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1.
J Clin Transl Sci ; 8(1): e63, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38655451

RESUMO

Background: Impaired motor and cognitive function can make travel cumbersome for People with Parkinson's disease (PwPD). Over 50% of PwPD cared for at the University of Arkansas for Medical Sciences (UAMS) Movement Disorders Clinic reside over 30 miles from Little Rock. Improving access to clinical care for PwPD is needed. Objective: To explore the feasibility of remote clinic-to-clinic telehealth research visits for evaluation of multi-modal function in PwPD. Methods: PwPD residing within 30 miles of a UAMS Regional health center were enrolled and clinic-to-clinic telehealth visits were performed. Motor and non-motor disease assessments were administered and quantified. Results were compared to participants who performed at-home telehealth visits using the same protocols during the height of the COVID pandemic. Results: Compared to the at-home telehealth visit group (n = 50), the participants from regional centers (n = 13) had similar age and disease duration, but greater disease severity with higher total Unified Parkinson's disease rating scale scores (Z = -2.218, p = 0.027) and lower Montreal Cognitive Assessment scores (Z = -3.350, p < 0.001). Regional center participants had lower incomes (Pearson's chi = 21.3, p < 0.001), higher costs to attend visits (Pearson's chi = 16.1, p = 0.003), and lived in more socioeconomically disadvantaged neighborhoods (Z = -3.120, p = 0.002). Prior research participation was lower in the regional center group (Pearson's chi = 4.5, p = 0.034) but both groups indicated interest in future research participation. Conclusions: Regional center research visits in PwPD in medically underserved areas are feasible and could help improve access to care and research participation in these traditionally underrepresented populations.

2.
Learn Health Syst ; 8(1): e10404, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38249841

RESUMO

Introduction: Research driven by real-world clinical data is increasingly vital to enabling learning health systems, but integrating such data from across disparate health systems is challenging. As part of the NCATS National COVID Cohort Collaborative (N3C), the N3C Data Enclave was established as a centralized repository of deidentified and harmonized COVID-19 patient data from institutions across the US. However, making this data most useful for research requires linking it with information such as mortality data, images, and viral variants. The objective of this project was to establish privacy-preserving record linkage (PPRL) methods to ensure that patient-level EHR data remains secure and private when governance-approved linkages with other datasets occur. Methods: Separate agreements and approval processes govern N3C data contribution and data access. The Linkage Honest Broker (LHB), an independent neutral party (the Regenstrief Institute), ensures data linkages are robust and secure by adding an extra layer of separation between protected health information and clinical data. The LHB's PPRL methods (including algorithms, processes, and governance) match patient records using "deidentified tokens," which are hashed combinations of identifier fields that define a match across data repositories without using patients' clear-text identifiers. Results: These methods enable three linkage functions: Deduplication, Linking Multiple Datasets, and Cohort Discovery. To date, two external repositories have been cross-linked. As of March 1, 2023, 43 sites have signed the LHB Agreement; 35 sites have sent tokens generated for 9 528 998 patients. In this initial cohort, the LHB identified 135 037 matches and 68 596 duplicates. Conclusion: This large-scale linkage study using deidentified datasets of varying characteristics established secure methods for protecting the privacy of N3C patient data when linked for research purposes. This technology has potential for use with registries for other diseases and conditions.

