Codon Bias Patterns of E.coliE.coli's Interacting Proteins

Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, $CompAI$, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for $E.coli$, comparing $CompAI$ with other widely used indices: $tAI$, $CAI$, and $Nc$. We show that $CompAI$ and $tAI$ capture similar information by being positively correlated with gene conservation, measured by ERI, and essentiality, whereas, $CAI$ and $Nc$ appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of $tAI$ and $CompAI$ with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in $E.coli$. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by $CompAI$ and $tAI$). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, $CompAI$ turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation

Is Vivaldi smooth and takete? Non-verbal sensory scales for describing music qualities

Studies on the perception of music qualities (such as induced or perceived emotions, performance styles, or timbre nuances) make a large use of verbal descriptors. Although many authors noted that particular music qualities can hardly be described by means of verbal labels, few studies have tried alternatives. This paper aims at exploring the use of non-verbal sensory scales, in order to represent different perceived qualities in Western classical music. Musically trained and untrained listeners were required to listen to six musical excerpts in major key and to evaluate them from a sensorial and semantic point of view (Experiment 1). The same design (Experiment 2) was conducted using musically trained and untrained listeners who were required to listen to six musical excerpts in minor key. The overall findings indicate that subjects\u2019 ratings on non-verbal sensory scales are consistent throughout and the results support the hypothesis that sensory scales can convey some specific sensations that cannot be described verbally, offering interesting insights to deepen our knowledge on the relationship between music and other sensorial experiences. Such research can foster interesting applications in the field of music information retrieval and timbre spaces explorations together with experiments applied to different musical cultures and contexts

Mozart is still blue: a comparison of sensory and verbal scales to describe qualities in music

An experiment was carried out in order to assess the use of non-verbal sensory scales for evaluating perceived music qualities, by comparing them with the analogous verbal scales. Participants were divided into two groups; one group (SV) completed a set of non-verbal scales responses and then a set of verbal scales responses to short musical extracts. A second group (VS) completed the experiment in the reverse order. Our hypothesis was that the ratings of the SV group can provide information unmediated (or less mediated) by verbal association in a much stronger way than the VS group. Factor analysis performed separately on the SV group, the VS group and for all participants shows a recurring patterning of the majority of sensory scales versus the verbal scales into different factors. Such results suggest that the sensory scale items are indicative of a different semantic structure than the verbal scales in describing music, and so they are indexing different qualities (perhaps ineffable), making them potentially special contributors to understanding musical experience

SARS-CoV-2 Vaccination in Solid-Organ Transplant Recipients

The coronavirus disease 2019 (COVID-19) pandemic has posed significant global challenges for solid organ transplant (SOT) recipients. Mortality rates of COVID-19 in this patient population remain high, despite new available therapeutic options and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) vaccination. Priority access to SARS-CoV-2 vaccination for waitlisted candidates and for SOT patients and their family members is recommended since the advantage from vaccination reduces the risk of COVID-19-related complications. However, immunogenicity and efficacy of COVID-19 vaccines are lower in waitlisted candidates and SOT recipients than in the general population. Routine systematic assessment of humoral and cellular immune responses after SARS-CoV-2 vaccination is controversial, although highly recommended for investigation and improvement of knowledge. SOT recipients should continue to adhere to preventive protective measures despite vaccination and may undergo passive antibody prophylaxis. This article seeks to provide an update on SARS-CoV-2 vaccination and preventive measures in SOT recipients based on existing literature and international guidelines

Enhancing allocentric spatial recall in pre-schoolers through navigational training programme

Unlike for other abilities, children do not receive systematic spatial orientation training at school, even though navigational training during adulthood improves spatial skills. We investigated whether navigational training programme (NTP) improved spatial orientation skills in pre-schoolers. We administered 12-week NTP to seventeen 4- to 5-year-old children (training group, TG). The TG children and 17 age-matched children (control group, CG) who underwent standard didactics were tested twice before (T0) and after (T1) the NTP using tasks that tap into landmark, route and survey representations. We determined that the TG participants significantly improved their performances in the most demanding navigational task, which is the task that taps into survey representation. This improvement was significantly higher than that observed in the CG, suggesting that NTP fostered the acquisition of survey representation. Such representation is typically achieved by age seven. This finding suggests that NTP improves performance on higher-level navigational tasks in pre-schooler

Modelling the spread of Covid19 in Italy using a revised version of the SIR model

In this paper, we present a model to predict the spread of the Covid-19 epidemic and apply it to the specific case of Italy. We started from a simple Susceptible, Infected, Recovered (SIR) model and we added the condition that, after a certain time, the basic reproduction number $R_0$ exponentially decays in time, as empirically suggested by world data. Using this model, we were able to reproduce the real behavior of the epidemic with an average error of 5\%. Moreover, we illustrate possible future scenarios, associated to different intervals of $R_0$. This model has been used since the beginning of March 2020, predicting the Italian peak of the epidemic in April 2020 with about 100.000 detected active cases. The real peak of the epidemic happened on the 20th of April 2020, with 108.000 active cases. This result shows that the model had predictive power for the italian case.Comment: The model presented in this paper has been adopted on Covstat.it. Errata corrige in the abstrac

Towards a Hybrid Design Approach of Anchored Drapery Systems

Anchored drapery meshes represent a worldwide adopted protective solution against rockfall. The mechanical performance of a wire mesh is evaluated through laboratory procedures in which the boundary conditions strongly differ from the ones typical of field applications. This shows that the laboratory characterization is, in general, not representative of the field behavior. In this work, referring to a double-twisted wire mesh, a simple approach allowing the extension of the laboratory characteristic values to field conditions is proposed. The approach is based on the definition of analytical relations for evaluating the effects of both the mesh’s system geometry and the loading condition on the force–displacement response. These relations are derived from previously calibrated laboratory tests and are extended to different configurations on the basis of a large number of discrete element simulations. A master curve allowing the prediction of the entire force–displacement response of a general configuration of the drapery system is then defined. The results of this study can provide useful information for designing anchored drapery systems and can be easily associated with standard limit equilibrium calculations to move toward a hybrid design approach that couples forces with mesh deformations

Equipment review: Mechanical effects of heat-moisture exchangers in ventilated patients

Although they represent a valuable alternative to heated humidifiers, artificial noses have unfavourable mechanical effects. Most important of these is the increase in dead space, with consequent increase in the ventilation requirement. Also, artificial noses increase the inspiratory and expiratory resistance of the apparatus, and may mildly increase intrinsic positive end-expiratory pressure. The significance of these effects depends on the design and function of the artificial nose. The pure humidifying function results in just a moderate increase in dead space and resistance of the apparatus, whereas the combination of a filtering function with the humidifying function may critically increase the volume and the resistance of the artificial nose, especially when a mechanical filter is used. The increase in the inspiratory load of ventilation that is imposed by artificial noses, which is particularly significant for the combined heat-moisture exchanger filters, should be compensated for by an increase either in ventilator output or in patient's work of breathing. Although both approaches can be tolerated by most patients, some exceptions should be considered. The increased pressure and volume that are required to compensate for the artificial nose application increase the risk of barotrauma and volutrauma in those patients who have the most severe alterations in respiratory mechanics. Moreover, those patients who have very limited respiratory reserve may not be able to compensate for the inspiratory work imposed by an artificial nose. When we choose an artificial nose, we should take into account the volume and resistance of the available devices. We should also consider the mechanical effects of the artificial noses when setting mechanical ventilation and when assessing a patient's ability to breathe spontaneously