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1.
BMC Med Inform Decis Mak ; 21(1): 182, 2021 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-34098959

RESUMO

BACKGROUND: Early diagnosis for the diabetes complications is clinically demanding with great significancy. Regarding the complexity of diabetes complications, we applied a multi-label classification (MLC) model to predict four diabetic complications simultaneously using data in the modern electronic health records (EHRs), and leveraged the correlations between the complications to further improve the prediction accuracy. METHODS: We obtained the demographic characteristics and laboratory data from the EHRs for patients admitted to Changzhou No. 2 People's Hospital, the affiliated hospital of Nanjing Medical University in China from May 2013 to June 2020. The data included 93 biochemical indicators and 9,765 patients. We used the Pearson correlation coefficient (PCC) to analyze the correlations between different diabetic complications from a statistical perspective. We used an MLC model, based on the Random Forest (RF) technique, to leverage these correlations and predict four complications simultaneously. We explored four different MLC models; a Label Power Set (LP), Classifier Chains (CC), Ensemble Classifier Chains (ECC), and Calibrated Label Ranking (CLR). We used traditional Binary Relevance (BR) as a comparison. We used 11 different performance metrics and the area under the receiver operating characteristic curve (AUROC) to evaluate these models. We analyzed the weights of the learned model and illustrated (1) the top 10 key indicators of different complications and (2) the correlations between different diabetic complications. RESULTS: The MLC models including CC, ECC and CLR outperformed the traditional BR method in most performance metrics; the ECC models performed the best in Hamming loss (0.1760), Accuracy (0.7020), F1_Score (0.7855), Precision (0.8649), F1_micro (0.8078), F1_macro (0.7773), Recall_micro (0.8631), Recall_macro (0.8009), and AUROC (0.8231). The two diabetic complication correlation matrices drawn from the PCC analysis and the MLC models were consistent with each other and indicated that the complications correlated to different extents. The top 10 key indicators given by the model are valuable in medical application. CONCLUSIONS: Our MLC model can effectively utilize the potential correlation between different diabetic complications to further improve the prediction accuracy. This model should be explored further in other complex diseases with multiple complications.


Assuntos
Complicações do Diabetes , Diabetes Mellitus , China , Atenção à Saúde , Complicações do Diabetes/diagnóstico , Diabetes Mellitus/diagnóstico , Registros Eletrônicos de Saúde , Humanos , Curva ROC
2.
Zhonghua Er Ke Za Zhi ; 59(6): 471-477, 2021 Jun 02.
Artigo em Chinês | MEDLINE | ID: mdl-34102820

RESUMO

Objective: To explore the consistency of peripheral whole blood and venous serum procalcitonin (PCT) levels, and the value of peripheral whole blood PCT in evaluating pediatric bacterial infection. Methods: This multicenter cross-sectional parallel control study was conducted in 11 children's hospital. All the 1 898 patients older than 28 days admitted to these hospitals from March 2018 to February 2019 had their peripheral whole blood and venous serum PCT detected simultaneously with unified equipment, reagent and method. According to the venous serum PCT level, the patients were stratified to subgroups. Analysis of variance and chi-square test were used to compare the demographic characteristics among groups. And the correlation between the peripheral blood and venous serum PCT level was investigated by quantitative Pearson correlation analysis.The PCT resultes were also converted into ranked data to further test the consistency between the two sampling methods by Spearman's rank correlation test. Furthermore, the ranked data were converted into binary data to evaluate the consistency and investigate the best cut-off of peripheral blood PCT level in predicting bacterial infection. Results: A total of 1 898 valid samples were included (1 098 males, 800 females),age 27.4(12.2,56.7) months. There was a good correlation between PCT values of peripheral whole blood and venous serum (r=0.97, P<0.01). The linear regression equation was PCTvenous serum=0.135+0.929×PCTperipheral whole blood. However, when stratified to 5 levels, PCT results showed diverse and unsatisfied consistency between the two sampling methods (r=0.51-0.92, all P<0.01). But after PCT was converted to ordinal categorical variables, the stratified analysis showed that the coincidence rate of the measured values by the two sampling methods in each boundary area was 84.9%-97.1%. The dichotomous variables also showed a good consistency (coincidence rate 96.8%-99.3%, Youden index 0.82-0.89). According to the severity of disease, the serum PCT value was classified into 4 intervals(<0.5、0.5-<2.0、2.0-<10.0、≥10.0 µg/L), and the peripheral blood PCT value also showed a good predictive value (AUC value was 0.991 2-0.997 9). The optimal cut points of peripheral whole blood PCT value 0.5、1.0、2.0、10.0 µg/L corresponding to venous serum PCT values were 0.395, 0.595, 1.175 and 3.545 µg/L, respectively. Conclusions: There is a good correlation between peripheral whole blood PCT value and the venous serum PCT value, which means that the peripheral whole blood PCT could facilitate the identification of infection and clinical severity. Besides, the sampling of peripheral whole blood is simple and easy to repeat.


Assuntos
Pró-Calcitonina , Sepse , Adulto , Biomarcadores , Proteína C-Reativa , Calcitonina , Criança , Estudos Transversais , Feminino , Humanos , Masculino , Prognóstico , Curva ROC , Estudos Retrospectivos
3.
Zhonghua Er Ke Za Zhi ; 59(6): 489-494, 2021 Jun 02.
Artigo em Chinês | MEDLINE | ID: mdl-34102823