3.
Clin Pharmacol Ther ; 115(2): 231-238, 2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-37926939

RESUMO

Children with asthma and obesity are more likely to have lower vitamin D levels, but the optimal replacement dose is unknown in this population. The objective of this study is identifying a vitamin D dose in children with obesity-related asthma that safely achieves serum vitamin D levels of ≥ 40 ng/mL. This prospective multisite randomized controlled trial recruited children/adolescents with asthma and body mass index ≥ 85% for age/sex. Part 1 (dose finding), evaluated 4 oral vitamin D regimens for 16 weeks to identify a replacement dose that achieved serum vitamin D levels ≥ 40 ng/mL. Part 2 compared the replacement dose calculated from part 1 (50,000 IU loading dose with 8,000 IU daily) to standard of care (SOC) for 16 weeks to identify the proportion of children achieving target serum 25(OH)D level. Part 1 included 48 randomized participants. Part 2 included 64 participants. In Part 1, no SOC participants achieved target serum level, but 50-72.7% of participants in cohorts A-C achieved the target serum level. In part 2, 78.6% of replacement dose participants achieved target serum level compared with none in the SOC arm. No related serious adverse events were reported. This trial confirmed a 50,000 IU loading dose plus 8,000 IU daily oral vitamin D as safe and effective in increasing serum 25(OH)D levels in children/adolescents with overweight/obesity to levels ≥ 40 ng/mL. Given the critical role of vitamin D in many conditions complicating childhood obesity, these data close a critical gap in our understanding of vitamin D dosing in children.


Assuntos
Asma , Obesidade Infantil , Deficiência de Vitamina D , Adolescente , Criança , Humanos , Vitamina D , Colecalciferol/efeitos adversos , Estudos Prospectivos , Deficiência de Vitamina D/diagnóstico , Deficiência de Vitamina D/tratamento farmacológico , Obesidade Infantil/complicações , Obesidade Infantil/tratamento farmacológico , Obesidade Infantil/induzido quimicamente , Vitaminas , Asma/tratamento farmacológico , Suplementos Nutricionais
4.
Sci Rep ; 13(1): 20615, 2023 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-37996478

RESUMO

Machine learning approaches have been used for the automatic detection of Parkinson's disease with voice recordings being the most used data type due to the simple and non-invasive nature of acquiring such data. Although voice recordings captured via telephone or mobile devices allow much easier and wider access for data collection, current conflicting performance results limit their clinical applicability. This study has two novel contributions. First, we show the reliability of personal telephone-collected voice recordings of the sustained vowel /a/ in natural settings by collecting samples from 50 people with specialist-diagnosed Parkinson's disease and 50 healthy controls and applying machine learning classification with voice features related to phonation. Second, we utilize a novel application of a pre-trained convolutional neural network (Inception V3) with transfer learning to analyze the spectrograms of the sustained vowel from these samples. This approach considers speech intensity estimates across time and frequency scales rather than collapsing measurements across time. We show the superiority of our deep learning model for the task of classifying people with Parkinson's disease as distinct from healthy controls.


Assuntos
Doença de Parkinson , Voz , Humanos , Doença de Parkinson/diagnóstico , Reprodutibilidade dos Testes , Fonação , Aprendizado de Máquina
5.
Semin Radiat Oncol ; 33(4): 395-406, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37684069

RESUMO

Clinical trials have been the center of progress in modern medicine. In oncology, we are fortunate to have a structure in place through the National Clinical Trials Network (NCTN). The NCTN provides the infrastructure and a forum for scientific discussion to develop clinical concepts for trial design. The NCTN also provides a network group structure to administer trials for successful trial management and outcome analyses. There are many important aspects to trial design and conduct. Modern trials need to ensure appropriate trial conduct and secure data management processes. Of equal importance is the quality assurance of a clinical trial. If progress is to be made in oncology clinical medicine, investigators and patient care providers of service need to feel secure that trial data is complete, accurate, and well-controlled in order to be confident in trial analysis and move trial outcome results into daily practice. As our technology has matured, so has our need to apply technology in a uniform manner for appropriate interpretation of trial outcomes. In this article, we review the importance of quality assurance in clinical trials involving radiation therapy. We will include important aspects of institution and investigator credentialing for participation as well as ongoing processes to ensure that each trial is being managed in a compliant manner. We will provide examples of the importance of complete datasets to ensure study interpretation. We will describe how successful strategies for quality assurance in the past will support new initiatives moving forward.


