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1.
J Am Med Inform Assoc ; 31(3): 727-731, 2024 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-38146986

RESUMO

OBJECTIVES: Clinical text processing offers a promising avenue for improving multiple aspects of healthcare, though operational deployment remains a substantial challenge. This case report details the implementation of a national clinical text processing infrastructure within the Department of Veterans Affairs (VA). METHODS: Two foundational use cases, cancer case management and suicide and overdose prevention, illustrate how text processing can be practically implemented at scale for diverse clinical applications using shared services. RESULTS: Insights from these use cases underline both commonalities and differences, providing a replicable model for future text processing applications. CONCLUSIONS: This project enables more efficient initiation, testing, and future deployment of text processing models, streamlining the integration of these use cases into healthcare operations. This project implementation is in a large integrated health delivery system in the United States, but we expect the lessons learned to be relevant to any health system, including smaller local and regional health systems in the United States.


Assuntos
Suicídio , Veteranos , Humanos , Estados Unidos , United States Department of Veterans Affairs , Atenção à Saúde , Administração de Caso
2.
Cardiorenal Med ; 14(1): 34-44, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38151011

RESUMO

INTRODUCTION: Angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) improve outcomes but are underutilized in patients with chronic kidney disease (CKD). Little is known about reasons for discontinuation and lack of reinitiating these medications. We aimed to explore clinicians' and patients' experiences and perceptions of ACEI/ARB use in CKD. METHODS: A multi-profession sample of health care clinicians and patients with documented ACEI/ARB-associated side effects in the past 6 months. Participants were recruited from 2 Veterans Affairs healthcare systems in Texas and Tennessee. A total of 15 clinicians and 10 patients completed interviews. We used inductive and deductive qualitative data analysis approaches to identify themes related to clinician and patient experiences with ACEI/ARB. Thematic analysis focused on prescribing decisions and practices, clinical guidelines, and perception of side effects. Data were analyzed as they amassed, and recruitment was stopped at the point of thematic saturation. RESULTS: Clinicians prescribe ACEI/ARB for blood pressure control and kidney protection and underscored the importance of these medications in patients with diabetes. While clinicians described providing comprehensive patient education about ACEI/ARB in CKD, patient interviews revealed significant knowledge gaps about CKD and ACEI/ARB use. Many patients were unaware of their CKD status, and some did not know why they were prescribed ACEI/ARB. Clinicians' drug management strategies varied widely, as did their understanding of prescribing guidelines. They identified structural and patient-level barriers to prescribing and many endorsed the development of a decision support tool to facilitate ACEI/ARB prescribing and management. DISCUSSION/CONCLUSION: Our qualitative study of clinicians and providers identified key target areas for improvement to increase ACEI/ARB utilization in patients with CKD with the goal to improve long-term outcomes in high-risk patients. These findings will also inform the development of a decision support tool to assist with prescribing ACEI/ARBs for patients with CKD.


Assuntos
Inibidores da Enzima Conversora de Angiotensina , Insuficiência Renal Crônica , Humanos , Inibidores da Enzima Conversora de Angiotensina/efeitos adversos , Antagonistas de Receptores de Angiotensina/uso terapêutico , Antagonistas de Receptores de Angiotensina/farmacologia , Sistema Renina-Angiotensina , Insuficiência Renal Crônica/complicações , Insuficiência Renal Crônica/tratamento farmacológico , Anti-Hipertensivos/uso terapêutico , Avaliação de Resultados da Assistência ao Paciente
3.
J Clin Psychiatry ; 84(4)2023 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-37341477