RESUMO

Objective: To investigate the predictive value of lactate concentration within 1 h after admission combined with lactate clearance rate (LC) at 6 h after fluid resuscitation in prognosis of neonatal septic shock. Methods: In this retrospective study, 58 newborns with septic shock admitted to the Neonatal Intensive Care Unit of Xi'an Children's Hospital,Xi'an Jiao Tong University from June 2016 to March 2020 were enrolled. According to the mortality within 60 days after admission,which was also set as the end point, the patients were divided into death group and survival group. The general demographic data and clinical variables including blood cell counts, procalcitonin, C-reactive protein, D-dimer, serum creatinine, and lactate concentration within 1 h after admission (Lac1) and at 6 h after fluid resuscitation (Lac2) were collected. The differences in the clinical variables between the survival and death group were compared by independent sample t test or Rank-Sum test, and the risk factors of poor prognosis were analyzed by binary Logistic regression. The predictive values of these risk factors were tested by receiver operating characteristic (ROC) curve. Furthermore, the cut-off of the risk factors were used to analyze the accumulative survival rate by Kaplan-Meier curve. Results: A total of 58 neonates were enrolled, among whom 24 survived and 34 died within 60 days after admission. The rate of premature rupture of membranes in the death group was higher than that in the survival group (41% (14/34) vs.13%(3/24), P=0.021). There were also significant differences in infection site, pathogenic characteristics, total fluid volume of resuscitation, vasoactive drug index, rate and complications of mechanical ventilation between the two groups (all P<0.05). The levels of Lac1, Lac2, procalcitonin, D-dimer and serum creatinine in the death group were higher than those in the survival group ((12±6) vs. (7±4) mmol/L, (14±6) vs. (4±2) mmol/L, (59±23) vs.(24±14) ng/L, (24±11) vs.(11±6) mg/L, (167±31) vs.(92±23) µmol/L, t=3.549, 3.112, 3.859, 4.499, 3.288, all P<0.05). While the blood pressure and LC at 6 h after fluid resuscitation were lower than those in the survival group ((41±12) vs. (52±5) mmHg (1 mmHg=0.133 kPa), t =4.230;-16 (-40, 20) % vs. 40 (18, 70) %, Z= 3.558, all P<0.05). Binary Logistic regression analysis showed that LC was negatively associated with the risk of death in neonates with septic shock (odds ratio (OR) and 95% confidence interval (CI): 0.679 (0.662-0.999), P<0.05), while Lac1 was the risk factor and positively associated with the risk of death (OR and 95% CI: 1.203 (0.965-1.500), P<0.05). Furthermore, the predictive values of LC, Lac1 and the combination of these two variables in the prognosis of neonatal septic shock were analyzed by ROC curve analysis, and the area under the curve (AUC) were 0.699, 0.875, 0.965, respectively, with the sensitivity of 83.32%, 89.65% and 94.31%, and the specificity of 72.52%, 77.18% and 88.76%, respectively. According to the cut-off value of Lac1, the newborns with Lac1>4 mmol/L had significantly lower accumulative survival rate than those with Lac1≤4 mmol/L by Kaplan-Meier analysis (21% (8/38) vs. 80% (16/20), χ²=54.520, P<0.05). According to the cut-off value of LC, the newborns with LC ≤ 10% had significantly lower accumulative survival rate than those with LC>10% by Kaplan-Meier analysis (19% (6/32) vs. 69% (18/26), χ²=14.140, P<0.05). Conclusion: The combination of lactate concentration and lactate clearance rate have an optimal predictive value in the prognosis of neonatal septic shock.


Assuntos
Choque Séptico , Criança , Humanos , Recém-Nascido , Ácido Láctico , Pró-Calcitonina , Prognóstico , Curva ROC , Estudos Retrospectivos
4.
World J Gastroenterol ; 27(21): 2910-2920, 2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34135561

RESUMO

BACKGROUND: Persistent liver inflammatory damage is the main risk factor for developing liver fibrosis, cirrhosis, and even hepatocellular carcinoma in chronic hepatitis B (CHB) patients. Thus, accurate prediction of the degree of liver inflammation is a high priority and a growing medical need. AIM: To build an effective and robust non-invasive model for predicting hepatitis B-related hepatic inflammation. METHODS: A total of 650 treatment-naïve CHB (402 HBeAg-positive and 248 HBeAg-negative) patients who underwent liver biopsy were enrolled in this study. Histological inflammation grading was assessed by the Ishak scoring system. Serum quantitative hepatitis B core antibody (qAnti-HBc) levels and 21 immune-related inflammatory factors were measured quantitatively using a chemiluminescent microparticle immunoassay. A backward feature elimination (BFE) algorithm utilizing random forest (RF) was used to select optional features and construct a combined model. The diagnostic abilities of the model or variables were evaluated based on the estimated area under the receiver operating characteristics curve (AUROC) and compared using the DeLong test. RESULTS: Four features were selected to predict moderate-to-severe inflammation in CHB patients using the RF-BFE method. These predictive features included qAnti-HBc, ALT, AST, and CXCL11. Spearman's correlation analysis indicated that serum qAnti-HBc, ALT, AST, and CXCL11 levels were positively correlated with the histology activity index (HAI) score. These selected features were incorporated into the model to establish a novel model named I-3A index. The AUROC [0.822; 95% confidence interval (CI): 0.790-0.851] of the I-3A index was significantly increased compared with qAnti-HBc alone (0.760, 95%CI: 0.724-0.792, P < 0.0001) in all CHB patients. The use of an I-3A index cutoff value of 0.41 produced a sensitivity of 69.17%, specificity of 81.44%, and accuracy of 73.8%. Additionally, the I-3A index showed significantly improved diagnostic performance for predicting moderate-to-severe inflammation in HBeAg-positive and HBeAg-negative CHB patients (0.829, 95%CI: 0.789-0.865 and 0.810, 95%CI: 0.755-0.857, respectively). CONCLUSION: The selected features of the I-3A index constructed using the RF-BFE algorithm can effectively predict moderate-to-severe liver inflammation in CHB patients.


Assuntos
Hepatite B Crônica , Alanina Transaminase , Algoritmos , Biomarcadores , Antígenos E da Hepatite B , Vírus da Hepatite B/genética , Hepatite B Crônica/complicações , Hepatite B Crônica/diagnóstico , Humanos , Inflamação , Cirrose Hepática/diagnóstico , Curva ROC
5.
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue ; 33(5): 568-572, 2021 May.
Artigo em Chinês | MEDLINE | ID: mdl-34112294

