423 research outputs found
Dizionario di miti, leggende, costumi greco-romani
No full textDizionario di miti, leggende, costumi greco-romani / Giovanni Stano. - Manduria : Prem. tip. cav. B. D\u27Errico, 1925
Dedica manoscritta dell\u27autore: A Sua Eccell. / Bodrero / Omaggio / Giovanni Stano / R. Ginnasio - Taranto
https://galileodiscovery.unipd.it/discovery/fulldisplay?context=L&vid=39UPD_INST:VU1&search_scope=MyInst_and_CI&tab=Everything&docid=alma99000192265020604
General Lines, Routes and Perspectives of Wetware Embodied AI. From its Organizational Bases to a Glimpse on Social Chemical Robotics
No full textBottom-Up Synthetic Biology Leads to Artificial Cells as Innovative Materials and Calls for the Adoption of Systemic Perspectives
No full textOPEN QUESTIONS IN ORIGIN OF LIFE: EXPERIMENTAL STUDIES ON THE ORIGIN OF NUCLEIC ACIDS AND PROTEINS WITH SPECIFIC AND FUNCTIONAL SEQUENCES BY A CHEMICAL SYNTHETIC BIOLOGY APPROACH
No full textIn this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the chemical viewpoint, macromolecules are formed by chemical pathways leading to the condensation of building blocks (amino acids, or nucleotides) in long-chain copolymers (proteins and nucleic acids, respectively). The second difficulty deals with a conceptual problem, namely with the emergence of specific sequences among a vast array of possible ones, the huge “sequence space”, leading to the question “why these macromolecules, and not the others?”
We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides, like Ser-His, with respect to peptide- and nucleotides-condensation, as a realistic model of primitive organocatalysis. We have also set up a strategy for exploring the sequence space of random proteins and RNAs (the so-called “never born biopolymer” project) with respect to the production of folded structures. Being still far from solved, the main aspects of these “open questions” are discussed here, by commenting on recent results obtained in our groups and by providing a unifying view on the problem and possible solutions. In particular, we propose a general scenario for macromolecule formation via fragment-condensation, as a scheme for the emergence of specific sequences based on molecular growth and selection
Nonlinear State and Parameter Estimation for Hopper Dredgers
No full textA Trailing Suction Hopper Dredger (TSHD) is a ship that excavates sediments from the sea bottom while sailing. In situ material is excavated with a special tool called the Drag-Head, then it is hydraulically transported through a pipe to the hopper where it is temporarily stored. After the dredging is completed the collected material is transported and discharged at a specified location. The efficiency of this process is highly dependent on the detailed knowledge of the excavated soil. The optimization of dredging operations is of vital importance for future improvement in efficiency, accuracy and from the viewpoint of labor saving. The automated onboard systems that have been developed to optimize the dredging performance require knowledge of several uncertain soil-dependent parameters. These cannot be directly measured but have to be estimated online from the available measurements. Such estimation is a challenging task due to lack of sufficient sensors, severe nonlinearities in models, and time-varying nature of the parameters of interest. In this thesis we focus on two of the most important TSHD-related models. These are: I. Drag-Head Model - describing the excavation process, II. Hopper Model - describing the sedimentation process occurring inside the hopper. They contain several uncertain soil-dependent parameters that need to be estimated. These are: I. horizontal cutting force coefficient kch (Drag-Head Model ), II. ratio kvh between the horizontal and vertical cutting forces (Drag-Head Model ), III. in situ permeability ksi (Drag-Head Model ), IV. average grain diameter dm (Hopper Model ). Both processes, together with the corresponding estimation problems, are discussed in detail in Chapter 2. The highly uncertain and time-varying nature of the soil-dependent parameters and the nonlinear dynamics of the models used to describe dredging process make the estimation a challenging task. The algorithms that are capable of tackling these type of problems are Nonlinear Bayesian Filters (NBF). In Chapter 3 we review several types of NBF, namely: I. parametric filters based on the Taylor series expansion (EKF, IEKF), II. parametric filters based on statistical approximations (UKF, GHF, CDF), III. parametric filters based on Gaussian Sum approximations (GSF), IV. nonparametric filters based on the importance sampling (BPF), V. nonparametric filters based on the mean-field control-oriented approach (FPF). In Chapter 4 we investigate the applicability of these nonlinear filters to the estimation problems that originate from the Drag-Head Model. The problems are: the Cutting Estimation Problem and the Cutting and Jetting Estimation Problem. The Cutting Estimation Problem applies for any cutting excavation tool whereas the Cutting and Jetting Estimation Problem is applicable only for tools equipped with cutting and jetting components. The former problem considers estimation of the ratio kvh between