104 research outputs found
MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems
No full textMulti-omics analysis aims at extracting previously uncovered biological knowledge by integrating information across multiple single-omic sources. Past approaches have focused on the simultaneous analysis of a small number of omic data sets. Current challenges face the problem of integrating multiple omic sources into a unified complex model, or of combining already available tools for two-by-two omics analyses and merging their outcomes. By doing so and leveraging integrated system-level knowledge, multi-omic approaches ought to enable the development of better qualitative and quantitative models for descriptive and predictive analyses. To move this area forward, new statistical and algorithmic frameworks are needed, for example for generalizing classical graph theory results to heterogeneous networks, and applying them to diverse problems such as drug repurposing or understanding the immune response to infections. Thus, in short, this workshop aims at investigating novel methodologies for providing crucial insights into multi-omics data management, integration, and analysis to enable biological discoveries. The workshop will be sponsored by the InfoLife CINI National Laboratory (https://www.consorzio-cini.it/index.php/en/ )
Blake e Pernice: due metodi a confronto
No full textThe article compares M.E. Blake and E. Pernice books, both issued in the '30 of the past century. Based on work conducted by the Author in Pompeii and Paestum, differences between the two publications are stressed, in order to better evaluate their scope and the impact on fieldwor
Una donna con tre anime di Rosa Rosà. Futurismo, fantascienza, questione femminile
No full textUna donna con tre anime (A Woman with Three Souls) (1918) is the debut novel by Futurist writer, painter and illustrator Rosa Rosà. It tells the story of Giorgina Rossi, a ‘dusty’ and ‘insignificant’ housewife who finds herself experiencing three different transformations of personality. This happens after a storm dispersed some radioactive elements that Professor Ipsilon was working on: a thunderbolt threw them on Giorgina’s house, creating ‘materialized abstractions of time’, making her live fragments of future times. The three souls by which the insignificant housewife is possessed therefore represent as many views of ‘what a woman’s life will be in the future’.After a brief presentation of the author and her work, this paper aims to inquire whether the short novel belongs to the literary genres of utopia and science fiction. Furthermore, it will try to put the work of Rosa Rosà into context within the lively debate on the (Futurist) woman question caused by the release of How to Seduce Women (1917) by F.T. Marinetti. Before publishing her novel, Rosà took part in the discussion through some articles on L’Italia futurista. After taking into account the most significant positions involved, this contribution will analyse the role played by A Woman with Three Souls within the dispute.
Keywords: Futurist woman, science fiction, futurism, Rosa Rosà, uchroni
Estimating Daclizumab effects in Multiple Sclerosis using Stochastic Symmetric Nets
No full textMultiple Sclerosis (MS) is an immune-mediated inflammatory disease of the central nervous system which damages the myelin sheath enveloping nerve cells causing severe physical disability in patients. Relapsing Remitting Multiple Sclerosis (RRMS) is one of the most common form of MS and it is characterized by a series of attacks of new or increasing neurologic symptoms, followed by periods of remission. Recently, many treatments were proposed and studied to contrast the RRMS progression. Among these drugs Daclizumab, an antibody tailored against the interleukin -2 receptor of T cells, exhibited promising results. Unfortunately, more recent studies on Daclizumab highlight severe adverse effects, that led to its retirement from the EU marketing authorization process. Motivated by these recent studies, in this paper we describe how computational modelling can be efficiently exploited to improve our understanding on Daclizumab mechanism of action, and on how this mechanism leads towards the observed undesirable effects
Reply: "An expert forum for the histologic of endometriomas"
No full textFertil Steril. 2007 Feb;87(2):362-6. Epub 2006 Nov 13. Histologic analysis of endometriomas: what the surgeon needs to know. Muzii L, Bianchi A, Bellati F, Cristi E, Pernice M, Zullo MA, Angioli R, Panici PB. Source Department of Obstetrics and Gynecology, University Campus Bio-Medico of Rome, Rome, Italy. [email protected] Abstract OBJECTIVE: To evaluate by thorough pathologic analysis the histologic features of the endometrioma wall excised at laparoscopy. DESIGN: Prospective series of consecutive patients. SETTING: Tertiary care, university hospital. PATIENT(S): Fifty-nine patients with ovarian endometriomas. A total of 70 cysts were examined. INTERVENTION(S): Patients underwent operative laparoscopy with the stripping technique for excision of the ovarian endometrioma. MAIN OUTCOME MEASURE(S): A thorough histologic examination was performed on the entire cyst wall specimen. RESULT(S): Histologic examination confirmed the endometriotic nature of the cyst in 100% of the cases. The inner wall of the endometrioma was covered by endometriotic tissue on 60% of the surface. The mean cyst wall thickness was 1.4 mm. The mean value of maximal depth of endometriosis penetration in the endometrioma wall was 0.6 mm. In 99% of the cases the maximal penetration of the endometriotic tissue was 1.5 mm. These histologic data may help the gynecologic laparoscopist select the surgical approach that maximally preserves healthy ovarian tissue. Comment in Fertil Steril. 2007 Oct;88(4):1017-8; author reply 1018-9. Fertil Steril. 2007 Aug;88(2):534; author reply 534-5
Exploiting Stochastic Petri Net formalism to capture the Relapsing Remitting Multiple Sclerosis variability under Daclizumab administration
No full textUnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale
No full textThis project has received funding from: Ministero dell’Univerisita’ e della Ricerca (MUR) PRIN 2022 project MEDICA: Modelling and vErification of alkaptonuria and multiple sclerosis Driven by biomedICAl data [No 2022RNTYWZ] (MEDICA project to Marco Beccuti) and from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 825410 (ONCOBIOME project to Francesca Cordero and Simone Pernice). The scientific activities of the CINI InfoLife Laboratory supported this research.Motivation
Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognizable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, e.g. to the cancer evolution study.
