Automated analysis of calcium spiking profiles with CaSA software: two case studies from root-microbe symbioses

BACKGROUND: Repeated oscillations in intracellular calcium (Ca(2+)) concentration, known as Ca(2+) spiking signals, have been described in plants for a limited number of cellular responses to biotic or abiotic stimuli and most notably the common symbiotic signaling pathway (CSSP) which mediates the recognition by their plant hosts of two endosymbiotic microbes, arbuscular mycorrhizal (AM) fungi and nitrogen fixing rhizobia. The detailed analysis of the complexity and variability of the Ca(2+) spiking patterns which have been revealed in recent studies requires both extensive datasets and sophisticated statistical tools. RESULTS: As a contribution, we have developed automated Ca(2+) spiking analysis (CaSA) software that performs i) automated peak detection, ii) statistical analyses based on the detected peaks, iii) autocorrelation analysis of peak-to-peak intervals to highlight major traits in the spiking pattern. We have evaluated CaSA in two experimental studies. In the first, CaSA highlighted unpredicted differences in the spiking patterns induced in Medicago truncatula root epidermal cells by exudates of the AM fungus Gigaspora margarita as a function of the phosphate concentration in the growth medium of both host and fungus. In the second study we compared the spiking patterns triggered by either AM fungal or rhizobial symbiotic signals. CaSA revealed the existence of different patterns in signal periodicity, which are thought to contribute to the so-called Ca(2+) signature. CONCLUSIONS: We therefore propose CaSA as a useful tool for characterizing oscillatory biological phenomena such as Ca(2+) spiking

COVID-19 and slowdown of residents' activity: Feedback from a novel e-learning event and overview of the literature

Objective: To evaluate the impact of an e-learning online event, created for supporting resident's training during the slowdown of surgical and clinical activities caused by COVID-19 pandemic. An overview of PubMed literature depicting the state of the art of urology residency in the COVID-19 era was performed as well, to contextualize the issue.Methods: An online learning event for residents was set up at the beginning of the pandemic; the faculty consisted of experts in urology who provided on-line lectures and videos on surgical anatomy, procedures, updates in guidelines, technology, training. The audience was composed of 30-500 attendees from Italy, USA, India and Belgium. A questionnaire to analyze relevance, satisfaction and popularity of the lessons was mailed to 30 local residents.Results and limitations: Almost all residents defined the web environment suitable to achieve the learning outcomes; the method, the number and the competence of the faculty were appropriate/excellent. Most of the younger residents (81.8%) stated their surgical knowledge would improve after the course; 72.7% declared they would take advantage into routine inpatients clinical activity. Nineteen more expert residents agreed that the course would improve their surgical knowledge and enhance their practical skills; almost all stated that the initiative would change their outpatients and inpatients practice. Overall, 44 articles available in PubMed have addressed the concern of urological learning and training during the pandemic from different standpoints; four of them considered residents' general perception towards web-based learning programs.Conclusions: The paper confirms residents' satisfaction with e-learning methods and, to our knowledge, is the first one focusing on a specific event promptly settled up at the beginning of the outbreak. Web-based educational experience developed during the pandemic may represent the very basis for the implementation of prospective on-site training and overall scientific update of future urologists

Clinical characteristics and predictors of death among hospitalized patients infected with SARS-CoV-2 in Sicily, Italy: A retrospective observational study

Since late December 2019, severe acute respiratory syndrome coronavirus 2 has spread across the world, which resulted in the World Health Organization declaring a global pandemic. Coronavirus disease 2019 (COVID-19) presents a highly variable spectrum with regard to the severity of illness. Most infected individuals exhibit a mild to moderate illness (81%); however, 14% have a serious disease and 5% develop severe acute respiratory distress syndrome (ARDS), requiring intensive care support. The mortality rate of COVID-19 continues to rise across the world. Data regarding predictors of mortality in patients with COVID 19 are still scarce but are being actively investigated. The present multicenter retrospective observational study provides a complete description of the demographic and clinical characteristics, comorbidities and laboratory abnormalities in a population of 421 hospitalized patients recruited across eight infectious disease units in Southern Italy (Sicily) with the aim of identifying the baseline characteristics predisposing COVID-19 patients to critical illness or death. In this study, older age, pre-existing comorbidities and certain changes in laboratory markers (such as neutrophilia, lymphocytopenia and increased C-reactive protein levels) at the time of admission were associated with a higher risk of mortality. Male sex, on the other hand, was not significantly associated with increased risk of mortality. Symptoms such as fatigue, older age, a number of co-pathologies and use of continuous positive airway pressure were the most significant contributors in the estimation of clinical prognosis. Further research is required to better characterize the epidemiological features of COVID-19, to understand the related predictors of death and to develop new effective therapeutic strategies

Prevalence of CKD in Northeastern Italy: Results of the INCIPE Study and Comparison with NHANES

Background and objectives: Sufficiently powered studies to investigate the CKD prevalence are few and do not cover southern Europe

Proceedings Third International Workshop on Computational Models for Cell Processes

This volume contains the final versions of the papers presented at the 3rd International Workshop on Computational Models for Cell Processes (CompMod 2011). The workshop took place on September 10, 2011 at the University of Aachen, Germany, in conjunction with CONCUR 2011. The first edition of the workshop (2008) took place in Turku, Finland, in conjunction with Formal Methods 2008 and the second edition (2009) took place in Eindhoven, the Netherlands, as well in conjunction with Formal Methods 2009. The goal of the CompMod workshop series is to bring together researchers in Computer Science (especially in Formal Methods) and Mathematics (both discrete and continuous), interested in the opportunities and the challenges of Systems Biology