Identifying Strong Neoantigen MHC-I/II Binding Candidates for Targeted Immunotherapy with SINE.

The discovery of tumor-derived neoantigens which elicit an immune response through major histocompatibility complex (MHC-I/II) binding has led to significant advancements in immunotherapy. While many neoantigens have been discovered through the identification of non-synonymous mutations, the rate of these is low in some cancers, including head and neck squamous cell carcinoma. Therefore, the identification of neoantigens through additional means, such as aberrant splicing, is necessary.

Stroke-induced neuroplasticity in spiny mice in the absence of tissue regeneration.

Stroke is a major cause of disability for adults over 40 years of age. While research into animal models has prioritized treatments aimed at diminishing post-stroke damage, no studies have investigated the response to a severe stroke injury in a highly regenerative adult mammal. Here we investigate the effects of transient ischemia on adult spiny mice, Acomys cahirinus, due to their ability to regenerate multiple tissues without scarring.

Exploring the relationship between shared identity and interoperability: a mixed methods analysis of discussion-based multi-agency emergency response exercises.

Previous research has shown ongoing difficulties between Police, Fire and Rescue, and Ambulance Service responders during multi-agency emergencies. Recently, researchers have used the Social Identity Approach to gain insight into these challenges, offering a psychological framework for understanding relations within and between response organisations. This study builds upon previous work by engaging responders from the emergency services in six discussion-based exercises.

Session Introduction: Precision Medicine: Multi-modal and multi-scale methods to promote mechanistic understanding of disease.

Precision medicine focuses on developing treatments and preventative strategies tailored to an individual's genomic profile, lifestyle, and environmental context. The Precision Medicine sessions at the Pacific Symposium on Biocomputing (PSB) have consistently spotlighted progress in this domain. Our 2025 manuscript collection features algorithmic innovations that integrate data across scales and diverse data modalities, presenting novel techniques to derive clinically relevant insights from molecular datasets.

What is a unit of nature? Measurement challenges in the emerging biodiversity credit market.

Bending the curve of biodiversity loss requires the business and financial sectors to disclose and reduce their biodiversity impacts and help fund nature recovery. This has sparked interest in developing generalizable, standardized measurements of biodiversity-essentially a 'unit of nature'. We examine how such units are defined in the rapidly growing voluntary biodiversity credits market and present a framework exploring how biodiversity is quantified, how delivery of positive outcomes is detected and attributed to the investment and how the number of credits issued is adjusted to account for uncertainties.

MHC-Hammer decodes HLA disruption in tumors.

Tumors utilize various mechanisms of HLA disruption in order to evade immune surveillance. Previous computational tools have interrogated specific aspects of this process, yet a holistic picture of HLA loss of heterozygosity (LOH), transcriptomic suppression, and alternative splicing has remained challenging. In a recent Nature Genetics study, Puttick and colleagues introduced MHC Hammer, a robust computational toolkit designed to dissect the complexities of HLA disruptions that mediate immune evasion in cancer.

Association of advance care planning with hospital use and costs at the end of life: a population-based retrospective cohort study.

Objective: To investigate associations between the availability and timing of digitally available advance care planning (ACP) documents and hospital use and costs during the last 6 months of life.

Design: Retrospective population-based cohort study using data linkage.

Setting: 11 public hospitals in Queensland, Australia.

Pre-operative stereotactic radiosurgery and peri-operative dexamethasone for resectable brain metastases: a two-arm pilot study evaluating clinical outcomes and immunological correlates.

Enhancing the efficacy of immunotherapy in brain metastases (BrM) requires an improved understanding of the immune composition of BrM and how this is affected by radiation and dexamethasone. Our two-arm pilot study (NCT04895592) allocated 26 patients with BrM to either low (Arm A) or high (Arm B) dose peri-operative dexamethasone followed by pre-operative stereotactic radiosurgery (pSRS) and resection (n= 13 per arm). The primary endpoint, a safety analysis at 4 months, was met.

Cost-effectiveness analysis of microwave ablation versus robot-assisted partial nephrectomy for patients with small renal masses in Australia.

Objectives: Microwave ablation (MWA) has gained attention as a minimally invasive and safe alternative to surgical intervention for patients with small renal masses; however, its cost-effectiveness in Australia remains unclear. This study conducted a cost-effectiveness analysis to evaluate the relative clinical and economic merits of MWA compared to robotic-assisted partial nephrectomy (RA-PN) in the treatment of small renal masses.

Methods: A Markov state-transition model was constructed to simulate the progression of Australian patients with small renal masses treated with MWA versus RA-PN over a 10-year horizon.

The development of rapid immunoassays for the urinary analysis of 1-hydroxypyrene glucuronide facilitate both laboratory and on-site polycyclic aromatic hydrocarbon biomonitoring.

