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1.
Artigo em Inglês | MEDLINE | ID: mdl-34995752

RESUMO

Hypothermic circulatory arrest is a protective technique used when complete cessation of circulation is required during cardiac surgery. Prior efforts to decrease neurologic injury with the NMDA receptor antagonist MK801 were limited by unacceptable side effects. We hypothesized that ketamine would provide neuroprotection without dose-limiting side effects. Canines were peripherally cannulated for cardiopulmonary bypass, cooled to 18°C, and underwent 90 minutes of circulatory arrest. Ketamine-treated canines (n = 5; total dose 2.85 mg/kg) were compared to untreated controls (n = 10). A validated neurobehavioral deficit score was obtained at 24, 48, and 72 hours (0 = no deficits/normal exam; higher score represents increasing deficits). Biomarkers of neuronal injury in the cerebrospinal fluid were examined at baseline and at 8, 24, 48, and 72 hours. Brain histopathologic injury was scored at 72 hours (higher score indicates more necrosis and apoptosis). Ketamine-treated canines had significantly improved, lower neurobehavioral deficit scores compared to controls (overall P = 0.003; 24 hours: median 72 vs 112, P = 0.030; 48 hours: 47 vs 90, P = 0.021; 72 hours: 30 vs 89, P = 0.069). Although the histopathologic injury scores of ketamine-treated canines (median 12) were lower than controls (16), there was no statistical difference (P = 0.10). Levels of phosphorylated neurofilament-H and neuron specific enolase, markers of neuronal injury, were significantly lower in ketamine-treated animals (P = 0.010 and = 0.039, respectively). Ketamine significantly reduced neurologic deficits and biomarkers of injury in canines after hypothermic circulatory arrest. Ketamine represents a safe and approved medication that may be useful as a pharmacologic neuroprotectant during cardiac surgery with circulatory arrest.

2.
BMC Bioinformatics ; 22(Suppl 1): 598, 2021 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-34920707

RESUMO

BACKGROUND: Automated assignment of specific ontology concepts to mentions in text is a critical task in biomedical natural language processing, and the subject of many open shared tasks. Although the current state of the art involves the use of neural network language models as a post-processing step, the very large number of ontology classes to be recognized and the limited amount of gold-standard training data has impeded the creation of end-to-end systems based entirely on machine learning. Recently, Hailu et al. recast the concept recognition problem as a type of machine translation and demonstrated that sequence-to-sequence machine learning models have the potential to outperform multi-class classification approaches. METHODS: We systematically characterize the factors that contribute to the accuracy and efficiency of several approaches to sequence-to-sequence machine learning through extensive studies of alternative methods and hyperparameter selections. We not only identify the best-performing systems and parameters across a wide variety of ontologies but also provide insights into the widely varying resource requirements and hyperparameter robustness of alternative approaches. Analysis of the strengths and weaknesses of such systems suggest promising avenues for future improvements as well as design choices that can increase computational efficiency with small costs in performance. RESULTS: Bidirectional encoder representations from transformers for biomedical text mining (BioBERT) for span detection along with the open-source toolkit for neural machine translation (OpenNMT) for concept normalization achieve state-of-the-art performance for most ontologies annotated in the CRAFT Corpus. This approach uses substantially fewer computational resources, including hardware, memory, and time than several alternative approaches. CONCLUSIONS: Machine translation is a promising avenue for fully machine-learning-based concept recognition that achieves state-of-the-art results on the CRAFT Corpus, evaluated via a direct comparison to previous results from the 2019 CRAFT shared task. Experiments illuminating the reasons for the surprisingly good performance of sequence-to-sequence methods targeting ontology identifiers suggest that further progress may be possible by mapping to alternative target concept representations. All code and models can be found at: https://github.com/UCDenver-ccp/Concept-Recognition-as-Translation .

