SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation

Given the relevance of the pig proteome in different studies, including human complex maladies, a statistical validation of the annotation is required for a better understanding of the role of specific genes and proteins in the complex networks underlying biological processes in the animal. Presently, approximately 80% of the pig proteome is still poorly annotated, and the existence of protein sequences is routinely inferred automatically by sequence alignment towards preexisting sequences. In this article, we introduce SUS-BAR, a database that derives information mainly from UniProt Knowledgebase and that includes 26 206 pig protein sequences. In SUS-BAR, 16 675 of the pig protein sequences are endowed with statistically validated functional and structural annotation. Our statistical validation is determined by adopting a cluster-centric annotation procedure that allows transfer of different types of annotation, including structure and function. Each sequence in the database can be associated with a set of statistically validated Gene Ontologies (GOs) of the three main sub-ontologies (Molecular Function, Biological Process and Cellular Component), with Pfam functional domains, and when possible, with a cluster Hidden Markov Model that allows modelling the 3D structure of the protein. A database search allows some statistics demonstrating the enrichment in both GO and Pfam annotations of the pig proteins as compared with UniProt Knowledgebase annotation. Searching in SUS-BAR allows retrieval of the pig protein annotation for further analysis. The search is also possible on the basis of specific GO terms and this allows retrieval of all the pig sequences participating into a given biological process, after annotation with our system. Alternatively, the search is possible on the basis of structural information, allowing retrieval of all the pig sequences with the same structural characteristics

Low-Cost Potentiometric Sensor for Chloride Measurement in Continuous Industrial Process Control

Recently, the new updates in legislation about drinking water control and human health have increased the demand for novel electrochemical low-cost sensors, such as potentiometric ones. Nowadays, the determination of chloride ion in aqueous solutions has attracted great attention in several fields, from industrial processes to drinking water control. Indeed, chloride plays a crucial role in corrosion, also influencing the final taste of beverages, especially coffee. The main goal is to obtain devices suitable for continuous and real-time analysis. For these reasons, we investigated the possibility to develop an easy, low-cost potentiometric chloride sensor, able to perform analysis in aqueous mediums for long immersion time and reducing the need of periodic calibration. We realized a chloride ion selective electrode made of Ag/AgCl sintered pellet and we tested its response in model solutions compatible with drinking water. The sensor was able to produce a stable, reproducible, and accurate quantification of chloride in 900 s, without the need for a preliminary calibration test. This opens the route to potential applications of this sensor in continuous, in situ, and real time measurement of chloride ions in industrial processes, with a reduced need for periodic maintenance

The Role of Postoperative Irradiation in the Treatment of Locally Recurrent Incompletely Resected Extra-Abdominal Desmoid Tumors

Background: To define the efficacy of postoperative irradiation in patients with recurrent extra-abdominal desmoid tumors in whom surgical intervention has resulted in microscopically or grossly positive surgical margins

How personality relates to distress in parents during the COVID-19 lockdown: The mediating role of child’s emotional and behavioral difficulties and the moderating effect of living with other people

Since the initiation of the COVID-19 lockdown, Italian parents have been forced to manage their children at home. The present study aimed at investigating the psychological distress of parents during the lockdown, identifying contributing factors. An online survey was administered to 833 participants from 3 to 15 April 2020. Mediation and moderated mediation models were run to explore the association between parent neuroticism and parent distress, mediated by child hyperactivity–inattention and child emotional symptoms, and the moderating effect of living only with child(ren) on the direct and indirect effects of parent neuroticism on parent distress. For parents living only with child(ren), high levels of psychological distress depended exclusively on their levels of neuroticism. For parents living with at least one other person in addition to child(ren), distress levels were also mediated by child behavioral and emotional difficulties. Motherhood emerged as a significant factor contributing to greater distress. Furthermore, parent psychological distress decreased in line with increased child age. The results confirm that neuroticism is an important risk factor for mental health. Preventive measures should be primarily target multicomponent families with younger children and directed towards parents who are already known to present emotional instability and to parents of children who have received local mental health assistance for behavioral and/or emotional difficulties

An Experimental and Simulation Study of Early Flame Development in a Homogeneous-Charge Spark-Ignition Engine

An integrated experimental and Large-Eddy Simulation (LES) study is presented for homogeneous premixed combustion in a spark-ignition engine. The engine is a single-cylinder two-valve optical research engine with transparent liner and piston: the Transparent Combustion Chamber (TCC) engine. This is a relatively simple, open engine configuration that can be used for LES model development and validation by other research groups. Pressure-based combustion analysis, optical diagnostics and LES have been combined to generate new physical insight into the early stages of combustion. The emphasis has been on developing strategies for making quantitative comparisons between high-speed/high-resolution optical diagnostics and LES using common metrics for both the experiments and the simulations, and focusing on the important early flame development period. Results from two different LES turbulent combustion models are presented, using the same numerical methods and computational mesh. Both models yield Cycle-to-Cycle Variations (CCV) in combustion that are higher than what is observed in the experiments. The results reveal strengths and limitations of the experimental diagnostics and the LES models, and suggest directions for future diagnostic and simulation efforts. In particular, it has been observed that flame development between the times corresponding to the laminar-to-turbulent transition and 1% mass-burned fraction are especially important in establishing the subsequent combustion event for each cycle. This suggests a range of temporal and spatial scales over which future experimental and simulation efforts should focus