RESUMO

OBJECTIVE: To evaluate the diagnostic value of circulating microRNA-1 (miR-1) in early coronary artery plaque rupture in patients with stable coronary artery disease (SCAD). METHODS: A prospective cohort study was conducted. Sixty-seven patients with SCAD admitted to the department of cardiology of the Third Affiliated Hospital of Soochow University from January to June in 2019 were enrolled. All patients had completed coronary angiography (CAG), percutaneous coronary intervention (PCI) single stent implantation or only CAG was performed according to the CAG results. Blood samples were collected before (0 hour) and 3 hours after the procedure. The expression of plasma miR-1 was detected by real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR), and electrocardiogram was used to detect cardiac troponin I (cTnI) levels. The difference of miR-1 and cTnI levels in PCI or CAG patients before and after procedure were compared, and the value for early diagnosis of coronary artery plaque rupture in SCAD patients was evaluated. The diagnostic efficacy was evaluated by the receiver operating characteristic curve (ROC curve). RESULTS: There were 38 CAG patients and 29 PCI patients. There were no significant differences in gender, age, previous history (without hypertension history) and baseline data of cardiac function between the two groups. The expression of miR-1 after PCI was significantly higher than that before PCI [2-ΔΔCt: 2.11 (1.56, 2.73) vs. 1.26 (1.07, 1.92), P < 0.01], and there was no significant difference in cTnI level before and after PCI [µg/L: 0.00 (0.00, 0.02) vs. 0.00 (0.00, 0.02), P > 0.05]. There were no significant differences in miR-1 and cTnI levels before and after procedure in the CAG group [miR-1 (2-ΔΔCt): 1.09 (1.00, 1.40) vs. 1.21 (1.00, 1.71), cTnI (µg/L): 0.00 (0.00, 0.02) vs. 0.00 (0.00, 0.02), both P > 0.05]. ROC curve analysis showed that the area under ROC curve (AUC) and 95% confidence interval (95%CI) of miR-1 in the diagnosis of coronary plaque rupture were 0.794 (0.687-0.900), P < 0.01, the sensitivity was 82.8%, the specificity was 68.4%, and the optimal cut-off value was 1.51. The AUC and 95%CI of the difference of miR-1 before and after operation (ΔmiR-1) were 0.704 (0.567-0.842), P = 0.004, the sensitivity was 62.1%, the specificity was 84.2%, and the optimal cut-off value was 0.39. The efficancy of miR-1 and ΔmiR-1 after procedure to diagnose coronary plaque rupture in patients with SCAD was similar (Z = 1.287, P = 0.198). However, baseline miR-1 might not predict whether patients with SCAD need PCI or not (AUC = 0.630, P > 0.05). Multivariate binary Logistic regression analysis showed that increased postoperative miR-1 expression was an independent risk factor for coronary plaque rupture in SCAD patients [odds ratios (OR) = 2.887, 95%CI was 1.044-7.978, P = 0.041]. CONCLUSIONS: Circulating miR-1 might have the value for early diagnosis of coronary artery plaque rupture in SCAD patients.


Assuntos
MicroRNA Circulante/sangue , Doença da Artéria Coronariana , MicroRNAs/sangue , Placa Aterosclerótica/diagnóstico , Doença da Artéria Coronariana/diagnóstico , Diagnóstico Precoce , Humanos , Intervenção Coronária Percutânea , Estudos Prospectivos , Curva ROC
6.
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue ; 33(5): 573-577, 2021 May.
Artigo em Chinês | MEDLINE | ID: mdl-34112295

RESUMO

OBJECTIVE: To investigate the predictive value of plasma high-sensitivity C-reactive protein/albumin ratio (HCRP/ALB) for the death in patients with acute coronary syndrome (ACS). METHODS: The clinical data of patients with ACS [including unstable angina (UA), non-ST segment elevation myocardial infarction (NSTEMI), ST segment elevation myocardial infarction (STEMI)] admitted to Beijing Anzhen Hospital Affiliated to Capital Medical University from January 2018 to August 2020 were retrospectively analyzed. The plasma HCRP and ALB were recorded and the HCRP/ALB ratio was calculated. Patients were divided into death group and survival group according to the hospital outcome. The differences of baseline data and biochemical indexes between the two groups were compared. Receiver operating characteristic curve (ROC curve) was used to analyze the predictive value of each variable to death. Logistic regression was used to analyze the risk factors of death. RESULTS: Among the 1 722 ACS patients, 74 died in hospital. Comparison of baseline data between death group and survival group showed that the other baseline data were statistically different except for the rate of hyperlipidemia. Among them, patients in death group had higher heart rate (HR), HCRP, B-type natriuretic peptide (BNP), HCRP/ALB [HR (bpm): 89±19 vs. 73±15, HCRP (mg/L): 23.24 (9.79, 33.69) vs. 3.57 (1.03, 14.26), BNP (ng/L): 424.0 (164.3, 1 596.1) vs. 79.0 (31.0, 211.4), HCRP/ALB: 0.700 (0.289, 1.017) vs. 0.089 (0.026, 0.368), all P < 0.01], while ALB was lower (g/L: 35.37±5.16 vs. 39.97±6.43, P < 0.01). ROC curve analysis showed that area under ROC curve and 95% confidence interval [AUC (95%CI)] of BNP, HCRP and HCRP/ALB for predicting death were 0.781 (0.717-0.845), 0.790 (0.724-0.856) and 0.803 (0.738-0.869), respectively. The Youden index of HCRP/ALB was 0.559, and the corresponding HCRP/ALB was 0.246. The patients were divided into low HCRP/ALB group (HCRP/ALB ≤ 0.246, 1 163 cases) and high HCRP/ALB group (HCRP/ALB > 0.246, 559 cases). Except for gender, previous smoking, hypertension and diabetes rates, the other baseline data were statistically different between the two groups. Patients in the high HCRP/ALB group had a higher mortality (10.4% vs. 1.4%, P < 0.01), higher rates of implanted intra-aortic balloon pump (IABP, 12.7% vs. 2.7%, P < 0.01), higher BNP, HCRP, HCRP/ALB [BNP (ng/L): 253.0 (82.8, 749.0) vs. 60.0 (26.0, 145.2), HCRP (mg/L): 25.42±17.47 vs. 2.62±2.43, HCRP/ALB: 0.700±0.435 vs. 0.066±0.062, all P < 0.01], while lower ALB (g/L: 36.89±4.30 vs. 41.17±6.83, P < 0.01). Logistic regression analysis showed that higher HR [odds ratio (OR) = 1.037, 95%CI was 1.020-1.055, P = 0.000] and higher HCRP/ALB (OR = 3.835, 95%CI was 1.612-9.125, P = 0.002) were independent risk factors for the death in ACS patients, while higher ALB could reduce the mortality in ACS patients (OR = 0.884, 95%CI was 0.818-0.957, P = 0.002). CONCLUSIONS: The higher the HCRP/ALB, the higher the risk of death in patients with ACS. When HCRP/ALB is greater than 0.246, the patient has a higher mortality. Therefore, HCRP/ALB in patients with ACS can be used as an effective predictor for death risk.


