Category: Statistics

PLoS One. 2021 Aug 6;16(8):e0255269. doi: 10.1371/journal.pone.0255269. eCollection 2021.

ABSTRACT

The Sine-Cosine algorithm (SCA) is a population-based metaheuristic algorithm utilizing sine and cosine functions to perform search. To enable the search process, SCA incorporates several search parameters. But sometimes, these parameters make the search in SCA vulnerable to local minima/maxima. To overcome this problem, a new Multi Sine-Cosine algorithm (MSCA) is proposed in this paper. MSCA utilizes multiple swarm clusters to diversify & intensify the search in-order to avoid the local minima/maxima problem. Secondly, during update MSCA also checks for better search clusters that offer convergence to global minima effectively. To assess its performance, we tested the MSCA on unimodal, multimodal and composite benchmark functions taken from the literature. Experimental results reveal that the MSCA is statistically superior with regards to convergence as compared to recent state-of-the-art metaheuristic algorithms, including the original SCA.

PMID:34358237 | DOI:10.1371/journal.pone.0255269

PLoS Comput Biol. 2021 Aug 6;17(8):e1009275. doi: 10.1371/journal.pcbi.1009275. Online ahead of print.

ABSTRACT

In modern computational biology, there is great interest in building probabilistic models to describe collections of a large number of co-varying binary variables. However, current approaches to build generative models rely on modelers’ identification of constraints and are computationally expensive to infer when the number of variables is large (N~100). Here, we address both these issues with Super-statistical Generative Model for binary Data (SiGMoiD). SiGMoiD is a maximum entropy-based framework where we imagine the data as arising from super-statistical system; individual binary variables in a given sample are coupled to the same ‘bath’ whose intensive variables vary from sample to sample. Importantly, unlike standard maximum entropy approaches where modeler specifies the constraints, the SiGMoiD algorithm infers them directly from the data. Due to this optimal choice of constraints, SiGMoiD allows to model collections of a very large number (N>1000) of binary variables. Finally, SiGMoiD offers a reduced dimensional description of the data, allowing us to identify clusters of similar data points as well as binary variables. We illustrate the versatility of SiGMoiD using several datasets spanning several time- and length-scales.

PMID:34358223 | DOI:10.1371/journal.pcbi.1009275

PLoS One. 2021 Aug 6;16(8):e0253425. doi: 10.1371/journal.pone.0253425. eCollection 2021.

ABSTRACT

Statistical models for outcome prediction are central to traumatic brain injury research and critical to baseline risk adjustment. Glasgow coma score (GCS) and pupil reactivity are crucial covariates in all such models but may be measured at multiple time points between the time of injury and hospital and are subject to a variable degree of unreliability and/or missingness. Imputation of missing data may be undertaken using full multiple imputation or by simple substitution of measurements from other time points. However, it is unknown which strategy is best or which time points are more predictive. We evaluated the pseudo-R2 of logistic regression models (dichotomous survival) and proportional odds models (Glasgow Outcome Score-extended) using different imputation strategies on the The Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study dataset. Substitution strategies were easy to implement, achieved low levels of missingness (<< 10%) and could outperform multiple imputation without the need for computationally costly calculations and pooling multiple final models. While model performance was sensitive to imputation strategy, this effect was small in absolute terms and clinical relevance. A strategy of using the emergency department discharge assessments and working back in time when these were missing generally performed well. Full multiple imputation had the advantage of preserving time-dependence in the models: the pre-hospital assessments were found to be relatively unreliable predictors of survival or outcome. The predictive performance of later assessments was model-dependent. In conclusion, simple substitution strategies for imputing baseline GCS and pupil response can perform well and may be a simple alternative to full multiple imputation in many cases.

PMID:34358231 | DOI:10.1371/journal.pone.0253425

Echocardiography. 2021 Aug 6. doi: 10.1111/echo.15170. Online ahead of print.

ABSTRACT

AIM: Chest computed tomography (CT) imaging plays a diagnostic and prognostic role in Coronavirus disease 2019 (COVID-19) patients. This study aimed to investigate and compare predictive capacity of main pulmonary artery diameter (MPA), ascending aorta diameter (AAo), and MPA-to-AAo ratio to determine in-hospital mortality in COVID-19 patients.

MATERIALS AND METHODS: This retrospective study included 255 hospitalized severe or critical COVID-19 patients. MPA was measured at the level of pulmonary artery bifurcation perpendicular to the direction of the vessel through transverse axial images and AAo was measured by using the same CT slice at its maximal diameter. MPA-to-AAo ratio was calculated by division of MPA to AAo.