4.
J Surg Res ; 264: 260-273, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-33839341

RESUMO

BACKGROUND: Hypothermic circulatory arrest (HCA) is a technique used for complex repair of the aorta, but it can be associated with neurologic morbidity. To better understand the molecular changes that underlie ischemic brain injury, we assessed gene expression and cytokine/chemokine polypeptide concentration in brain tissue and cerebrospinal fluid (CSF) of canines that underwent two hours of HCA. MATERIALS AND METHODS: Adult male canines were cannulated peripherally for cardiopulmonary bypass, cooled to 18°C, and arrested for two hours. Animals were euthanized two, eight, or 24 hours post-HCA (n = 8 per group), and their brains were compared to brains from eight normal canines, using gene expression microarray analysis, cytokine assay, and histopathology. RESULTS: Two to eight hours after HCA, pro-inflammatory cytokine mRNAs increased markedly, and gene expression was enriched within signaling pathways related to neuroinflammation or ischemic injury. Concentrations of pro-inflammatory cytokine polypeptides IL-6, IL-8, IL-1ß, and CCL2 were very low in normal canine brain, whereas anti-inflammatory IL-10 and TGF-ß1 were expressed at moderate levels. Pro-inflammatory cytokine concentrations rose robustly in cerebral tissue and CSF after HCA. IL-6 and IL-8 peaked at eight hours and declined at 24 hours, while IL-1ß and CCL2 remained elevated. Concentrations of anti-inflammatory IL-10 and TGF-ß1 were maintained after HCA, with a significant increase in TGF-ß1 at 24 hours. CONCLUSIONS: These cytokines represent potential diagnostic markers for ischemic neurologic injury that could be used to assess neurologic injury in patients undergoing HCA. The cellular mechanisms underlying this pro-inflammatory, ischemic-induced injury represent potential targets for neuroprotection in the future.


Assuntos
Isquemia Encefálica/imunologia , Parada Circulatória Induzida por Hipotermia Profunda/efeitos adversos , Citocinas/metabolismo , Mediadores da Inflamação/metabolismo , Animais , Biomarcadores/líquido cefalorraquidiano , Biomarcadores/metabolismo , Encéfalo/irrigação sanguínea , Encéfalo/imunologia , Encéfalo/patologia , Isquemia Encefálica/líquido cefalorraquidiano , Isquemia Encefálica/diagnóstico , Isquemia Encefálica/patologia , Citocinas/líquido cefalorraquidiano , Modelos Animais de Doenças , Cães , Perfilação da Expressão Gênica , Humanos , Mediadores da Inflamação/líquido cefalorraquidiano , Masculino
5.
Chest ; 157(1): 151-161, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31446063

RESUMO

BACKGROUND: At the recent 6th World Symposium on Pulmonary Hypertension (PH), the definition of PH was redefined to include lower pulmonary artery pressures in the setting of elevated pulmonary vascular resistance (PVR). However, the relevance of this change to subjects with PH due to left-heart disease as well as the preoperative assessment of heart transplant (HT) recipients is unknown. METHODS: The United Network for Organ Sharing database was queried to identify adult recipients who underwent primary HT from 1996 to 2015. Recipients were subdivided into those with mean pulmonary artery pressure (mPAP) < 25 mm Hg and ≥ 25 mm Hg. Exploratory univariable analysis was undertaken to identify candidate risk factors associated with 30-day and 1-year survival (conditional on 30-day survival) in recipients with mPAP < 25 mm Hg, and subsequently, parsimonious multivariable Cox proportional hazards models were constructed to assess the independent association with PVR. RESULTS: Over the study period, 32,465 patients underwent HT, including 12,257 (38%) with mPAP < 25 mm Hg. The median age was 55 years (interquartile range, 47-62) and the median PVR was 1.5 Wood units (WU) (interquartile range, 1-2.2) in recipients with mPAP < 25 mm Hg. After controlling for confounders, PVR was independently associated with increased risk for 30-day mortality (hazard ratio, 1.16; 95% CI, 1.05-1.27; P < .01), but not conditional 1-year mortality (hazard ratio, 1.03; 95% CI, 0.94-1.12; P = .55). PVR ≥ 3 WU was associated with an absolute 1.9% increase in 30-day mortality in those with mPAP < 25 mm Hg, a similar risk to recipients with PVR ≥ 3 WU and mPAP ≥ 25 mm Hg. CONCLUSIONS: Elevated PVR remains associated with a significant increase in the hazard for 30-day mortality after cardiac transplantation, even in the setting of lower pulmonary artery pressures. These data support the validity of the new definition of pulmonary hypertension.


