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11.
The excess of phosphorus in soil reduces physiological performances over time but enhances prompt recovery of salt-stressed Arundo donax plants
Claudia Cocozza, Federico Brilli, Sara Pignattelli, Susanna Pollastri, Cecilia Brunetti, Cristina Gonnelli, Roberto Tognetti, Mauro Centritto, Francesco Loreto, 2020, izvirni znanstveni članek

Opis: Arundo donax L. is an invasive grass species with high tolerance to a wide range of environmental stresses. The response of potted A. donax plants to soil stress characterized by prolonged exposure (43 days) to salinity (+Na), to high concentration of phosphorus (+P), and to the combination of high Na and P (+NaP) followed by 14 days of recovery under optimal nutrient solution, was investigated along the entire time-course of the experiment. After an exposure of 43 days, salinity induced a progressive decline in stomatal conductance that hampered A. donax growth through diffusional limitations to photosynthesis and, when combined with high P, reduced the electron transport rate. Isoprene emission from A. donax leaves was stimulated as Na+ concentration raised in leaves. Prolonged growth in P-enriched substrate did not significantly affect A. donax performance, but decreased isoprene emission from leaves. Prolonged exposure of A. donax to + NaP increased the leaf level of H2O2, stimulated the production of carbohydrates, phenylpropanoids, zeaxanthin and increased the de-epoxidation state of the xanthophylls. This might have resulted in a higher stress tolerance that allowed a fast and full recovery following stress relief. Moreover, the high amount of ABA-glucose ester accumulated in leaves of A. donax exposed to + NaP might have favored stomata re-opening further sustaining the observed prompt recovery of photosynthesis. Therefore, prolonged exposure to high P exacerbated the negative effects of salt stress in A. donax plants photosynthetic performances, but enhanced activation of physiological mechanisms that allowed a prompt and full recovery after stress.
Ključne besede: Arundo donax Phosphorus Salinity Stress tolerance Biomass production
Objavljeno v RUNG: 20.04.2020; Ogledov: 2898; Prenosov: 0
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12.
A map-matching algorithm dealing with sparse cellular fingerprint observations
Andrea Dalla Torre, Paolo Gallo, Donatella Gubiani, Chris Marshall, Angelo Montanari, Federico Pittino, Andrea Viel, 2019, izvirni znanstveni članek

Opis: The widespread availability of mobile communication makes mobile devices a resource for the collection of data about mobile infrastructures and user mobility. In these contexts, the problem of reconstructing the most likely trajectory of a device on the road network on the basis of the sequence of observed locations (map-matching problem) turns out to be particularly relevant. Different contributions have demonstrated that the reconstruction of the trajectory of a device with good accuracy is technically feasible even when only a sparse set of GNSS positions is available. In this paper, we face the problem of coping with sparse sequences of cellular fingerprints. Compared to GNSS positions, cellular fingerprints provide coarser spatial information, but they work even when a device is missing GNSS positions or is operating in an energy saving mode. We devise a new map-matching algorithm, that exploits the well-known Hidden Markov Model and Random Forests to successfully deal with noisy and sparse cellular observations. The performance of the proposed solution has been tested over a medium-sized Italian city urban environment by varying both the sampling of the observations and the density of the fingerprint map as well as by including some GPS positions into the sequence of fingerprint observations.
Ključne besede: Map-matching algorithm, trajectory, cellular fingerprint, Hidden Markov Model
Objavljeno v RUNG: 11.06.2019; Ogledov: 3320; Prenosov: 97
.pdf Celotno besedilo (3,93 MB)

13.
Map matching with sparse cellular fingerprint observations
Andrea Viel, Donatella Gubiani, Paolo Gallo, Angelo Montanari, Andrea Dalla Torre, Federico Pittino, Chris Marshall, 2018, objavljeni znanstveni prispevek na konferenci

Ključne besede: map matching, fingerprint, trajectories
Objavljeno v RUNG: 09.12.2018; Ogledov: 3619; Prenosov: 0
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14.
Dealing with network changes in cellular fingerprint positioning systems
Andrea Viel, Paolo Gallo, Angelo Montanari, Donatella Gubiani, Andrea Dalla Torre, Federico Pittino, Chris Marshall, 2017, objavljeni znanstveni prispevek na konferenci

Opis: Besides being a fundamental infrastructure for communication, cellular networks are exploited for positioning through signal fingerprinting. Maintaining the fingerprint database consistent and up-to-date is a challenging task in many fingerprint positioning systems, e.g., in those populated by a crowd-sourcing effort. To this end, detecting and tracking the changes in the configurations of cellular networks over time is recognized as a relevant problem. In this paper, we show that to cope with this problem we can successfully exploit information provided by Timing Advance (TA). As a by-product, we prove that TA can improve the fingerprint candidate selection phase, reducing the number of fingerprints to provide as input to positioning algorithms. The effectiveness of the proposed improvements has been tested on a fingerprint positioning system with a large fingerprint dataset collected over a period of 2 years.
Ključne besede: fingerprint positioning systems, cellular communication networks, network changes
Objavljeno v RUNG: 13.06.2018; Ogledov: 3901; Prenosov: 0
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15.
Hair cortisol concentrations in New Zealand white rabbits subjected to surgery
Tanja Peric, Antonella Comin, Mirco Corazzin, Marta Montillo, Federico Canavese, Marco Stebel, Alberto Prandi, 2018, izvirni znanstveni članek