RESUMO

Background: Suicide risk prediction models frequently rely on structured electronic health record (EHR) data, including patient demographics and health care usage variables. Unstructured EHR data, such as clinical notes, may improve predictive accuracy by allowing access to detailed information that does not exist in structured data fields. To assess comparative benefits of including unstructured data, we developed a large case-control dataset matched on a state-of-the-art structured EHR suicide risk algorithm, utilized natural language processing (NLP) to derive a clinical note predictive model, and evaluated to what extent this model provided predictive accuracy over and above existing predictive thresholds.Methods: We developed a matched case-control sample of Veterans Health Administration (VHA) patients in 2017 and 2018. Each case (all patients that died by suicide in that interval, n = 4,584) was matched with 5 controls (patients who remained alive during treatment year) who shared the same suicide risk percentile. All sample EHR notes were selected and abstracted using NLP methods. We applied machine-learning classification algorithms to NLP output to develop predictive models. We calculated area under the curve (AUC) and suicide risk concentration to evaluate predictive accuracy overall and for high-risk patients.Results: The best performing NLP-derived models provided 19% overall additional predictive accuracy (AUC = 0.69; 95% CI, 0.67, 0.72) and 6-fold additional risk concentration for patients at the highest risk tier (top 0.1%), relative to the structured EHR model.Conclusions: The NLP-supplemented predictive models provided considerable benefit when compared to conventional structured EHR models. Results support future structured and unstructured EHR risk model integrations.


Assuntos
Registros Eletrônicos de Saúde , Processamento de Linguagem Natural , Humanos , Saúde dos Veteranos , Algoritmos , Aprendizado de Máquina
4.
Am J Nephrol ; 54(3-4): 126-135, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37231800

RESUMO

INTRODUCTION: Angiotensin-converting enzyme inhibitors (ACEis) and angiotensin receptor blockers (ARBs) are frequently discontinued in patients with chronic kidney disease (CKD). Documented adverse drug reactions (ADRs) in medical records may provide insight into the reasons for treatment discontinuation. METHODS: In this retrospective cohort of US veterans from 2005 to 2019, we identified individuals with CKD and a current prescription for an ACEi or ARB (current user group) or a discontinued prescription within the preceding 5 years (discontinued group). Documented ADRs in structured datasets associated with an ACEi or ARB were categorized into 17 pre-specified groups. Logistic regression assessed associations of documented ADRs with treatment discontinuation. RESULTS: There were 882,441 (73.0%) individuals in the current user group and 326,794 (27.0%) in the discontinued group. There were 26,434 documented ADRs, with at least one documented ADR in 7,520 (0.9%) current users and 9,569 (2.9%) of the discontinued group. ADR presence was associated with treatment discontinuation, aOR 4.16 (95% CI: 4.03, 4.29). The most common documented ADRs were cough (37.3%), angioedema (14.2%), and allergic reaction (10.4%). ADRs related to angioedema (aOR 3.81, 95% CI: 3.47, 4.17), hyperkalemia (aOR 2.03, 95% CI: 1.84, 2.24), peripheral edema (aOR 1.53, 95% CI: 1.33, 1.77), or acute kidney injury (aOR 1.32, 95% CI: 1.15, 1.51) were associated with treatment discontinuation. CONCLUSION: ADRs leading to drug discontinuation were infrequently documented. ADR types were differentially associated with treatment discontinuation. An understanding of which ADRs lead to treatment discontinuation provides an opportunity to address them at a healthcare system level.


Assuntos
Angioedema , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Insuficiência Renal Crônica , Humanos , Inibidores da Enzima Conversora de Angiotensina/efeitos adversos , Antagonistas de Receptores de Angiotensina/efeitos adversos , Estudos Retrospectivos , Insuficiência Renal Crônica/complicações , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos/epidemiologia , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos/etiologia , Angioedema/induzido quimicamente , Angioedema/epidemiologia , Angioedema/complicações
6.
Psychiatry Res ; 315: 114703, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35841702

RESUMO

Electronic medical record (EMR)-based suicide risk prediction methods typically rely on analysis of structured variables such as demographics, visit history, and prescription data. Leveraging unstructured EMR notes may improve predictive accuracy by allowing access to nuanced clinical information. We utilized natural language processing (NLP) to analyze a large EMR note corpus to develop a data-driven suicide risk prediction model. We developed a matched case-control sample of U.S. Department of Veterans Affairs (VA) patients in 2015 and 2016. We randomly matched each case (all patients that died by suicide in that interval, n = 5029) with five controls (patients that remained alive). We processed note corpus using NLP methods and applied machine-learning classification algorithms to output. We calculated area under the curve (AUC) and risk tiers to determine predictive accuracy. NLP-derived models demonstrated strong predictive accuracy. Patients that scored within top 10% of risk model accounted for up to 29% of suicide decedents. NLP-derived model compares positively to other leading prediction methods. Our approach is highly implementable, only requiring access to text data and open-source software. Additional studies should evaluate ensemble models incorporating NLP-derived information alongside more typical structured variables.