Assuntos
Síndrome Coronariana Aguda , Proteína C-Reativa , Albumina Sérica , Síndrome Coronariana Aguda/diagnóstico , Síndrome Coronariana Aguda/mortalidade , Proteína C-Reativa/análise , Humanos , Prognóstico , Curva ROC , Estudos Retrospectivos
7.
Sci Rep ; 11(1): 11591, 2021 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078950

RESUMO

Making timely assessments of disease progression in patients with COVID-19 could help offer the best personalized treatment. The purpose of this study was to explore an effective model to predict the outcome of patients with COVID-19. We retrospectively included 188 patients (124 in the training set and 64 in the test set) diagnosed with COVID-19. Patients were divided into aggravation and improvement groups according to the disease progression. Three kinds of models were established, including the radiomics, clinical, and combined model. Receiver operating characteristic curves, decision curves, and Delong's test were used to evaluate and compare the models. Our analysis showed that all the established prediction models had good predictive performance in predicting the progress and outcome of COVID-19.


Assuntos
COVID-19/diagnóstico por imagem , Tomografia Computadorizada por Raios X , Idoso , COVID-19/etiologia , Diagnóstico por Computador/métodos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Modelos Teóricos , Prognóstico , Curva ROC
8.
Eur Rev Med Pharmacol Sci ; 25(10): 3868-3878, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-34109595

RESUMO

OBJECTIVE: This study aimed to compare the mortality rate between advanced-stage non-small cell lung cancer patients (NSCLC) with and without COVID-19. This study also explores the possible laboratory characteristics used for prognostication in patients with NSCLC and COVID-19. Additionally, this study evaluated potential differences in laboratory values between the case and control groups. PATIENTS AND METHODS: This is a single-center retrospective cohort study conducted in Dharmais National Cancer Hospital, Indonesia, enrolling patients with NSCLC undergoing chemotherapy or targeted therapy between May 2020 and January 2021. All patients with NSCLC and COVID-19 in these periods were enrolled into the case group. The control group was age-matched NSCLC patients without COVID-19 that was derived from the NSCLC cohort through randomization. RESULTS: There were 342 patients with NSCLC between May 2020 and January 2021. Twenty-seven (7.9%) of the patients were infected by COVID-19. To facilitate comparison, thirty-five age-matched controls with NSCLC were selected from the cohort. The mortality rate in patients with COVID-19 was 46.2%. Eleven patients (40.7%) had severe COVID-19, of which none survived. NLR >8.35 has a sensitivity of 83.3%, specificity of 92.9%, LR+ of 12, and LR- of 0.18. The AUC was 0.946 (95% CI 0.867-1.000), p<0.001. PLR >29.14 has a sensitivity of 75.0%, specificity of 71.4%, LR+ 2.62, LR- 0.35, and AUC 0.851 (95% CI 0.706-0.996), p=0.002. Both NLR and PLR were associated with shorter time-to-mortality in the unadjusted and adjusted model CONCLUSIONS: NLR and PLR are independent predictors of mortality in COVID-19 patients with NSCLC.


Assuntos
Plaquetas/citologia , COVID-19/diagnóstico , Carcinoma Pulmonar de Células não Pequenas/mortalidade , Neoplasias Pulmonares/mortalidade , Linfócitos/citologia , Neutrófilos/citologia , Idoso , Área Sob a Curva , COVID-19/complicações , COVID-19/virologia , Carcinoma Pulmonar de Células não Pequenas/complicações , Carcinoma Pulmonar de Células não Pequenas/patologia , Feminino , Humanos , Indonésia , Neoplasias Pulmonares/complicações , Neoplasias Pulmonares/patologia , Masculino , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Curva ROC , Estudos Retrospectivos , SARS-CoV-2/isolamento & purificação , Sensibilidade e Especificidade , Taxa de Sobrevida
9.
NPJ Prim Care Respir Med ; 31(1): 33, 2021 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-34083541

RESUMO

Accurate prediction of the risk of progression of coronavirus disease (COVID-19) is needed at the time of hospitalization. Logistic regression analyses are used to interrogate clinical and laboratory co-variates from every hospital admission from an area of 2 million people with sporadic cases. From a total of 98 subjects, 3 were severe COVID-19 on admission. From the remaining subjects, 24 developed severe/critical symptoms. The predictive model includes four co-variates: age (>60 years; odds ratio [OR] = 12 [2.3, 62]); blood oxygen saturation (<97%; OR = 10.4 [2.04, 53]); C-reactive protein (>5.75 mg/L; OR = 9.3 [1.5, 58]); and prothrombin time (>12.3 s; OR = 6.7 [1.1, 41]). Cutoff value is two factors, and the sensitivity and specificity are 96% and 78% respectively. The area under the receiver-operator characteristic curve is 0.937. This model is suitable in predicting which unselected newly hospitalized persons are at-risk to develop severe/critical COVID-19.


Assuntos
COVID-19/diagnóstico , Hospitalização/estatística & dados numéricos , Adolescente , Adulto , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Proteína C-Reativa/análise , COVID-19/patologia , Criança , Pré-Escolar , Progressão da Doença , Feminino , Humanos , Lactente , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Oxigênio/sangue , Prognóstico , Tempo de Protrombina , Curva ROC , Medição de Risco , Sensibilidade e Especificidade , Adulto Jovem
10.
Medicine (Baltimore) ; 100(22): e25878, 2021 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-34087829

RESUMO

ABSTRACT: The study aimed to explore the value of ultrasound (US) texture analysis in the differential diagnosis of triple-negative breast cancer (TNBC) and non-TNBC.Retrospective analysis was done on 93 patients with breast cancer (35 patients with TNBC and 38 patients with non-TNBC) who were admitted to Taizhou people's hospital from July 2015 to June 2019. All lesions were pathologically proven at surgery. US images of all patients were collected. Texture analysis of US images was performed using MaZda software package. The differences between textural features in TNBC and non-TNBC were assessed. Receiver operating characteristic curve analysis was used to compare the diagnostic performance of textural parameters showing significant difference.Five optimal texture feature parameters were extracted from gray level run-length matrix, including gray level non-uniformity (GLNU) in horizontal direction, vertical gray level non-uniformity, GLNU in the 45 degree direction, run length non-uniformity in 135 degree direction, GLNU in the 135 degree direction. All these texture parameters were statistically higher in TNBC than in non-TNBC (P <.05). Receiver operating characteristic curve analysis indicated that at a threshold of 268.9068, GLNU in horizontal direction exhibited best diagnostic performance for differentiating TNBC from non-TNBC. Logistic regression model established based on all these parameters showed a sensitivity of 69.3%, specificity of 91.4% and area under the curve of 0.834.US texture features were significantly different between TNBC and non-TNBC, US texture analysis can be used for preliminary differentiation of TNBC from non-TNBC.


