Coherent transport in Josephson-Junction rhombi chain with quenched disorder

We consider a chain of Josephson-junction rhombi (proposed originally by Doucot and Vidal) in quantum regime. In a regular chain with no disorder in the maximally frustrated case when magnetic flux through each rhombi \Phi_r is equal to one half of superconductive flux quantum \Phi_0, Josephson current is due to correlated transport of pairs of Cooper pairs, i.e. charge is quantized in units of $4e$. Sufficiently strong deviation \delta\Phi =|\Phi_r-\Phi_0/2| > \delta\Phi^c from the maximally frustrated point brings the system back to usual $2e$-quantized supercurrent. For a regular chain \delta\Phi^c was calculated by us previously. Here we present detailed analysis of the effect of quenched disorder (random stray charges and random fluxes piercing rhombi) on the pairing effect.Comment: 21 pages, 5 figure

Magnetic screening in proximity effect Josephson-junction arrays

The modulation with magnetic field of the sheet inductance measured on proximity effect Josephson-junction arrays (JJAs) is progressively vanishing on lowering the temperature, leading to a low temperature field-independent response. This behaviour is consistent with the decrease of the two-dimensional penetration length below the lattice parameter. Low temperature data are quantitatively compared with theoretical predictions based on the XY model in absence of thermal fluctuations. The results show that the description of a JJA within the XY model is incomplete and the system is put well beyond the weak screening limit which is usually assumed in order to invoke the well known frustrated XY model describing classical Josephson-junction arrays.Comment: 6 pages, 5 figure

Automatic generation of pseudoknotted RNAs taxonomy

Background: The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as 16S rRNA. Most comparison methods and benchmarks in the literature focus on pseudoknot-free structures due to the difficulty of mapping pseudoknots in classical tree representations. Some approaches exist that permit to cluster pseudoknotted RNAs but there is not a general framework for evaluating their performance. Results: We introduce an evaluation framework based on a similarity/dissimilarity measure obtained by a comparison method and agglomerative clustering. Their combination automatically partition a set of molecules into groups. To illustrate the framework we define and make available a benchmark of pseudoknotted (16S and 23S) and pseudoknot-free (5S) rRNA secondary structures belonging to Archaea, Bacteria and Eukaryota. We also consider five different comparison methods from the literature that are able to manage pseudoknots. For each method we clusterize the molecules in the benchmark to obtain the taxa at the rank phylum according to the European Nucleotide Archive curated taxonomy. We compute appropriate metrics for each method and we compare their suitability to reconstruct the taxa

Bone Remodelling in BioShape

AbstractMany biological phenomena are inherently multiscale, i.e. they are characterised by interactions involving different scales at the same time. This is the case of bone remodelling, where macroscopic behaviour (at organ and tissue scale) and microstructure (at cell scale) strongly influence each other. Consequently, several approaches have been defined to model such a process at different spatial and temporal levels and, in particular, in terms of continuum properties, abstracting in this way from a realistic – and more complex – cellular scenario. While a large amount of information is available to validate such models separately, more work is needed to integrate all levels fully in a faithful multiscale model.In this scenario, we propose the use of BioShape, a 3D particle-based, scale-independent, geometry and space oriented simulator. It is used to define and integrate a cell and tissue scale model for bone remodelling in terms of shapes equipped with perception, interaction and movement capabilities. Their in-silico simulation allows for tuning continuum-based tissutal and cellular models, as well as for better understanding – both in qualitative and in quantitative terms – the blurry synergy between mechanical and metabolic factors triggering bone remodelling

Timed Operational Semantics and Well-Formedness of Shape Calculus

The Shape Calculus is a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel that models naturally binding sites on the surface of shapes. In this paper, the full formal timed operational semantics of the calculus is provided, together with examples that illustrate the use of the calculus in a well-known biological scenario. Moreover, a result of well-formedness about the evolution of a given network of well-formed 3D processes is proved