Assuntos
Registros Eletrônicos de Saúde , Suicídio , Algoritmos , Humanos , Processamento de Linguagem Natural , Fatores de Risco
7.
Circ Cardiovasc Interv ; 15(3): e011092, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35176872

RESUMO

BACKGROUND: Despite its high prevalence and clinical impact, research on peripheral artery disease (PAD) remains limited due to poor accuracy of billing codes. Ankle-brachial index (ABI) and toe-brachial index can be used to identify PAD patients with high accuracy within electronic health records. METHODS: We developed a novel natural language processing (NLP) algorithm for extracting ABI and toe-brachial index values and laterality (right or left) from ABI reports. A random sample of 800 reports from 94 Veterans Affairs facilities during 2015 to 2017 was selected and annotated by clinical experts. We trained the NLP system using random forest models and optimized it through sequential iterations of 10-fold cross-validation and error analysis on 600 test reports and evaluated its final performance on a separate set of 200 reports. We also assessed the accuracy of NLP-extracted ABI and toe-brachial index values for identifying patients with PAD in a separate cohort undergoing ABI testing. RESULTS: The NLP system had an overall precision (positive predictive value) of 0.85, recall (sensitivity) of 0.93, and F1 measure (accuracy) of 0.89 to correctly identify ABI/toe-brachial index values and laterality. Among 261 patients with ABI testing (49% PAD), the NLP system achieved a positive predictive value of 92.3%, sensitivity of 83.1%, and specificity of 93.1% to identify PAD when compared with a structured chart review. The above findings were consistent in a range of sensitivity analysis. CONCLUSIONS: We successfully developed and validated an NLP system for identifying patients with PAD within the Veterans Affairs electronic health record. Our findings have broad implications for PAD research and quality improvement.


Assuntos
Índice Tornozelo-Braço , Doença Arterial Periférica , Tornozelo , Índice Tornozelo-Braço/métodos , Humanos , Extremidade Inferior , Doença Arterial Periférica/diagnóstico , Doença Arterial Periférica/epidemiologia , Valor Preditivo dos Testes , Resultado do Tratamento
8.
Am J Prev Cardiol ; 9: 100300, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-34950914

RESUMO

OBJECTIVE: To determine whether natural language processing (NLP) of unstructured medical text can improve identification of ASCVD patients not using high-intensity statin therapy (HIST) due to statin-associated side effects (SASEs) and other reasons. METHODS: Reviewers annotated reasons for not prescribing HIST in notes of 1152 randomly selected patients from across the VA healthcare system treated for ASCVD but not receiving HIST. Developers used reviewer annotations to train the Canary NLP tool to detect and extract notes containing one or more of these reasons. Negative predictive value (NPV), sensitivity, specificity and Area Under the Curve (AUC) were used to assess accuracy at detecting documents containing reasons when using structured data, NLP-extracted unstructured data, or both data sources combined. RESULTS: At least one documented reason for not prescribing HIST occurred in 47% of notes. The most frequent reasons were SASEs (41%) and general intolerance (20%). When identifying notes containing any documented reason for not using HIST, adding NLP-extracted, unstructured data significantly (p<0.05) increased sensitivity (0.69 (95% confidence interval [CI] 0.60-0.76) to 0.89 (95% CI 0.81-0.93)), NPV (0.90 (95% CI 0.87 to 0.93) to 0.96 (95% CI 0.93-0.98)), and AUC (0.84 (95% confidence interval [CI] 0.81-0.88) to 0.91 (95% CI 0.90-0.93)) compared to structured data alone. CONCLUSIONS: NLP extraction of data from unstructured text can improve identification of reasons for patients not being on HIST over structured data alone. The additional information provided through NLP of unstructured free text should help in tailoring and implementing system-level interventions to improve HIST use in patients with ASCVD.