Assuntos
Neoplasias da Mama/diagnóstico por imagem , Neoplasias da Mama/patologia , Processamento de Imagem Assistida por Computador/métodos , Ultrassonografia/métodos , Adulto , Idoso , Idoso de 80 Anos ou mais , Neoplasias da Mama/cirurgia , Feminino , Humanos , Pessoa de Meia-Idade , Curva ROC , Estudos Retrospectivos , Neoplasias de Mama Triplo Negativas/diagnóstico por imagem , Neoplasias de Mama Triplo Negativas/patologia
11.
Int J Mol Sci ; 22(11)2021 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-34072601

RESUMO

The high mortality rate in septic shock patients is likely due to environmental and genetic factors, which influence the host response to infection. Two genome-wide association studies (GWAS) on 832 septic shock patients were performed. We used integrative bioinformatic approaches to annotate and prioritize the sepsis-associated single nucleotide polymorphisms (SNPs). An association of 139 SNPs with death based on a false discovery rate of 5% was detected. The most significant SNPs were within the CISH gene involved in cytokine regulation. Among the 139 SNPs associated with death and the 1311 SNPs in strong linkage disequilibrium with them, we investigated 1439 SNPs within non-coding regions to identify regulatory variants. The highest integrative weighted score (IW-score) was obtained for rs143356980, indicating that this SNP is a robust regulatory candidate. The rs143356980 region is located in a non-coding region close to the CISH gene. A CRISPR-Cas9-mediated deletion of this region and specific luciferase assays in K562 cells showed that rs143356980 modulates the enhancer activity in K562 cells. These analyses allowed us to identify several genes associated with death in patients with septic shock. They suggest that genetic variations in key genes, such as CISH, perturb relevant pathways, increasing the risk of death in sepsis patients.


Assuntos
Elementos Facilitadores Genéticos , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Choque Séptico/etiologia , Choque Séptico/mortalidade , Proteínas Supressoras da Sinalização de Citocina/genética , Alelos , Biomarcadores , Biologia Computacional/métodos , Humanos , Interleucina-6/sangue , Anotação de Sequência Molecular , Polimorfismo de Nucleotídeo Único , Prognóstico , Mapeamento de Interação de Proteínas , Mapas de Interação de Proteínas , Curva ROC , Sequências Reguladoras de Ácido Nucleico , Reprodutibilidade dos Testes , Choque Séptico/metabolismo
12.
Int J Mol Sci ; 22(9)2021 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-34067072

RESUMO

Numbers of patients with coronavirus disease 2019 (COVID-19) have increased rapidly worldwide. Plasma levels of full-length galectin-9 (FL-Gal9) and osteopontin (FL-OPN) as well as their truncated forms (Tr-Gal9, Ud-OPN, respectively), are representative inflammatory biomarkers. Here, we measured FL-Gal9, FL-OPN, Tr-Gal9, and Ud-OPN in 94 plasma samples obtained from 23 COVID-19-infected patients with mild clinical symptoms (CV), 25 COVID-19 patients associated with pneumonia (CP), and 14 patients with bacterial infection (ID). The four proteins were significantly elevated in the CP group when compared with healthy individuals. ROC analysis between the CV and CP groups showed that C-reactive protein had the highest ability to differentiate, followed by Tr-Gal9 and ferritin. Spearman's correlation analysis showed that Tr-Gal9 and Ud-OPN but not FL-Gal9 and FL-OPN, had a significant association with laboratory markers for lung function, inflammation, coagulopathy, and kidney function in CP patients. CP patients treated with tocilizumab had reduced levels of FL-Gal9, Tr-Gal9, and Ud-OPN. It was suggested that OPN is cleaved by interleukin-6-dependent proteases. These findings suggest that the cleaved forms of OPN and galectin-9 can be used to monitor the severity of pathological inflammation and the therapeutic effects of tocilizumab in CP patients.


Assuntos
COVID-19/sangue , Galectinas/sangue , Osteopontina/sangue , Pneumonia/sangue , Síndrome Respiratória Aguda Grave/sangue , Adulto , Idoso , Idoso de 80 Anos ou mais , Anticorpos Monoclonais Humanizados/uso terapêutico , Biomarcadores/metabolismo , COVID-19/tratamento farmacológico , COVID-19/fisiopatologia , Feminino , Humanos , Inflamação/metabolismo , Rim/metabolismo , Rim/patologia , Rim/virologia , Masculino , Pessoa de Meia-Idade , Pneumonia/complicações , Pneumonia/tratamento farmacológico , Pneumonia/virologia , Curva ROC , Síndrome Respiratória Aguda Grave/complicações , Síndrome Respiratória Aguda Grave/tratamento farmacológico , Síndrome Respiratória Aguda Grave/virologia , Índice de Gravidade de Doença , Adulto Jovem
13.
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue ; 33(5): 557-562, 2021 May.
Artigo em Chinês | MEDLINE | ID: mdl-34112292