Assuntos
Ensaios Clínicos como Assunto , Radioterapia (Especialidade) , Humanos , Gerenciamento de Dados , Oncologia , Registros
6.
J Parkinsons Dis ; 13(6): 961-973, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37522218

RESUMO

BACKGROUND: Freezing of gait (FOG) is a debilitating, variably expressed motor symptom in people with Parkinson's disease (PwPD) with limited treatments. OBJECTIVE: To determine if the rate of progression in spatiotemporal gait parameters in people converting from a noFOG to a FOG phenotype (FOGConv) was faster than non-convertors, and determine if gait parameters can help predict this conversion. METHODS: PwPD were objectively monitored longitudinally, approximately every 6 months. Non-motor assessments were performed at the initial visit. Steady-state gait in the levodopa ON-state was collected using a gait mat (Protokinetics) at each visit. The rate of progression in 8 spatiotemporal gait parameters was calculated. FOG convertors (FOGConv) were classified if they did not have FOG at initial visit and developed FOG at a subsequent visit. RESULTS: Thirty freezers (FOG) and 30 non-freezers were monitored an average of 3.5 years, with 10 non-freezers developing FOG (FOGConv). FOGConv and FOG had faster decline in mean stride-length, swing-phase-percent, and increase in mean total-double-support percent, coefficient of variability (CV) foot-strike-length and CV swing-phase-percent than the remaining non-freezers (noFOG). On univariate modeling, progression rates of mean stride-length, stride-velocity, swing-phase-percent, total-double-support-percent and of CV swing-phase-percent had high discriminative power (AUC > 0.83) for classification of the FOGConv and noFOG groups. CONCLUSION: FOGConv had a faster temporal decline in objectively quantified gait than noFOG, and progression rates of spatiotemporal gait parameters were more predictive of FOG phenotype conversion than initial (static) parameters Objectively monitoring gait in disease prediction models may help define FOG prone groups for testing putative treatments.


Assuntos
Transtornos Neurológicos da Marcha , Doença de Parkinson , Humanos , Doença de Parkinson/complicações , Doença de Parkinson/terapia , Transtornos Neurológicos da Marcha/diagnóstico , Transtornos Neurológicos da Marcha/etiologia , Marcha , Levodopa
7.
Eur Radiol Exp ; 7(1): 20, 2023 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-37150779

RESUMO

Artificial intelligence (AI) is transforming the field of medical imaging and has the potential to bring medicine from the era of 'sick-care' to the era of healthcare and prevention. The development of AI requires access to large, complete, and harmonized real-world datasets, representative of the population, and disease diversity. However, to date, efforts are fragmented, based on single-institution, size-limited, and annotation-limited datasets. Available public datasets (e.g., The Cancer Imaging Archive, TCIA, USA) are limited in scope, making model generalizability really difficult. In this direction, five European Union projects are currently working on the development of big data infrastructures that will enable European, ethically and General Data Protection Regulation-compliant, quality-controlled, cancer-related, medical imaging platforms, in which both large-scale data and AI algorithms will coexist. The vision is to create sustainable AI cloud-based platforms for the development, implementation, verification, and validation of trustable, usable, and reliable AI models for addressing specific unmet needs regarding cancer care provision. In this paper, we present an overview of the development efforts highlighting challenges and approaches selected providing valuable feedback to future attempts in the area.Key points• Artificial intelligence models for health imaging require access to large amounts of harmonized imaging data and metadata.• Main infrastructures adopted either collect centrally anonymized data or enable access to pseudonymized distributed data.• Developing a common data model for storing all relevant information is a challenge.• Trust of data providers in data sharing initiatives is essential.• An online European Union meta-tool-repository is a necessity minimizing effort duplication for the various projects in the area.


Assuntos
Inteligência Artificial , Neoplasias , Humanos , Diagnóstico por Imagem , Previsões , Big Data
9.
Contemp Clin Trials ; 126: 107110, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36738915

RESUMO

Children have historically been underrepresented in randomized controlled trials and multi-center studies. This is particularly true for children who reside in rural and underserved areas. Conducting multi-center trials in rural areas presents unique informatics challenges. These challenges call for increased attention towards informatics infrastructure and the need for development and application of sound informatics approaches to the collection, processing, and management of data for clinical studies. By modifying existing local infrastructure and utilizing open source tools, we have been able to successfully deploy a multi-site data coordinating and operations center. We report our implementation decisions for data collection and management for the IDeA States Pediatric Clinical Trial Network (ISPCTN) based on the functionality needed for the ISPCTN, our synthesis of the extant literature in data collection and management methodology, and Good Clinical Data Management Practices.


