HERV‐K(HML7) integrations in the human genome: Comprehensive characterization and comparative analysis in non‐human primates

Endogenous Retroviruses (ERVs) are ancient relics of infections that affected the primate germ line and constitute about 8% of our genome. Growing evidence indicates that ERVs had a major role in vertebrate evolution, being occasionally domesticated by the host physiology. In ad-dition, human ERV (HERV) expression is highly investigated for a possible pathological role, even if no clear associations have been reported yet. In fact, on the one side, the study of HERV expression in high‐throughput data is a powerful and promising tool to assess their actual dysregulation in diseased conditions; but, on the other side, the poor knowledge about the various HERV group genomic diversity and individual members somehow prevented the association between specific HERV loci and a given molecular mechanism of pathogenesis. The present study is focused on the HERV‐K(HML7) group that—differently from the other HERV‐K members—still remains poorly characterized. Starting from an initial identification performed with the software RetroTector, we collected 23 HML7 proviral insertions and about 160 HML7 solitary LTRs that were analyzed in terms of genomic distribution, revealing a significant enrichment in chromosome X and the frequent localization within human gene introns as well as in pericentromeric and centromeric regions. Phy-logenetic analyses showed that HML7 members form a monophyletic group, which based on age estimation and comparative localization in non‐human primates had its major diffusion between 20 and 30 million years ago. Structural characterization revealed that besides 3 complete HML7 pro-viruses, the other group members shared a highly defective structure that, however, still presents recognizable functional domains, making it worth further investigation in the human population to assess the presence of residual coding potential

Centroid moment tensor catalog with 3D lithospheric wavespeed model. The 2016–2017 Central Apennines sequence

Moment tensor inversions of broadband velocity data are usually managed by adopting Green's functions for 1D layered seismic wave speed models. This assumption can impact on source parameter estimates in regions with complex 3D heterogeneous structures and discontinuities in rock properties. In this work, we present a new centroid moment tensor (CMT) catalog for the Amatrice-Visso-Norcia (AVN) seismic sequence based on a recently generated 3D wave speed model for the Italian lithosphere. Forward synthetic seismograms and Fréchet derivatives for CMT-3D inversions of 159 earthquakes with Mw ≥ 3.0 are simulated using a spectral-element method (SEM) code. By comparing the retrieved solutions with those from time domain moment tensor (TDMT) catalog, obtained with a 1D wave speed model calibrated for Central Apennines (Italy), we observe a remarkable degree of consistency in terms of source geometry, kinematics, and magnitude. Significant differences are found in centroid depths, which are more accurately estimated using the 3D model. Finally, we present a newly designed parameter, τ, to better quantify and compare a-posteriori the reliability of the obtained MT solutions. τ measures the goodness of fit between observed and synthetic seismograms accounting for differences in amplitude, arrival time, percentage of fitted seconds, and the usual L2-norm estimate. The CMT-3D solutions represent the first Italian CMT catalog based on a full-waveform 3D wave speed model. They provide reliable source parameters with potential implications for the structures activated during the sequence. The developed approach can be readily applied to more complex Italian regions where 1D models are underperforming and not representative of the area

Early and long-term results of pectoralis muscle flap reconstruction versus sternal rewiring following failed sternal closure

Objectives: The aim of the study was to compare early and long-term results of pectoralis muscle flap reconstruction with those of sternal rewiring following failed sternal closure. Primary outcomes of the study were survival and failure rate. Respiratory function, chronic pain and quality of life were also evaluated. Methods: In a propensity-score matching analysis, of 94 patients who underwent sternal reconstruction, 40 were selected; 20 underwent sternal reconstruction with bilateral pectoralis muscle flaps (Group 1) and 20 underwent sternal rewiring (Group 2). Survival and failure rates were evaluated by in-hospital records and at follow-up. Respiratory function measures, including vital capacity (VC), were evaluated both by spirometry and computed tomography (CT) volumetry. Chronic pain was evaluated by the visual analogue pain scale. Results: At 85 ± 24 months of follow-up, survival and procedure failure were 95 and 90% in Group 1 and 60 and 55% in Group 2, respectively (P < 0.01, for both comparisons). Based on CT-scan volumetry, in Group 1, severe non-union and hemisternal paradoxical movement occurred less frequently (2 vs 7, P = 0.01). At spirometry assessment, postoperative VC was greater in Group 1 (3220 ± 290 vs 3070 ± 290 ml, P = 0.04). The same trend was detected by CT-scan in-expiratory measures (4034 ± 1800 vs 3182 ± 862 mm3, P < 0.05). Correspondingly, in Group 1, less patients presented in NYHA Class III (P < 0.05), and both chronic persistent pain score and physical health quality-of-life score were significantly better in the same group. Conclusions: In our study, muscle flap reconstruction guaranteed better early and late-term results as shown by lower rates of mortality, procedure failure and hemisternum stability. Moreover, Group 1 patients had greater postoperative VC, lower NYHA class and better quality of life. These results suggest that, in patients with multiple bone fracture, the rewiring approach does not promote physiological bone consolidation, whereas the muscle flap reconstruction can assure more physiological ventilatory dynamics.© The Author 2013. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved

Early and long-term results of pectoralis muscle flap reconstruction vs sternal rewiring following failed sternal closure.