cutting forces and the horizontal cutting force coefficient kch, the latter problem deals with the estimation of the horizontal cutting force coefficient kch and the in situ permeability ksi. To solve the aforementioned estimation problems one needs to handle time-varying delay in the measurement of incoming density ?i, which is discussed separately. It is concluded that among the tested methods the best solution to the Cutting Estimation Problem is provided by the CDF and, in case of large uncertainty in the initial states, by the GSF. To solve the Cutting and Jetting Estimation Problem it is crucial to exploit the correlation between the horizontal cutting force coefficient kch and the in situ permeability ksi. This is done by a cascaded filter, which uses the PF to obtain an estimate of ksi, which will be further filtered by a Steady State Identification (SSI) filter, and finally by the BF to produce a final estimate of kch. In Chapter 5 we develop a novel class of nonlinear particle filters: the Saturated Particle Filter (SPF) that is used to solve the Hopper Estimation Problem. The SPF is a general method designed for Saturated Stochastic Dynamical Systems (SSDS), which are severely nonlinear systems often used in modeling real-life problems. They are characterized by a constrained probability distribution exhibiting singularity on the boundary of the saturation region. Such singularities make it difficult to estimate the states or the parameters of SSDSs by standard nonlinear filters. Our new method exploits the specific structure of the SSDS in order to design an importance sampling distribution that accounts for the most recent measurements in the prediction step of the filtering algorithm. Chapter 6 deals with the asymptotic properties of the SPF. We establish the conditions under which the SPF converges to the optimal theoretical filter. The convergence of our method is closely related to the appropriate resampling scheme. This led to the development of the improved Saturated Particle Filter (iSPF) which combines the importance sampling of the SPF with a novel resampling algorithm. In Chapter 7 the iSPF together with other nonparametric methods from Chapter 3 are used to estimate the average grain diameter dm, which solves the Hopper Estimation Problem. Because the sedimentation process is naturally divided into three regimes, to find the most efficient filtering method we considered each mode separately. We conclude that: I. for the No-Overflow loading phase the best estimate of dm is obtained by the FPF, II. for the Overflow loading phases with weak erosion, the recommended filtering method is the Reduced-Order PF, III. for the Overflow loading phases with strong erosion, the best estimation performance is achieved by the Reduced-Order PF when the excavated soil is fine and the Hybrid SPF when the excavated soil is coarse. The final solution to the Hopper Estimation Problem is obtained by integrating the filters designed for separate modes into a global estimator. Chapter 8 concludes the thesis.Delft Center for Systems and ControlMechanical, Maritime and Materials Engineerin
Quasi-cellular systems: stochastic simulation analysis at nanoscale range
No full textBackground: The wet-lab synthesis of the simplest forms of life (minimal cells) is a challenging aspect in modern
synthetic biology. Quasi-cellular systems able to produce proteins directly from DNA can be obtained by
encapsulating the cell-free transcription/translation system PURESYSTEMTM(PS) in liposomes. It is possible to detect
the intra-vesicle protein production using DNA encoding for GFP and monitoring the fluorescence emission over
time. The entrapment of solutes in small-volume liposomes is a fundamental open problem. Stochastic simulation
is a valuable tool in the study of biochemical reaction at nanoscale range. QDC (Quick Direct-Method Controlled), a
stochastic simulation software based on the well-known Gillespie’s SSA algorithm, was used. A suitable model
formally describing the PS reactions network was developed, to predict, from inner species concentrations (very
difficult to measure in small-volumes), the resulting fluorescence signal (experimentally observable).
Results: Thanks to suitable features specific of QDC, we successfully formalized the dynamical coupling between
the transcription and translation processes that occurs in the real PS, thus bypassing the concurrent-only
environment of Gillespie’s algorithm. Simulations were firstly performed for large liposomes (2.67μm of diameter)
entrapping the PS to synthetize GFP. By varying the initial concentrations of the three main classes of molecules
involved in the PS (DNA, enzymes, consumables), we were able to stochastically simulate the time-course of GFPproduction.
The sigmoid fit of the GFP-production curves allowed us to extract three quantitative parameters
which are significantly dependent on the various initial states. Then we extended this study for small-volume
liposomes (575 nm of diameter), where it is more complex to infer the intra-vesicle composition, due to the
expected anomalous entrapment phenomena. We identified almost two extreme states that are forecasted to give
rise to significantly different experimental observables.