Opis: The aim of this study was to assess hair cortisol concentrations in New Zealand white rabbits (Oryctolagus cuniculus) that were subjected to relocation and surgery to evaluate HPA-axis activity; in addition, we used this marker of cortisol secretion to evaluate the allostatic load of animals undergoing surgery. After a period of acclimatisation, which lasted 40 days from their arrival at the enclosure, 19 rabbits were subjected to T1–T12 dorsal arthrodesis (RS), 19 were sham-operated (SS), and 19 were non-operated (CON). Hair samples were collected at the time of arrival (ST1) at the animal facility, and seven other sets of hair samples were collected at 40-day intervals from the same area of skin for a period of 240 days as re-shaved hair (anagen phase): immediately before surgery (ST2) and after the surgery (ST3, ST4, ST5, ST6, ST7, and ST8). The transition from the rabbitry to the animal breeding facility led to a significant increase in cortisol concentration (ST2) in all of the groups. At ST3, the RS group presented higher cortisol concentrations than those of the SS group and the CON group. At ST4, the experimental groups showed similar values that remained constant until ST8. The results show that the management of rabbits undergoing surgery should be evaluated very carefully, and hair cortisol concentrations may provide a means of avoiding the dangerous cumulative effects of additional stressors close to surgery.
Ključne besede: animal welfare, cortisol, hair, HPA axis, rabbit, surgery
Objavljeno v RUNG: 09.02.2018; Ogledov: 4030; Prenosov: 0
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Distance-based configurational entropy of proteins from molecular dynamics simulations
Federico Fogolari, Alessandra Corazza, Sara Fortuna, Miguel Angel Soler, Bryan VanSchouwen, Giorgia Brancolini, Stefano Corni, Giuseppe Melacini, Gennaro Esposito, 2015, izvirni znanstveni članek

Opis: Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements; the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state; backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy); the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Ključne besede: entropy, protein, molecular dynamics, simulations, MD
Objavljeno v RUNG: 12.10.2016; Ogledov: 4234; Prenosov: 221
.pdf Celotno besedilo (2,40 MB)

19.
Chelating effect in short polymers for the design of bidentate binders of increased affinity and selectivity
Sara Fortuna, Federico Fogolari, Giacinto Scoles, 2015, izvirni znanstveni članek

Opis: The design of new strong and selective binders is a key step towards the development of new sensing devices and effective drugs. Both affinity and selectivity can be increased through chelation and here we theoretically explore the possibility of coupling two binders through a flexible linker. We prove the enhanced ability of double binders of keeping their target with a simple model where a polymer composed by hard spheres interacts with a spherical macromolecule, such as a protein, through two sticky spots. By Monte Carlo simulations and thermodynamic integration we show the chelating effect to hold for coupling polymers whose radius of gyration is comparable to size of the chelated particle. We show the binding free energy of flexible double binders to be higher than that of two single binders and to be maximized when the binding sites are at distances comparable to the mean free polymer end-to-end distance. The affinity of two coupled binders is therefore predicted to increase non linearly and in turn, by targeting two non-equivalent binding sites, this will lead to higher selectivity.
Ključne besede: chelation, polymer, multivalency, bidentate, free energy, thermodynamic integration, Monte Carlo
Objavljeno v RUNG: 11.10.2016; Ogledov: 4022; Prenosov: 152
.pdf Celotno besedilo (1,68 MB)

20.
Accurate estimation of the entropy of rotation-translation probability distributions
Federico Fogolari, Cedrix Jurgal Dongmo Foumthuim, Sara Fortuna, Miguel Angel Soler, Alessandra Corazza, Gennaro Esposito, 2016, izvirni znanstveni članek

Opis: The estimation of rotational and translational entropies in the context of ligand binding has been the subject of long-time investigations. The high dimensionality (six) of the problem and the limited amount of sampling often prevent the required resolution to provide accurate estimates by the histogram method. Recently, the nearest-neighbor distance method has been applied to the problem, but the solutions provided either address rotation and translation separately, therefore lacking correlations, or use a heuristic approach. Here we address rotational–translational entropy estimation in the context of nearest-neighbor-based entropy estimation, solve the problem numerically, and provide an exact and an approximate method to estimate the full rotational–translational entropy.
Ključne besede: entropy, probability distribution, molecular dynamics, nearest-neighbor
Objavljeno v RUNG: 11.10.2016; Ogledov: 4368; Prenosov: 0
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