9.
J Biomed Inform ; 120: 103851, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34174396

RESUMO

Social determinants of health (SDoH) are increasingly important factors for population health, healthcare outcomes, and care delivery. However, many of these factors are not reliably captured within structured electronic health record (EHR) data. In this work, we evaluated and adapted a previously published NLP tool to include additional social risk factors for deployment at Vanderbilt University Medical Center in an Acute Myocardial Infarction cohort. We developed a transformation of the SDoH outputs of the tool into the OMOP common data model (CDM) for re-use across many potential use cases, yielding performance measures across 8 SDoH classes of precision 0.83 recall 0.74 and F-measure of 0.78.


Assuntos
Registros Eletrônicos de Saúde , Determinantes Sociais da Saúde , Centros Médicos Acadêmicos , Estudos de Coortes , Atenção à Saúde , Humanos
10.
Kidney Int ; 97(2): 263-265, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31980076

RESUMO

Much of medical data is buried in the free text of clinical notes and not captured by structured data, such as administrative codes. Natural language processing (NLP) can locate and use information that resides in unstructured free text. Chan et al. demonstrate that NLP is sensitive for identifying symptoms in hemodialysis patients. These findings highlight the benefit NLP may bring to nephrology and should prompt discussion of important considerations for NLP system design and implementation.


Assuntos
Processamento de Linguagem Natural , Nefrologia , Registros Eletrônicos de Saúde , Humanos , Diálise Renal
11.
J Clin Lipidol ; 13(5): 797-803.e1, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31501043

RESUMO

BACKGROUND: Accurate identification of patients with statin-associated side effects (SASEs) is critical for health care systems to institute strategies to improve guideline-concordant statin use. OBJECTIVE: The objective of this study was to determine whether adverse drug reaction (ADR) entry by clinicians in the electronic medical record can accurately identify SASEs. METHODS: We identified 1,248,214 atherosclerotic cardiovascular disease (ASCVD) patients seeking care in the Department of Veterans Affairs. Using an ADR data repository, we identified SASEs in 15 major symptom categories. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were assessed using a chart review of 256 ASCVD patients with identified SASEs, who were not on high-intensity statin therapy. RESULTS: We identified 171,189 patients (13.71%) with documented SASEs over a 15-year period (9.9%, 2.7%, and 1.1% to 1, 2, or >2 statins, respectively). Statin use, high-intensity statin use, low-density lipoprotein cholesterol, and non-high-density lipoprotein cholesterol levels were 72%, 28.1%, 99 mg/dL, and 129 mg/dL among those with vs 81%, 31.1%, 84 mg/dL, and 111 mg/dL among those without SASEs. Progressively lower statin and high-intensity statin use, and higher low-density lipoprotein cholesterol and non-high-density lipoprotein cholesterol levels were noted among those with SASEs to 1, 2, or >2 statins. Two-thirds of SASEs were related to muscle symptoms. Sensitivity, specificity, PPV, NPV compared with manual chart review were 63.4%, 100%, 100%, and 85.3%, respectively. CONCLUSION: A strategy of using ADR entry in the electronic medical record is feasible to identify SASEs with modest sensitivity and NPV but high specificity and PPV. Health care systems can use this strategy to identify ASCVD patients with SASEs and operationalize efforts to improve guideline-concordant lipid-lowering therapy use in such patients. The sensitivity of this approach can be further enhanced by the use of unstructured text data.


Assuntos
Aterosclerose/tratamento farmacológico , Inibidores de Hidroximetilglutaril-CoA Redutases/efeitos adversos , Inibidores de Hidroximetilglutaril-CoA Redutases/uso terapêutico , United States Department of Veterans Affairs , Veteranos , Idoso , Aterosclerose/sangue , HDL-Colesterol/sangue , LDL-Colesterol/sangue , Feminino , Humanos , Masculino , Valor Preditivo dos Testes , Sensibilidade e Especificidade , Estados Unidos
12.
J Nucl Cardiol ; 26(6): 1878-1885, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-29696484