Self-association of a highly charged, arginine-rich cell-penetrating peptide

Small angle X-ray scattering (SAXS) measurements reveal a striking difference in intermolecular interactions between two short, highly charged peptides, namely deca-arginine (R10) and deca-lysine (K10). Comparison of SAXS curves at high and low salt concentration shows that R10 self-associates, while interactions between K10 chains are purely repulsive. The self-association of R10 occurs to a larger extent at low ionic strength indicating that the attraction between R10 molecules has an important electrostatic component. SAXS data is complemented by potentials of mean force between the peptides calculated by means of umbrella sampling molecular dynamics (MD) simulations. Atomistic MD simulations elucidate the origin of the R10-R10 attraction by providing structural information on the dimeric state: the last two C-terminal residues of R10 constitute an adhesive patch achieved by stacking of the side chains of two arginine residues and by salt bridges formed between the like-charge ion-pair and C-terminal carboxyl groups. A statistical analysis of the protein data bank reveals that this mode of interaction commonly occurs in proteins. Please click Additional Files below to see the full abstract

In vitro irradiation system for radiobiological experiments

Background: Although two-dimensional (2-D) monolayer cell cultures provide important information on basic tumor biology and radiobiology, they are not representative of the complexity of three-dimensional (3-D) solid tumors. In particular, new models reproducing clinical conditions as closely as possible are needed for radiobiological studies to provide information that can be translated from bench to bedside. Methods: We developed a novel system for the irradiation, under sterile conditions, of 3-D tumor spheroids, the in vitro model considered as a bridge between the complex architectural organization of in vivo tumors and the very simple one of in vitro monolayer cell cultures. The system exploits the same equipment as that used for patient treatments, without the need for dedicated and highly expensive instruments. To mimic the passage of radiation beams through human tissues before they reach the target tumor mass, 96-multiwell plates containing the multicellular tumor spheroids (MCTS) are inserted into a custom-built phantom made of plexiglass, the material most similar to water, the main component of human tissue. Results: The system was used to irradiate CAEP- and A549-derived MCTS, pre-treated or not with 20 \u3bcM cisplatin, with a dose of 20 Gy delivered in one session. We also tested the same treatment schemes on monolayer CAEP and A549 cells. Our preliminary results indicated a significant increment in radiotoxicity 20 days after the end of irradiation in the CAEP spheroids pre-treated with cisplatin compared to those treated with cisplatin or irradiation alone. Conversely, the effect of the radio- chemotherapy combination in A549-derived MCTS was similar to that induced by cisplatin or irradiation alone. Finally, the 20 Gy dose did not affect cell survival in monolayer CAEP and A549 cells, whereas cisplatin or cisplatin plus radiation caused 100% cell death, regardless of the type of cell line used. Conclusions: We set up a system for the irradiation, under sterile conditions, of tumor cells grown in 3-D which allows for the use of the same dose intensities and schedules utilized in clinical practice. This irradiation system, coupled with 3-D cell cultures, has the potential to generate information that could be used to individually tailor radiotherap

Determinazione del carvacrolo mediante HRGC-MS/FID nell'orata (Sparus aurata) di acquacoltura

Le proprietà antimicrobiche del carvacrolo sono state ampiamente descritte soprattutto sulla base di osservazioni in vitro. L’ampia diffusione “zootecnica” di Sparus aurata ha determinato in questi ultimi decenni il diffondersi di patologie batteriche come la pasteurellosi e la vibriosi. La sperimentazione è stata condotta per 45 giorni su orate (Sparus aurata) del peso medio di 150 g la cui razione alimentare giornaliera è stata incorporata con l’1% di carvacrolo, e su orate alimentate con il mangime base nello stesso periodo (gruppo controllo). La frazione lipidica è stata estratta dal muscolo mediante metodo di Folch modificato. L’identificazione del carvacrolo è stata effettuata via HRGC-MS. L’analisi quantitativa è stata valutata nelle stesse condizioni cromatografiche ma con detector a ionizzazione di fiamma (FID) in presenza di standard interno (n-dodecanolo). La procedura ha consentito il recupero del 98,97% circa del carvacrolo con un limite di rilevabilità pari a 0,5 ppm

CDKN1A upregulation and cisplatin-pemetrexed resistance in non-small cell lung cancer cells