Assuntos
Gerenciamento de Dados , Informática , Criança , Humanos , Coleta de Dados , População Rural
10.
Front Oncol ; 13: 1015596, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36776318

RESUMO

Clinical trials have become the primary mechanism to validate process improvements in oncology clinical practice. Over the past two decades there have been considerable process improvements in the practice of radiation oncology within the structure of a modern department using advanced technology for patient care. Treatment planning is accomplished with volume definition including fusion of multiple series of diagnostic images into volumetric planning studies to optimize the definition of tumor and define the relationship of tumor to normal tissue. Daily treatment is validated by multiple tools of image guidance. Computer planning has been optimized and supported by the increasing use of artificial intelligence in treatment planning. Informatics technology has improved, and departments have become geographically transparent integrated through informatics bridges creating an economy of scale for the planning and execution of advanced technology radiation therapy. This serves to provide consistency in department habits and improve quality of patient care. Improvements in normal tissue sparing have further improved tolerance of treatment and allowed radiation oncologists to increase both daily and total dose to target. Radiation oncologists need to define a priori dose volume constraints to normal tissue as well as define how image guidance will be applied to each radiation treatment. These process improvements have enhanced the utility of radiation therapy in patient care and have made radiation therapy an attractive option for care in multiple primary disease settings. In this chapter we review how these changes have been applied to clinical practice and incorporated into clinical trials. We will discuss how the changes in clinical practice have improved the quality of clinical trials in radiation therapy. We will also identify what gaps remain and need to be addressed to offer further improvements in radiation oncology clinical trials and patient care.

11.
J Med Imaging (Bellingham) ; 10(6): 061403, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-36814939

RESUMO

Purpose: Deep learning has shown great promise as the backbone of clinical decision support systems. Synthetic data generated by generative models can enhance the performance and capabilities of data-hungry deep learning models. However, there is (1) limited availability of (synthetic) datasets and (2) generative models are complex to train, which hinders their adoption in research and clinical applications. To reduce this entry barrier, we explore generative model sharing to allow more researchers to access, generate, and benefit from synthetic data. Approach: We propose medigan, a one-stop shop for pretrained generative models implemented as an open-source framework-agnostic Python library. After gathering end-user requirements, design decisions based on usability, technical feasibility, and scalability are formulated. Subsequently, we implement medigan based on modular components for generative model (i) execution, (ii) visualization, (iii) search & ranking, and (iv) contribution. We integrate pretrained models with applications across modalities such as mammography, endoscopy, x-ray, and MRI. Results: The scalability and design of the library are demonstrated by its growing number of integrated and readily-usable pretrained generative models, which include 21 models utilizing nine different generative adversarial network architectures trained on 11 different datasets. We further analyze three medigan applications, which include (a) enabling community-wide sharing of restricted data, (b) investigating generative model evaluation metrics, and (c) improving clinical downstream tasks. In (b), we extract Fréchet inception distances (FID) demonstrating FID variability based on image normalization and radiology-specific feature extractors. Conclusion: medigan allows researchers and developers to create, increase, and domain-adapt their training data in just a few lines of code. Capable of enriching and accelerating the development of clinical machine learning models, we show medigan's viability as platform for generative model sharing. Our multimodel synthetic data experiments uncover standards for assessing and reporting metrics, such as FID, in image synthesis studies.

