Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs

The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested subgenomic RNAsused to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5 ' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs

Rapporto 2007 su consumo e dipendenze da sostanze in Emilia-Romagna.

Report on the state of legal and illegal substances use in the territory of Emilia-Romagna Region.Il report analizza il fenomeno delle dipendenze nel territorio della Regione Emilia-Romagna. La descrizione del fenomeno si sviluppa intorno all\u27analisi degli indicatori individuati dall\u27Osservatorio Europeo delle Dipendenze di Lisbona (OEDT): 1-uso di sostanze nella popolazione generale (questo indicatore va a rilevare i comportamenti nei confronti di alcol e sostanze psicoattive da parte della popolazione generale); 2-prevalenza d\u27uso problematico delle sostanze psicoattive; 3-domanda di trattamento degli utilizzatori di sostanze; 4-mortalit? degli utilizzatori di sostanze; 5-malattie infettive. Altri due importanti indicatori che si stanno sviluppando, e che vengono qui illustrati, sono l\u27analisi delle Schede di Dimissione Ospedaliera (SDO) e gli indicatori relativi alle conseguenza sociali dell\u27uso di droghe (criminalit? droga correlata). Inoltre sono state applicate diverse metodologie standard di stima sia per quantificare la quota parte sconosciuta di utilizzatori di sostanze che non afferiscono ai servizi, sia per identificarne alcune caratteristiche

Control of postharvest fungal pathogens by antifungal compounds from Penicillium expansum

The fungicidal effects of secondary metabolites produced by a strain of Penicillium expansum (R82) in culture filtrate and in a double petri dish assay were tested against one isolate each of Botrytis cinerea, Colletotrichum acutatum, and Monilinia laxa and six isolates of P. expansum, revealing inhibitory activity against every pathogen tested. The characterization of volatile organic compounds released by the R82 strain was performed by solid-phase microextraction-gas chromatographic techniques, and several compounds were detected, one of them identified as phenethyl alcohol (PEA). Synthetic PEA, tested in vitro on fungal pathogens, showed strong inhibition at a concentration of 1,230 μg/ml of airspace, and mycelium appeared more sensitive than conidia; nevertheless, at the concentration naturally emitted by the fungus (0.726 ± 0.16 m g/ml), commercial PEA did not show any antifungal activity. Therefore, a combined effect between different volatile organic compounds produced collectively by R82 can be hypothesized. This aspect suggests further investigation into the possibility of exploiting R82 as a nonchemical alternative in the control of some plant pathogenic fungi

Control of postharvest grey mould (Botrytis cinerea Per.: Fr.) on strawberries by glucosinolate-derived allyl-isothiocyanate treatments

The vapours of allyl-isothiocyanate (AITC) were evaluated in in vitro and in vivo trials against Botrytiscinerea, a severe pathogen of strawberries. In in vitro trials AITC activity was assayed on conidial germi-nation and mycelial growth of the fungus. The mycelium appeared less sensitive to AITC than conidia(EC50values of 1.35 mg L−1and 0.62 mg L−1, respectively). In addition, AITC had a fungistatic effect againstthe pathogen, since the values of EC50, for both parameters, increased by around 30% after AITC removal.In in vivo trials, ‘Tecla’ and ‘Monterey’ strawberries (spring-bearing and day-neutral cultivars, respec-tively) obtained from organic production and naturally infected by B. Cinerea, were exposed for 4 h in anatmosphere enriched by pure AITC or derived from defatted seed meals of Brassica carinata (0.1 mg L−1,in a 0.1 m3treatment cabinet). After 2 days at 0◦C and another 3–4 days at 20◦C, the fruit were evalu-ated for grey mould infections. The AITC treatment reduced the decay caused by the pathogen by over47.4% up to 91.5%, significantly different from the untreated fruit. No significant differences were foundbetween synthetic and glucosinolate-derived AITC. Residue analysis performed on fruit at the end ofstorage (7 d after treatment) showed values lower than 1 mg kg−1. Total phenolic content and antioxi-dant capacity estimated in treated and untreated strawberries showed no significant difference betweencontrol and AITC treated fruit. Our results show it is possible to reduce the incidence of postharvest greymould on strawberries with a treatment of AITC (0.1 mg L−1) for 4 h, opening a potential application ofbiofumigation in the postharvest control of B. cinerea in strawberry