RESUMO

OBJECTIVE: To explore the value of radiographic assessment of lung edema (RALE) score in evaluating the severity and prognosis of patients with acute respiratory distress syndrome (ARDS). METHODS: A retrospective study was conducted. Patients with ARDS admitted to the department of intensive care unit (ICU) of Affiliated Nantong Third Hospital of Nantong University from January 2016 to November 2020 were enrolled. Clinical data of those patients were collected, and two senior radiologists who did not know the outcome of the patients independently scored each chest radiograph, the mean value of which was taken as the RALE score. The patients were divided into death group and survival group according to the 28-day prognosis. The differences of the basic data, PaO2/FiO2, sequential organ failure assessment (SOFA) score, acute physiology and chronic health evaluation II (APACHE II) score and RALE score between groups were analyzed. ARDS patients were classified according to the Berlin standard and RALE scores were compared between groups. Then, the correlations between RALE score and PaO2/FiO2, SOFA score, APACHE II score were analyzed. The prognostic capacity of RALE score for 28-day prognosis of ARDS patients were analyzed by Kaplan-Meier survival curve. RESULTS: Of the 98 ARDS patients, 62 were included in the final analysis, 39 patients survived and 23 patients died. The 28-day mortality was 37.1%. Compared with the survival group, patients in the death group were older (years old: 72.83±12.21 vs. 64.44±14.68), had lower PaO2/FiO2 [mmHg (1 mmHg = 0.133 kPa): 122.66±48.32 vs. 150.26±50.40], and higher SOFA score and greater difference of RALE score between the third day and the first day after admission (D3-D1 RALE score) (SOFA score: 11.26±3.91 vs. 9.04±3.72, D3-D1 RALE score: 1.35±6.42 vs. -2.74±7.35), with statistically significant differences (all P < 0.05). However, there were no significant differences in gender, cause of ARDS, APACHE II score, and RALE scores on the first and the third day of admission (D1 RALE, D3 RALE) between the two groups. Among the 62 patients, there were 11 mild cases (17.7%), 36 moderate cases (58.1%), and 15 severe cases (24.2%). The D1 RALE score of patients with mild and moderate ARDS were lower than those of patients with severe ARDS (19.09±3.65, 22.58±6.79 vs. 27.07±5.23, both P < 0.05). Correlation analysis showed that D1 RALE score was negatively correlated with PaO2/FiO2 (r = -0.385, P = 0.002), and positively correlated with SOFA score and APACHE II score (r1 = 0.433, r2 = 0.442, both P < 0.001). Kaplan-Meier survival curve analysis showed that the 28-day survival rate of ARDS patients in D3-D1 RALE score ≥ -1 group was significantly higher than that in D3-D1 RALE score < -1 group (73.08% vs. 55.56%; log-rank test: χ2 = 3.979, P = 0.046). CONCLUSIONS: The RALE score is a simple and reliable non-invasive evaluation index, which can be used to evaluate the severity of ARDS patients. The difference of RALE score in early stage is helpful to identify ARDS patients with poor prognosis.


Assuntos
Síndrome do Desconforto Respiratório , Berlim , Edema , Humanos , Unidades de Terapia Intensiva , Pulmão , Prognóstico , Curva ROC , Síndrome do Desconforto Respiratório/diagnóstico por imagem , Estudos Retrospectivos
14.
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue ; 33(5): 582-586, 2021 May.
Artigo em Chinês | MEDLINE | ID: mdl-34112297

RESUMO

OBJECTIVE: To investigate the correlation of monocyte/lymphocyte ratio (MLR) with the prognosis and adverse event in critically ill patients. METHODS: Basic information of patients were extracted from Medical Information Mart for Intensive Care-III (MIMIC-III), including demographics, blood routine, biochemical indexes, systemic inflammatory response syndrome score (SIRS), sequential organ failure assessment (SOFA) score, and outcome, etc. MLR on the first day of intensive care unit (ICU) admission was calculated. The receiver operating characteristic curve (ROC curve) was applied to evaluate the prognostic value of MLR on the 30-day mortality and its cut-off value. According to the cut-off value, the patients were divided into two groups, and the differences between the groups were compared. Logistic regression model was used to analyze the relationship of MLR with 30-day mortality, continuous renal replacement therapy (CRRT), mechanical ventilation, the length of ICU stay, and total hospitalization time. RESULTS: (1) A total of 43 174 critically ill patients were included. ROC curve showed that area under ROC curve (AUC) of MLR in predicting 30-day mortality was 0.655 [95% confidence interval (95%CI) was 0.632-0.687]. The cut-off value of MLR calculated according to the maximum Yoden index was 0.5. There were 16 948 patients with MLR ≥ 0.5 (high MLR group) and 26 226 patients with MLR < 0.5 (low MLR group). (2) Compared with the low MLR group, the high MLR group had higher age, proportion of male, body mass index (BMI) [age (years old): 66.0 (51.7, 78.4) vs. 57.6 (27.1, 74.6), proportion of male: 57.2% vs. 52.5%, BMI (kg/m2): 26.5 (22.5, 31.1) vs. 24.7 (14.3, 29.7)]. The high MLR group also had higher incidence of complications (hypertension: 49.2% vs. 44.6%, chronic heart failure: 32.6% vs. 21.7%, diabetes mellitus: 27.0% vs. 23.4%, chronic obstructive pulmonary disease: 21.5% vs. 16.1%, renal insufficiency: 19.3% vs. 13.1%), and higher white blood cell count (WBC), blood glucose, lactate (Lac), serum creatinine (SCr), SIRS score and SOFA score [WBC (×109/L): 13.8 (9.6, 19.2) vs. 11.5 (8.4, 15.6), blood glucose (mmol/L): 8.66 (6.88, 11.49) vs. 8.27 (6.55, 10.88), Lac (mmol/L): 2.2 (1.5, 3.7) vs. 2.1 (1.4, 3.3), SCr (µmol/L): 106.1 (70.7, 176.8) vs. 88.4 (70.7, 132.6), SIRS score: 3 (2, 4) vs. 2 (2, 3), SOFA score: 4 (2, 7) vs. 3 (1, 5)]. The 30-day mortality, and the proportion of patients with length of ICU stay > 5 days, total hospitalization time > 14 days, CRRT and mechanical ventilation > 5 days were significantly higher in high MLR group (30-day mortality: 20.0% vs. 8.3%, length of ICU stay > 5 days: 33.2% vs. 20.4%, total hospitalization time > 14 days: 33.7% vs. 16.2%, CRRT: 3.6% vs. 0.7%, mechanical ventilation > 5 days: 18.4% vs. 5.7%), with statistically significant differences (all P < 0.05). (3) After adjusted with the related factors, multivariate Logistic regression analysis showed that elevated MLR was an independent risk factor for increased 30-day mortality [odd ratio (OR) = 1.54, 95%CI was 1.37-1.72, P < 0.001]. Moreover, the increased MLR was independently associated with the increased risk of usage of CRRT (OR = 2.77, 95%CI was 2.18-3.51), mechanical ventilation > 5 days (OR = 2.45, 95%CI was 2.21-2.72), the length of ICU stay > 5 days (OR = 2.29, 95%CI was 2.10-2.49), and total hospitalization time > 14 days (OR = 2.28, 95%CI was 2.08-2.49), all P < 0.001. CONCLUSIONS: Retrospective analysis of large sample shows that MLR elevation is an independent risk factor for 30-day mortality, usage of CRRT, prolonged mechanical ventilation time, prolonged hospitalization, prolonged length of ICU stay. MLR can be used for risk stratification of severe patients.