12.
Drug Saf ; 46(2): 129-143, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36547811

RESUMO

INTRODUCTION: Drug-induced liver injury is a significant health issue, yet the exposure-based incidence remains to be characterized. OBJECTIVE: We aimed to assess the frequency, phenotypes, and outcomes of acute liver injury associated with amoxicillin/clavulanate using a large electronic health record system. METHODS: Using the Veterans Health Administration electronic health record system, we developed the framework to identify unexplained acute liver injury, defined by alanine aminotransferase and/or alkaline phosphatase elevation temporally linked to prescription records of amoxicillin/clavulanate, a major culprit of clinically significant drug-induced liver injury, excluding other competing causes. The population was subcategorized by pre-existing liver conditions and inpatient status at the time of exposure for the analysis. RESULTS: Among 1,445,171 amoxicillin/clavulanate first exposures in unique individuals [92% men; mean age (standard deviation): 59 (15) years], 6476 (incidence: 0.448%) acute liver injuries were identified. Of these, 4427 (65%) had alternative causes, yielding 2249 (incidence: 0.156%) with unexplained acute liver injuries. The incidence of unexplained acute liver injury was lowest in outpatients without underlying liver disease (0.067%) and highest in inpatients with pre-existing liver conditions (0.719%). Older age, male sex, and American Indian or Alaska Native (vs White) were associated with a higher incidence of unexplained acute liver injury. Cholestatic injury affected 74%, exhibiting a higher frequency with advanced age, inpatient exposure, and pre-existing liver conditions. Hepatocellular injury with bilirubin elevation affected 0.003%, with a higher risk at age >45 years. During a 12-month follow-up, patients with unexplained acute liver injury had a higher adjusted overall mortality risk than those without evident acute liver injury. CONCLUSIONS: This framework identifies unexplained acute liver injury following drug exposure in large electronic health record datasets. After validating in other systems, this framework can aid in deducing drug-induced liver injury in the general patient population and regulatory decision making to promote drug safety and public health.


Assuntos
Doença Hepática Induzida por Substâncias e Drogas , Hepatopatias , Humanos , Masculino , Feminino , Saúde dos Veteranos , Combinação Amoxicilina e Clavulanato de Potássio/efeitos adversos , Doença Hepática Induzida por Substâncias e Drogas/epidemiologia , Doença Hepática Induzida por Substâncias e Drogas/etiologia , Fenótipo
13.
Phys Med Biol ; 68(1)2022 12 23.
Artigo em Inglês | MEDLINE | ID: mdl-36279873

RESUMO

The cancer imaging archive (TICA) receives and manages an ever-increasing quantity of clinical (non-image) data containing valuable information about subjects in imaging collections. To harmonize and integrate these data, we have first cataloged the types of information occurring across public TCIA collections. We then produced mappings for these diverse instance data using ontology-based representation patterns and transformed the data into a knowledge graph in a semantic database. This repository combined the transformed instance data with relevant background knowledge from domain ontologies. The resulting repository of semantically integrated data is a rich source of information about subjects that can be queried across imaging collections. Building on this work we have implemented and deployed a REST API and a user-facing semantic cohort builder tool. This tool allows allow researchers and other users to search and identify groups of subject-level records based on non-image data that were not queryable prior to this work. The search results produced by this interface link to images, allowing users to quickly identify and view images matching the selection criteria, as well as allowing users to export the harmonized clinical data.


Assuntos
Neoplasias , Software , Humanos , Semântica , Neoplasias/diagnóstico por imagem , Diagnóstico por Imagem , Bases de Dados Factuais
14.
Commun Med (Lond) ; 2: 133, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36310650

RESUMO

An increasing array of tools is being developed using artificial intelligence (AI) and machine learning (ML) for cancer imaging. The development of an optimal tool requires multidisciplinary engagement to ensure that the appropriate use case is met, as well as to undertake robust development and testing prior to its adoption into healthcare systems. This multidisciplinary review highlights key developments in the field. We discuss the challenges and opportunities of AI and ML in cancer imaging; considerations for the development of algorithms into tools that can be widely used and disseminated; and the development of the ecosystem needed to promote growth of AI and ML in cancer imaging.

