ROBustness In Network (robin): an R Package for Comparison and Validation of Communities

In network analysis, many community detection algorithms have been developed. However, their implementation leaves unaddressed the question of the statistical validation of the results. Here, we present robin (ROBustness In Network), an R package to assess the robustness of the community structure of a network found by one or more methods to give indications about their reliability. The procedure initially detects if the community structure found by a set of algorithms is statistically significant and then compares two selected detection algorithms on the same graph to choose the one that better fits the network of interest. We demonstrate the use of our package on the American College Football benchmark dataset

Quantification of Myocardial Contraction Fraction with Three-Dimensional Automated, Machine-Learning-Based Left-Heart-Chamber Metrics: Diagnostic Utility in Hypertrophic Phenotypes and Normal Ejection Fraction

Aims: The differentiation of left ventricular (LV) hypertrophic phenotypes is challenging in patients with normal ejection fraction (EF). The myocardial contraction fraction (MCF) is a simple dimensionless index useful for specifically identifying cardiac amyloidosis (CA) and hypertrophic cardiomyopathy (HCM) when calculated by cardiac magnetic resonance. The purpose of this study was to evaluate the value of MCF measured by three-dimensional automated, machine-learning-based LV chamber metrics (dynamic heart model [DHM]) for the discrimination of different forms of hypertrophic phenotypes. Methods and Results: We analyzed the DHM LV metrics of patients with CA (n = 10), hypertrophic cardiomyopathy (HCM, n = 36), isolated hypertension (IH, n = 87), and 54 healthy controls. MCF was calculated by dividing LV stroke volume by LV myocardial volume. Compared with controls (median 61.95%, interquartile range 55.43–67.79%), mean values for MCF were significantly reduced in HCM—48.55% (43.46–54.86% p < 0.001)—and CA—40.92% (36.68–46.84% p < 0.002)—but not in IH—59.35% (53.22–64.93% p < 0.7). MCF showed a weak correlation with EF in the overall cohort (R2 = 0.136) and the four study subgroups (healthy adults, R2 = 0.039 IH, R2 = 0.089; HCM, R2 = 0.225; CA, R2 = 0.102). ROC analyses showed that MCF could differentiate between healthy adults and HCM (sensitivity 75.9%, specificity 77.8%, AUC 0.814) and between healthy adults and CA (sensitivity 87.0%, specificity 100%, AUC 0.959). The best cut-off values were 55.3% and 52.8%. Conclusions: The easily derived quantification of MCF by DHM can refine our echocardiographic discrimination capacity in patients with hypertrophic phenotype and normal EF. It should be added to the diagnostic workup of these patients

Determinants of cardiac structure in frail and sarcopenic elderly adults

Background: Cardiac structure and function change with age. The higher prevalence of left ventricular hypertrophy (LVH) with concentric remodeling is indicative of a typical geometric pattern of aging associated with a higher cardiovascular (CV) risk and diseases. The recent associations found between low left ventricular and skeletal mass in older patients with frailty and sarcopenia have raised great interest in investigating cardiac characteristics and determinants of left ventricular mass (LVM) in this population. Design: Cross-sectional study. Methods: We evaluated 100 sarcopenic and physically frail outpatients, 33 men (M), 67 women (F), aged ≥70 years (mean age 79 ± 5) and enrolled in the Parma site of European multicenter SPRINTT population. Results: All male and female participants showed LVH, assessed as indexed LVM to body surface area (LVM/BSA) (M = 128 ± 39 g/m2; F = 104 ± 26 g/m2), and were more prone to have concentric geometry, as demonstrated by relative wall thickness value (0.41 in both sexes). After backward regression analysis, including covariates such as age, sex, office or ABPM systolic blood pressure (SBP), heart rate, BSA, use of β blockers, ACE-inhibitors, angiotensin receptor blockers, calcium channel blockers, diuretics, physical activity, hemoglobin level, and Mini Mental State examination - the most powerful determinants of LVM were clinical SBP (β = 1.51 ± 0.31, p = 0.0005), BSA (β = 165.9 ± 41.4, p = 0.0001), while less powerful determinants were 24 h, daily and nightly SBP (p = 0.02, p = 0.002, p = 0.004 respectively). Conclusions: Older sarcopenic and physically frail patients showed LVH with a tendency towards concentric geometry. The main determinant of LVM was SBP, highlighting the key role that hemodynamic condition plays in determining LVH in this population

