectively for biomedical and clinical natural language processing (NLP) tasks, still, our newly trained BioGottBERT model outperformed GottBERT on both clinical NER tasks. However, training new biomedical models from scratch proved ineffective.DiscussionThe domain-adaptation strategy's potential is currently limited due to a lack of pre-training data. Since general-purpose language models are only marginally inferior to domain-specific models, both options are suitable for developing German-language biomedical applications.ConclusionGeneral-purpose language models perform remarkably well on biomedical and clinical NLP tasks. If larger corpora become available in the future, domain-adapting these models may improve performances.

Project description:BackgroundData on emergency and critical care (ECC) capacity in low-income countries (LICs) are needed to improve outcomes and make progress towards realizing the goal of Universal Health Coverage.MethodsWe developed a novel research instrument to assess public sector ECC capacity and service readiness in LICs. From January 20th to February 18th, 2020 we administered the instrument at all four central hospitals and a simple random sample of nine of 24 district hospitals in Malawi, a landlocked and predominantly rural LIC of 19·1 million people in Southern Africa. The instrument contained questions on the availability of key resources across three domains and was administered to hospital administrators and clinicians from outpatient departments, emergency departments, and inpatient units. Results were used to generate an ECC Readiness Score, with a possible range of 0 to 1, for each facility.FindingsA total of 114 staff members across 13 hospitals completed interviews for this study. Three (33%) district hospitals and all four central hospitals had ECC Readiness Scores above 0·5 (p-value 0·070). Absent equipment was identified as the most common barrier to ECC Readiness. Central hospitals had higher median ECC Readiness Scores with less variability 0·82 (interquartile range: 0·80-0·89) than district hospitals (0·33, 0·23 to 0·50, p-value 0·021).InterpretationThis is the first study to employ a systematic approach to assessing ECC capacity and service readiness at both district and central hospitals in Malawi and provides a framework for measuring ECC capacity in other LICs. Prior ECC assessments potentially overestimated equipment availability and our methodology may provide a more accurate approach. There is an urgent need for investments in ECC services, particularly at district hospitals which are more accessible to Malawi's predominantly rural population. These findings highlight the need for long-term investments in health systems strengthening and underscore the importance of understanding capacity in LIC settings to inform these efforts.FundingDivision of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Department of Emergency Medicine, Brigham and Women's Hospital.

Project description:ObjectivesCharacterize current practices for PICU-based rehabilitation, and physician perceptions and attitudes, barriers, resources, and outcome assessment in contemporary PICU settings.DesignInternational, self-administered, quantitative, cross-sectional survey.SettingOnline survey distributed from March 2017 to April 2017.Patients or subjectsPediatric critical care physicians who subscribed to email distribution lists of the Pediatric Acute Lung Injury and Sepsis Investigators, the Pediatric Neurocritical Care Research Group, or the Prevalence of Acute Critical Neurological Disease in Children: A Global Epidemiological Assessment study group, and visitors to the World Federation of Pediatric Intensive and Critical Care Societies website.InterventionsNone.Measurements and main resultsOf the 170 subjects who began the survey, 148 completed it. Of those who completed the optional respondent information, most reported working in an academic medical setting and were located in the United States. The main findings were 1) a large majority of PICU physicians reported working in institutions with no guidelines for PICU-based rehabilitation, but expressed interest in developing and implementing such guidelines; 2) despite this lack of guidelines, an overwhelming majority of respondents reported that their current practices would involve consultation of multiple rehabilitation services for each case example provided; 3) PICU physicians believed that additional research evidence is needed to determine efficacy and optimal implementation of PICU-based rehabilitation; 4) PICU physicians reported significant barriers to implementation of PICU-based rehabilitation across centers; and 5) low routine assessment of long-term functional outcomes of PICU patients, although some centers have developed multidisciplinary follow-up programs.ConclusionsPhysicians lack PICU-based rehabilitation guidelines despite great interest and current practices involving a high degree of PICU-based rehabilitation consultation. Data are needed to identify best practices and necessary resources in the delivery of ICU-based multidisciplinary rehabilitation and long-term functional outcomes assessment to optimize recovery of children and families affected by critical illness.

Project description:Invasive listeriosis, due to its severe nature in susceptible populations, has been the focus of many quantitative risk assessment (QRA) models aiming to provide a valuable guide in future risk management efforts. A review of the published QRA models of Listeria monocytogenes in seafood was performed, with the objective of appraising the effectiveness of the control strategies at different points along the food chain. It is worth noting, however, that the outcomes of a QRA model are context-specific, and influenced by the country and target population, the assumptions that are employed, and the model architecture itself. Studies containing QRA models were retrieved through a literature search using properly connected keywords on Scopus and PubMed®. All 13 QRA models that were recovered were of short scope, covering, at most, the period from the end of processing to consumption; the majority (85%) focused on smoked or gravad fish. Since the modelled pathways commenced with the packaged product, none of the QRA models addressed cross-contamination events. Many models agreed that keeping the product's temperature at 4.0-4.5 °C leads to greater reductions in the final risk of listeriosis than reducing the shelf life by one week and that the effectiveness of both measures can be surpassed by reducing the initial occurrence of L. monocytogenes in the product (at the end of processing). It is, therefore, necessary that future QRA models for RTE seafood contain a processing module that can provide insight into intervention strategies that can retard L. monocytogenes' growth, such as the use of bacteriocins, ad hoc starter cultures and/or organic acids, and other strategies seeking to reduce cross-contamination at the facilities, such as stringent controls for sanitation procedures. Since risk estimates were shown to be moderately driven by growth kinetic parameters, namely, the exponential growth rate, the minimum temperature for growth, and the maximum population density, further work is needed to reduce uncertainties.

Dataset Information

Chlamydomonas immunophilins and parvulins: survey and critical assessment of gene models.

Publications

Chlamydomonas immunophilins and parvulins: survey and critical assessment of gene models.

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