Survival analysis of oropharyngeal squamous cell carcinoma patients linked to histopathology, disease stage, tumor stage, risk factors, and received therapy

Publisher Copyright: Copyright © Experimental Oncology, 2020. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Survival of oropharyngeal squamous cell carcinoma (OSCC) patients depends on the risk and environmental factors, tumor biology, achievements in diagnostics and treatment approaches. Aim: To perform a survival analysis of the patients with OSCC treated over a 10-year period in a single hospital in Latvia linking these data to histopathological findings, risk factors and received therapy. Materials and Methods: The main outcome measures were overall and disease-specific survival (OS and DS) along with histopathology analysis. Results: Kaplan - Meier survival analysis showed better survival for females, younger patients lacking bad habits, operated and received radiotherapy, with lower T grade and disease stage. Cox regression showed diminished early death risk in patients with lower T grade, no regional metastases (N0) and bad habits, operated and received radiotherapy. A vast majority of tumors were localized in palatine tonsils and the base of the tongue. The localization did not correlate with mean survival time/survival. Lower OS (p = 0.03) and DS (p = 0.026) were estimated for patients with pharyngeal wall and tonsillar involvement compared to tumors localized in the soft palate. A histological variant of tumor seemed irrelevant estimating OS and DS, whereas therapeutic modalities significantly affected survival. Conclusions: OSCC patients with lower T grade, N0 status, lacking bad habits, and surgically treated had better survival.publishersversionPeer reviewe

Production and purification of chimeric HBc virus-like particles carrying influenza virus LAH domain as vaccine candidates

Background: The lack of a universal influenza vaccine is a global health problem. Interest is now focused on structurally conserved protein domains capable of eliciting protection against a broad range of influenza virus strains. The long alpha helix (LAH) is an attractive vaccine component since it is one of the most conserved influenza hemagglutinin (HA) stalk regions. For an improved immune response, the LAH domain from H3N2 strain has been incorporated into virus-like particles (VLPs) derived from hepatitis B virus core protein (HBc) using recently developed tandem core technology. Results: Fermentation conditions for recombinant HBc-LAH were established in yeast Pichia pastoris and a rapid and efficient purification method for chimeric VLPs was developed to match the requirements for industrial scale-up. Purified VLPs induced strong antibody responses against both group 1 and group 2 HA proteins in mice. Conclusion: Our results indicate that the tandem core technology is a useful tool for incorporation of highly hydrophobic LAH domain into HBc VLPs. Chimeric VLPs can be successfully produced in bioreactor using yeast expression system. Immunologic data indicate that HBc VLPs carrying the LAH antigen represent a promising universal influenza vaccine component

The RCSB Protein Data Bank: redesigned web site and web services

The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education

Rapid Proton-Detected NMR Assignment for Proteins with Fast Magic Angle Spinning

Using a set of six 1H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5–30 kDa proteins. The approach relies on perdeuteration, amide 2H/1H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary 13C/15N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR

The effectiveness of helmets in bicycle collisions with motor vehicles: a case-control study

There has been an ongoing debate in Australia and internationally regarding the effectiveness of bicycle helmets in preventing head injury. This study aims to examine the effectiveness of bicycle helmets in preventing head injury amongst cyclists in crashes involving motor vehicles, and to assess the impact of ‘risky cycling behaviour’ among helmeted and unhelmeted cyclists. This analysis involved a retrospective, case-control study using linked police-reported road crash, hospital admission and mortality data in New South Wales (NSW), Australia during 2001 to 2009. The study population was cyclist casualties who were involved in a collision with a motor vehicle. Cases were those that sustained a head injury and were admitted to hospital. Controls were those admitted to hospital who did not sustain a head injury, or those not admitted to hospital. Standard multiple variable logistic regression modelling was conducted, with multinomial outcomes of injury severity. There were 6,745 cyclist collisions with motor vehicles where helmet use was known. Helmet use was associated with reduced risk of head injury in bicycle collisions with motor vehicles of up to 74%, and the more severe the injury considered, the greater the reduction. This was also found to be true for particular head injuries such as skull fractures, intracranial injury and open head wounds. Around one half of children and adolescents less than 19 years were not wearing a helmet, an issue that needs to be addressed in light of the demonstrated effectiveness of helmets. Non-helmeted cyclists were more likely to display risky riding behaviour, however, were less likely to cycle in risky areas; the net result of which was that they were more likely to be involved in more severe crashes

Three dimensional structure of 22 uncultured ssRNA bacteriophages Flexibility of the coat protein fold and variations in particle shapes

The single stranded RNA ssRNA bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins CPs in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome derived ssRNA phage CPs to produce virus like particles and determined the three dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage based vaccine desig

Is protein deuteration beneficial for proton detected solid-state NMR at and above 100 kHz magic-angle spinning?

1H-detection in solid-state NMR of proteins has been traditionally combined with deuteration for both resolution and sensitivity reasons, with the optimal level of proton dilution being dependent on MAS rate. Here we present 1H-detected 15N and 13C CP-HSQC spectra on two microcrystalline samples acquired at 60 and 111 kHz MAS and at ultra-high field. We critically compare the benefits of three labeling schemes yielding different levels of proton content in terms of resolution, coherence lifetimes and feasibility of scalar-based 2D correlations under these experimental conditions. We observe unexpectedly high resolution and sensitivity of aromatic resonances in 2D 13C-1H correlation spectra of protonated samples. Ultrafast MAS reduces or even removes the necessity of 1H dilution for high-resolution 1H-detection in biomolecular solid-state NMR. It yields 15N,1H and 13C,1H fingerprint spectra of exceptional resolution for fully protonated samples, with notably superior 1H and 13C lineshapes for side-chain resonances

Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ

Microscopic imaging and technolog