Boolean versus continuous dynamics on simple two-gene modules

We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a generalized method, we study within a single framework different continuous models and different types of regulatory functions, and establish conditions under which the system can display stable oscillations. These conditions concern the time scales, the degree of cooperativity of the regulating interactions, and the signs of the interactions. Not all models that show oscillations under Boolean dynamics can have oscillations under continuous dynamics, and vice versa.Comment: 8 pages, 10 figure

E-Defense 2015 ten-story building: beam–column joint assessment according to different code-based design

Recent devastating earthquakes worldwide pointed out the importance of seismic detailing and their influence on the observed damage and subsequent repairability of reinforced concrete buildings. Several studies and post-earthquake observations remarked the role of beam–column joints (BCJs) on the global building response and the effectiveness of transverse reinforcement in increasing the joint shear strength and the ultimate deformation. Although number of experimental and theoretical studies focused on the seismic response of BCJs, their mechanical behaviour is still a discussed topic. This resulted in number of design approaches available in worldwide code or standards that lead to different quantity of joint stirrups. This study focuses on the response of BCJs of a 10-story prototype building designed according to Japanese standards and tested in 2015 on the E-Defense shaking table. First the damage assessment at global (building) and local (joint) level is performed at increasing intensities and considering the building in the base slip and base fixed configurations. A refined numerical model is then developed and validated against global and local experimental results. Then, the joint stirrups are re-designed according to different international standards (ACI, EC8, NZS) and different numerical models are developed. The numerical results are then compared in terms of interstorey drift demand and joint shear strain. Finally, a comparison in terms of expected damage varying the design approach of joint stirrups is proposed

The germination niche of coastal dune species as related to their occurrence along a sea–inland gradient

Aims: The early phases in the life cycle of a plant are the bottleneck for successful species establishment thereby affecting population dynamics and distribution. In coastal environments, the spatial pattern of plant communities (i.e. vegetation zonation) follows the ecological gradient of abiotic stress changing with the distance from the sea. This pattern has been mainly explained based on the adaptation and tolerance to the abiotic stress of adult plants. However, the adult niche may considerably differ from the germination niche of a plant species. The aim of this work was to investigate to what extent abiotic factors (specifically salinity, temperature, nitrogen and their interactions) constrain seed germination along the sea–inland gradient. Location: Latium coast (Central Italy). Methods: Germination tests were performed on seeds of focal species of three different plant communities which establish at increasing distances from the coastline: Cakile maritima subsp. maritima, Elymus farctus, Crucianella maritima. We tested increasing concentrations of NaCl (one of the main abiotic factors which decrease across the sea–inland gradient), and their interactions with temperature and KNO3, to consider other factors which drive germination processes. Results: The tolerance to salinity significantly decreased in relation to the position of species along the coastal zonation. Crucianella maritima was shown to be the least tolerant species, having a decrease in germination >80% across all conditions. KNO3 significantly (although slightly) increased the germination percentage in Cakile maritima subsp. maritima and Elymus farctus. When combined with NaCl, KNO3 alleviated the negative effects of salinity only in Cakile maritima subsp. maritima. Conclusions: The germination responses to the interaction among the tested factors suggest that the germination niche may explain vegetation zonation filtering species at their early stages. Quantifying environmental niches in different phases of the life cycle of plants may provide important insights into community assembly processes

Effects of Short-Term Fasting on mRNA Expression of Ghrelin and the Peptide Transporters PepT1 and 2 in Atlantic Salmon (Salmo salar)

Food intake is a vital process that supplies necessary energy and essential nutrients to the body. Information regarding luminal composition in the gastrointestinal tract (GIT) collected through mechanical and nutrient sensing mechanisms are generally conveyed, in both mammals and fish, to the hypothalamic neurocircuits. In this context, ghrelin, the only known hormone with an orexigenic action, and the intestinal peptide transporters 1 and 2, involved in absorption of dietary di- and tripeptides, exert important and also integrated roles for the nutrient uptake. Together, both are potentially involved in signaling pathways that control food intake originating from different segments of the GIT. However, little is known about the role of different paralogs and their response to fasting. Therefore, after 3 weeks of acclimatization, 12 Atlantic salmon (Salmo salar) post-smolt were fasted for 4 days to explore the gastrointestinal response in comparison with fed control (n = 12). The analysis covered morphometric (weight, length, condition factor, and wet content/weight fish %), molecular (gene expression variations), and correlation analyses. Such short-term fasting is a common and recommended practice used prior to any handling in commercial culture of the species. There were no statistical differences in length and weight but a significant lower condition factor in the fasted group. Transcriptional analysis along the gastrointestinal segments revealed a tendency of downregulation for both paralogous genes slc15a1a and slc15a1b and with significant lowered levels in the pyloric ceca for slc15a1a and in the pyloric ceca and midgut for slc15a1b. No differences were found for slc15a2a and slc15a2b (except a higher expression of the fasted group in the anterior midgut), supporting different roles for slc15 paralogs. This represents the first report on the effects of fasting on slc15a2 expressed in GIT in teleosts. Transcriptional analysis of ghrelin splicing variants (ghrl-1 and ghrl-2) showed no difference between treatments. However, correlation analysis showed that the mRNA expression for all genes (restricted to segment with the highest levels) were affected by the residual luminal content. Overall, the results show minimal effects of 4 days of induced fasting in Atlantic salmon, suggesting that more time is needed to initiate a large GIT response