Assuntos
Estado Terminal , Sepse , Cuidados Críticos , Humanos , Unidades de Terapia Intensiva , Linfócitos , Masculino , Monócitos , Prognóstico , Curva ROC , Estudos Retrospectivos
15.
Medicine (Baltimore) ; 100(22): e26212, 2021 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-34087897

RESUMO

ABSTRACT: To investigate the diagnostic value of a computed tomography (CT) scan-based radiomics model for acute aortic dissection.For the dissection group, we retrospectively selected 50 patients clinically diagnosed with acute aortic dissection between October 2018 and November 2019, for whom non-contrast CT and CT angiography images were available. Fifty individuals with available non-contrast CT and CT angiography images for other causes were selected for inclusion in the non-dissection group. Based on the aortic dissection locations on the CT angiography images, we marked the corresponding regions-of-interest on the non-contrast CT images of both groups. We collected 1203 characteristic parameters from these regions by extracting radiomics features. Subsequently, we used a random number table to include 70 individuals in the training group and 30 in the validation group. Finally, we used the Lasso regression for dimension reduction and predictive model construction. The diagnostic performance of the model was evaluated by a receiver operating characteristic (ROC) curve.Fourteen characteristic parameters with non-zero coefficients were selected after dimension reduction. The accuracy, sensitivity, specificity, and area under the ROC curve of the prediction model for the training group were 94.3% (66/70), 91.2% (31/34), 97.2% (35/36), and 0.988 (95% confidence interval [CI]: 0.970-0.998), respectively. The respective values for the validation group were 90.0% (27/30), 94.1% (16/17), 84.6% (11/13), and 0.952 (95% CI: 0.883-0.986).Our non-contrast CT scan-based radiomics model accurately facilitated acute aortic dissection diagnosis.


Assuntos
Aneurisma Dissecante/diagnóstico por imagem , Aorta/patologia , Aneurisma Aórtico/complicações , Tomografia Computadorizada por Raios X/métodos , Doença Aguda , Adulto , Idoso , Angiografia por Tomografia Computadorizada/métodos , Feminino , Humanos , Aumento da Imagem/instrumentação , Processamento de Imagem Assistida por Computador/métodos , Masculino , Pessoa de Meia-Idade , Curva ROC , Estudos Retrospectivos , Sensibilidade e Especificidade
16.
Medicine (Baltimore) ; 100(22): e26219, 2021 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-34087900

RESUMO

BACKGROUND: Autophagy is closely related to skin cutaneous melanoma (SKCM), but the mechanism involved is unclear. Therefore, exploration of the role of autophagy-related genes (ARGs) in SKCM is necessary. MATERIALS AND METHODS: Differential expression autophagy-related genes (DEARGs) were first analysed. Univariate and multivariate Cox regression analyses were used to evaluate the expression of DEARGs and prognosis of SKCM. Further, the expression levels of prognosis-related DEARGs were verified by immunohistochemical (IHC) staining. Finally, gene set enrichment analysis (GSEA) was used to explore the underlying molecular mechanisms of SKCM. RESULTS: Five ARGs (APOL1, BIRC5, EGFR, TP63, and SPNS1) were positively correlated with the prognosis of SKCM. IHC verified the results of the differential expression of these 5 ARGs in the bioinformatics analysis. According to the receiver operating characteristic curve, the signature had a good performance at predicting overall survival in SKCM. The signature could classify SKCM patients into high-risk or low-risk groups according to distinct overall survival. The nomogram confirmed that the risk score has a particularly large impact on the prognosis of SKCM. Calibration plot displayed excellent agreement between nomogram predictions and actual observations. Principal component analysis indicated that patients in the high-risk group could be distinguished from those in low-risk group. Results of GSEA indicated that the low-risk group is enriched with aggressiveness-related pathways such as phosphatidylinositol-3-kinase/protein kinase B and mitogen-activated protein kinase signalling pathways. CONCLUSION: Our study identified a 5-gene signature. It revealed the mechanisms of autophagy that lead to the progression of SKCM and established a prognostic nomogram that can predict overall survival of patients with SKCM. The findings of this study provide novel insights into the relationship between ARGs and prognosis of SKCM.


Assuntos
Autofagia/genética , Biologia Computacional/métodos , Melanoma/genética , Neoplasias Cutâneas/patologia , Proteínas Adaptadoras de Transdução de Sinal/genética , Apolipoproteína L1/genética , Receptores ErbB/genética , Feminino , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , Melanoma/mortalidade , Proteínas de Membrana/genética , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Nomogramas , Fosfatidilinositol 3-Quinase/metabolismo , Prognóstico , Estudos Prospectivos , Proteínas Proto-Oncogênicas c-akt/metabolismo , Curva ROC , Fatores de Risco , Survivina/genética , Fatores de Transcrição/genética , Proteínas Supressoras de Tumor/genética
17.
BMC Surg ; 21(1): 279, 2021 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-34082725