Cisplatin-pemetrexed is a frequently adopted first-line treatment for patients with advanced non-small cell lung cancer (NSCLC) ineligible for biological therapy, notwithstanding its limited efficacy. In the present study, the RAL cell line, an epidermal growth factor receptor (EGFR)-wild-type, p53- and KRAS-mutated model of NSCLC, was used to investigate novel biomarkers of resistance to this treatment. Cells were analyzed 96 h (96 h-post wo) and 21 days (21 days-post wo) after the combined treatment washout. Following an initial moderate sensitivity to the treatment, the cell growth proliferative capability had fully recovered. Gene expression analysis of the resistant surviving cells revealed a significant upregulation of CDKN1A expression in the cells at 96-h post-wo and, although to a lesser extent, in the cells at 21 days-post wo, accompanied by an enrichment of acetylated histone H3 in its promoter region. CDKN1A was also upregulated at the protein level, being mainly detected in the cytoplasm of the cells at 96 h-post wo. A marked increase in the number of apoptotic cells, together with a significant G1 phase block, were observed at 96-h post wo in the cells in which CDKN1A was knocked down, suggesting its involvement in the modulation of the response of RAL cells to the drug combination. On the whole, these data suggest that CDKN1A plays a role in the response to the cisplatin-pemetrexed combination in advanced KRAS-mutated NSCLC, thus suggesting that it may be used as a promising predictive marker

Curva di apprendimento nella scialoendoscopia diagnostica e interventistica per le patologie salivari ostruttive

La scialoendoscopia è un nuovo strumento diagnostico e chirurgico che offre l’opportunità di trattare alcune patologie delle ghiandole salivari con procedure non invasive e con risultati potenzialmente superiori alle precedenti tecniche. Come per tutte le nuove tecniche, per raggiungere rapidamente risultati paragonabili a quelli riportati in letteratura, è indispensabile un corretto programma di formazione che segua una graduale curva di apprendimento. Questo include un appropriato programma diagnostico, una corretta selezione dei pazienti e la conoscenza delle possibili insidie operatorie. Abbiamo eseguito uno studio retrospettivo confrontando le prime 141 procedure (74 parotidee e 67 sottomandibolari) eseguite con questa tecnica nel nostro Dipartimento dal 2009 al 2013 con analoghe esperienze riportate in letteratura. I pazienti sono stati divisi in 3 gruppi: Gruppo A (le prime 49 procedure effettuate), gruppo B (le successive 50), Gruppo C (le ultime 42 procedure effettuate). Fra i tre gruppi non sono state evidenziate differenze statisticamente significative nei tempi medi di durata delle procedure, nella percentuale di ricorrenza della sintomatologia dopo il trattamento, nel numero di pazienti che hanno necessitato di più trattamenti e nell’incidenza di complicanze minori. Non sono state riportate complicanze maggiori. Con l’acquisizione di una maggiore esperienza da parte dei chirurghi si è evidenziato un progressivo calo del numero di interventi eseguiti in anestesia generale rispetto a quelli in anestesia locale (51% vs 18% vs 14%). Solo in tre casi su 130 ghiandole trattate (2.3%) è stato necessario eseguire un’asportazione ghiandolare. Per i calcoli salivari è stato valutato il tipo di tecnica utilizzato per l’estrazione e la percentuale d’insuccesso che era analoga nei tre gruppi (13.6% vs 15% vs 15%). I nostri risultati non differiscono sostanzialmente da quelli riportati in letteratura. Abbiamo risolto la difficoltà iniziale nella cateterizzazione del dotto con esercizi chirurgici su cadavere o su teste di maiale. La mancanza di precisione degli strumenti diagnostici radiologici può essere migliorata autonomizzando il chirurgo nell’esecuzione delle ecografie pre e post-operatorie. Viene infine sottolineata l’opportunità di creare dei centri di scialoendoscopia con un bacino di utenza di circa 1 o 2 milioni di abitanti in modo da concentrare le patologie, far fronte agli elevati costi della strumentazione necessaria e poter guadagnare la necessaria esperienza nelle gestione delle varie tecniche chirurgiche