MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins

MobiDB (ext-link-type="uri" xlink:href="http://mobidb.bio.unipd.it/" xlink:type="simple">http://mobidb.bio.unipd.it/) is a database of intrinsically disordered and mobile proteins. Intrinsically disordered regions are key for the function of numerous proteins. Here we provide a new version of MobiDB, a centralized source aimed at providing the most complete picture on different flavors of disorder in protein structures covering all UniProt sequences (currently over 80 million). The database features three levels of annotation: manually curated, indirect and predicted. Manually curated data is extracted from the DisProt database. Indirect data is inferred from PDB structures that are considered an indication of intrinsic disorder. The 10 predictors currently included (three ESpritz flavors, two IUPred flavors, two DisEMBL flavors, GlobPlot, VSL2b and JRONN) enable MobiDB to provide disorder annotations for every protein in absence of more reliable data. The new version also features a consensus annotation and classification for long disordered regions. In order to complement the disorder annotations, MobiDB features additional annotations from external sources. Annotations from the UniProt database include post-translational modifications and linear motifs. Pfam annotations are displayed in graphical form and are link-enabled, allowing the user to visit the corresponding Pfam page for further information. Experimental protein-protein interactions from STRING are also classified for disorder content

Exploration of alternative splicing events in ten different grapevine cultivars

Background: The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results: Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions: Our analysis shows that similar to 70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars

Concomitant Intubation with Minimal Cuffed Tube and Rigid Bronchoscopy for Severe Tracheo-Carinal Obstruction

Background: Our aim was to report on the use of an innovative technique for airway management utilizing a small diameter, short-cuffed, long orotracheal tube for assisting operative rigid bronchoscopy in critical airway obstruction. Methods: We retrospectively reviewed the clinical data of 36 patients with life-threatening critical airway stenosis submitted for rigid bronchoscopy between January 2008 and July 2021. The supporting ventilatory tube, part of the Translaryngeal Tracheostomy KIT (Fantoni method), was utilized in tandem with the rigid bronchoscope during endoscopic airway reopening. Results: Indications for collateral intubation were either tumors of the trachea with near-total airway obstruction (13), or tumors of the main carina with total obstruction of one main bronchus and possible contralateral involvement (23). Preliminary dilation was necessary before tube placement in only 2/13 patients with tracheal-obstructing tumors (15.4%). No postoperative complications were reported. There was one case of an intraoperative cuff tear, with no further technical problems. Conclusions: In our experience, this innovative method proved to be safe, allowing for continuous airway control. It enabled anesthesia inhalation, use of neuromuscular blockage and reliable end-tidal CO2 monitoring, along with protection of the distal airway from blood flooding. The shorter time of the procedure was due to the lack of need for pauses to ventilate the patient

The dermatological effects and occupational impacts of personal protective equipment on a large sample of healthcare workers during the COVID-19 pandemic

Introduction: Working during the Sars-CoV-2 pandemic healthcare workers (HCWs) had to wear Personal Protective Equipment (PPEs) for extended periods of time, leading to an increase in dermatological reactions. The study evaluates the prevalence of adverse skin reactions to PPEs among Italian healthcare workers during the COVID-19 pandemic, and aims to determine whether prolonged PPEs usage poses a significant occupational health risk, by measuring the loss of work days and the eligibility of workers that requested health surveillance due to dermatological PPEs reactions. Materials and methods: An online ad hoc questionnaire was administered to a sample of Italian HCWs. Questions verted on sociodemographic characteristics, PPEs usage, and occupational well-being. Descriptive analyses and logistic regressions were performed to explore possible associations between variables. Results: Two types of PPEs, Gloves and Masks, were tested. The sample included 1,223 interviewed HCWs, 1,184 gave their consent for participation. A total of 90 medical surveillance visits were requested due to PPEs related dermatological issues: in 30 cases were recognized limitations in working duties and in one case the worker was deemed not fit to keep working. Furthermore, 25 workers had a loss of occupational days due to dermatological issues. A statistically significant correlation was observed with being a nurse or midwife (OR = 1.91, IC = 1.38-2.63, p < 0.001), and being female (OR = 2.04, IC = 1.49-2.78, p < 0.001), which acted as risk factors. Discussion: The enhanced protection measures put in place during the COVID-19 pandemic, highlight the importance of occupational dermatology. This study could contribute to assess the issue, aiming to develop better prevention strategies in the workplace in order to improve well-being of HCWs and reduce the impact of dermatological adverse reactions to PPEs

Adverse skin reactions to personal protective equipment during COVID-19 pandemic in Italian health care workers