Polycylic Aromatic Hydrocarbons (PAHs) are produced during the incomplete burning of organic materials. PAH sources include vehicle exhaust, tobacco smoke and waste incineration. Environmental and occupational exposures to PAHs are known to occur.

The United Nations' General Assembly High-Level Meeting on antimicrobial resistance: a joint statement from the Heads of Government and Chief Medical Officers of the United Kingdom's Overseas Territories.

The UK Overseas Territories (UKOTs) are small, often remote territories with historical and territorial links to the UK. They range from densely populated areas (Cayman, Bermuda, Gibraltar) to land with no permanent inhabitants (British Antarctic Territory, South Georgia). However, they are linked by ecosystem instability (the permacrisis) including antimicrobial resistance (AMR), climate change and biodiversity disruption.

'Going through the motions'; a rich account of the complexity of the anterior cruciate ligament reconstruction pathway, a UK qualitative study.

Objectives: This study aimed to understand the lived experiences of patients on the anterior cruciate ligament reconstruction (ACLR) pathway up to 3 months before, 3 months after and 1 year after surgery. Study objectives were to explore (1) patient experiences of preoperative and postoperative treatment, (2) views of/involvement in prehabilitation and (3) sources and consistency of healthcare advice.

Design: Semi-structured interviews analysed using reflexive thematic analysis.

Exome capture of Antarctic krill (Euphausia superba) for cost effective genotyping and population genetics with historical collections.

Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean ecosystem, with ecological and commercial significance. However, its vulnerability to climate change requires an urgent investigation of its adaptive potential to future environmental conditions. Historical museum collections of krill from the early 20th century represent an ideal opportunity to investigate how krill have changed over time due to predation, fishing and climate change.

Integrated Germline and Somatic Features Reveal Divergent Immune Pathways Driving Response to Immune Checkpoint Blockade.

Immune checkpoint blockade (ICB) has revolutionized cancer treatment; however, the mechanisms determining patient response remain poorly understood. Here, we used machine learning to predict ICB response from germline and somatic biomarkers and interpreted the learned model to uncover putative mechanisms driving superior outcomes. Patients with higher infiltration of T-follicular helper cells had responses even in the presence of defects in the MHC class-I (MHC-I).

So is it better than something else? Using the results of a random-effects meta-analysis to characterize the magnitude of an effect size as a percentile.

The characterization of an effect size is best made in reference to effect sizes found in the literature. A random-effects meta-analysis is the systematic synthesis of related effects from across a literature, producing an estimate of the distribution of effects in the population. We propose using the estimated mean and variance from a random-effects meta-analysis to inform the characterization of an observed effect size.

Evaluating the tailored implementation of a multisite care navigation service for mental health in rural and remote Australia (The Bridging Study): protocol for a community-engaged hybrid effectiveness-implementation study.

Background: A dramatic decline in mental health of people worldwide in the early COVID-19 pandemic years has not recovered. In rural and remote Australia, access to appropriate and timely mental health services has been identified as a major barrier to people seeking help for mental ill-health. From 2020 to 2021 a care navigation model, Navicare, was co-designed with rural and remote communities in the Greater Whitsunday Region of Central Queensland in Australia.

Current Recommendations for the Use of Sound Therapy in Adults with Hyperacusis: A Scoping Review.

Hyperacusis is a condition that is characterized by hypersensitivity to normal everyday sounds or reduced sound tolerance and can affect patients in distressing ways. Sound therapy is a treatment intervention that is used to desensitize patients. However, as yet, there is a lack of understanding on how it is used in clinical practice, the different types of devices, or how to use them.

A systematic review of health state utility values for older people with acute myeloid leukaemia.

Purpose: Older people with acute myeloid leukaemia (AML) have a poor prognosis, reduced health-related quality of life (HRQoL) and require substantial healthcare resources. The objectives of this systematic review were to determine what health state utility values (HSUVs) are reported in the literature that can be used in economic evaluations of interventions for older people with AML, identify research gaps, and discuss directions for future research.

Methods: The following databases were searched for studies published from inception until Feb 2023: PubMed, EMBASE, CINAHL, PsycINFO, Cochrane, and EconLit.

Genetic association and machine learning improves discovery and prediction of type 1 diabetes.

Type 1 diabetes (T1D) has a large genetic component, and expanded genetic studies of T1D can lead to novel biological and therapeutic discovery and improved risk prediction. In this study, we performed genetic association and fine-mapping analyses in 817,718 European ancestry samples genome-wide and 29,746 samples at the MHC locus, which identified 165 independent risk signals for T1D of which 19 were novel. We used risk variants to train a machine learning model (named T1GRS) to predict T1D, which highly differentiated T1D from non-disease and type 2 diabetes (T2D) in Europeans as well as African Americans at or beyond the level of current standards.