Seed cryopreservation of Fraxinus angustifolia Vahl

Fraxinus angustifolia is used for afforestation and for production of both valuable timber and manna, a substance with pharmacological applications. The aim of this research was to establish the optimized condition for cryopreservation of F. angustifolia seeds, in order to protect the germplasm of this species. Germination percentage and mean time of germination of non-treated seeds (control) and liquid nitrogen-treated seeds were established in water or in 10-6 M gibberellic acid (GA3). The seeds could be cryopreserved with 3% of moisture content (MC) and germinated easily in water (70.0 ± 5.0%), while seeds cryopreserved with 6% MC showed a physiological dormancy. This state could be efficiently removed by addition of GA3, which increased germination to 76.0 ± 2.4%. Liquid nitrogen did not impair embryo viability, allowing a successful cryopreservation of seeds. The results are particularly useful for both germplasm conservation programs and in narrow leaved ash nurseries.Keywords: Fraxinus angustifolia, germination, germplasm conservation, seed cryopreservationAfrican Journal of Biotechnology Vol. 12(16), pp. 1930-193

HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA). HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA)

Algoritmi efficienti per la scoperta di pattern ripetuti a intervalli

Dal momento che non esiste ancora sufficiente conoscenza per costruire un adeguato modello dell'informazione, e tale da filtrare sequenze di caratteri rilevanti da altre apparentemente senza significato, si ricorre spesso ad approcci che non prevedono l'uso di un modello di dati. La formulazione di notazioni massimali, senza introdurre perdita d'informazione, cattura importanti caratteristiche sulla struttura interna dei motif e ne riduce drasticamente il numero da analizzare, conferendo un senso all'enorme numero di risultati. In questa tesi propongo un approccio alla codifica delle sequenze nucleotidiche altamente ridondanti, tale da produrre permutazioni numeriche. Questa metodologia, che usa i Suffix Tree, mira a generare codifiche esenti da alterazioni o artefatti dell'informazione genetica producendo, per design, permutazioni "compatibili" con i minimal consensus PQ Tree, i quali sono usati per la creazione della notazione massimale. Si forniscono le motivazioni che hanno ispirato questo approccio, basato sull'analisi della struttura permutativa interna delle stringhe. Si delineano alcuni possibili sviluppi e si forniscono molti esempi accompagnati da un caso d'uso reale

Biomedical Event Extraction as Sequence Labeling

We introduce Biomedical Event Extraction as Sequence Labeling (BeeSL), a joint end-to-end neural information extraction model. BeeSL recasts the task as sequence labeling, taking advantage of a multi-label aware encoding strategy and jointly modeling the intermediate tasks via multi-task learning. BeeSL is fast, accurate, end-to-end, and unlike current methods does not require any external knowledge base or preprocessing tools. BeeSL outperforms the current best system (Li et al., 2019) on the Genia 2011 benchmark by 1.57% absolute F1 score reaching 60.22% F1, establishing a new state of the art for the task. Importantly, we also provide first results on biomedical event extraction without gold entity information. Empirical results show that BeeSL's speed and accuracy makes it a viable approach for large-scale real-world scenarios

HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA). HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA)

Geometric phases along quantum trajectories

A monitored quantum system undergoing a cyclic evolution of the parameters governing its Hamiltonian accumulates a geometric phase that depends on the quantum trajectory followed by the system on its evolution. The phase value will be determined both by the unitary dynamics and by the interaction of the system with the environment. Consequently, the geometric phase will acquire a stochastic character due to the occurrence of random quantum jumps. Here we study the distribution function of geometric phases in monitored quantum systems and discuss when/if different quantities, proposed to measure geometric phases in open quantum systems, are representative of the distribution. We also consider a monitored echo protocol and discuss in which cases the distribution of the interference pattern extracted in the experiment is linked to the geometric phase. Furthermore, we unveil, for the single trajectory exhibiting no quantum jumps, a topological transition in the phase acquired after a cycle and show how this critical behavior can be observed in an echo protocol. For the same parameters, the density matrix does not show any singularity. We illustrate all our main results by considering a paradigmatic case, a spin-1/2 immersed in time-varying a magnetic field in presence of an external environment. The major outcomes of our analysis are however quite general and do not depend, in their qualitative features, on the choice of the model studied.Comment: 20 pages, 15 figure

Adsorption of triblock copolymers and their homopolymers at laponite clay/solution interface. Role played by the copolymer nature

The adsorption thermodynamics of copolymers, based on ethylene oxide (EO) and propylene oxide ( PO) units, at the laponite (RD) clay/liquid interface was determined at 298 K. The copolymer nature was tuned at molecular level by changing the hydrophilicity, the architecture and the molecular weight (Mw) keeping constant the EO/PO ratio. Polyethylene (PEGs) and polypropylene (PPGs) glycols with varying Mw and their mixture were also investigated to discriminate the role of the EO and the PO segments in the adsorption process. Enthalpies of transfer of RD, at fixed concentration, from water to the aqueous macromolecule solutions as functions of the macromolecule molality were determined. They were treated quantitatively by means of a model based on two equilibria: ( 1) one-to-one binding between the macromolecule and the site on the solid and ( 2) two-to-one binding following which one macromolecule interacts with another one adsorbed onto the solid. The good agreement between the equilibrium constants obtained from calorimetry and those determined from kinetic experiments conformed the reliability of the experimental and theoretical approaches. Almost all of the systems investigated are highlighted by the one-to-one binding; the L35 and 10R5 systems present both equilibria. The insights provided by the thermodynamics of adsorption of their homopolymers onto RD were fruitful in obtaining detailed information on the nature of the forces involved between RD and the copolymers. The data obtained in the present work clearly evidenced that for comparable polymer Mw, PPG is more suitable in building up a steric barrier around the RD particles and, indeed, exhibits several advantages and no drawbacks. Moreover, the parent copolymers may properly functionalize the RD surface by exploiting both their high affinity to the solid surface and the ability to self-assemble onto it as L35 and 10R5 clearly showed