Relationship between the loss of neutralizing antibody binding and fusion activity of the F protein of human respiratory syncytial virus

To elucidate the relationship between resistance to HRSV neutralizing antibodies directed against the F protein and the fusion activity of the F protein, a recombinant approach was used to generate a panel of mutations in the major antigenic sites of the F protein. These mutant proteins were assayed for neutralizing mAb binding (ch101F, palivizumab, and MAb19), level of expression, post-translational processing, cell surface expression, and fusion activity. Functional analysis of the fusion activity of the panel of mutations revealed that the fusion activity of the F protein is tolerant to multiple changes in the site II and IV/V/VI region in contrast with the somewhat limited spectrum of changes in the F protein identified from the isolation of HRSV neutralizing antibody virus escape mutants. This finding suggests that aspects other than fusion activity may limit the spectrum of changes tolerated within the F protein that are selected for by neutralizing antibodies

Towards a generic test of the strong field dynamics of general relativity using compact binary coalescence: Further investigations

In this paper we elaborate on earlier work by the same authors in which a novel Bayesian inference framework for testing the strong-field dynamics of General Relativity using coalescing compact binaries was proposed. Unlike methods that were used previously, our technique addresses the question whether one or more 'testing coefficients' (e.g. in the phase) parameterizing deviations from GR are non-zero, rather than all of them differing from zero at the same time. The framework is well-adapted to a scenario where most sources have low signal-to-noise ratio, and information from multiple sources as seen in multiple detectors can readily be combined. In our previous work, we conjectured that this framework can detect generic deviations from GR that can in principle not be accomodated by our model waveforms, on condition that the change in phase near frequencies where the detectors are the most sensitive is comparable to that induced by simple shifts in the lower-order phase coefficients of more than a few percent ($\sim 5$ radians at 150 Hz). To further support this claim, we perform additional numerical experiments in Gaussian and stationary noise according to the expected Advanced LIGO/Virgo noise curves, and coherently injecting signals into the network whose phasing differs structurally from the predictions of GR, but with the magnitude of the deviation still being small. We find that even then, a violation of GR can be established with good confidence.Comment: 15 pages, 7 figures, Amaldi 9 proceeding

Testing consumers’ acceptance for an extra-virgin olive oil with a naturally increased content in polyphenols: The case of ultrasounds extraction

Innovation is fundamental for all agri-food companies to increase competitiveness. Being extra-virgin olive oil (EVOO) a traditional food product (TFP), the main obstacle to innovation is its traditional nature. This study evaluated consumers’ acceptance for an EVOO with a naturally increased content of poliphenols, as it has been extracted through ultrasounds. This product has been compared with a set of emerging innovations that may be introduced in the next future. To this end, a choice experiment was carried out bent on the estimation of a Latent Class Model (LCM). A nationally-representative sample of EVOO consumers were involved in a web-based interview. The LCM analysis highlighted three segments of consumers: (1) innovative; (2) traditionalist; (3) cautious. Results showed that there is cluster of consumers willing to accept this innovation, therefore its introduction on the market appears to be possibly successful

Testing consumers' acceptance for an extra-virgin olive oil with a naturally increased content in polyphenols: The case of ultrasounds extraction

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Contribution of cysteine residues in the extracellular domain of the F protein of human respiratory syncytial virus to its function

The mature F protein of all known isolates of human respiratory syncytial virus (HRSV) contains fifteen absolutely conserved cysteine (C) residues that are highly conserved among the F proteins of other pneumoviruses as well as the paramyxoviruses. To explore the contribution of the cysteines in the extracellular domain to the fusion activity of HRSV F protein, each cysteine was changed to serine. Mutation of cysteines 37, 313, 322, 333, 343, 358, 367, 393, 416, and 439 abolished or greatly reduced cell surface expression suggesting these residues are critical for proper protein folding and transport to the cell surface. As expected, the fusion activity of these mutations was greatly reduced or abolished. Mutation of cysteine residues 212, 382, and 422 had little to no effect upon cell surface expression or fusion activity at 32°C, 37°C, or 39.5°C. Mutation of C37 and C69 in the F2 subunit either abolished or reduced cell surface expression by 75% respectively. None of the mutations displayed a temperature sensitive phenotype