Results
To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It enables functional studies by combining the analysis of the system’s multi-level stable states with its fluctuating conditions. This approach helps to investigate the functional relationships and dependencies among biological entities. This is achieved, thanks to the hybridization of two analysis approaches that capture a system’s different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal’s effectiveness was demonstrated by mechanistically simulating the metabolic output of Escherichia coli under environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells to Clostridium difficile infection.
Availability and implementation
GreatMod https://qbioturin.github.io/epimod/, epimod_FBAfunctions https://github.com/qBioTurin/epimod_FBAfunctions, first case study E. coli https://github.com/qBioTurin/Ec_coli_modelling, second case study C. difficile https://github.com/qBioTurin/EpiCell_CDifficile.Ministero dell’Univerisita’ e della RicercaEuropean CommissionDepto. de Biodiversidad, Ecología y EvoluciónFac. de Ciencias BiológicasTRUEpu
From compositional Petri Net modeling to macro and micro simulation by means of Stochastic Simulation and Agent-Based models
No full textComputational modeling has become a widespread approach for studying real-world phenomena by using different modeling perspectives, in particular, the microscopic point of view concentrates on the behavior of the single components and their interactions from which the global system evolution emerges, while the macroscopic point of view represents the system’s overall behavior abstracting as much as possible from that of the single components. The preferred point of view depends on the effort required to develop the model, on the detail level of the available information about the system to be modeled, and on the type of measures that are of interest to the modeler; each point of view may lead to a different modeling language and simulation paradigm. An approach adequate for the microscopic point of view is Agent-Based Modeling and Simulation, which has gained popularity in the last few decades but lacks a formal definition common to the different tools supporting it. This may lead to modeling mistakes and wrong interpretation of the results, especially when comparing models of the same system developed according to different points of view. The aim of the work described in this paper is to provide a common compositional modeling language from which both a macro and a micro simulation model can be automatically derived: these models are coherent by construction and may be studied through different simulation approaches and tools. A framework is thus proposed in which a model can be composed using a Petri Net formalism and then studied through both an Agent-Based Simulation and a classical Stochastic Simulation Algorithm, depending on the study goal
Feasibility of conductive embroidered threads for I2C sensors in microcontroller-based wearable electronics
No full textIn recent years, the importance of flexible and textile electronics in the field of wearable devices has continuously increased, as they are expected to replace conventional wires that exhibit limited resistance to the mechanical stress occurring in on-body applications. Wearable health devices (WHDs) can provide physiological information about various body parts and employ distributed sensor networks. Among the sensors typically integrated within WHDs, those based on the I2C communication protocol are very common and exploit signals transmitted at frequencies up to hundreds of kilohertz. Therefore, robust communication is required to guarantee a proper transmission of the signal at those frequencies. In this context, we have realized embroidered conductive threads exhibiting a lower resistance, appositely designed to replace conventional wires in a microcontroller-based wearable device employing I2C sensors. A commercial conductive thread (silver coated polyamide) was used to embroider the conductive lines on to cotton fabric. Preliminary measurements were performed to characterize the response of these materials to signals typically operated within the I2C communication protocol at different path lengths. Resistive measurements have also been performed to stimulate different environmental conditions, that is, temperature, the effect of sweating, and repeated washing cycles, also apply mechanical stress, i.e. twisting, with promising results that validate our conductive paths for digital signal communication
Wearable Multisensor Ring-Shaped Probe for Assessing Stress and Blood Oxygenation: Design and Preliminary Measurements
No full textThe increasing interest in innovative solutions for health and physiological monitoring has recently fostered the development of smaller biomedical devices. These devices are capable of recording an increasingly large number of biosignals simultaneously, while maximizing the user’s comfort. In this study, we have designed and realized a novel wearable multisensor ring-shaped probe that enables synchronous, real-time acquisition of photoplethysmographic (PPG) and galvanic skin response (GSR) signals. The device integrates both the PPG and GSR sensors onto a single probe that can be easily placed on the finger, thereby minimizing the device footprint and overall size. The system enables the extraction of various physiological indices, including heart rate (HR) and its variability, oxygen saturation (SpO2), and GSR levels, as well as their dynamic changes over time, to facilitate the detection of different physiological states, e.g., rest and stress. After a preliminary SpO2 calibration procedure, measurements have been carried out in laboratory on healthy subjects to demonstrate the feasibility of using our system to detect rapid changes in HR, skin conductance, and SpO2 across various physiological conditions (i.e., rest, sudden stress-like situation and breath holding). The early findings encourage the use of the device in daily-life conditions for real-time monitoring of different physiological states
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