Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data.

Motivation: Phage therapy offers a viable alternative for bacterial infections amid rising antimicrobial resistance. Its success relies on selecting safe and effective phage candidates that require comprehensive genomic screening to identify potential risks. However, this process is often labor intensive and time-consuming, hindering rapid clinical deployment.

phage therapy candidates from Sphae: An automated toolkit for predicting sequencing data.

Motivation: Phage therapy is a viable alternative for treating bacterial infections amidst the escalating threat of antimicrobial resistance. However, the therapeutic success of phage therapy depends on selecting safe and effective phage candidates. While experimental methods focus on isolating phages and determining their lifecycle and host range, comprehensive genomic screening is critical to identify markers that indicate potential risks, such as toxins, antimicrobial resistance, or temperate lifecycle traits.

Evaluation of mucosal barrier disruption due to Staphylococcus lugdunensis and Staphylococcus epidermidis exoproteins in patients with chronic rhinosinusitis.

Background: Chronic rhinosinusitis (CRS) is a persistent inflammatory condition of the sinus mucosa. While Staphylococcus aureus has been shown to play a significant role in mucosal barrier disruption in CRS patients, coagulase-negative staphylococci (CoNS) such as Staphylococcus epidermidis and Staphylococcus lugdunensis are also implicated in CRS pathophysiology. This study investigates the effects of exoproteins secreted by planktonic and biofilm forms of clinical isolates of S.

Differential proteomic expression in non-functional pituitary neuroendocrine tumours and pituitary glands.

Introduction: Pituitary neuroendocrine tumours (PitNETs) are common accounting for 10 to 25 % of all intracranial tumours. This project describes the feasibility of developing a novel membrane-based biomarker that could be used for fluorescent guided surgery. The aim was to catalogue the differential expression of membrane proteins between non-functional PitNETs and pituitary glands.

Solving genomic puzzles: computational methods for metagenomic binning.

Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels.

Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages.

The majority of bacteriophage diversity remains uncharacterized, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the , repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and its subsequent impacts on functional annotation.

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.

It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing is usually required for perfection. However, the effect of short-read depth on polishing performance is not well understood. Here, we introduce Pypolca (with default and careful parameters) and Polypolish v0.

Pilot Validation of a 3-Dimensional Printed Pituitary Adenoma, Vascular Injury, and Cerebrospinal Fluid Leak Surgical Simulator.

Background And Objectives: Endoscopic skull base surgery is a subspecialty field which would benefit significantly from high-fidelity surgical simulators. Giving trainees the opportunity to flatten their learning curve by practicing a variety of procedures on surgical simulators will inevitably improve patient outcomes.

Methods: Four neurosurgeons, 8 otolarynologists, and 6 expert course faculty agreed to participate.

Emergence characteristics comparing endotracheal tube to reinforced laryngeal mask airway during endoscopic sinus surgery - A randomised controlled study.

Background And Aims: During endoscopic sinus surgery, anaesthetic conditions significantly impact the intraoperative surgical field and bleeding during emergence. While the endotracheal tube (ETT) has been traditionally used in sinus surgery, a reinforced laryngeal mask airway (RLMA) that produces less upper airway stimulation may result in smoother emergence.

Methods: A randomised controlled trial of 72 patients undergoing elective sinus surgery was conducted, with the allocation of airway technique to either ETT with a throat pack or RLMA.

Increased antibiotic resistance of isolates from chronic rhinosinusitis patients grown in anaerobic conditions.

Introduction: In chronic rhinosinusitis (CRS), the congestion and blockage of the nose can cause anaerobic conditions within the sinus cavities which may promote the expression of virulence and antibiotic resistance genes in invading pathogens. is a facultative anaerobic bacteria and causes severe recalcitrant CRS. In this study, we aimed to evaluate the antimicrobial resistance of isolates of CRS patients in planktonic and biofilm form grown in aerobic and anaerobic conditions.

Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies.

Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches.

A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.

Describing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S rRNA short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification.

Chitogel with deferiprone following endoscopic sinus surgery: improved wound healing and microbiome.

Background: Adhesion formation, sinus ostial narrowing, and presence of pathogenic bacteria are associated with poor outcomes following endoscopic sinus surgery (ESS) for chronic rhinosinusitis. Chitogel has been shown to improve wound healing, restore a healthier microbiome, and reduce post-operative infections post ESS. Deferiprone has antibacterial properties and has been shown to reduce adhesion formation.

