Protein structure and functionally-oriented dynamics: from atomistic to Coarse-grained models

The overwhelming majority of biological processes relies on the capability of proteins to sustain conformational changes so to selectively recognise, bind and process other molecules, being them proteins, nucleic acids or other chemical compounds. The paradigmatic tripartite characterization of proteins in terms of sequence\u2192structure\u2192function has served to interpret the above-mentioned capability as being encoded in proteins' native structures, which is in turn determined by the amino acidic sequence..

Network Effects in Technology Acceptance: Laboratory Evidence

This research analyzes network effects in technology acceptance on the hypothesis that the larger the user network, the more likely technology acceptance is. Still today, empirical measurement of network effects is challenging and there is a lack of experimental evidence, particularly in technology acceptance research. To overcome this limitation we reproduce a particular class of technology acceptance processes in a laboratory experiment, controlling for the user network size to verify if it can make a difference in user perceptions and, ultimately, in acceptance decisions. We measured user perceptions and analyzed the data set using standard technology acceptance models. The experiments confirm our working hypothesis, showing a significant role of network effects on key user perceptions influencing technology acceptance

Comprehensive analysis of the membrane phosphoproteome regulated by oligogalacturonides in Arabidopsis thaliana

Early changes in the Arabidopsis thaliana membrane phosphoproteome in response to oligogalacturonides (OGs), a class of plant damage-associated molecular patterns (DAMPs), were analyzed by two complementary proteomic approaches. Differentially phosphorylated sites were determined through phosphopeptide enrichment followed by LC-MS/MS using label-free quantification; differentially phosphorylated proteins were identified by 2D-DIGE combined with phospho-specific fluorescent staining (phospho-DIGE). This large-scale phosphoproteome analysis of early OG-signaling enabled us to determine 100 regulated phosphosites using LC-MS/MS and 46 differential spots corresponding to 34 pdhosphoproteins using phospho-DIGE. Functional classification showed that the OG-responsive phosphoproteins include kinases, phosphatases and receptor-like kinases, heat shock proteins (HSPs), reactive oxygen species (ROS) scavenging enzymes, proteins related to cellular trafficking, transport, defense and signaling as well as novel candidates for a role in immunity, for which elicitor-induced phosphorylation changes have not been shown before. A comparison with previously identified elicitor-regulated phosphosites shows only a very limited overlap, uncovering the immune-related regulation of 70 phosphorylation sites and revealing novel potential players in the regulation of elicitor-dependent immunity

Changes in the microsomal proteome of tomato fruit during ripening

The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress

Deductive Controller Synthesis for Probabilistic Hyperproperties

Probabilistic hyperproperties specify quantitative relations between the probabilities of reaching different target sets of states from different initial sets of states. This class of behavioral properties is suitable for capturing important security, privacy, and system-level requirements. We propose a new approach to solve the controller synthesis problem for Markov decision processes (MDPs) and probabilistic hyperproperties. Our specification language builds on top of the logic HyperPCTL and enhances it with structural constraints over the synthesized controllers. Our approach starts from a family of controllers represented symbolically and defined over the same copy of an MDP. We then introduce an abstraction refinement strategy that can relate multiple computation trees and that we employ to prune the search space deductively. The experimental evaluation demonstrates that the proposed approach considerably outperforms HyperProb, a state-of-the-art SMT-based model checking tool for HyperPCTL. Moreover, our approach is the first one that is able to effectively combine probabilistic hyperproperties with additional intra-controller constraints (e.g. partial observability) as well as inter-controller constraints (e.g. agreements on a common action)

Working with Tweets: The Effectiveness of Lean Communication in Collaborative Problem-Solving

Among social network sites and tools, Twitter and other microblogging tools are characterized by their particularly "lean" communication form, based on quick and short messages, particularly appealing for personal use by the so called "generation Y". In this paper we investigate whether lean communication - and particularly Twitter - can be used as a tool for teamwork in organizations. Therefore, our research question is focused on whether Twitter could represent a viable communication tool in the future enterprise for collaborative problem solving. More specifically, whether the 140 characters limit would actually make a difference. To answer this research question, we propose here a comparative study of Twitter, a well-known SNS for microblogging, and Skype, a typical communication platform for individuals and organizations. The laboratory experiment method was selected in order to conduct a rigorous comparison with well- defined measurements. Different teams of the same size carry out a well structured problem- solving task communicating via Twitter or Skype. Comparative group performance is measured in terms of task completion time. Our results show that the lower volume of information exchanged via Twitter does not negatively affect group performance: Twitter teams are just as effective as Skype teams. These results can be partly explained in terms of media richness theory, but more interestingly they may be related to the different group dynamics within teams using different systems, and to further dimensions of investigation including the subjects, the task, the technological features and the organizational coordination modes, disclosing new paths for further research

Efficacy of a new technique - INtubate-RECruit-SURfactant-Extubate - "IN-REC-SUR-E" - in preterm neonates with respiratory distress syndrome: Study protocol for a randomized controlled trial

Background: Although beneficial in clinical practice, the INtubate-SURfactant-Extubate (IN-SUR-E) method is not successful in all preterm neonates with respiratory distress syndrome, with a reported failure rate ranging from 19 to 69 %. One of the possible mechanisms responsible for the unsuccessful IN-SUR-E method, requiring subsequent re-intubation and mechanical ventilation, is the inability of the preterm lung to achieve and maintain an "optimal" functional residual capacity. The importance of lung recruitment before surfactant administration has been demonstrated in animal studies showing that recruitment leads to a more homogeneous surfactant distribution within the lungs. Therefore, the aim of this study is to compare the application of a recruitment maneuver using the high-frequency oscillatory ventilation (HFOV) modality just before the surfactant administration followed by rapid extubation (INtubate-RECruit-SURfactant-Extubate: IN-REC-SUR-E) with IN-SUR-E alone in spontaneously breathing preterm infants requiring nasal continuous positive airway pressure (nCPAP) as initial respiratory support and reaching pre-defined CPAP failure criteria. Methods/design: In this study, 206 spontaneously breathing infants born at 24+0-27+6 weeks' gestation and failing nCPAP during the first 24 h of life, will be randomized to receive an HFOV recruitment maneuver (IN-REC-SUR-E) or no recruitment maneuver (IN-SUR-E) just prior to surfactant administration followed by prompt extubation. The primary outcome is the need for mechanical ventilation within the first 3 days of life. Infants in both groups will be considered to have reached the primary outcome when they are not extubated within 30 min after surfactant administration or when they meet the nCPAP failure criteria after extubation. Discussion: From all available data no definitive evidence exists about a positive effect of recruitment before surfactant instillation, but a rationale exists for testing the following hypothesis: a lung recruitment maneuver performed with a step-by-step Continuous Distending Pressure increase during High-Frequency Oscillatory Ventilation (and not with a sustained inflation) could have a positive effects in terms of improved surfactant distribution and consequent its major efficacy in preterm newborns with respiratory distress syndrome. This represents our challenge. Trial registration: ClinicalTrials.gov identifier: NCT02482766. Registered on 1 June 2015