RESUMO

BACKGROUND: Reporting standards promote clarity and consistency of stress myocardial perfusion imaging (MPI) reports, but do not require an assessment of post-test risk. Natural Language Processing (NLP) tools could potentially help estimate this risk, yet it is unknown whether reports contain adequate descriptive data to use NLP. METHODS: Among VA patients who underwent stress MPI and coronary angiography between January 1, 2009 and December 31, 2011, 99 stress test reports were randomly selected for analysis. Two reviewers independently categorized each report for the presence of critical data elements essential to describing post-test ischemic risk. RESULTS: Few stress MPI reports provided a formal assessment of post-test risk within the impression section (3%) or the entire document (4%). In most cases, risk was determinable by combining critical data elements (74% impression, 98% whole). If ischemic risk was not determinable (25% impression, 2% whole), inadequate description of systolic function (9% impression, 1% whole) and inadequate description of ischemia (5% impression, 1% whole) were most commonly implicated. CONCLUSIONS: Post-test ischemic risk was determinable but rarely reported in this sample of stress MPI reports. This supports the potential use of NLP to help clarify risk. Further study of NLP in this context is needed.


Assuntos
Angiografia Coronária , Teste de Esforço , Imagem de Perfusão do Miocárdio , Processamento de Linguagem Natural , Cardiopatias/diagnóstico por imagem , Humanos , Infarto do Miocárdio/diagnóstico por imagem , Isquemia Miocárdica/diagnóstico por imagem , Medição de Risco/métodos , Estados Unidos , United States Department of Veterans Affairs
13.
JMIR Res Protoc ; 6(1): e3, 2017 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-28104580

RESUMO

BACKGROUND: Pressure ulcers (PrUs) are a frequent, serious, and costly complication for veterans with spinal cord injury (SCI). The health care team should periodically identify PrU risk, although there is no tool in the literature that has been found to be reliable, valid, and sensitive enough to assess risk in this vulnerable population. OBJECTIVE: The immediate goal is to develop a risk assessment model that validly estimates the probability of developing a PrU. The long-term goal is to assist veterans with SCI and their providers in preventing PrUs through an automated system of risk assessment integrated into the veteran's electronic health record (EHR). METHODS: This 5-year longitudinal, retrospective, cohort study targets 12,344 veterans with SCI who were cared for in the Veterans Health Administration (VHA) in fiscal year (FY) 2009 and had no record of a PrU in the prior 12 months. Potential risk factors identified in the literature were reviewed by an expert panel that prioritized factors and determined if these were found in structured data or unstructured form in narrative clinical notes for FY 2009-2013. These data are from the VHA enterprise Corporate Data Warehouse that is derived from the EHR structured (ie, coded in database/table) or narrative (ie, text in clinical notes) data for FY 2009-2013. RESULTS: This study is ongoing and final results are expected in 2017. Thus far, the expert panel reviewed the initial list of risk factors extracted from the literature; the panel recommended additions and omissions and provided insights about the format in which the documentation of the risk factors might exist in the EHR. This list was then iteratively refined through review and discussed with individual experts in the field. The cohort for the study was then identified, and all structured, unstructured, and semistructured data were extracted. Annotation schemas were developed, samples of documents were extracted, and annotations are ongoing. Operational definitions of structured data elements have been created and steps to create an analytic dataset are underway. CONCLUSIONS: To our knowledge, this is the largest cohort employed to identify PrU risk factors in the United States. It also represents the first time natural language processing and statistical text mining will be used to expand the number of variables available for analysis. A major strength of this quantitative study is that all VHA SCI centers were included in the analysis, reducing potential for selection bias and providing increased power for complex statistical analyses. This longitudinal study will eventually result in a risk prediction tool to assess PrU risk that is reliable and valid, and that is sensitive to this vulnerable population.

14.
J Am Med Inform Assoc ; 24(e1): e40-e46, 2017 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-27413122

RESUMO

OBJECTIVE: This paper describes a new congestive heart failure (CHF) treatment performance measure information extraction system - CHIEF - developed as part of the Automated Data Acquisition for Heart Failure project, a Veterans Health Administration project aiming at improving the detection of patients not receiving recommended care for CHF. DESIGN: CHIEF is based on the Apache Unstructured Information Management Architecture framework, and uses a combination of rules, dictionaries, and machine learning methods to extract left ventricular function mentions and values, CHF medications, and documented reasons for a patient not receiving these medications. MEASUREMENTS: The training and evaluation of CHIEF were based on subsets of a reference standard of various clinical notes from 1083 Veterans Health Administration patients. Domain experts manually annotated these notes to create our reference standard. Metrics used included recall, precision, and the F 1 -measure. RESULTS: In general, CHIEF extracted CHF medications with high recall (>0.990) and good precision (0.960-0.978). Mentions of Left Ventricular Ejection Fraction were also extracted with high recall (0.978-0.986) and precision (0.986-0.994), and quantitative values of Left Ventricular Ejection Fraction were found with 0.910-0.945 recall and with high precision (0.939-0.976). Reasons for not prescribing CHF medications were more difficult to extract, only reaching fair accuracy with about 0.310-0.400 recall and 0.250-0.320 precision. CONCLUSION: This study demonstrated that applying natural language processing to unlock the rich and detailed clinical information found in clinical narrative text notes makes fast and scalable quality improvement approaches possible, eventually improving management and outpatient treatment of patients suffering from CHF.


Assuntos
Cardiotônicos/uso terapêutico , Insuficiência Cardíaca/tratamento farmacológico , Armazenamento e Recuperação da Informação/métodos , Processamento de Linguagem Natural , Função Ventricular Esquerda , Registros Eletrônicos de Saúde , Insuficiência Cardíaca/fisiopatologia , Hospitais de Veteranos , Humanos , Aprendizado de Máquina
15.
J Am Med Inform Assoc ; 21(5): 833-41, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24431336

RESUMO

OBJECTIVE: To determine whether assisted annotation using interactive training can reduce the time required to annotate a clinical document corpus without introducing bias. MATERIALS AND METHODS: A tool, RapTAT, was designed to assist annotation by iteratively pre-annotating probable phrases of interest within a document, presenting the annotations to a reviewer for correction, and then using the corrected annotations for further machine learning-based training before pre-annotating subsequent documents. Annotators reviewed 404 clinical notes either manually or using RapTAT assistance for concepts related to quality of care during heart failure treatment. Notes were divided into 20 batches of 19-21 documents for iterative annotation and training. RESULTS: The number of correct RapTAT pre-annotations increased significantly and annotation time per batch decreased by ~50% over the course of annotation. Annotation rate increased from batch to batch for assisted but not manual reviewers. Pre-annotation F-measure increased from 0.5 to 0.6 to >0.80 (relative to both assisted reviewer and reference annotations) over the first three batches and more slowly thereafter. Overall inter-annotator agreement was significantly higher between RapTAT-assisted reviewers (0.89) than between manual reviewers (0.85). DISCUSSION: The tool reduced workload by decreasing the number of annotations needing to be added and helping reviewers to annotate at an increased rate. Agreement between the pre-annotations and reference standard, and agreement between the pre-annotations and assisted annotations, were similar throughout the annotation process, which suggests that pre-annotation did not introduce bias. CONCLUSIONS: Pre-annotations generated by a tool capable of interactive training can reduce the time required to create an annotated document corpus by up to 50%.


Assuntos
Inteligência Artificial , Registros Eletrônicos de Saúde , Processamento de Linguagem Natural , Insuficiência Cardíaca/tratamento farmacológico , Insuficiência Cardíaca/fisiopatologia , Humanos
16.
J Biomed Inform ; 48: 54-65, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24316051

