Community detection in networks: a heuristic version of Girvan Newman algorithm

I grafi permettono di modellare problemi complessi di diversa natura. Una delle questioni più stimolanti e importanti è il rilevamento delle comunità, cioè l’identificazione di componenti altamente connesse. L’algoritmo di Girvan Newman è in grado di identificare tali componenti con successo, ma non è computazionalmente adatto ad un’analisi di grafi di grandi dimensioni. Pertanto, proponiamo una versione euristica di questo algoritmo, approssimando la misura di betweenness degli archi. Analizziamo le prestazioni della nostra proposta utilizzando reti benchmark.Complex problems in different fields can be modeled by graph data structures. An important and challenging task is the community detection, i.e. the identification of highly connected components. The Girvan Newman algorithm identifies high-quality communities but is not computationally suitable for huge graph analysis. Therefore, we propose a heuristic version of this algorithm, by considering an approximated measure of the edge betweenness. We evaluate the performances of our proposal on benchmark networks

DIAMIN: a software library for the distributed analysis of large-scale molecular interaction networks

Background Huge amounts of molecular interaction data are continuously produced and stored in public databases. Although many bioinformatics tools have been proposed in the literature for their analysis, based on their modeling through different types of biological networks, several problems still remain unsolved when the problem turns on a large scale. Results We propose DIAMIN, that is, a high-level software library to facilitate the development of applications for the efficient analysis of large-scale molecular interaction networks. DIAMIN relies on distributed computing, and it is implemented in Java upon the framework Apache Spark. It delivers a set of functionalities implementing different tasks on an abstract representation of very large graphs, providing a built-in support for methods and algorithms commonly used to analyze these networks. DIAMIN has been tested on data retrieved from two of the most used molecular interactions databases, resulting to be highly efficient and scalable. As shown by different provided examples, DIAMIN can be exploited by users without any distributed programming experience, in order to perform various types of data analysis, and to implement new algorithms based on its primitives. Conclusions The proposed DIAMIN has been proved to be successful in allowing users to solve specific biological problems that can be modeled relying on biological networks, by using its functionalities. The software is freely available and this will hopefully allow its rapid diffusion through the scientific community, to solve both specific data analysis and more complex tasks

Rhythm outcomes of minimally-invasive off-pump surgical versus catheter ablation in atrial fibrillation: A meta-analysis of reconstructed time-to-event data

Background: Mid- and long-term rhythm outcomes of catheter ablation (CA) for atrial fibrillation (AF) are reported to be suboptimal. Minimally invasive surgical off-pump ablation (MISOA), including both thoracoscopic and trans-diaphragmatic approaches, has been developed to reduce surgical invasiveness and overcome on-pump surgery drawbacks. We sought to compare the efficacy and safety of MISOA and CA for AF treatment. Methods: A systematic review and meta-analysis of the literature was performed including studies comparing MISOA and CA. The primary endpoint was survival freedom from AF at follow-up after a 3-month blanking period. Subgroup analysis of the primary endpoint was performed according to the type of surgical incision and hybrid approach. Results: Freedom from AF at 4 years was 52.1% ± 3.2% vs 29.1% ± 3.5%, between MISOA and CA respectively (log-rank p < 0.001; Hazard Ratio: 0.60 [95%Confidence Interval (CI):0.50-0.72], p < 0.001). At landmark analysis, a significant improvement in rhythm outcomes was observed in the MISOA group after the 5th month of follow-up (2 months from the blanking period). The Odds Ratio between MISOA and CA of postoperative cerebrovascular accident incidence and postoperative permanent pacemaker implant (PPM) were 2.00 (95%CI:0.91-4.40, p = 0.084) and 1.55 (95%CI:0.61-3.95, p = 0.358), respectively. The incidence rate ratio of late CVA between MISOA and CA was 0.86 (95%CI:0.28-2.65, p = 0.787), while for late PPM implant was 0.45 (95%CI:0.11-1.78, p = 0.256). Conclusions: The current meta-analysis suggests that MISOA provides superior rhythm outcomes when compared to CA in terms of sinus rhythm restoration. Despite the rhythm outcome superiority of MISOA, it is associated to higher postoperative complications compared to CA

Bladder‐sparing, combined‐modality approach for muscle‐invasive bladder cancer

AbstractBACKGROUND.The authors evaluated their long‐term experience with combined‐modality, conservative treatment in patients with muscle‐invasive bladder cancer.METHODS.In total, 121 patients with T2, T3, or T4 bladder cancer (mean age, 63 years; ratio of men to women, 3:1) underwent induction by transurethral resection (TUR) of the tumor and received 2 cycles of neoadjuvant chemotherapy followed by radiotherapy (RT) (n = 43 patients) or radiochemotherapy (RCT) (n = 78 patients). Six weeks after RT or RCT, responses were evaluated by restaging TUR. Patients who achieved a complete response (CR) were observed at regular intervals. In patients who had persistent or recurrent invasive tumor, further treatment was recommended.RESULTS.Local response evaluation by restaging TUR was possible in 119 patients, and 102 of those patients (85.7%) achieved a CR. After a median follow‐up of 66 months (range, 6–182 months), no local or distant disease recurrences were observed in 67 of 102 complete responders (65.7%), 17 of 102 complete responders (16.7%) experienced superficial local disease recurrence, and 18 of 102 complete responders (17.6%) had a muscle‐invasive relapse. The 5‐year tumor‐specific, overall, and bladder‐intact survival rates were 73.5%, 67.7%, and 51.2%, respectively. Treatment modality, tumor classification, and resection status after initial TUR had an impact on survival rates (P = .04, P = .02, and P = .02, respectively).CONCLUSIONS.The current results indicated that conservative combined treatment is a reasonable alternative to radical cystectomy in selected patients with muscle‐invasive bladder cancer. Cancer 2008. © 2007 American Cancer Society