Targeted metabolomic profiles of piglet plasma reveal physiological changes over the suckling period

The suckling phase is a critical period for the piglets due to their incomplete immune system development and their rapid growth rates. In this study, we analysed the metabolomic profiles of piglets over this period. Eighteen piglets (nine males and nine females) from three different litters were included in the study. Body weight was recorded at birth (T0), 12 (T1) and 21 (T2) days after birth. Plasma samples were collected at two critical time points of the suckling phase (T1 and T2) and about 180 metabolites of five different biochemical classes (glycerophospholipids, amino acids, biogenic amines, hexoses and acylcarnitines) were analyzed using a target metabolomics approach based on Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). Metabolites whose levels could discriminate the plasma profiles at T1 and T2 were identified using the sparse version of Multilevel Partial Least Squares Discriminant Analysis (sMLPLS-DA), coupled with a stability test based on a Leave One Out (LOO) procedure. The level of twenty-three metabolites differed significantly (P < 0.1; both for stability and the effect size) between the two time points. Higher levels of six acylcarnitine (C14:1, C14:1-OH, C16-OH, C4, C5 and C5-OH), serine, threonine and tyrosine, and one phosphatidylcholine (PC ae C42:3) were observed at T1, whereas one biogenic amine (creatinine), eight phosphatidylcholines including PC aa C30:2, PC ae C30:0, PC ae C32:1, PC ae C38:4, PC ae C40:4, PC ae C42:4, PC ae C42:5 and PC ae C44:6, and four sphingomyelins, including SM (OH) C22:1, SM C16:0, SM C16:1 and SM C18:0, were more abundant at T2. The Metabolite Set Enrichment Analysis and the Pathway Analysis modules suggested a perturbation of the \u201cglycine and serine metabolism\u201d and the \u201csphingolipid metabolism\u201d. Differences of these metabolites between these two time points might be related to the rapid growth and immunological maturation phases of the piglets in this period. Our results provided new information that could describe the biological changes of the piglets over the suckling period. The identified metabolites may be useful markers of the developmental processes occurring in the piglets over this critical pre-weaned phase

Redox-Active Ferrocene grafted on H-Terminated Si(111): Electrochemical Characterization of the Charge Transport Mechanism and Dynamics

Electroactive self-assembled monolayers (SAMs) bearing a ferrocene (Fc) redox couple were chemically assembled on H-terminated semiconducting degenerate-doped n-type Si(111) substrate. This allows to create a Si(111)|organic-spacer|Fc hybrid interface, where the ferrocene moiety is covalently immobilized on the silicon, via two alkyl molecular spacers of different length. Organic monolayer formation was probed by Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) and X-ray photoelectron spectroscopy (XPS) measurements, which were also used to estimate thickness and surface assembled monolayer (SAM) surface coverage. Atomic force microscopy (AFM) measurements allowed to ascertain surface morphology and roughness. The single electron transfer process, between the ferrocene redox probe and the Si electrode surface, was probed by cyclic voltammetry (CV) measurements. CVs recorded at different scan rates, in the 10 to 500 mV s−1 range, allowed to determine peak-to-peak separation, half-wave potential, and charge-transfer rate constant (KET). The experimental findings suggest that the electron transfer is a one electron quasi-reversible process. The present demonstration of surface engineering of functional redox-active organometallic molecule can be efficient in the field of molecular electronics, surface-base redox chemistry, opto-electronic applications

The BovMAS Consortium: investigation of bovine chromosome 14 for quantitative trait loci affecting milk production and quality traits in the Italian Holstein Friesian breed

Many studies have demonstrated that quantitative trait loci (QTL) can be identified and mapped in commercial dairy cattle populations using genetic markers in daughter and granddaughter designs.The final objective of these studies is to identify genes or markers that can be used in breeding schemes via marker assisted selection (MAS)

Polariton Condensation in a One-Dimensional Disordered Potential

We study the coherence and density modulation of a non-equilibrium exciton-polariton condensate in a one-dimensional valley with disorder. By means of interferometric measurements we evidence a modulation of the first-order coherence function and we relate it to a disorder-induced modulation of the condensate density, that increases as the pump power is increased. The non-monotonous spatial coherence function is found to be the result of the strong non-equilibrium character of the one-dimensional system, in the presence of disorder

Correlation function of weakly interacting bosons in a disordered lattice

One of the most important issues in disordered systems is the interplay of the disorder and repulsive interactions. Several recent experimental advances on this topic have been made with ultracold atoms, in particular the observation of Anderson localization, and the realization of the disordered Bose-Hubbard model. There are however still questions as to how to differentiate the complex insulating phases resulting from this interplay, and how to measure the size of the superfluid fragments that these phases entail. It has been suggested that the correlation function of such a system can give new insights, but so far little experimental investigation has been performed. Here, we show the first experimental analysis of the correlation function for a weakly interacting, bosonic system in a quasiperiodic lattice. We observe an increase in the correlation length as well as a change in shape of the correlation function in the delocalization crossover from Anderson glass to coherent, extended state. In between, the experiment indicates the formation of progressively larger coherent fragments, consistent with a fragmented BEC, or Bose glass.Comment: 16 pages, 8 figure