Prediction of hepatocellular carcinoma response to radiation segmentectomy using an MRI-based machine learning approach.

Purpose: To evaluate the value of pre-treatment MRI-based radiomics in patients with hepatocellular carcinoma (HCC) for the prediction of response to Yttrium 90 radiation segmentectomy.

Methods: This retrospective study included 154 patients (38 female; mean age 66.8 years) who underwent contrast-enhanced MRI prior to radiation segmentectomy.

Precision and Test-Retest Repeatability of Stiffness Measurement with MR Elastography: A Multicenter Phantom Study.

Background MR elastography (MRE) has been shown to have excellent performance for noninvasive liver fibrosis staging. However, there is limited knowledge regarding the precision and test-retest repeatability of stiffness measurement with MRE in the multicenter setting. Purpose To determine the precision and test-retest repeatability of stiffness measurement with MRE across multiple centers using the same phantoms.

Differential Regulation of the STING Pathway in Human Papillomavirus-Positive and -Negative Head and Neck Cancers.

Unlabelled: Squamous cell carcinomas, which arise from the cells that line the mucosal surfaces of the head and neck, represent the most common type of head and neck cancers (HNSCC). Human papillomavirus (HPV) infection has been strongly associated with the development of oropharyngeal cancers, which are cancers that occur in the back of the throat, including the tonsils and base of the tongue. HNSCCs with and without HPV infection have distinct pathology, with HPV-positive patients having higher levels of immune infiltration, activation in the tumor microenvironment and better response to radiation and chemotherapy.

Understanding cancer patient cohorts in virtual reality environment for better clinical decisions: a usability study.

Background: Visualising patient genomic data in a cohort with embedding data analytics models can provide relevant and sensible patient comparisons to assist a clinician with treatment decisions. As immersive technology is actively used around the medical world, there is a rising demand for an efficient environment that can effectively display genomic data visualisations on immersive devices such as a Virtual Reality (VR) environment. The VR technology will allow clinicians, biologists, and computer scientists to explore a cohort of individual patients within the 3D environment.

Soluble CTLA-4 attenuates T cell activation and modulates anti-tumor immunity.

CTLA-4 is a crucial immune checkpoint receptor involved in the maintenance of immune homeostasis, tolerance, and tumor control. Antibodies targeting CTLA-4 have been promising treatments for numerous cancers, but the mechanistic basis of their anti-tumoral immune-boosting effects is poorly understood. Although the ctla4 gene also encodes an alternatively spliced soluble variant (sCTLA-4), preclinical/clinical evaluation of anti-CTLA-4-based immunotherapies have not considered the contribution of this isoform.

Inferring actual treatment pathways from patient records.

Objective: Treatment pathways are step-by-step plans outlining the recommended medical care for specific diseases; they get revised when different treatments are found to improve patient outcomes. Examining health records is an important part of this revision process, but inferring patients' actual treatments from health data is challenging due to complex event-coding schemes and the absence of pathway-related annotations. The objective of this study is to develop a method for inferring actual treatment steps for a particular patient group from administrative health records - a common form of tabular healthcare data - and address several technique- and methodology-based gaps in treatment pathway-inference research.

Neuroblastoma: an ongoing cold front for cancer immunotherapy.

Neuroblastoma is the most frequent extracranial childhood tumour but effective treatment with current immunotherapies is challenging due to its immunosuppressive microenvironment. Efforts to date have focused on using immunotherapy to increase tumour immunogenicity and enhance anticancer immune responses, including anti-GD2 antibodies; immune checkpoint inhibitors; drugs which enhance macrophage and natural killer T (NKT) cell function; modulation of the cyclic GMP-AMP synthase-stimulator of interferon genes pathway; and engineering neuroblastoma-targeting chimeric-antigen receptor-T cells. Some of these strategies have strong preclinical foundation and are being tested clinically, although none have demonstrated notable success in treating paediatric neuroblastoma to date.