S. aureus biofilm properties correlate with immune B cell subset frequencies and severity of chronic rhinosinusitis.

Staphylococcus aureus mucosal biofilms are associated with recalcitrant chronic rhinosinusitis (CRS). However, S. aureus colonisation of sinus mucosa is frequent in the absence of mucosal inflammation.

Neuronavigation in endoscopic skull base surgery and the accuracy of different MRI sequences.

Objective: Neuronavigation is common technology used by skull base teams when performing endoscopic endonasal surgery. A common practice of MRI imagining is to obtain 3D isotopic gadolinium enhanced T1W magnetisation prepared rapid gradient echo (MPRAGE) sequences. These are prone to distortion when undertaken on 3 T magnets.

Biofilm-Secreted Factors Cause Mucosal Damage, Mast Cell Infiltration, and Goblet Cell Hyperplasia in a Rat Rhinosinusitis Model.

Chronic rhinosinusitis (CRS) is an inflammatory condition of the sinonasal mucosa. Despite being a common health issue, the exact cause of CRS is yet to be understood. However, research suggests that , particularly in its biofilm form, is associated with the disease.

A Novel Model of -Induced Lymphoplasmacytic Rhinosinusitis in Rats.

Chronic rhinosinusitis (CRS) is characterized by sinonasal mucosal inflammation. is associated with severe CRS phenotypes. Different animal models have been proposed to study the association of CRS and .

Preclinical characterization and in silico safety assessment of three virulent bacteriophages targeting carbapenem-resistant uropathogenic Escherichia coli.

Phage therapy has recently been revitalized in the West with many successful applications against multi-drug-resistant bacterial infections. However, the lack of geographically diverse bacteriophage (phage) genomes has constrained our understanding of phage diversity and its genetics underpinning host specificity, lytic capability, and phage-bacteria co-evolution. This study aims to locally isolate virulent phages against uropathogenic Escherichia coli (E.

Chitogel improves long-term health economic outcomes following endoscopic sinus surgery in severe chronic rhinosinusitis patients.

Introduction: Chronic rhinosinusitis causes severe symptoms that can affect patient quality of life. Endoscopic sinus surgery can be effective in improving symptoms, although surgical outcomes can be compromised post-operatively, and revision surgery is required in a proportion of patients. This study compares outcomes and healthcare resource use in patients undergoing sinus surgery with or without Chitogel as a post-operative dressing.

Double blind randomized controlled trial measuring the efficacy of nebulized steroid at half dose in comparison to high volume squeeze bottle steroid irrigation in management of patients with chronic rhinosinusitis.

Nebulized budesonide is effective at half dose compared to budesonide irrigation in CRS. Nasal nebulizers provide an alternative for delivery of topical steroids to the sinuses.

Quality of life after emergency laparotomy: a systematic review.

Background: Emergency laparotomy is a commonly performed surgical procedure that has higher post-operative morbidity and mortality than elective surgery. Previous research has identified that patients valued postoperative quality of life (QoL) more than the risk of mortality when deciding to undergo emergency surgery. Current pre-operative scoring and risk stratification systems for emergency laparotomy do not account for or provide prediction tools for post-operative QoL.

The role of decompressive craniectomy following microsurgical repair of a ruptured aneurysm: Analysis of a South Australian cerebrovascular registry.

Objective: Decompressive craniectomy (DC) remains a controversial intervention for intracranial hypertension among patients with aneurysmal subarachnoid haemorrhage (aSAH).

Methods: We identified aSAH patients who underwent DC following microsurgical aneurysm repair from a prospectively maintained registry and compared their outcomes with a propensity-matched cohort who did not. Logistic regression was used to identify predictors of undergoing decompressive surgery and post-operative outcome.

Identification of consensus head and neck cancer-associated microbiota signatures: a systematic review and meta-analysis of 16S rRNA and The Cancer Microbiome Atlas datasets.

Multiple reports have attempted to describe the tumour microbiota in head and neck cancer (HNSC). However, these have failed to produce a consistent microbiota signature, which may undermine understanding the importance of bacterial-mediated effects in HNSC. The aim of this study is to consolidate these datasets and identify a consensus microbiota signature in HNSC.

Predicting stop codon reassignment improves functional annotation of bacteriophages.

The majority of bacteriophage diversity remains uncharacterised, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the , repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and subsequent impacts on functional annotation.