RESULTS: Multivariate logistic regression model yielded MPA ≥29.15 mm (OR: 4.95, 95% CI: 2.01-12.2, p = 0.001), MPA (OR: 1.28, 95% CI: 1.13-1.46, p < 0.001), AAo (OR: .90, 95% CI: .81-.99, p = 0.040), and MPA-to-AAo ratio ≥.82 (OR: 4.67, 95% CI: 1.86-11.7, p = 0.001) as independent predictors of in-hospital mortality. Time-dependent multivariate Cox-proportion regression model demonstrated MPA ≥29.15 mm (HR: 1.96, 95% CI: 1.03-3.90, p = 0.047) and MPA (HR: 1.08, 95% CI: 1.01-1.17, p = 0.048) as independent predictors of in-hospital mortality, whereas AAo and MPA-to-AAo ratio did not reach statistical significance.

CONCLUSION: Pulmonary artery enlargement strongly predicts in-hospital mortality in hospitalized COVID-19 patients. MPA, which can be calculated easily from chest CT imaging, can be beneficial in the prognostication of these patients.

PMID:34355824 | DOI:10.1111/echo.15170

J Magn Reson Imaging. 2021 Aug 6. doi: 10.1002/jmri.27871. Online ahead of print.

ABSTRACT

BACKGROUND: CD8⁺ T cell in pancreatic ductal adenocarcinoma (PDAC) is closely related to the prognosis and treatment response of patients. Accurate preoperative CD8⁺ T-cell expression can better identify the population benefitting from immunotherapy.

PURPOSE: To develop and validate a machine learning classifier based on noncontrast magnetic resonance imaging (MRI) for the preoperative prediction of CD8⁺ T-cell expression in patients with PDAC.

STUDY TYPE: Retrospective cohort study.

POPULATION: Overall, 114 patients with PDAC undergoing MR scan and surgical resection; 97 and 47 patients in the training and validation cohorts. FIELD STRENGTH/SEQUENCE/3 T: Breath-hold single-shot fast-spin echo T2-weighted sequence and noncontrast T1-weighted fat-suppressed sequences.

ASSESSMENT: CD8⁺ T-cell expression was quantified using immunohistochemistry. For each patient, 2232 radiomics features were extracted from noncontrast T1- and T2-weighted images and reduced using the Wilcoxon rank-sum test and least absolute shrinkage and selection operator method. Linear discriminative analysis was used to construct radiomics and mixed models. Model performance was determined by its discriminative ability, calibration, and clinical utility.

STATISTICAL TESTS: Kaplan-Meier estimates, Student’s t-test, the Kruskal-Wallis H test, and the chi-square test, receiver operating characteristic curve, and decision curve analysis.

RESULTS: A log-rank test showed that the survival duration in the CD8-high group (25.51 months) was significantly longer than that in the CD8-low group (22.92 months). The mixed model included all MRI characteristics and 13 selected radiomics features, and the area under the curve (AUC) was 0.89 (95% confidence interval [CI], 0.77-0.92) and 0.69 (95% CI, 0.53-0.82) in the training and validation cohorts. The radiomics model included 13 radiomics features, which showed good discrimination in the training cohort (AUC, 0.85; 95% CI, 0.77-0.92) and the validation cohort (AUC, 0.76; 95% CI, 0.61-0.87).

DATA CONCLUSIONS: This study developed a noncontrast MRI-based radiomics model that can preoperatively determine CD8⁺ T-cell expression in patients with PDAC and potentially immunotherapy planning.

EVIDENCE LEVEL: 5 TECHNICAL EFFICACY: Stage 2.

PMID:34355834 | DOI:10.1002/jmri.27871

Clin Cardiol. 2021 Aug 6. doi: 10.1002/clc.23708. Online ahead of print.

ABSTRACT

BACKGROUND: Recent reports have indicated the beneficial role of strain measurement in COVID-19 patients.

HYPOTHESIS: To determine the association between right and left global longitudinal strain (RVGLS, LVGLS) and COVID-19 patients’ outcomes.

METHODS: Hospitalized COVID-19 patients between June and August 2020 were included. Two-dimensional echocardiography and biventricular global longitudinal strain measurement were performed. The outcome measure was defined as mortality, ICU admission, and need for intubation. Appropriate statistical tests were used to compare different groups.