15.
Front Oncol ; 12: 931294, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36033446

RESUMO

The future of radiation oncology is exceptionally strong as we are increasingly involved in nearly all oncology disease sites due to extraordinary advances in radiation oncology treatment management platforms and improvements in treatment execution. Due to our technology and consistent accuracy, compressed radiation oncology treatment strategies are becoming more commonplace secondary to our ability to successfully treat tumor targets with increased normal tissue avoidance. In many disease sites including the central nervous system, pulmonary parenchyma, liver, and other areas, our service is redefining the standards of care. Targeting of disease has improved due to advances in tumor imaging and application of integrated imaging datasets into sophisticated planning systems which can optimize volume driven plans created by talented personnel. Treatment times have significantly decreased due to volume driven arc therapy and positioning is secured by real time imaging and optical tracking. Normal tissue exclusion has permitted compressed treatment schedules making treatment more convenient for the patient. These changes require additional study to further optimize care. Because data exchange worldwide have evolved through digital platforms and prisms, images and radiation datasets worldwide can be shared/reviewed on a same day basis using established de-identification and anonymization methods. Data storage post-trial completion can co-exist with digital pathomic and radiomic information in a single database coupled with patient specific outcome information and serve to move our translational science forward with nimble query elements and artificial intelligence to ask better questions of the data we collect and collate. This will be important moving forward to validate our process improvements at an enterprise level and support our science. We have to be thorough and complete in our data acquisition processes, however if we remain disciplined in our data management plan, our field can grow further and become more successful generating new standards of care from validated datasets.

16.
Contemp Clin Trials ; 120: 106861, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35907490

RESUMO

Obesity and asthma are epidemic in the United States and obesity is an independent risk factor for asthma. Low vitamin D levels (i.e. serum 25-hydroxyvitamin D) have been reported in patients with reduced lung function, more frequent respiratory infections, and asthma exacerbations. Experts have proposed that serum levels > 40 ng/mL are required to offer the immunomodulatory benefits of vitamin D. Low vitamin D levels are common in both obesity and asthma, but it is not known whether supplementation with vitamin D improves asthma symptoms. Guidance for drug development stresses the importance of early phase studies to establish accurate population pharmacokinetics (PK) and drug dosing prior to larger phase 3 trials. The PK of this fat-soluble vitamin in children with increased adiposity are unknown; as are the doses need to reach proposed immunomodulatory levels. The objective of this study is to characterize the PK of vitamin D in children with obesity. Children ages 6--18 years who had physician diagnosed asthma and a body mass index (BMI) >85th percentile will be randomized to receive either standard daily dosing or loading doses followed by standard daily dosing. Blood samples will be obtained to characterize the PK of vitamin D. The results of this study will be used to identify a sufficient dose of vitamin D supplement to raise serum levels above a pre-specified value that may result in anti-inflammatory actions that could improve asthma symptoms.


Assuntos
Asma , Deficiência de Vitamina D , Adolescente , Asma/tratamento farmacológico , Asma/epidemiologia , Criança , Humanos , Obesidade , Ensaios Clínicos Controlados Aleatórios como Assunto , Estados Unidos , Vitamina D , Deficiência de Vitamina D/tratamento farmacológico , Deficiência de Vitamina D/epidemiologia , Vitaminas/uso terapêutico
17.
Artigo em Inglês | MEDLINE | ID: mdl-35373222

RESUMO

Colonoscopy is a screening and diagnostic procedure for detection of colorectal carcinomas with specific quality metrics that monitor and improve adenoma detection rates. These quality metrics are stored in disparate documents i.e., colonoscopy, pathology, and radiology reports. The lack of integrated standardized documentation is impeding colorectal cancer research. Clinical concept extraction using Natural Language Processing (NLP) and Machine Learning (ML) techniques is an alternative to manual data abstraction. Contextual word embedding models such as BERT (Bidirectional Encoder Representations from Transformers) and FLAIR have enhanced performance of NLP tasks. Combining multiple clinically-trained embeddings can improve word representations and boost the performance of the clinical NLP systems. The objective of this study is to extract comprehensive clinical concepts from the consolidated colonoscopy documents using concatenated clinical embeddings. We built high-quality annotated corpora for three report types. BERT and FLAIR embeddings were trained on unlabeled colonoscopy related documents. We built a hybrid Artificial Neural Network (h-ANN) to concatenate and fine-tune BERT and FLAIR embeddings. To extract concepts of interest from three report types, 3 models were initialized from the h-ANN and fine-tuned using the annotated corpora. The models achieved best F1-scores of 91.76%, 92.25%, and 88.55% for colonoscopy, pathology, and radiology reports respectively.