ROBustness In Network(robin): an R package for Comparison and Validation of Communities

In network analysis, many community detection algorithms have been developed. However, their implementation leaves unaddressed the question of the statistical validation of the results. Here, we present robin (ROBustness In Network), an R package to assess the robustness of the community structure of a network found by one or more methods to give indications about their reliability. The procedure initially detects if the community structure found by a set of algorithms is statistically significant and then compares two selected detection algorithms on the same graph to choose the one that better fits the network of interest. We demonstrate the use of our package on the American College Football benchmark dataset

Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells

The T-box transcription factor TBX1 has critical roles in the cardiopharyngeal lineage and the gene is haploinsufficient in DiGeorge syndrome, a typical developmental anomaly of the pharyngeal apparatus. Despite almost two decades of research, if and how TBX1 function triggers chromatin remodeling is not known. Here, we explored genome-wide gene expression and chromatin remodeling in two independent cellular models of Tbx1 loss of function, mouse embryonic carcinoma cells P19Cl6, and mouse embryonic stem cells (mESCs). The results of our study revealed that the loss or knockdown of TBX1 caused extensive transcriptional changes, some of which were cell type-specific, some were in common between the two models. However, unexpectedly we observed only limited chromatin changes in both systems. In P19Cl6 cells, differentially accessible regions (DARs) were not enriched in T-BOX binding motifs; in contrast, in mESCs, 34% (n = 47) of all DARs included a T-BOX binding motif and almost all of them gained accessibility in Tbx1–/– cells. In conclusion, despite a clear transcriptional response of our cell models to loss of TBX1 in early cell differentiation, chromatin changes were relatively modest

Atrial fibrillation in vascular surgery: a systematic review and meta-analysis on prevalence, incidence and outcome implications

Aims: To know the prevalence of atrial fibrillation (AF), as well as the incidence of postoperative AF (POAF) in vascular surgery for arterial diseases and its outcome implications. Methods: We performed a systematic review and meta-analysis following the PRISMA statement. Results: After the selection process, we analyzed 44 records (30 for the prevalence of AF history and 14 for the incidence of POAF). The prevalence of history of AF was 11.5% [95% confidence interval (CI) 1-13.3] with high heterogeneity (I2 = 100%). Prevalence was higher in the case of endovascular procedures. History of AF was associated with a worse outcome in terms of in-hospital death [odds ratio (OR) 3.29; 95% CI 2.66-4.06; P < 0.0001; I2 94%] or stroke (OR 1.61; 95% CI 1.39-1.86; P < 0.0001; I2 91%). The pooled incidence of POAF was 3.6% (95% CI 2-6.4) with high heterogeneity (I2 = 100%). POAF risk was associated with older age (mean difference 4.67 years, 95% CI 2.38-6.96; P = 0.00007). The risk of POAF was lower in patients treated with endovascular procedures as compared with an open surgical procedure (OR 0.35; 95% CI 0.13-0.91; P = 0.03; I2 = 61%). Conclusions: In the setting of vascular surgery for arterial diseases a history of AF is found overall in 11.5% of patients, more frequently in the case of endovascular procedures, and is associated with worse outcomes in terms of short-term mortality and stroke. The incidence of POAF is overall 3.6%, and is lower in patients treated with an endovascular procedure as compared with open surgery procedures. The need for oral anticoagulants for preventing AF-related stroke should be evaluated with randomized clinical trials

Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics

Medicine, Faculty ofNon UBCPathology and Laboratory Medicine, Department ofReviewedFacultyResearche

Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics (Genome Biology, (2021), 22, 1, (220), 10.1186/s13059-021-02433-9)

Following publication of the original article [1], the authors identified that author Dario Righelli had erroneously been omitted from the author panel. The author group above has been updated and the original article [1] has been corrected