RESULTS: In this study 207 patients (88 females) were enrolled. During 64 ± 4 days of follow-up, 22 (10.6%) patients died. Mortality, ICU admission, and intubation were significantly associated with LVGLS and RVGLS tertiles. LVGLS tertiles could predict poor outcome with significant odds ratios in the total population (OR = 0.203, 95% CI: 0.088-0.465; OR = 0.350, 95% CI: 0.210-0.585; OR = 0.354, 95% CI: 0.170-0.736 for mortality, ICU admission, and intubation). Although odds ratios of LVGLS for the prediction of outcome were statistically significant among hypertensive patients, these odds ratios did not reach significance among non-hypertensive patients. RVGLS tertiles revealed significant odds ratios for the prediction of mortality (OR = 0.322, 95% CI: 0.162-0.640), ICU admission (OR = 0.287, 95% CI: 0.166-0.495), and need for intubation (OR = 0.360, 95% CI: 0.174-0.744). Odds ratios of RVGLS remained significant even after adjusting for hypertension when considering mortality and ICU admission.

CONCLUSION: RVGLS and LVGLS can be acceptable prognostic factors to predict mortality, ICU admission, and intubation in hospitalized COVID-19 patients. However, RVGLS seems more reliable, as it is not confounded by hypertension.

PMID:34355809 | DOI:10.1002/clc.23708

Echocardiography. 2021 Aug 6. doi: 10.1111/echo.15175. Online ahead of print.

ABSTRACT

BACKGROUND: The evaluation of the tricuspid annular plane systolic excursion (TAPSE) is recommended to assess the right ventricular (RV) systolic function. We performed an updated meta-analysis of the association between TAPSE and short-term mortality in COVID-19 patients.

METHODS: MEDLINE and Scopus databases were searched to locate all the articles published up to May 1, 2021, reporting data on TAPSE among COVID-19 survivors and non-survivors. The difference of TAPSE between the two groups was expressed as mean difference (MD) with the corresponding 95% confidence interval (CI) using the Mantel-Haenszel random effects model. Both Q value and I² statistics were used to assess heterogeneity across studies. Sensitivity analysis, meta-regression, and evaluation of bias were performed.

RESULTS: Twelve studies, enrolling 1272 COVID-19 patients (778 males, mean age 69.3 years), met the inclusion criteria and were included in the final analysis. Non-survivors had a lower TAPSE compared to survivors (MD = -3.089 mm, 95% CI = -4.087 to -2.091, p < 0.0001, I² = 79.0%). Both the visual inspection of the funnel plot and the Egger’s tests (t = 1.195, p = 0.259) revealed no evidence of publication bias. Sensitivity analysis confirmed yielded results. Meta-regression analysis evidenced that the difference in TAPSE between the two groups was only influenced by pre-existing chronic obstructive pulmonary disease (COPD, p = 0.02).

CONCLUSION: COVID-19 non-survivors have a lower TAPSE when compared to survivors, especially in COPD subjects. Current data suggest that the TAPSE assessment may provide useful information regarding the short-term prognosis of COVID-19 patients during the infection.

PMID:34355816 | DOI:10.1111/echo.15175

Cardiol J. 2021 Aug 6. doi: 10.5603/CJ.a2021.0083. Online ahead of print.

ABSTRACT

BACKGROUND: Atrial fibrillation (AF) is the leading cause of stroke. The European Society of Cardiology (ESC) advises opportunistic AF screening among patients aged ≥ 65 years. Considering this, the aim herein, was compare the feasibility of two different systems of smartphone-based electrocardiogram (ECG) recordings to identify AF among those without a previous arrhythmia history.

METHODS: Prospective AF screening was conducted at six pharmacies using Kardia Mobile and Hartmann Veroval 2 in 1. A single-lead ECG was acquired by the placement of fingers on the pads. A cardiologist evaluated findings from both devices.

RESULTS: Atrial fibrillation was identified in 3.60% and previously unknown AF was detected in 1.92% of the study participants. Sensitivity and specificity of the Kardia application in detecting AF were 66.7% (95% confidence interval [CI] 38.4-88.2%) and 98.5% (95% CI 96.7-99.5%), and for Veroval 10.0% (95% CI 0.23-44.5%) and 94.96% (95% CI 92.15-96.98%), accordingly. Inter-rater agreement was k = 0.088 (95% CI 1.59-16.1%).