Precursor-Directed Biosynthesis and Biological Testing of -Alicyclic- and -Branched Tunicamycin -Acyl Variants.

Tunicamycins (TUNs) are -derived natural products, widely used to block protein -glycosylation in eukaryotes or cell wall biosynthesis in bacteria. Modified or synthetic TUN analogues that uncouple these activities have considerable potential as novel mode-of-action antibacterial agents. Chemically modified TUNs reported previously with attenuated activity on yeast have pinpointed eukaryotic-specific chemophores in the uridyl group and the -acyl chain length and terminal branching pattern.

Machine learning for administrative health records: A systematic review of techniques and applications.

Machine learning provides many powerful and effective techniques for analysing heterogeneous electronic health records (EHR). Administrative Health Records (AHR) are a subset of EHR collected for administrative purposes, and the use of machine learning on AHRs is a growing subfield of EHR analytics. Existing reviews of EHR analytics emphasise that the data-modality of the EHR limits the breadth of suitable machine learning techniques, and pursuable healthcare applications.

Magnetic resonance elastography for noninvasive detection of liver fibrosis: is there an added value of 3D acquisition?

Purpose: (1) Assess the diagnostic performance of liver 3D magnetic resonance elastography (MRE) parameters (including stiffness, storage/loss modulus and damping ratio) compared to liver stiffness measured with 2D MRE for noninvasive detection of advanced liver fibrosis (F3-F4) and cirrhosis (F4) in patients with chronic liver disease. (2) Assess the value of serum markers (FIB-4) in detecting advanced liver fibrosis and cirrhosis in the same patients.

Methods: This was a single center, prospective IRB-approved cross-sectional study that included 49 patients (M/F: 23/26, mean age 50.

A review of the machine learning datasets in mammography, their adherence to the FAIR principles and the outlook for the future.

The increasing rates of breast cancer, particularly in emerging economies, have led to interest in scalable deep learning-based solutions that improve the accuracy and cost-effectiveness of mammographic screening. However, such tools require large volumes of high-quality training data, which can be challenging to obtain. This paper combines the experience of an AI startup with an analysis of the FAIR principles of the eight available datasets.

Transcriptome and Genome Analysis Uncovers a Structural Variant: A Case Report.

Objective: Duchenne muscular dystrophy (DMD) is caused by pathogenic variants in the dystrophin gene (). Hypermethylated CGG expansions within 5' UTR are associated with an intellectual development disorder. Here, we demonstrate the diagnostic utility of genomic short-read sequencing (SRS) and transcriptome sequencing to identify a novel structural variant (SV) and a CGG expansion in a patient with DMD for whom conventional diagnostic testing failed to yield a genetic diagnosis.

A guide to current methodology and usage of reverse vaccinology towards in silico vaccine discovery.

Reverse vaccinology (RV) was described at its inception in 2000 as an in silico process that starts from the genomic sequence of the pathogen and ends with a list of potential protein and/or peptide candidates to be experimentally validated for vaccine development. Twenty-two years later, this process has evolved from a few steps entailing a handful of bioinformatics tools to a multitude of steps with a plethora of tools. Other in silico related processes with overlapping workflow steps have also emerged with terms such as subtractive proteomics, computational vaccinology, and immunoinformatics.

4D flow MRI in abdominal vessels: prospective comparison of k-t accelerated free breathing acquisition to standard respiratory navigator gated acquisition.

Volumetric phase-contrast magnetic resonance imaging with three-dimensional velocity encoding (4D flow MRI) has shown utility as a non-invasive tool to examine altered blood flow in chronic liver disease. Novel 4D flow MRI pulse sequences with spatio-temporal acceleration can mitigate the long acquisition times of standard 4D flow MRI, which are an impediment to clinical adoption. The purpose of our study was to demonstrate feasibility of a free-breathing, spatio-temporal (k-t) accelerated 4D flow MRI acquisition for flow quantification in abdominal vessels and to compare its image quality, flow quantification and inter-observer reproducibility with a standard respiratory navigator-gated 4D flow MRI acquisition.