OBJECTIVES: The aim of the study was to compare early and long-term results of pectoralis muscle flap reconstruction with those of sternal rewiring following failed sternal closure. Primary outcomes of the study were survival and failure rate. Respiratory function, chronic pain and quality of life were also evaluated. METHODS: In a propensity-score matching analysis, of 94 patients who underwent sternal reconstruction, 40 were selected; 20 underwent sternal reconstruction with bilateral pectoralis muscle flaps (Group 1) and 20 underwent sternal rewiring (Group 2). Survival and failure rates were evaluated by in-hospital records and at follow-up. Respiratory function measures, including vital capacity (VC), were evaluated both by spirometry and computed tomography (CT) volumetry. Chronic pain was evaluated by the visual analogue pain scale. RESULTS: At 85 ± 24 months of follow-up, survival and procedure failure were 95 and 90% in Group 1 and 60 and 55% in Group 2, respectively (P < 0.01, for both comparisons). Based on CT-scan volumetry, in Group 1, severe non-union and hemisternal paradoxical movement occurred less frequently (2 vs 7, P = 0.01). At spirometry assessment, postoperative VC was greater in Group 1 (3220 ± 290 vs 3070 ± 290 ml, P = 0.04). The same trend was detected by CT-scan in-expiratory measures (4034 ± 1800 vs 3182 ± 862 mm3, P < 0.05). Correspondingly, in Group 1, less patients presented in NYHA Class III (P < 0.05), and both chronic persistent pain score and physical health quality-of-life score were significantly better in the same group. CONCLUSIONS: In our study, muscle flap reconstruction guaranteed better early and late-term results as shown by lower rates of mortality, procedure failure and hemisternum stability. Moreover, Group 1 patients had greater postoperative VC, lower NYHA class and better quality of life. These results suggest that, in patients with multiple bone fracture, the rewiring approach does not promote physiological bone consolidation, whereas the muscle flap reconstruction can assure more physiological ventilatory dynamics

Novel atrazine-binding biomimetics inspired to the D1 protein from the photosystem II of Chlamydomonas reinhardtii

Biomimetic design represents an emerging field for improving knowledge of natural molecules, as well as to project novel artificial tools with specific functions for biosensing. Effective strategies have been exploited to design artificial bioreceptors, taking inspiration from complex supramolecular assemblies. Among them, size-minimization strategy sounds promising to provide bioreceptors with tuned sensitivity, stability, and selectivity, through the ad hoc manipulation of chemical species at the molecular scale. Herein, a novel biomimetic peptide enabling herbicide binding was designed bioinspired to the D1 protein of the Photosystem II of the green alga Chlamydomonas reinhardtii. The D1 protein portion corresponding to the QB plastoquinone binding niche is capable of interacting with photosynthetic herbicides. A 50-mer peptide in the region of D1 protein from the residue 211 to 280 was designed in silico, and molecular dynamic simulations were performed alone and in complex with atrazine. An equilibrated structure was obtained with a stable pocked for atrazine binding by three H-bonds with SER222, ASN247, and HIS272 residues. Computational data were confirmed by fluorescence spectroscopy and circular dichroism on the peptide obtained by automated synthesis. Atrazine binding at nanomolar concentrations was followed by fluorescence spectroscopy, highlighting peptide suitability for optical sensing of herbicides at safety limits

Pediatric Injury Surveillance From Uncoded Emergency Department Admission Records in Italy: Machine Learning-Based Text-Mining Approach