RESUMO

Rapid, automated determination of the mapping of free text phrases to pre-defined concepts could assist in the annotation of clinical notes and increase the speed of natural language processing systems. The aim of this study was to design and evaluate a token-order-specific naïve Bayes-based machine learning system (RapTAT) to predict associations between phrases and concepts. Performance was assessed using a reference standard generated from 2860 VA discharge summaries containing 567,520 phrases that had been mapped to 12,056 distinct Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) concepts by the MCVS natural language processing system. It was also assessed on the manually annotated, 2010 i2b2 challenge data. Performance was established with regard to precision, recall, and F-measure for each of the concepts within the VA documents using bootstrapping. Within that corpus, concepts identified by MCVS were broadly distributed throughout SNOMED CT, and the token-order-specific language model achieved better performance based on precision, recall, and F-measure (0.95±0.15, 0.96±0.16, and 0.95±0.16, respectively; mean±SD) than the bag-of-words based, naïve Bayes model (0.64±0.45, 0.61±0.46, and 0.60±0.45, respectively) that has previously been used for concept mapping. Precision, recall, and F-measure on the i2b2 test set were 92.9%, 85.9%, and 89.2% respectively, using the token-order-specific model. RapTAT required just 7.2ms to map all phrases within a single discharge summary, and mapping rate did not decrease as the number of processed documents increased. The high performance attained by the tool in terms of both accuracy and speed was encouraging, and the mapping rate should be sufficient to support near-real-time, interactive annotation of medical narratives. These results demonstrate the feasibility of rapidly and accurately mapping phrases to a wide range of medical concepts based on a token-order-specific naïve Bayes model and machine learning.


Assuntos
Inteligência Artificial , Processamento de Linguagem Natural , Algoritmos , Automação , Teorema de Bayes , Bases de Dados Factuais , Registros Eletrônicos de Saúde , Hospitais de Veteranos , Humanos , Modelos Estatísticos , Reprodutibilidade dos Testes , Software , Systematized Nomenclature of Medicine , Tennessee , Terminologia como Assunto , Unified Medical Language System , Vocabulário Controlado
17.
Int J Med Inform ; 82(2): 118-27, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22595284

RESUMO

BACKGROUND: Clinical practice and epidemiological information aggregation require knowing when, how long, and in what sequence medically relevant events occur. The Temporal Awareness and Reasoning Systems for Question Interpretation (TARSQI) Toolkit (TTK) is a complete, open source software package for the temporal ordering of events within narrative text documents. TTK was developed on newspaper articles. We extended TTK to support medical notes using veterans' affairs (VA) clinical notes and compared it to TTK. METHODS: We used a development set consisting of 200 VA clinical notes to modify and append rules to TTK's time tagger, creating Med-TTK. We then evaluated the performances of TTK and Med-TTK on an independent random selection of 100 clinical notes. Evaluation tasks were to identify and classify time-referring expressions as one of four temporal classes (DATE, TIME, DURATION, and SET). The reference standard for this test set was generated by dual human manual review with disagreements resolved by a third reviewer. Outcome measures included recall and precision for each class, and inter-rater agreement scores. RESULTS: There were 3146 temporal expressions in the reference standard. TTK identified 1595 temporal expressions. Recall was 0.15 (95% confidence interval [CI] 0.12-0.15) and precision was 0.27 (95% CI 0.25-0.29) for TTK. Med-TTK identified 3174 expressions. Recall was 0.86 (95% CI 0.84-0.87) and precision was 0.85 (95% CI 0.84-0.86) for Med-TTK. CONCLUSION: The algorithms for identifying and classifying temporal expressions in medical narratives developed within Med-TTK significantly improved performance compared to TTK. Natural language processing applications such as Med-TTK provide a foundation for meaningful longitudinal mapping of patient history events among electronic health records. The tool can be accessed at the following site: http://code.google.com/p/med-ttk/.


Assuntos
Registros Eletrônicos de Saúde/estatística & dados numéricos , Registros de Saúde Pessoal , Narração , Processamento de Linguagem Natural , Reconhecimento Automatizado de Padrão/métodos , Fatores de Tempo , Vocabulário Controlado , Software , Estados Unidos
18.
AMIA Annu Symp Proc ; 2012: 753-62, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23304349

RESUMO

BACKGROUND: A practical data point for assessing information quality and value in the Electronic Health Record (EHR) is the professional category of the EHR author. We evaluated and compared free form electronic signatures against LOINC note titles in categorizing the profession of EHR authors. METHODS: A random 1000 clinical document sample was selected and divided into 500 document sets for training and testing. The gold standard for provider classification was generated by dual clinician manual review, disagreements resolved by a third reviewer. Text matching algorithms composed of document titles and author electronic signatures for provider classification were developed on the training set. RESULTS: Overall, detection of professional classification by note titles alone resulted in 76.1% sensitivity and 69.4% specificity. The aggregate of note titles with electronic signatures resulted in 95.7% sensitivity and 98.5% specificity. CONCLUSIONS: Note titles alone provided fair professional classification. Inclusion of author electronic signatures significantly boosted classification performance.