CONCLUSIONS: Mobile devices can detect AF, but each finding must be verified by a professional. The Kardia application appeared to be more user-friendly than Veroval. Cardiovascular screening using mobile devices is feasible at pharmacies. Hence it might be considered for routine use.

PMID:34355779 | DOI:10.5603/CJ.a2021.0083

Folia Morphol (Warsz). 2021 Aug 6. doi: 10.5603/FM.a2021.0075. Online ahead of print.

ABSTRACT

BACKGROUND: To evaluate the relationship between the horizontal condylar angle (HCA), temporomandibular joint osteoarthritis (TMJ OA), and condylar position on cone-beam computed tomography (CBCT) images.

MATERIALS AND METHODS: Based on TMJ OA, joints were classified as affected and the unaffected. According to the OA condition of their joints, three groups of patients were formed: control group (n = 159, 41.1%), unilateral group (n = 121, 31.3%), and bilateral group (n = 107, 27.6%). In total, the HCAs of 774 TMJs of 387 patients were measured and their condylar positions were determined as concentric (n = 184, 23.8%), posterior (n = 338, 43.7%), and anterior (n = 252, 32.5%).

RESULTS: The mean HCA of the bilateral group (22.7° ± 7.6°) was greater than those in both the control (19.5° ± 6.4°) and the unilateral (20.5° ± 6.5°) groups (p < 0.05). However, the difference was not statistically significant between the control and unilateral group (p > 0.05). In total patients, unlike the unilateral group, the affected joints had a greater mean HCA than the unaffected joints (p < 0.05). The mean HCAs of the joints according to the condylar position were as concentric: 20.6° ± 6.7°, posterior: 21.1° ± 7.8°, and anterior: 20.2° ± 7.9° (p > 0.05).

CONCLUSIONS: While the HCA increased in the presence of TMJ OA, no relationship was found between HCA and three different condylar positions.

PMID:34355786 | DOI:10.5603/FM.a2021.0075

Folia Morphol (Warsz). 2021 Aug 6. doi: 10.5603/FM.a2021.0074. Online ahead of print.

ABSTRACT

BACKGROUND: Bone wax, a hemostatic agent, is widely used in craniospinal surgical procedures for a long time, inspite of controversial results regarding its negative influence upon bone regeneration. In this experimental study, the effects of Ankaferd Blood Stopper (ABS), as an alternative hemostatic agent, were evaluated through histochemical, immunohistochemical and scintigraphic studies.

MATERIALS AND METHODS: The total of 30 adult female Wistar-Albino rats was randomly divided into three groups: intact control group (n=10), bone wax group (n=10), and ABS group (n=10). Surgically, a 3.0 mm hole in diameter was drilled on the right side of calvarium of the rats using a Class Mini Grinder set in all three groups, as described previously. At the end of 8 weeks, bone healing and connective tissue alterations surrounding drilled calvarial defect areas of the rats were determined via Hematoxylin and Eosin (H&E) and the Mallory’s trichrome staining and anti-bone sialoprotein (BSP) immunohistochemistry. Image Pro Express 4.5 program was used for histomorphometric calculation of new bone and fibrotic tissue areas. All statistical analyzes were made with SPSS 25.0 and analysis of variance (one-way ANOVA) followed by Bonferroni post hoc test was performed, p<0.001 was considered as significance level.

RESULTS: Histomorphometrically, it was found that he had the largest hole diameter and the least fibrotic scar area in the bone-wax group. In the bone wax group, it was observed that the material closed the hole and there was only a fibrotic scar tissue in the area between the bone tissue at the edge of the hole and bone wax, and a fibrotic tissue was formed in the bone wax area. During the histological procedure, this bone-wax material was poured and the sections were seen as a gap in this area. In the ABS hemostat group, the smallest hole diameter and the least fibrotic scar tissue were observed. Fibrotic scar tissue close to each other was found in the ABS hemostat and bone wax groups. Histological analysis of samples also showed a statistical significance for fibrotic connective tissue area between groups (p <0.05). Scintigraphically, osteoblastic activity related to blood flow in the animal taken from the group with application of ABS hemostat was more pronounced compared to the other two groups.

CONCLUSIONS: In our study, it has been concluded that the ABS yields affirmative effects on the bone healing, while bone wax leads to negative impact on the bone regeneration. Scintigraphic, histochemical and immunohistochemical data support the affirmative impact of the ABS hemostat application upon the bone regeneration apart from the quick stop of hemorrhage.

PMID:34355787 | DOI:10.5603/FM.a2021.0074