RESUMO

INTRODUCTION: The drain output volume (DOV) after pancreaticoduodenectomy (PD) is an easily assessable indicator in clinical settings. We explored the utility of the DOV as a possible warning sign of complications after PD. METHODS: A total of 404 patients undergoing PD were considered for inclusion. The predictability of the DOV for overall morbidity, major complications, intraabdominal infection (IAI), clinically relevant (CR) postoperative pancreatic fistula (POPF), CR delayed gastric emptying (DGE), CR chyle leak (CL), and CR post-pancreatectomy hemorrhaging (PPH) was evaluated. RESULTS: One hundred (24.8%) patients developed major complications, and 131 (32.4%) developed IAI. Regarding CR post-pancreatectomy complications, 75 (18.6%) patients developed CR-POPF, 23 (5.7%) developed CR-DGE, 20 (5.0%) developed CR-CL, and 28 (6.9%) developed CR-PPH. The median DOV on postoperative day (POD) 1 and POD 3 was 266 and 234.5 ml, respectively. A low DOV on POD 1 was an independent predictor of CR-POPF, and a high DOV on POD 3 was an independent predictor of CR-CL. A receiver operating characteristics (ROC) analysis revealed that the DOV on POD 1 had a negative predictive value (area under the curve [AUC] 0.655, sensitivity 65.0%, specificity 65.3%, 95% confidence interval [CI]: 0.587-0.724), with a calculated optimal cut-off value of 227 ml. An ROC analysis also revealed that the DOV on POD 3 had a positive predictive value (AUC 0.753, sensitivity 70.1%, specificity 75.0%, 95% CI: 0.651-0.856), with a calculated optimal cut-off value of 332 ml. CONCLUSION: A low DOV on POD 1 might be a postoperative warning sign for CR-POPF, similar to high drain amylase (DA) on POD 1, high DA on POD 3, and high CRP on POD 3. When the DOV on POD 1 after PD was low, surgeons should evaluate the reasons of a low DOV. A high DOV on POD 3 was a postoperative warning sign CR-CL, and might require an appropriate management of protein loss.


Assuntos
Pancreatectomia , Pancreaticoduodenectomia , Drenagem , Humanos , Fístula Pancreática/diagnóstico , Fístula Pancreática/etiologia , Fístula Pancreática/cirurgia , Pancreaticoduodenectomia/efeitos adversos , Complicações Pós-Operatórias/epidemiologia , Complicações Pós-Operatórias/cirurgia , Curva ROC , Fatores de Risco
18.
BMJ Open ; 11(6): e044496, 2021 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-34117044

RESUMO

OBJECTIVE: During the influenza epidemic season, the fragile elderlies are not only susceptible to influenza infections, but are also more likely to develop severe symptoms and syndromes. Such circumstances may pose a significant burden to the medical resources especially in the emergency department (ED). Disposition of the elderly patients with influenza infections to either the ward or intensive care unit (ICU) accurately is therefore a crucial issue. STUDY DESIGN: Retrospective cohort study. SETTING AND PARTICIPANTS: Elderly patients (≥65 years) with influenza visiting the ED of a medical centre between 1 January 2010 and 31 December 2015. PRIMARY OUTCOME MEASURES: Demographic data, vital signs, medical history, subtype of influenza, national early warning score (NEWS) and outcomes (mortality) were analysed. We investigated the ability of NEWS to predict ICU admission via logistic regression and the receiver operating characteristic (ROC) analysis. RESULTS: We included 409 geriatric patients in the ED with a mean age of 79.5 years and approximately equal sex ratio. The mean NEWS ±SD was 3.4±2.9, and NEWS ≥8 was reported in 11.0% of the total patients. Logistic regression revealed that NEWS ≥8 predicted ICU admission with an OR of 5.37 (95% CI 2.61 to 11.04). The Hosmer-Lemeshow goodness-of-fit test was calculated as 0.95, and the adjusted area under the ROC was 0.72. An NEWS ≥8 is associated with ICU-admission and may help to triage elderly patients with influenza infections during the influenza epidemic season. CONCLUSION: The high specificity of NEWS ≥8 to predict ICU admission in elderly patients with influenza infection during the epidemic season may avoid unnecessary ICU admissions and ensure proper medical resource allocation.


Assuntos
Escore de Alerta Precoce , Influenza Humana , Idoso , Serviço Hospitalar de Emergência , Mortalidade Hospitalar , Humanos , Influenza Humana/diagnóstico , Influenza Humana/epidemiologia , Unidades de Terapia Intensiva , Curva ROC , Estudos Retrospectivos , Estações do Ano
19.
Rev Saude Publica ; 55: 23, 2021.
Artigo em Inglês, Português | MEDLINE | ID: mdl-34133618

RESUMO

OBJECTIVE: To predict the risk of absence from work due to morbidities of teachers working in early childhood education in the municipal public schools, using machine learning algorithms. METHODS: This is a cross-sectional study using secondary, public and anonymous data from the Relação Anual de Informações Sociais, selecting early childhood education teachers who worked in the municipal public schools of the state of São Paulo between 2014 and 2018 (n = 174,294). Data on the average number of students per class and number of inhabitants in the municipality were also linked. The data were separated into training and testing, using records from 2014 to 2016 (n = 103,357) to train five predictive models, and data from 2017 to 2018 (n = 70,937) to test their performance in new data. The predictive performance of the algorithms was evaluated using the value of the area under the ROC curve (AUROC). RESULTS: All five algorithms tested showed an area under the curve above 0.76. The algorithm with the best predictive performance (artificial neural networks) achieved 0.79 of area under the curve, with accuracy of 71.52%, sensitivity of 72.86%, specificity of 70.52%, and kappa of 0.427 in the test data. CONCLUSION: It is possible to predict cases of sickness absence in teachers of public schools with machine learning using public data. The best algorithm showed a better result of the area under the curve when compared with the reference model (logistic regression). The algorithms can contribute to more assertive predictions in the public health and worker health areas, allowing to monitor and help prevent the absence of these workers due to morbidity.


Assuntos
Absenteísmo , Aprendizado de Máquina , Brasil , Pré-Escolar , Estudos Transversais , Humanos , Curva ROC , Instituições Acadêmicas
20.
Nat Commun ; 12(1): 3438, 2021 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-34103501

RESUMO

DNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a consensus approach, METEORE ( https://github.com/comprna/METEORE ), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are also provided for reproducibility and to enable the systematic application of our analyses to other datasets.


Assuntos
Ilhas de CpG/genética , Metilação de DNA/genética , Sequenciamento por Nanoporos , Benchmarking , Proteína 9 Associada à CRISPR/metabolismo , Citosina/metabolismo , DNA/metabolismo , Escherichia coli/genética , Genoma Bacteriano , Curva ROC
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