Sarcina Ventriculi infection: a rare but fearsome event. A Systematic Review of the Literature

Objectives: This study is aimed to report a case of SV-related gastritis and the results of a systematic review of SV infections in the literature. Methods: Following a case presentation, we systematically searched different databases (MEDLINE, PubMed, Scopus, Web of Science, EMBASE) for the items "sarcina," "ventriculi," "clostridium" with AND/OR. Results: A total of 55 articles reporting 65 cases of Sarcina Ventriculi were found. Thus, 66 patients, including our case, were reviewed. Median age was 51 years (IQR: 0-87 years). Females accounted for 51% of cases. 68% of patients had one or more comorbidities. SV was isolated in the gastrointestinal tract (88%), respiratory (5%), urine (4%), and bloodstream (3%) systems. Upper endoscopy was performed in 52 patients (79%). Biopsies were obtained in all 52 cases, and resulted normal in 23%. Surgery was warranted in 15 patients (23%), and specific antimicrobial therapy was delivered in 34 (52%) patients. Mortality was 14%. At follow-up, 88% of patients showed complete eradication of the SV infection. Conclusions: Upper gastrointestinal biopsy positive for SV should prompt an evaluation of the clinical conditions, being the risk of gastric perforation not negligible. Antibiotic therapy may eradicate the infection and prevent complications. Emergency surgery is required in case of source control

Open data from the first and second observing runs of Advanced LIGO and Advanced Virgo

Advanced LIGO and Advanced Virgo are monitoring the sky and collecting gravitational-wave strain data with sufficient sensitivity to detect signals routinely. In this paper we describe the data recorded by these instruments during their first and second observing runs. The main data products are gravitational-wave strain time series sampled at 16384 Hz. The datasets that include this strain measurement can be freely accessed through the Gravitational Wave Open Science Center at http://gw-openscience.org, together with data-quality information essential for the analysis of LIGO and Virgo data, documentation, tutorials, and supporting software

Global variation in postoperative mortality and complications after cancer surgery: a multicentre, prospective cohort study in 82 countries

© 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 licenseBackground: 80% of individuals with cancer will require a surgical procedure, yet little comparative data exist on early outcomes in low-income and middle-income countries (LMICs). We compared postoperative outcomes in breast, colorectal, and gastric cancer surgery in hospitals worldwide, focusing on the effect of disease stage and complications on postoperative mortality. Methods: This was a multicentre, international prospective cohort study of consecutive adult patients undergoing surgery for primary breast, colorectal, or gastric cancer requiring a skin incision done under general or neuraxial anaesthesia. The primary outcome was death or major complication within 30 days of surgery. Multilevel logistic regression determined relationships within three-level nested models of patients within hospitals and countries. Hospital-level infrastructure effects were explored with three-way mediation analyses. This study was registered with ClinicalTrials.gov, NCT03471494. Findings: Between April 1, 2018, and Jan 31, 2019, we enrolled 15 958 patients from 428 hospitals in 82 countries (high income 9106 patients, 31 countries; upper-middle income 2721 patients, 23 countries; or lower-middle income 4131 patients, 28 countries). Patients in LMICs presented with more advanced disease compared with patients in high-income countries. 30-day mortality was higher for gastric cancer in low-income or lower-middle-income countries (adjusted odds ratio 3·72, 95% CI 1·70–8·16) and for colorectal cancer in low-income or lower-middle-income countries (4·59, 2·39–8·80) and upper-middle-income countries (2·06, 1·11–3·83). No difference in 30-day mortality was seen in breast cancer. The proportion of patients who died after a major complication was greatest in low-income or lower-middle-income countries (6·15, 3·26–11·59) and upper-middle-income countries (3·89, 2·08–7·29). Postoperative death after complications was partly explained by patient factors (60%) and partly by hospital or country (40%). The absence of consistently available postoperative care facilities was associated with seven to 10 more deaths per 100 major complications in LMICs. Cancer stage alone explained little of the early variation in mortality or postoperative complications. Interpretation: Higher levels of mortality after cancer surgery in LMICs was not fully explained by later presentation of disease. The capacity to rescue patients from surgical complications is a tangible opportunity for meaningful intervention. Early death after cancer surgery might be reduced by policies focusing on strengthening perioperative care systems to detect and intervene in common complications. Funding: National Institute for Health Research Global Health Research Unit