DiscovEpi: automated whole proteome MHC-I-epitope prediction and visualization.

BACKGROUND: Antigen presentation is a central step in initiating and shaping the adaptive immune response. To activate CD8+ T cells, pathogen-derived peptides are presented on the cell surface of antigen-presenting cells bound to major histocompatibility complex (MHC) class I molecules. CD8+ T cells that recognize these complexes with their T cell receptor are activated and ideally eliminate infected cells. Prediction of putative peptides binding to MHC class I (MHC-I) is crucial for understanding pathogen recognition in specific immune responses and for supporting drug and vaccine design. There are reliable databases for epitope prediction algorithms available however they primarily focus on the prediction of epitopes in single immunogenic proteins. RESULTS: We have developed the tool DiscovEpi to establish an interface between whole proteomes and epitope prediction. The tool allows the automated identification of all potential MHC-I-binding peptides within a proteome and calculates the epitope density and average binding score for every protein, a protein-centric approach. DiscovEpi provides a convenient interface between automated multiple sequence extraction by organism and cell compartment from the database UniProt for subsequent epitope prediction via NetMHCpan. Furthermore, it allows ranking of proteins by their predicted immunogenicity on the one hand and comparison of different proteomes on the other. By applying the tool, we predict a higher immunogenic potential of membrane-associated proteins of SARS-CoV-2 compared to those of influenza A based on the presented metrics epitope density and binding score. This could be confirmed visually by comparing the epitope maps of the influenza A strain and SARS-CoV-2. CONCLUSION: Automated prediction of whole proteomes and the subsequent visualization of the location of putative epitopes on sequence-level facilitate the search for putative immunogenic proteins or protein regions and support the study of adaptive immune responses and vaccine design.

A multicentre, clinical evaluation of a hydro-responsive wound dressing: the Glasgow experience.

OBJECTIVE: Our aim was to assess the effectiveness of hydro-responsive wound dressing (HRWD) in debridement and wound bed preparation of a variety of acute and chronic wounds that presented with devitalised tissue needing removal so that healing may proceed. METHOD: This was a non-comparative evaluation of acute and chronic wounds that required debridement as part of their normal treatment regimen. Clinicians recorded wound changes including a subjective assessment level of devitalised tissue and wound bed preparation, presence of pain, wound status (e.g., wound size) and periwound skin condition. Data was also collected from clinicians and patients to provide information on clinical performance of the dressing. RESULTS: We recruited 100 patients with a variety of wound types into the study. Over 90% of the clinicians reported removal of devitalised tissue to enable a healing response in both chronic and acute wounds. Specifically, over the course of the evaluation period, levels of devitalised tissue (necrosis and slough) reduced from 85.5% to 26.3%, and this was accompanied by an increase in wound bed granulation from 12.0% to 33.7%. Correspondingly, there was a 40% reduction in wound area, hence a clinically relevant healing response was seen upon treatment with HRWD. It is also noteworthy that this patient population included a significant proportion of chronic wounds (51.4%) that showed no signs of wound progression within <4 weeks before study inclusion. Of these chronic wounds, 93% demonstrated wound progression upon treatment with HRWD. Despite reported pain levels being low pre- and post-dressing change, overall wound pain improved (reduced) in 48% of patients. Periwound skin condition showed a tendency towards improvement, and the fluid management capabilities of the HRWD was reported as good to excellent in the majority of cases. Wound infections were reduced by at least 60% over the evaluation period. A simple cost-effective analysis demonstrated significant savings using HRWD (£6.33) over current standard practice regimens of a four-step debridement process (£8.05), larval therapy (£306.39) and mechanical pad debridement (£11.46). CONCLUSION: HRWD was well tolerated and was demonstrated to be an efficient debridement tool providing rapid, effective and pain free debridement in a variety of wound types.

Reasons for late detection of hip dislocation in childhood.

A retrospective study of 56 children with dislocation of the hip presenting late found that the mean age at which the parents first noticed that something was wrong (including hip abnormalities found at birth in 10 patients) was 11 months, but that at diagnosis was 26 months, a mean delay of 15 months. The reasons for delay were failure to examine the hips at birth (13 cases), failure to follow up abnormalities at birth (7), failure of symptoms noticed by the parents to alert the health-care professional to the possibility of a dislocated hip (36), failure to check the hips routinely after 3 months (27), and failure of the parents to appreciate the significance of abnormalities and to act on them (28). Hip screening should continue beyond the neonatal period and should include routine checks on all children until they are walking normally. A greater awareness in health-care professionals of the features of hip dislocation and further health education for parents are needed.