Assuntos
Transplante de Coração/mortalidade , Hipertensão Pulmonar/classificação , Hipertensão Pulmonar/complicações , Feminino , Hemodinâmica , Humanos , Masculino , Pessoa de Meia-Idade , Seleção de Pacientes , Fatores de Risco , Análise de Sobrevida , Resistência Vascular
6.
Ann Thorac Surg ; 108(6): 1895-1900, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31336069

RESUMO

BACKGROUND: Previous "high-stakes" examinations by the American Board of Thoracic Surgery (ABTS) required remote testing, were noneducational, and were not tailored to individual practices. Given the ABTS mission of public safety and diplomate education, the ABTS Maintenance of Certification (MOC) examination was revised in 2015 to improve the educational experience and validate knowledge acquired. METHODS: The ABTS-MOC Committee developed a web-based, secure examination tailored to the specialty-specific practice profile (cardiac, general thoracic, cardiothoracic, congenital) of the individual surgeon. After an initial answer to each question, an educational critique was reviewed before returning to the initial question and logging a second (final) response. Intraexam learning was assessed by comparing scores before and after reading the critique. Diplomate feedback was obtained. RESULTS: A total of 988 diplomates completed the 10-year MOC examination between 2015 and 2017. Substantive learning was demonstrated with an 18%, 17%, 20%, and 9% improvement in cardiac, general thoracic, cardiothoracic, and congenital final scores, respectively. This improvement was most notable among diplomates with the lowest initial scores. Fewer diplomates failed the new exam (<1% vs 2.3%). Diplomate postexam survey highlighted marked improvements in clinical relevance (35% vs 78%), convenience (37% vs 78%), and learning (15% vs 45%). Over 80% acknowledged educational value, and 97% preferred the new format. CONCLUSIONS: The new MOC process demonstrates increased knowledge acquisition through a convenient, secure, web-based practice-focused examination. This approach provides feedback, identifies baseline knowledge gaps for individual diplomates, and validates new knowledge attained.


Assuntos
Certificação , Competência Clínica , Educação de Pós-Graduação em Medicina/normas , Conselhos de Especialidade Profissional , Cirurgia Torácica/educação , Procedimentos Cirúrgicos Torácicos/normas , Avaliação Educacional , Humanos , Estudos Retrospectivos , Procedimentos Cirúrgicos Torácicos/educação , Estados Unidos
8.
Innovations (Phila) ; 14(1): 43-54, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30848712

RESUMO

INTRODUCTION: Frailty is an important component of risk prognostication in transcatheter aortic valve replacement (TAVR). Objective markers of frailty, including sarcopenia, the modified Frailty Index (mFI), and albumin levels, have emerged, but little is known how such markers compare to each other in predicting outcomes after TAVR. We sought to define and compare these markers in predicting long-term outcomes after TAVR. METHODS: Patients who underwent TAVR at our institution from 2011 to 2016 were included. Indexed cross-sectional areas of the lumbosacral muscles on preoperative computed tomography scans were used to assess sarcopenia. Optimal cutoffs for sarcopenia were defined using a statistically validated method. mFI was calculated using an 11-point scale of clinical characteristics. The primary outcome was 2-year all-cause mortality. Adjusted survival analysis was used to analyze outcomes. RESULTS: A total of 381 patients were included in this study. Sarcopenia of the psoas muscles was associated with an increased risk of mortality on univariate (HR: 2.3, P = 0.01) and multivariate (HR: 2.5, P = 0.01) analysis. Sarcopenia of the paravertebral muscles was associated with increased risk of mortality only on univariate analysis (HR: 2.1, P = 0.03). Increased preoperative albumin levels were associated with decreased risk of mortality on univariate (HR: 0.3, P < 0.01) and multivariate analysis (HR: 0.3, P < 0.01). The (mFI) was not associated with mortality on univariate or multivariate analysis. DISCUSSION: Novel cutoffs for sarcopenia of the psoas muscles were determined and associated with decreased survival after TAVR. Sarcopenia and albumin levels may be better tools for risk prediction than mFI in TAVR.