β-Arrestin-1 expression and epithelial-to-mesenchymal transition in laryngeal carcinoma.

Aim: The novel primary end-point of the present study was to ascertain β-arrestin-1 expression in a cohort of consecutive patients with laryngeal squamous cell carcinoma (LSCC) with information available on their cigarette-smoking habits. A secondary end-point was to conduct a preliminary clinical and pathological investigation into the possible role of β-arrestin-1 in the epithelial-to-mesenchymal transition (EMT), identified by testing for E-cadherin, Zeb1, and Zeb2 expression, in the setting of LSCC. Methods: The expression of β-arrestin-1, E-cadherin, zeb1, and zeb2 was ascertained in 20 consecutive LSCCs. Results: Statistical analysis showed no significant associations between β-arrestin-1 and EMT (based on the expression of E-cadherin, Zeb1, and Zeb2). The combined effect of nicotine and β-arrestin-1 was significantly associated with a shorter disease-free survival ( P=0.01) in our series of LSCC. This latter result was also confirmed in an independent, publicly available LSCC cohort ( P=0.047). Conclusions: Further investigations on larger series (ideally in prospective settings) are needed before we can consider closer follow-up protocols and/or more aggressive treatments for patients with LSCC and a combination of nicotine exposure and β-arrestin-1 positivity in tumor cells at the time of their diagnosis. Further studies on how β-arrestin functions in cancer via different signaling pathways might reveal potential targets for the treatment of even advanced laryngeal malignancies

Risk Factors of Right Ventricular Dysfunction and Adverse Cardiac Events in Patients with Repaired Tetralogy of Fallot

Aim: This study evaluates the risk factors associated with right ventricular (RV) dilation and dysfunction leading to pulmonary valve replacement (PVR) or adverse cardiac events in repaired Tetralogy of Fallot (rToF) patients. Methods: Data from all rToF patients who underwent magnetic resonance imaging (MRI) evaluation at our hospital between February 2007 and September 2020 were collected. Results: Three hundred and forty-two patients (60% males, 42% older than 18 years), with a median age of 16 years (IQR 13–24) at the time of MRI, were included. All patients underwent complete repair at a median age of 8 months (IQR 5–16), while palliation was performed in 56 patients (16%). One hundred and forty-four patients (42%) subsequently received pulmonary valve replacement (PVR). At the multivariate analysis, male gender was an independent predictor for significant RV dilation, RV and left ventricular (LV) dysfunction. Transventricular ventricular septal defect (VSD) closure and previous palliation significantly affected LV function and RV size, respectively. Male gender and the transventricular VSD closure were independent predictors for PVR. Conclusions: Male gender and surgical history (palliation, VSD closure approach) significantly affected the long-term outcomes in rToF patients and should be taken into consideration in the follow-up management and in PVR timing in this patient population

Recurrent differentiated thyroid cancer: to cut or burn

[No abstract available

Low serum total testosterone level as a predictor of upstaging and upgrading in low-risk prostate cancer patients meeting the inclusion criteria for active surveillance

Active surveillance (AS) is currently a widely accepted treatment option for men with clinically localized prostate cancer (PCa). Several reports have highlighted the association of low serum testosterone levels with high-grade, high-stage PCa. However, the impact of serum testosterone as a predictor of progression in men with low-risk PCa has been little assessed.In this study, we evaluated the association of circulating testosterone concentrations with a staging/grading reclassification in a cohort of low-risk PCa patients meeting the inclusion criteria for the AS protocol but opting for radical prostatectomy.Radical prostatectomy (RP) was performed in 338 patients, eligible for AS according to the following criteria: clinical stage T2a or less, PSApT2) and upgrading (GS≥7; primary Gleason pattern 4) disease. Unfavorable disease was defined as the occurrence of pathological stage>pT2 and predominant Gleason score 4. Total testosterone was measured before surgery.Low serum testosterone levels (<300 ng/dL) were significantly associated with upgrading, upstaging, unfavorable disease and positive surgical margins. The addition of testosterone to a base model, including age, PSA, PSA density, clinical stage and positive cancer involvement in cores, showed a significant independent influence of this variable on upstaging, upgrading and unfavorable disease.In conclusion, our results support the idea that total testosterone should be a selection criterion for inclusion of low-risk PCa patients in AS programs and suggest that testosterone level less than 300 ng/dL should be considered a discouraging factor when a close AS program is considered as treatment option