The serotonin receptor 3E variant is a risk factor for female IBS-D.

Irritable bowel syndrome (IBS) is a gut-brain disorder of multifactorial origin. Evidence of disturbed serotonergic function in IBS accumulated for the 5-HT receptor family. 5-HTRs are encoded by HTR3 genes and control GI function, and peristalsis and secretion, in particular.

Virtual reality for the observation of oncology models (VROOM): immersive analytics for oncology patient cohorts.

The significant advancement of inexpensive and portable virtual reality (VR) and augmented reality devices has re-energised the research in the immersive analytics field. The immersive environment is different from a traditional 2D display used to analyse 3D data as it provides a unified environment that supports immersion in a 3D scene, gestural interaction, haptic feedback and spatial audio. Genomic data analysis has been used in oncology to understand better the relationship between genetic profile, cancer type, and treatment option.

MR elastography outperforms shear wave elastography for the diagnosis of clinically significant portal hypertension.

Objectives: Portal hypertension (PH) is associated with complications such as ascites and esophageal varices and is typically diagnosed through invasive hepatic venous pressure gradient (HVPG) measurement, which is not widely available. In this study, we aim to assess the diagnostic performance of 2D/3D MR elastography (MRE) and shear wave elastography (SWE) measures of liver and spleen stiffness (LS and SS) and spleen volume, to noninvasively diagnose clinically significant portal hypertension (CSPH) using HVPG measurement as the reference.

Methods: In this prospective study, patients with liver disease underwent 2D/3D MRE and SWE of the liver and spleen, as well as HVPG measurement.

Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing.

The World Health Organisation reported in 2020 that six of the top 10 sources of death in low-income countries are parasites. Parasites are microorganisms in a relationship with a larger organism, the host. They acquire all benefits at the host's expense.

Towards Image Guided Magnetic Resonance Elastography via Active Driver Positioning Robot.

Unlabelled: Magnetic Resonance Elastography (MRE) is a developing imaging technique that enables non-invasive estimation of tissue mechanical properties through the combination of induced mechanical displacements in the tissue and Magnetic Resonance Imaging (MRI). The mechanical drivers necessary to produce shear waves in the tissue have been a focus of engineering effort in the development and refinement of MRE. The potential targeting of smaller and stiffer tissues calls for increases in actuation frequency and refinement of mechanical driver positioning.

CD8 T cells and fatty acids orchestrate tumor ferroptosis and immunity via ACSL4.

Tumor cell intrinsic ferroptosis-initiating mechanisms are unknown. Here, we discover that T cell-derived interferon (IFN)γ in combination with arachidonic acid (AA) induces immunogenic tumor ferroptosis, serving as a mode of action for CD8 T cell (CTL)-mediated tumor killing. Mechanistically, IFNγ stimulates ACSL4 and alters tumor cell lipid pattern, thereby increasing incorporations of AA into C16 and C18 acyl chain-containing phospholipids.

Neoadjuvant cemiplimab for resectable hepatocellular carcinoma: a single-arm, open-label, phase 2 trial.

Background: Surgical resection of early stage hepatocellular carcinoma is standard clinical practice; however, most tumours recur despite surgery, and no perioperative intervention has shown a survival benefit. Neoadjuvant immunotherapy has induced pathological responses in multiple tumour types and might decrease the risk of postoperative recurrence in hepatocellular carcinoma. We aimed to evaluate the clinical activity of neoadjuvant cemiplimab (an anti-PD-1) in patients with resectable hepatocellular carcinoma.

Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability.

There is increasing evidence that changes in the variability or overall distribution of gene expression are important both in normal biology and in diseases, particularly cancer. Genes whose expression differs in variability or distribution without a difference in mean are ignored by traditional differential expression-based analyses. Using a Bayesian hierarchical model that provides tests for both differential variability and differential distribution for bulk RNA-seq data, we report here an investigation into differential variability and distribution in cancer.