Assuntos
Albuminas/análise , Valva Aórtica/cirurgia , Sarcopenia/complicações , Substituição da Valva Aórtica Transcateter/métodos , Idoso , Idoso de 80 Anos ou mais , Biomarcadores , Comorbidade , Feminino , Fragilidade/complicações , Fragilidade/epidemiologia , Humanos , Masculino , Prognóstico , Músculos Psoas/patologia , Estudos Retrospectivos , Sarcopenia/diagnóstico por imagem , Sarcopenia/patologia , Análise de Sobrevida , Tomografia Computadorizada por Raios X/métodos , Substituição da Valva Aórtica Transcateter/efeitos adversos , Substituição da Valva Aórtica Transcateter/mortalidade , Resultado do Tratamento
10.
J Arthroplasty ; 33(9): 2752-2758, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-29858101

RESUMO

INTRODUCTION: Routine laboratory studies are often obtained daily after total joint arthroplasty (TJA) regardless of medical management. The purpose of this study was to investigate the utility of routine basic metabolic panel (BMP) tests after TJA. Furthermore, the goal was to identify factors that may predispose patients to abnormal laboratory values that require medical intervention. METHODS: A retrospective review was performed on 767 patients who underwent primary TJA at a single institution. Preoperative and postoperative potassium, sodium, creatinine, and glucose values were collected along with demographic data, comorbidities, and procedural characteristics. Multivariable logistic regression models were used to determine independent risk factors for abnormal postoperative laboratory values. RESULTS: Diabetes was associated with abnormal glucose (odds ratio [OR] 23.4, 95% confidence interval [CI] 10.7-51.0, P < .001), while chronic kidney disease was associated with abnormal creatinine (OR 3.1, 95% CI 1.7-5.8, P < .001) and potassium (OR 1.8, 95% CI 1.1-2.8, P = .014) requiring medical intervention. An abnormal preoperative laboratory value was also associated with medical treatment for each of sodium, potassium, and creatinine (all P < .001). Average number of BMP tests collected for patients who did not receive medical intervention was 2.8. This equated to $472,372.56 in total hospital charges. CONCLUSION: Cost containment while maintaining high-quality patient care is critical. Routine postoperative BMP tests in patients with normal preoperative values without major medical comorbidities do not contribute to actionable information. Patients with diabetes, chronic kidney disease, or with abnormal preoperative values should obtain a BMP after TJA.


Assuntos
Artroplastia de Quadril/efeitos adversos , Artroplastia do Joelho/efeitos adversos , Creatinina/sangue , Falência Renal Crônica/complicações , Adulto , Idoso , Idoso de 80 Anos ou mais , Complicações do Diabetes/metabolismo , Feminino , Custos de Cuidados de Saúde , Testes Hematológicos/economia , Humanos , Falência Renal Crônica/sangue , Masculino , Pessoa de Meia-Idade , Análise Multivariada , Razão de Chances , Pacotes de Assistência ao Paciente , Potássio/sangue , Estudos Retrospectivos , Fatores de Risco , Sódio/sangue , Adulto Jovem
11.
J Cardiothorac Vasc Anesth ; 32(6): 2485-2492, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-29903683