Conclusions: The present work is the first one describing in the detail the stochastic behavior of the PS. Thanks to our
results, an experimental approach is now possible, aimed at recording the GFP production kinetics in very small microemulsion
droplets or liposomes, and inferring, by using the simulation as a reverse-engineering procedure, the internal
solutes distribution, and shed light on the still unknown forces driving the entrapment phenomenon
Case report of gastrointestinal localization of SARS-CoV-2 and open abdomen technique in an Italian emergency surgery department for gastrointestinal bleeding
No full textThis article aims to present the case of a man affected by SARS CoV-2 and to discuss the association between this manifestation, viral infection and Open Abodmen. A 52 years old Caucasian man, affected by SARS CoV-2 infection, was admitted to the Emergency department of Arcispedale Sant'Anna of Ferrara for epigastralgia followed by syncopal episode, vomiting and diarrhea with bloody stools. The next day the patient underwent colonoscopy, which detected an ulceration proximally to the ileocecal valve without active bleeding. Subsequently an initial non-operative management and two pharyngeal swabs negative, for another rectorrhagia and hypotensive episode, underwent emerging surgery and an Open Abdomen was performed. The patient was discharged in 12th post-surgery day without complications. The IHC analysis with anti-SARS-CoV-2 nucleocapsid-protein revealed the presence of viral protein expression in epithelial cell of ulcerated intestinal mucosa. In this case report, we showed the presence of viral inclusion in small intestinal wall after two negative pharyngeal swabs for SARS-CoV-2 RNA. We can also say that the largest amount of viral inclusions was in the tissue of ulceration of the last ileal loop. This case report showed that SARS-CoV-2 can be unseen also after clinical healing. It's probably can be expelled with stools and rectal swabs search for SARS-Cov-2 RNA after pharyngeal swabs could be mandatory for declare heled a patient. Moreover, damage control surgery and Open Abdomen as a surgical technique can be a valid alternative in case of uncertainty of the bleeding source and when a second surgical look is necessary
Electrostatically Cross-Linked Reversible Gels - Effects of pH and Ionic Strength
No full textMixing of oppositely charged macromolecules can, under certain conditions, lead to the formation of electrostatically cross-linked coacervate gels. In this simulation study, we determine the conditions under which equimolar mixtures of oppositely charged monodisperse four-armed star copolymers with charged end-blocks are able to form such coacervate gels. The cationic charged blocks consist of quenched charges, whereas the anionic blocks contain pH-responsive weak acid groups. We used the Grand-reaction method to determine the phase stability, equilibrium composition, and structural properties of these systems in equilibrium with a supernatant solution at various pH levels and salt concentrations. Depending on the pH and hence on the charge state of the polyanion blocks, we observed the emergence of three regimes: a solution, a sol of isolated star clusters, and a gel-percolating network of stars. Moreover, we demonstrate that the charge state of the stars in the gel phase can be well described by the ideal Henderson-Hasselbalch (HH) equation, despite the presence of strong interactions violating ideality. We can backtrace this surprising result to two deviations from the ideal titration behavior that almost quantitatively cancel each other. This observation explains why various experiments on coacervate gels can be well described by the HH equation, even though the basic assumptions of ideality are clearly violated
Experimental evidences suggest high between-vesicle diversity of artificial vesicle populations: Results, models and implications
No full textIn the past years, artificial cellular models for origins-of-life research and synthetic biology have been extensively studied. At this aim, solute-filled lipid vesicles (liposomes) are widely used. Several evidences have been collected about the capture of water-soluble chemicals, the mechanism of vesicle self-reproduction, and the course of (bio)chemical reactions in the vesicle lumen. Among the several fascinating questions which emerged from these studies, here we focus on a peculiar feature, namely, the fact that a spontaneous heterogeneity of vesicle structure often emerges. In other words, vesicle populations created in the laboratory by classical batch methods include very ‘diverse’ vesicles with respect to size, morphology, and – importantly – solute content. The consequences of this between-vesicle diversity are shortly discussed
En route for implanting a minimal chemical perceptron into artificial cells
No full textThis paper describes a potentially rewarding research program
aimed at designing, modeling, analyzing and experimentally
realizing artificial cells in the wetware domain endowed with a
‘neural network’-like module for achieving minimal perception.
In particular, we present a possible implementation based on
bacterial phosphorylation signaling networks (dubbed as
“phospho-neural network” by Hellingwerf and collaborators in
1995 ). At this initial stage only preliminary discussions are
possible. The scenario we devise minimizes unrealistic
assumptions and it is based on the state-of-the-art of
contemporary artificial cell technology. This contribution is
intended as a plan to foster the construction and the theoretical
analysis of next-generation artificial cells
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