18.
Artigo em Inglês | MEDLINE | ID: mdl-35386186

RESUMO

Clinical named entity recognition (NER) is an essential building block for many downstream natural language processing (NLP) applications such as information extraction and de-identification. Recently, deep learning (DL) methods that utilize word embeddings have become popular in clinical NLP tasks. However, there has been little work on evaluating and combining the word embeddings trained from different domains. The goal of this study is to improve the performance of NER in clinical discharge summaries by developing a DL model that combines different embeddings and investigate the combination of standard and contextual embeddings from the general and clinical domains. We developed: 1) A human-annotated high-quality internal corpus with discharge summaries and 2) A NER model with an input embedding layer that combines different embeddings: standard word embeddings, context-based word embeddings, a character-level word embedding using a convolutional neural network (CNN), and an external knowledge sources along with word features as one-hot vectors. Embedding was followed by bidirectional long short-term memory (Bi-LSTM) and conditional random field (CRF) layers. The proposed model reaches or overcomes state-of-the-art performance on two publicly available data sets and an F1 score of 94.31% on an internal corpus. After incorporating mixed-domain clinically pre-trained contextual embeddings, the F1 score further improved to 95.36% on the internal corpus. This study demonstrated an efficient way of combining different embeddings that will improve the recognition performance aiding the downstream de-identification of clinical notes.

19.
Artigo em Inglês | MEDLINE | ID: mdl-35300321

RESUMO

Colonoscopy plays a critical role in screening of colorectal carcinomas (CC). Unfortunately, the data related to this procedure are stored in disparate documents, colonoscopy, pathology, and radiology reports respectively. The lack of integrated standardized documentation is impeding accurate reporting of quality metrics and clinical and translational research. Natural language processing (NLP) has been used as an alternative to manual data abstraction. Performance of Machine Learning (ML) based NLP solutions is heavily dependent on the accuracy of annotated corpora. Availability of large volume annotated corpora is limited due to data privacy laws and the cost and effort required. In addition, the manual annotation process is error-prone, making the lack of quality annotated corpora the largest bottleneck in deploying ML solutions. The objective of this study is to identify clinical entities critical to colonoscopy quality, and build a high-quality annotated corpus using domain specific taxonomies following standardized annotation guidelines. The annotated corpus can be used to train ML models for a variety of downstream tasks.

20.
Radiat Res ; 197(4): 434-445, 2022 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-35090025

RESUMO

With a widely attended virtual kickoff event on January 29, 2021, the National Cancer Institute (NCI) and the Department of Energy (DOE) launched a series of 4 interactive, interdisciplinary workshops-and a final concluding "World Café" on March 29, 2021-focused on advancing computational approaches for predictive oncology in the clinical and research domains of radiation oncology. These events reflect 3,870 human hours of virtual engagement with representation from 8 DOE national laboratories and the Frederick National Laboratory for Cancer Research (FNL), 4 research institutes, 5 cancer centers, 17 medical schools and teaching hospitals, 5 companies, 5 federal agencies, 3 research centers, and 27 universities. Here we summarize the workshops by first describing the background for the workshops. Participants identified twelve key questions-and collaborative parallel ideas-as the focus of work going forward to advance the field. These were then used to define short-term and longer-term "Blue Sky" goals. In addition, the group determined key success factors for predictive oncology in the context of radiation oncology, if not the future of all of medicine. These are: cross-discipline collaboration, targeted talent development, development of mechanistic mathematical and computational models and tools, and access to high-quality multiscale data that bridges mechanisms to phenotype. The workshop participants reported feeling energized and highly motivated to pursue next steps together to address the unmet needs in radiation oncology specifically and in cancer research generally and that NCI and DOE project goals align at the convergence of radiation therapy and advanced computing.


Assuntos
Radioterapia (Especialidade) , Academias e Institutos , Humanos , National Cancer Institute (U.S.) , Radioterapia (Especialidade)/educação , Estados Unidos
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