To avoid exposure to SARS-COV-2, healthcare professionals must use personal protective equipment (PPE). Their use has been related to a series of adverse effects; the most frequent adverse events were headache, dyspnoea, and pressure injuries. Skin adverse effects are very common, including contact dermatitis, itching, erythema, and acneiform eruptions. The objective of this study is to evaluate the skin problems caused by personal protection equipment (PPE) in health care workers (HCWs) and to individuate eventual risk factors. From May to June 2020 a retrospective observational multi-centric study conducted by an online survey sent by email, involving 10 hospital centers, was performed. We considered as independent variables gender and age, occupational group and sector, time of utilization, type and material of PPE. We tested 3 types of PPE: gloves, bonnet, and mask for different time of utilization (<1, 1-3, 3-6, >6 h). We performed a multiple logistic regression model to correlate them with skin adverse events occurrence. Among all the 1184 participants, 292 workers reported a dermatological pathology: 45 (15.41%) had psoriasis, 54 (18.49%) eczema, 38 (13.01%) acne, 48 (16.44%) seborrheic dermatitis, and 107 (36.64%) other. In our sample previous inflammatory dermatological conditions, female sex, prolonged use of PPE were significant risk factors for developing skin related adverse events considering all the PPE considered. The use of PPE is still mandatory in the hospital setting and skin adverse reactions still represent a global problem. Although data from Europe are limited, our study highlighted the importance of the problem of PPE skin reactions in a large sample of Italian healthcare professionals

Italian health care workers and Adverse skin reactions to personal protective equipment during Covid-19 pandemic

Introduction: During the pandemic, the use of personal protective equipment (PPE) has become essential for Healthcare Workers (HCWs) to fight safely against the virus. However, the extensive and prolonged use of PPE may cause various adverse skin reactions due to the use of alcohol hand cleanser and protracted use of masks and goggles. The aim of this study is to evaluate the skin problems caused by PPE in HCWs and the possible consequences on their work. Materials and methods: An online ad hoc questionnaire, composed by 35 questions about sociodemographic characteristics, work related issues and exposure/habits about PPE, was administered to a sample of Italian HCWs. Univariate and multivariate analyses were performed in order to explore possible associations between variables. Results: We tested 3 types of PPE: Gloves, Hair Bonnets and Masks for different time of utilization (<1, 1-3, 3-6, >6 hours). The sample included 1184 participants: 292 workers reported a dermatological pathology nested in four different pathological groups: 45 (15%) had Psoriasis, 54 (19%) Eczema, 38 (13%) Acne, 48 (16%), seborrheic dermatitis and 107 (36%) other. 25 workers had a loss of occupational days due to dermatological illness; 56 occupational physician surveillance visits were asked for; in 30 cases were recognized limitations in working duties. Conclusions: Protecting HCWs requires the use of PPE, but occupational dermatitis is an emerging problem in the midst of the COVID-19 pandemic. National data for affected healthcare professionals could contribute to a better understanding of the problem and prevention initiatives in the workplace

New Alien Plant Taxa for Italy and Europe: An Update

Abstract: Despite the wide amount of scientific contributions published on alien plant species, their diffusion dynamics, and their interactions with native taxa, it is increasingly difficult to slow down their spreading and their negative impact on habitats. Last recent years, in fact, a sharp rise in the number of new alien plant taxa introduced in Italy and Europe has been recorded. The aim of this work is to investigate most of the Italian territory in order to verify whether this alarming trend is still underway. Specimen collections and/or observations of alien plants have been performed in as many as 12 Italian regions. All the collected specimens are stored in public or private herbaria. Taxa have been identified according to the literature from the countries of origin of the investigated taxa, while the nomenclature followed the current international references. Updates on 106 taxa are reported. In particular, among 117 new records, 89 are first records, 27 are changes to status and there is 1 extinction. Seven new taxa for Italian alien flora are reported, two of which are new to Europe. The administrative regions with the highest number of records are Calabria (48), Sardegna (17) and Sicilia (15). Five of the surveyed taxa, for the first time, have been considered invasive aliens to Italian territory. The unfrequent amount of original results provided by this work, over the simple importance of data itself, proves how floristic investigation, still today, represents one of the most effective tools in broadening the current knowledge about alien taxa and their dynamics

Prospective validation of the CLIP score: a new prognostic system for patient with cirrhosis and hepatocellular carcinoma

Prognosis of patients with cirrhosis and hepatocellular carcinoma (HCC) depends on both residual liver function and tumor extension. The CLIP score includes Child-Pugh stage, tumor morphology and extension, serum alfa-fetoprotein (AFP) levels, and portal vein thrombosis. We externally validated the CLIP score and compared its discriminatory ability and predictive power with that of the Okuda staging system in 196 patients with cirrhosis and HCC prospectively enrolled in a randomized trial. No significant associations were found between the CLIP score and the age, sex, and pattern of viral infection. There was a strong correlation between the CLIP score and the Okuda stage, As of June 1999, 150 patients (76.5%) had died. Median survival time was 11 months, overall, and it was 36, 22, 9, 7, and 3 months for CLIP categories 0, 1, 2, 3, and 4 to 6, respectively. In multivariate analysis, the CLIP score had additional explanatory power above that of the Okuda stage. This was true for both patients treated with locoregional therapy or not. A quantitative estimation of 2-year survival predictive power showed that the CLIP score explained 37% of survival variability, compared with 21% explained by Okuda stage. In conclusion, the CLIP score, compared with the Okuda staging system, gives more accurate prognostic information, is statistically more efficient, and has a greater survival predictive power. It could be useful in treatment planning by improving baseline prognostic evaluation of patients with RCC, and could be used in prospective therapeutic trials as a stratification variable, reducing the variability of results owing to patient selection

Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio