PepServe: a web server for peptide analysis, clustering and visualization

Peptides, either as protein fragments or as naturally occurring entities are characterized by their sequence and function features. Many times the researchers need to massively manage peptide lists concerning protein identification, biomarker discovery, bioactivity, immune response or other functionalities. We present a web server that manages peptide lists in terms of feature analysis as well as interactive clustering and visualization of the given peptides. PepServe is a useful tool in the understanding of the peptide feature distribution among a group of peptides. The PepServe web application is freely available at http://bioserver-1.bioacademy.gr/Bioserver/PepServe/

Vaccine effectiveness against laboratory-confirmed influenza in Europe – Results from the DRIVE network during season 2018/19

The DRIVE project aims to establish a sustainable network to estimate brand-specific influenza vaccine effectiveness (IVE) annually. DRIVE is a public–private partnership launched in response to EMA guidance that requires effectiveness evaluation from manufacturers for all individual influenza vaccine brands every season. IVE studies are conducted by public partners in DRIVE. Private partners (vaccine manufacturers from the European Federation of Pharmaceutical Industries and Association (EFPIA)) provide written feedback moderated by an independent scientific committee. Test-negative design (TND) case-control studies (4 in primary care and five in hospital) were conducted in six countries in Europe during the 2018/19 season. Site-specific confounder-adjusted vaccine effectiveness (VE) estimates for any vaccine exposure were calculated by age group (<18 years (y), 18-64y and 65 + y) and pooled by setting (primary care, hospital) through random effects meta-analysis. In addition, one population-based cohort study was conducted in Finland. TND studies included 3339 cases and 6012 controls; seven vaccine brands were reported. For ages 65 + y, pooled VE against any influenza strain was estimated at 27% (95%CI 6–44) in hospital setting. Sample size was insufficient for meaningful IVE estimates in other age groups, in the primary care setting, or by vaccine brand. The population-based cohort study included 274,077 vaccinated and 494,337 unvaccinated person-years, two vaccine brands were reported. Brand-specific IVE was estimated for Fluenz Tetra (36% [95%CI 24–45]) for ages 2-6y, Vaxigrip Tetra (54% [43–62]) for ages 6 months to 6y, and Vaxigrip Tetra (30% [25–35]) for ages 65 + y. The results presented are from the second influenza season covered by the DRIVE network. While sample size from the pooled TND studies was still too low for precise (brand-specific) IVE estimates, the network has approximately doubled in size compared to the pilot season. Taking measures to increase sample size is an important focus of DRIVE for the coming years

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Polyamide capsules via soft templating with oil drops—1. Morphological studies of the capsule wall

Poly(terephthalamide) microcapsules can be reproducibly and easily prepared by interfacial polycondensation around emulsion droplets in water. Oil drops of cyclohexane/chloroform mixture stabilized with poly(vinyl alcohol) containing terephthaloylchloride serve as soft template. The interfacial polycondensation starts immediately after addition of an amine mixture (hexamethylenediamine/diethylenetriamine). Light and scanning electron microscopy prove the formation of capsules with size distribution in the range from a few up to 100 µm depending on particular composition of the reaction mixture. The morphology of the capsule wall is characterized by precipitated particles. If instead of pure organic solvents a reactive oil phase is used as template, the capsules can serve in subsequent reactions as templates for the synthesis of composite particles. In this way, styrene can be radically polymerized inside the capsule leading to composite capsules. The capsule morphology is determined by the partition of all components between all phases

Infected pancreatic necrosis: outcomes and clinical predictors of mortality. A post hoc analysis of the MANCTRA-1 international study

: The identification of high-risk patients in the early stages of infected pancreatic necrosis (IPN) is critical, because it could help the clinicians to adopt more effective management strategies. We conducted a post hoc analysis of the MANCTRA-1 international study to assess the association between clinical risk factors and mortality among adult patients with IPN. Univariable and multivariable logistic regression models were used to identify prognostic factors of mortality. We identified 247 consecutive patients with IPN hospitalised between January 2019 and December 2020. History of uncontrolled arterial hypertension (p = 0.032; 95% CI 1.135-15.882; aOR 4.245), qSOFA (p = 0.005; 95% CI 1.359-5.879; aOR 2.828), renal failure (p = 0.022; 95% CI 1.138-5.442; aOR 2.489), and haemodynamic failure (p = 0.018; 95% CI 1.184-5.978; aOR 2.661), were identified as independent predictors of mortality in IPN patients. Cholangitis (p = 0.003; 95% CI 1.598-9.930; aOR 3.983), abdominal compartment syndrome (p = 0.032; 95% CI 1.090-6.967; aOR 2.735), and gastrointestinal/intra-abdominal bleeding (p = 0.009; 95% CI 1.286-5.712; aOR 2.710) were independently associated with the risk of mortality. Upfront open surgical necrosectomy was strongly associated with the risk of mortality (p < 0.001; 95% CI 1.912-7.442; aOR 3.772), whereas endoscopic drainage of pancreatic necrosis (p = 0.018; 95% CI 0.138-0.834; aOR 0.339) and enteral nutrition (p = 0.003; 95% CI 0.143-0.716; aOR 0.320) were found as protective factors. Organ failure, acute cholangitis, and upfront open surgical necrosectomy were the most significant predictors of mortality. Our study confirmed that, even in a subgroup of particularly ill patients such as those with IPN, upfront open surgery should be avoided as much as possible. Study protocol registered in ClinicalTrials.Gov (I.D. Number NCT04747990)

2-fluoro-1-methylpyridinium p-toluene sulfonate: a new LC-MS/MS derivatization reagent for vitamin D metabolites

Vitamin D analysis by MS faces several analytical challenges, including inefficient ionization, nonspecific fragmentation, interferences from epimers, isomers, and isobars, as well as very low concentration levels. In this study, we used 2-fluoro-1-methylpyridinium (FMP) p-toluene sulfonate for derivatization of vitamin D3 metabolites to increase detection sensitivity and allow for full chromatographic separation of vitamin D isomers and epimers. UHPLC-MS/MS was used for measurement of five vitamin D3 metabolites in human serum. Compared with Amplifex and 4-phenyl-1,2,4-triazolin-3,5-dion, the FMP p-toluene sulfonate reaction required less time to be performed. The method was optimized and validated to ensure accuracy, precision, and reliability. In-house and commercial quality control samples were used to assure the quality of the results for 25-hydroxyvitamin D3. The method showed very good linearity and intraday and interday accuracy and precision; coefficients of determination (r2) ranged between 0.9977 and 0.9992, relative recovery from 95 to 111%, and coefficient of variation from 0.9 to 11.3. Stability tests showed that the extracted derivatized serum samples were stable for 24 h after storage at −20°C; 24,25-dihydroxyvitamin D3 and 1,25-dihydroxyvitamin D3-FMP derivatives were stable for 1 week at −80°C. The method was applied to samples of healthy individuals for quantitative determination of vitamin D3, the two epimers of 25-hydroxyvitamin D3 and 24,25-dihydroxyvitamin D3