RESUMO

OBJECTIVE: The authors sought to assess the relationship between low oxygen delivery (DO2) during cardiopulmonary bypass (CPB) and a neuron-specific biomarker of neurologic injury, ubiquitin C-terminal hydrolase L1 (UCH-L1). DESIGN: Retrospective analysis of patient charts and prospectively collected blood samples. SETTING: University-affiliated tertiary care hospital. PARTICIPANTS: Adult patients undergoing cardiac surgery on CPB. INTERVENTIONS: Serum UCH-L1 levels were drawn at baseline and 6 and 24 hours after CPB cessation. DO2 was computed from perfusion records, with area-under-the-curve (AUC) computations performed to account for distance of DO2 excursions below predefined DO2 thresholds and the amount of time spent below them. Strokes were defined radiographically using computed tomography and magnetic resonance imaging. MEASUREMENTS AND MAIN RESULTS: Forty-three adults were included (median age 65 y, interquartile range 59-72). Three patients experienced strokes (imaged at 2, 7, and 8 d postoperatively). Most patients underwent isolated coronary artery bypass grafting (41%, 18 patients) or isolated aortic valve replacement (30%, 13). Median UCH-L1 levels differed from baseline to 6 and 24 hours after CPB (40, 232, and 166 pg/mL, respectively; p < 0.001). On multivariable linear regression analysis controlling for baseline and surgical variables, only DO2 AUC <225 was significantly associated with 6-hour UCH-L1 levels (p = 0.001), whereas only DO2 AUC <300 was significantly associated with 24- hour levels (p < 0.001). The 3 patients who experienced radiographic strokes had nonsignificantly elevated 24-hour UCH-L1 levels compared with control patients (585 v 151 pg/mL, p = 0.11). CONCLUSIONS: This is the first study to demonstrate an independent association between DO2 during CPB and elevations of a brain injury biomarker; additional study is needed to clarify the clinical significance of these results.


Assuntos
Isquemia Encefálica/sangue , Ponte Cardiopulmonar/métodos , Complicações Intraoperatórias/sangue , Monitorização Intraoperatória/métodos , Oxigênio/metabolismo , Ubiquitina Tiolesterase/sangue , Idoso , Biomarcadores/sangue , Isquemia Encefálica/diagnóstico , Isquemia Encefálica/etiologia , Procedimentos Cirúrgicos Cardíacos/métodos , Ensaio de Imunoadsorção Enzimática , Feminino , Seguimentos , Humanos , Complicações Intraoperatórias/diagnóstico , Complicações Intraoperatórias/etiologia , Masculino , Pessoa de Meia-Idade , Prognóstico , Estudos Retrospectivos , Fatores de Tempo
12.
J Arthroplasty ; 33(10): 3211-3214, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29908797

RESUMO

BACKGROUND: Routine laboratory studies are often obtained following total hip arthroplasty (THA). Moreover, laboratory studies are often continued daily until the patient is discharged regardless of medical management. The purpose of this study was to investigate the use of routine complete blood count (CBC) tests following THA. Secondarily, the purpose was to identify patient factors associated with abnormal postoperative lab values. METHODS: This retrospective review identified 352 patients who underwent primary THA at a single institution from 2012 to 2014. Preoperative and postoperative CBC values were collected along with demographic data, use of tranexamic acid (TXA), and transfusion rates. Logistic regression models were used to identify factors associated with an abnormal postoperative lab and risk of transfusion. RESULTS: Of the 352 patients, 54 patients were transfused (15.3%). Patients who underwent transfusion had a significantly lower preoperative hemoglobin (Hb; 12.0 g/dL) compared to patients who did not undergo transfusion (13.5 g/dL; P < .001). Patients who did not receive TXA were 3.7 times more likely to receive a transfusion. No patients received medical intervention based on the outcome of postoperative platelet or white blood counts. A Hb value below 11.94 g/dL for patients who are anemic preoperative or did not receive TXA predicted transfusion after postoperative day 1. CONCLUSION: Under value-based care models, cost containment while maintaining high-quality patient care is critical. Routine postoperative CBC tests in patients with a normal preoperative Hb who receive TXA do not contribute to actionable information. Patients who are anemic before THA or do not receive TXA should at minimum obtain a CBC on postoperative day 1.