Background: Unintentional injury is the leading cause of death in young children. Emergency department (ED) diagnoses are a useful source of information for injury epidemiological surveillance purposes. However, ED data collection systems often use free-text fields to report patient diagnoses. Machine learning techniques (MLTs) are powerful tools for automatic text classification. The MLT system is useful to improve injury surveillance by speeding up the manual free-text coding tasks of ED diagnoses. Objective: This research aims to develop a tool for automatic free-text classification of ED diagnoses to automatically identify injury cases. The automatic classification system also serves for epidemiological purposes to identify the burden of pediatric injuries in Padua, a large province in the Veneto region in the Northeast Italy. Methods: The study includes 283, 468 pediatric admissions between 2007 and 2018 to the Padova University Hospital ED, a large referral center in Northern Italy. Each record reports a diagnosis by free text. The records are standard tools for reporting patient diagnoses. An expert pediatrician manually classified a randomly extracted sample of approximately 40, 000 diagnoses. This study sample served as the gold standard to train an MLT classifier. After preprocessing, a document-term matrix was created. The machine learning classifiers, including decision tree, random forest, gradient boosting method (GBM), and support vector machine (SVM), were tuned by 4-fold cross-validation. The injury diagnoses were classified into 3 hierarchical classification tasks, as follows: injury versus noninjury (task A), intentional versus unintentional injury (task B), and type of unintentional injury (task C), according to the World Health Organization classification of injuries. Results: The SVM classifier achieved the highest performance accuracy (94.14%) in classifying injury versus noninjury cases (task A). The GBM method produced the best results (92% accuracy) for the unintentional and intentional injury classification task (task B). The highest accuracy for the unintentional injury subclassification (task C) was achieved by the SVM classifier. The SVM, random forest, and GBM algorithms performed similarly against the gold standard across different tasks. Conclusions: This study shows that MLTs are promising techniques for improving epidemiological surveillance, allowing for the automatic classification of pediatric ED free-text diagnoses. The MLTs revealed a suitable classification performance, especially for general injuries and intentional injury classification. This automatic classification could facilitate the epidemiological surveillance of pediatric injuries by also reducing the health professionals' efforts in manually classifying diagnoses for research purposes

Biochemical Traits, 1H NMR Profile and Residual DNA Content of ‘Asprinio’, White Wine from Campania Region (Southern Italy)

‘Asprinio’ is a white dry wine characteristic for its acidity and aromatic flavour, known as emerging DOP wine in Southern Italy. Nevertheless, little information is available on the metabolomic profile of this wine. Thus, in this paper we evaluated the colourimetric parameters, 1H NMR profiles and free amino acids content of ‘Asprinio’ wines, bottled by two different wineries (hereafter ‘Asprinio_A’ and ‘Asprinio_B’) collected in 2019 and 2020, using ‘Greco di Tufo’ for comparison. The colourimetric parameters are similar for both ‘Asprinio’ wines and differ from ‘Greco di Tufo’ wines. On the other hand, both 1H NMR and free amino acid content profiles show different chemometric profiles among the three wines analysed, although the profiles are similar for both vintages. Moreover, the multivariate analyses carried out highlight differences between ‘Asprinio_A’ and ‘Asprinio_B’, which exbibit also different residual yeast and plant DNA. Overall, considering that the two-manufacturing wineries use 100% ‘Asprinio’ grape, the difference retrieved between the two ‘Asprinio’ wines could be explained by the different grapevine training systems: ‘vite maritata’ (training system inherited from Etruscans) for ‘Asprinio_A’ and ‘guyot’ for ‘Asprinio_B’

Expression and purification of the recombinant subunits of toluene/o-xylene monooxygenase and reconstitution of the active complex.

This paper describes the cloning of the genes coding for each component of the complex of toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1, their expression, purification and characterization. Moreover, the reconstitution of the active complex from the recombinant subunits has been obtained, and the functional role of each component in the electron transfer from the electron donor to molecular oxygen has been determined. The coexpression of subunits B, E and A leads to the formation of a subcomplex, named H, with a quaternary structure (BEA)2, endowed with hydroxylase activity. Tomo F component is an NADH oxidoreductase. The purified enzyme contains about 1 mol of FAD, 2 mol of iron, and 2 mol of acid labile sulfide per mol of protein, as expected for the presence of one [2Fe-2S] cluster, and exhibits a typical flavodoxin absorption spectrum. Interestingly, the sequence of the protein does not correspond to that previously predicted on the basis of DNA sequence. We have shown that this depends on minor errors in the gene sequence that we have corrected. C component is a Rieske-type ferredoxin, whose iron and acid labile sulfide content is in agreement with the presence of one [2Fe-2S] cluster. The cluster is very sensitive to oxygen damage. Mixtures of the subcomplex H and of the subunits F, C and D are able to oxidize p-cresol into 4-methylcathecol, thus demonstrating the full functionality of the recombinant subunits as purified. Finally, experimental evidence is reported which strongly support a model for the electron transfer. Subunit F is the first member of an electron transport chain which transfers electrons from NADH to C, which tunnels them to H subcomplex, and eventually to molecular oxyge

MedNet status report

MedNet is a network of very broadband seismic stations installed in countries bordering the Mediterranean area. The project started in 1987, with a final goal of 12-15 stations and a spacing of about 1000 km between stations. It was motivated both by research interest and by seismic hazard monitoring. The network presently comprises 23 operating stations, all of them equipped with state of the art seismographic stations. Presently, fully automatic network functions include: - daily monitoring of state of health; - data recover after link failures; - triggered retrieval of event waveforms; - update of web pages (http://mednet.ingv.it) for events and station information.PublishedS. Fernando (SPAIN)1.1. TTC - Monitoraggio sismico del territorio nazionaleope