Assuntos
Algoritmos , Autoria , Registros Eletrônicos de Saúde , Logical Observation Identifiers Names and Codes , Humanos , Sistemas de Informação , Estados Unidos , United States Department of Veterans Affairs/organização & administração , Veteranos
19.
Cell Transplant ; 20(11-12): 1901-6, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21457614

RESUMO

The technique of central nervous system cell implantation can affect the outcome of preclinical or clinical studies. Our goal was to evaluate the impact of various injection parameters that may be of consequence during the delivery of solute-suspended cells. These parameters included (1) the type and concentration of cells used for implantation, (2) the rate at which cells are injected (flow rate), (3) the acceleration of the delivery device, (4) the period of time between cell loading and injection into the CNS (delay), and (5) the length and gauge of the needle used to deliver the cells. Neural progenitor cells (NPCs) and bone marrow stromal cells (BMSCs) were injected an automated device. These parameters were assessed in relation to their effect on the volume of cells injected and cell viability. Longer and thinner cannulae and higher cell concentrations were detrimental for cell delivery. Devices and techniques that optimize these parameters should be of benefit.


Assuntos
Injeções/métodos , Células-Tronco Neurais/transplante , Células Estromais/transplante , Animais , Automação , Células da Medula Óssea/citologia , Encéfalo , Linhagem Celular , Sobrevivência Celular , Feminino , Injeções/instrumentação , Camundongos , Camundongos Endogâmicos C57BL , Células-Tronco Neurais/citologia , Células Estromais/citologia
20.
Neurosurgery ; 67(6): 1662-8; discussion 1668, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21107197

RESUMO

BACKGROUND: Cellular transplantation holds promise for the management of a variety of neurological disorders. However, there is great variability in cell type, preparation methods, and implantation technique, which are crucial to clinical outcomes. OBJECTIVE: We compared manual injection with automated injection using a prototype device to determine the possible value of a mechanized delivery system. METHODS: Neural progenitor cells and bone marrow stromal cells were injected using manual or automated methods. Consistency of injection volumes and cell number and viability were evaluated immediately or 1 day after injection. RESULTS: When cells were delivered as a series of 3 manual injections from the same syringe, the variation in fluid volume was greater than for single manual injections. Automated delivery of a series of 3 injections resulted in a lower variability in the amount of delivery than manual injection for both cell lines (1.2%-2.6% coefficient of variability for automated delivery vs 4.3%-24.0% for manual delivery). The amount delivered from injection 1 to injection 3 increased significantly with manual injections, whereas the amount injected did not vary over the 3 injections for the automated unit. Cell viability 1 day after injection was typically 30% to 40% of the value immediately after injection for the bone marrow stromal cells and 30% to 70% for the neural progenitor cells. There were no significant differences in viability attributed to the method of injection. CONCLUSION: The automated delivery device led to enhanced consistency of volumetric cell delivery but did not improve cell viability in the methods tested. Automated techniques could be useful in standardizing reproducible procedures for cell transplantation and improve both preclinical and clinical research.


Assuntos
Células-Tronco Adultas/transplante , Transplante de Células , Células-Tronco Neurais/transplante , Células-Tronco Adultas/fisiologia , Animais , Células da Medula Óssea/citologia , Células da Medula Óssea/fisiologia , Contagem de Células/métodos , Transplante de Células/instrumentação , Transplante de Células/fisiologia , Células Cultivadas , Processamento Eletrônico de Dados , Feminino , Injeções/métodos , Camundongos , Camundongos Endogâmicos C57BL , Células-Tronco Neurais/fisiologia , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Seringas
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