Assuntos
Artroplastia de Quadril , Contagem de Células Sanguíneas , Testes Diagnósticos de Rotina , Adulto , Idoso , Idoso de 80 Anos ou mais , Anemia/diagnóstico , Antifibrinolíticos/administração & dosagem , Perda Sanguínea Cirúrgica , Transfusão de Sangue , Feminino , Hemoglobinas/análise , Humanos , Masculino , Pessoa de Meia-Idade , Cuidados Pós-Operatórios , Estudos Retrospectivos , Fatores de Risco , Ácido Tranexâmico/administração & dosagem , Adulto Jovem
13.
Popul Health Manag ; 21(5): 357-365, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29393824

RESUMO

Accountable Care Organizations (ACOs), like other care entities, must be strategic about which initiatives they support in the quest for higher value. This article reviews the current strategic planning process for the Johns Hopkins Medicine Alliance for Patients (JMAP), a Medicare Shared Savings Program Track 1 ACO. It reviews the 3 focus areas for the 2017 strategic review process - (1) optimizing care coordination for complex, at-risk patients, (2) post-acute care, and (3) specialty care integration - reviewing cost savings and quality improvement opportunities, associated best practices from the literature, and opportunities to leverage and advance existing ACO and health system efforts in each area. It then reviews the ultimate selection of priorities for the coming year and early thoughts on implementation. After the robust review process, key stakeholders voted to select interventions targeted at care coordination, post-acute care, and specialty integration including Part B drug and imaging costs. The interventions selected incorporate a mixture of enhancing current ACO initiatives, working collaboratively and synergistically on other health system initiatives, and taking on new projects deemed targeted, cost-effective, and manageable in scope. The annual strategic review has been an essential and iterative process based on performance data and informed by the collective experience of other organizations. The process allows for an evidence-based strategic plan for the ACO in pursuit of the best care for patients.


Assuntos
Organizações de Assistência Responsáveis , Atenção à Saúde , Medicare , Guias de Prática Clínica como Assunto , Organizações de Assistência Responsáveis/economia , Organizações de Assistência Responsáveis/estatística & dados numéricos , Atenção à Saúde/economia , Atenção à Saúde/estatística & dados numéricos , Humanos , Medicare/economia , Medicare/estatística & dados numéricos , Melhoria de Qualidade , Estados Unidos
14.
Ann Thorac Surg ; 105(2): e51-e53, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29362191

RESUMO

We describe the novel use of bilateral cardiac sympathectomy in a woman with end-stage heart failure caused by ventricular tachycardia refractory to standard medical therapy who was under consideration for heart transplantation. Postoperatively, our patient has not experienced any symptoms of ventricular tachycardia, has returned to normal physical activity, and is no longer under consideration for transplantation as a result of the improvement in her cardiac function. Bilateral sympathectomy can be more effective than unilateral sympathectomy or percutaneous stellate ganglion blockade in patients with refractory ventricular tachycardia. Careful patient selection is necessary to identify patients who will benefit most from the procedure.


Assuntos
Antiarrítmicos/efeitos adversos , Resistência a Medicamentos , Insuficiência Cardíaca/cirurgia , Simpatectomia/métodos , Taquicardia Ventricular/cirurgia , Eletrocardiografia , Insuficiência Cardíaca/complicações , Humanos , Masculino , Pessoa de Meia-Idade , Taquicardia Ventricular/tratamento farmacológico , Taquicardia Ventricular/etiologia
15.
Heart Surg Forum ; 21(6): E489-E496, 2018 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-30604674

RESUMO

BACKGROUND: Atrial fibrillation (AF) is common after cardiac surgery and contributes to increased morbidity and mortality. Our objective was to derive and validate a predictive model for AF after CABG in patients, incorporating novel echocardiographic and laboratory values. METHODS: We retrospectively reviewed patients at our institution without preexisting dysrhythmia who underwent on-pump, isolated CABG from 2011-2015. The primary outcome was new onset AF lasting >1 hour on continuous telemetry or requiring medical treatment. Patients with a preoperative echocardiographic measurement of left atrial diameter were included in a risk model, and were randomly divided into derivation (80%) and validation (20%) cohorts. The predictors of AF after CABG (PAFAC) score was derived from a multivariable logistic regression model by multiplying the adjusted odds ratios of significant risk factors (P < .05) by a factor of 4 to derive an integer point system. RESULTS: 1307 patients underwent isolated CABG, including 762/1307 patients with a preoperative left atrial diameter measurement. 209/762 patients (27%) developed new onset AF including 165/611 (27%) in the derivation cohort. We identified four risk factors independently associated with postoperative AF which comprised the PAFAC score: age > 60 years (5 points), White race (5 points), baseline GFR < 90 mL/min (4 points) and left atrial diameter > 4.5 cm (4 points). Scores ranged from 0-18. The PAFAC score was then applied to the validation cohort and predicted incidence of AF strongly correlated with observed incidence (r = 0.92). CONCLUSION: The PAFAC score is easy to calculate and can be used upon ICU admission to reliably identify patients at high risk of developing AF after isolated CABG.


Assuntos
Fibrilação Atrial/etiologia , Ponte de Artéria Coronária/efeitos adversos , Medição de Risco/métodos , Fibrilação Atrial/diagnóstico , Ponte de Artéria Coronária/métodos , Feminino , Humanos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Complicações Pós-Operatórias , Estudos Retrospectivos , Fatores de Risco
16.
Pac Symp Biocomput ; 23: 133-144, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29218876

RESUMO

Our knowledge of the biological mechanisms underlying complex human disease is largely incomplete. While Semantic Web technologies, such as the Web Ontology Language (OWL), provide powerful techniques for representing existing knowledge, well-established OWL reasoners are unable to account for missing or uncertain knowledge. The application of inductive inference methods, like machine learning and network inference are vital for extending our current knowledge. Therefore, robust methods which facilitate inductive inference on rich OWL-encoded knowledge are needed. Here, we propose OWL-NETS (NEtwork Transformation for Statistical learning), a novel computational method that reversibly abstracts OWL-encoded biomedical knowledge into a network representation tailored for network inference. Using several examples built with the Open Biomedical Ontologies, we show that OWL-NETS can leverage existing ontology-based knowledge representations and network inference methods to generate novel, biologically-relevant hypotheses. Further, the lossless transformation of OWL-NETS allows for seamless integration of inferred edges back into the original knowledge base, extending its coverage and completeness.


Assuntos
Ontologias Biológicas/estatística & dados numéricos , Algoritmos , Biologia Computacional/métodos , Humanos , Internet , Bases de Conhecimento , Idioma , Aprendizado de Máquina , Modelos Biológicos , Semântica
17.
Pac Symp Biocomput ; 23: 566-577, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29218915

RESUMO

Most natural language processing applications exhibit a trade-off between precision and recall. In some use cases for natural language processing, there are reasons to prefer to tilt that trade-off toward high precision. Relying on the Zipfian distribution of false positive results, we describe a strategy for increasing precision, using a variety of both pre-processing and post-processing methods. They draw on both knowledge-based and frequentist approaches to modeling language. Based on an existing high-performance biomedical concept recognition pipeline and a previously published manually annotated corpus, we apply this hybrid rationalist/empiricist strategy to concept normalization for eight different ontologies. Which approaches did and did not improve precision varied widely between the ontologies.


Assuntos
Processamento de Linguagem Natural , Ontologias Biológicas/estatística & dados numéricos , Biologia Computacional/métodos , Mineração de Dados/métodos , Registros Eletrônicos de Saúde/estatística & dados numéricos , Reações Falso-Positivas , Humanos , Medicina de Precisão/estatística & dados numéricos , PubMed/estatística & dados numéricos , Reprodutibilidade dos Testes
18.
BMC Bioinformatics ; 18(1): 372, 2017 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-28818042

RESUMO

BACKGROUND: Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations. RESULTS: The corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases. The OntoNotes annotation guidelines, with minor adaptations, were used. Interannotator agreement ranges from 0.480 (entity-based CEAF) to 0.858 (Class-B3), depending on the metric that is used to assess it. The resulting corpus adds nearly 30,000 annotations to the previous release of the CRAFT corpus. Differences from related projects include a much broader definition of markables, connection to extensive annotation of several domain-relevant semantic classes, and connection to complete syntactic annotation. Tool performance was benchmarked on the data. A publicly available out-of-the-box, general-domain coreference resolution system achieved an F-measure of 0.14 (B3), while a simple domain-adapted rule-based system achieved an F-measure of 0.42. An ensemble of the two reached F of 0.46. Following the IDENTITY chains in the data would add 106,263 additional named entities in the full 97-paper corpus, for an increase of 76% percent in the semantic classes of the eight ontologies that have been annotated in earlier versions of the CRAFT corpus. CONCLUSIONS: The project produced a large data set for further investigation of coreference and coreference resolution in the scientific literature. The work raised issues in the phenomenon of reference in this domain and genre, and the paper proposes that many mentions that would be considered generic in the general domain are not generic in the biomedical domain due to their referents to specific classes in domain-specific ontologies. The comparison of the performance of a publicly available and well-understood coreference resolution system with a domain-adapted system produced results that are consistent with the notion that the requirements for successful coreference resolution in this genre are quite different from those of the general domain, and also suggest that the baseline performance difference is quite large.


Assuntos
Mineração de Dados/métodos , Publicações Periódicas como Assunto , Semântica
19.
Ann Thorac Surg ; 104(1): 169, 2017 07.
Artigo em Inglês | MEDLINE | ID: mdl-28633220
20.
Anesth Analg ; 125(1): 38-43, 2017 07.
Artigo em Inglês | MEDLINE | ID: mdl-28614129

RESUMO

BACKGROUND: Both patient characteristics and intraoperative factors have been associated with a higher risk of stroke after cardiac surgery. We hypothesized that poor systemic oxygenation in the perioperative period is associated with increased risk of stroke following cardiopulmonary bypass. METHODS: In this study of 251 adult patients who underwent cardiopulmonary bypass procedures at a single center from 2003 to 2006, cases (patients with a postoperative stroke at least 24 hours after surgery) were matched 1:2 to controls without stroke. Minimum and average partial pressure of oxygen in arterial blood (PaO2) values, from arterial blood gas values during and up to 24 hours after surgery, were evaluated as continuous and categorical predictors. Conditional logistic regression models adjusted for potential confounders (demographics, comorbidities, and intraoperative variables) were used to evaluate associations between PaO2 variables and stroke status. RESULTS: Lower nadir PaO2 values were associated with postoperative stroke, with estimated odds of stroke increasing over 20% (adjusted odds ratio [OR], 1.23; 95% confidence interval [CI], 1.07-1.41) per 10 mm Hg lower nadir PaO2, and similarly increased odds of stroke per lower quartile of nadir PaO2 (OR, 1.60; 95% CI, 1.19-2.16). When average PaO2 was considered, odds of stroke was also increased (adjusted OR, 1.39 per lower quartile of mean PaO2; 95% CI, 1.05-1.83). Having a nadir PaO2 value in the lowest versus any other quartile was associated with an estimated 2.41-fold increased odds of stroke (95% CI, 1.22-4.78). Quartile of nadir but not average PaO2 results remained significant after adjustment for multiple comparisons. CONCLUSIONS: Odds of stroke after cardiac surgery are increased in patients with a low minimum PaO2 within 24 hours of surgery. Results should be validated in an independent cohort. Further characterizing the underlying etiology of hypoxic episodes will be important to improve patient outcomes.


Assuntos
Procedimentos Cirúrgicos Cardíacos/efeitos adversos , Hipóxia/sangue , Oxigênio/sangue , Acidente Vascular Cerebral/etiologia , Idoso , Baltimore , Biomarcadores/sangue , Gasometria , Ponte Cardiopulmonar/efeitos adversos , Distribuição de Qui-Quadrado , Bases de Dados Factuais , Feminino , Humanos , Hipóxia/diagnóstico , Hipóxia/etiologia , Modelos Lineares , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Monitorização Intraoperatória/métodos , Dinâmica não Linear , Razão de Chances , Pressão Parcial , Período Perioperatório , Estudos Retrospectivos , Medição de Risco , Fatores de Risco , Acidente Vascular Cerebral/sangue , Acidente Vascular Cerebral/diagnóstico , Fatores de Tempo , Resultado do Tratamento
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