Utility of hybrid whole genome sequencing in assessing potential nosocomial VIM transmission.

Hybrid whole genome sequencing was used to investigate if nosocomial Verona integron-encoded metallo-β-lactamase (VIM) carbapenemase transmission occurred between two patients without epidemiological links or common pathogens. Challenges in genomic methodology and appropriate analytical depth for mobile carbapenemase outbreaks are described including how inappropriate choices can mislead results and impact infection control practices.

Genomic characterization of pathotype diversity and drug resistance among generic Escherichia coli isolated from broiler chickens in Canada.

Escherichia coli is a Gram-negative bacterium that is ubiquitous in animals and humans, with some strains capable of causing disease. The aim of this study was to perform a comparative genomic analysis of 2,732 generic E. coli isolates that were recovered from poultry samples collected from six regions in Canada as part of the National Microbiological Baseline study in Broiler Chicken.

A bivalent COVID-19 mRNA vaccine elicited broad immune responses and protection against Omicron subvariants infection.

Continuously emerging SARS-CoV-2 Omicron subvariants pose a threat thwarting the effectiveness of approved COVID-19 vaccines. Especially, the protection breadth and degree of these vaccines against antigenically distant Omicron subvariants is unclear. Here, we report the immunogenicity and efficacy of a bivalent mRNA vaccine, PTX-COVID19-M1.

Blood Plasma Methylated DNA Markers in the Detection of Lymphoma: Discovery, Validation, and Clinical Pilot.

Lymphoma is one of the leading causes of cancer and cancer deaths and yet has not been amenable to population screening. The role of methylated DNA markers (MDMs) in the detection of lymphoma has not been extensively studied. We aimed to discover, validate, and test tissue-derived MDMs of lymphoma in archival plasma specimens.

VSV drives CD8 T cell-mediated tumour regression through infection of both cancer and non-cancer cells.

Oncolytic viruses (OV) are designed to selectively infect and kill cancer cells, while simultaneously eliciting antitumour immunity. The mechanism is expected to originate from infected cancer cells. However, recent reports of tumour regression unaccompanied by cancer cell infection suggest a more complex mechanism of action.

Early detection of pancreatic cancer: Study design and analytical considerations in biomarker discovery and early phase validation studies.

Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease that is challenging to detect at an early stage. Biomarkers are needed that can detect PDAC early in the course of disease when interventions lead to the best outcomes. We highlight study design and statistical considerations that inform pancreatic cancer early detection biomarker evaluation.

The pore-forming apolipoprotein APOL7C drives phagosomal rupture and antigen cross-presentation by dendritic cells.

Conventional dendritic cells (cDCs) generate protective cytotoxic T lymphocyte (CTL) responses against extracellular pathogens and tumors. This is achieved through a process known as cross-presentation (XP), and, despite its biological importance, the mechanism(s) driving XP remains unclear. Here, we show that a cDC-specific pore-forming protein called apolipoprotein L 7C (APOL7C) is up-regulated in response to innate immune stimuli and is recruited to phagosomes.

3D ultrasound-augmented image guidance for surgery of high-grade gliomas - A quantitative analysis focused on the extent of resection.

Background: We have retrospectively reviewed our series of brain tumor patients operated on using 3D IntraOperative UltraSound (IOUS) to report technical advantages and areas of improvement.

Methods: Clinical and radiological data of patients with a diagnosis of high-grade glioma IV operated with and without IOUS were retrieved and analyzed.

Results: We have found 391 patients operated using IOUS coupled with neuronavigation and 257 using neuronavigation standalone.

Methylated DNA Markers in Voided Urine for the Identification of Clinically Significant Prostate Cancer.

Introduction: Non-invasive assays are needed to better discriminate patients with prostate cancer (PCa) to avoid over-treatment of indolent disease. We analyzed 14 methylated DNA markers (MDMs) from urine samples of patients with biopsy-proven PCa relative to healthy controls and further studied discrimination of clinically significant PCa (csPCa) from healthy controls and Gleason 6 cancers.

Methods: To evaluate the panel, urine from 24 healthy male volunteers with no clinical suspicion for PCa and 24 men with biopsy-confirmed disease across all Gleason scores was collected.

An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation.

Regular screening for colorectal cancer (CRC) is critical for early detection and long-term survival. Despite the current screening options available and advancements in therapies there will be around 53,000 CRC related deaths this year. There is great interest in non-invasive alternatives such as plasma cell-free RNA (cfRNA) for diagnostic, prognostic, and predictive applications.

Elucidating the influences of social determinants of health on perceived overall health among African American/Black and Hispanic ovarian cancer survivors using the NIH All of Us Research Program.

Objectives: To evaluate the influences of social determinants of health (SDOH) on perceived health and well-being among African American (AA)/Black and Hispanic ovarian cancer survivors.

Methods: A cross-sectional study was conducted using overall health and SDOH survey data collected by the National Institutes of Health All of Us Research Program from May 2017 to September 2023.

Results: While 1250 enrolled participants with ovarian cancer met the inclusion criteria, 414 (33%) completed SDOH surveys: 29 (7%) AA/Black, 33 (8%) Hispanic, and 352 (85%) White.

A computational pipeline for identifying gene targets and signalling pathways in cancer cells to improve lymphocyte infiltration and immune checkpoint therapy efficacy.

Background: Tumour-infiltrating lymphocytes (TILs) are crucial for effective immune checkpoint blockade (ICB) therapy in solid tumours. However, ∼70% of these tumours exhibit poor lymphocyte infiltration, rendering ICB therapies less effective.

Methods: We developed a bioinformatics pipeline integrating multiple previously unconsidered factors or datasets, including tumour cell immune-related pathways, copy number variation (CNV), and single tumour cell sequencing data, as well as tumour mRNA-seq data and patient survival data, to identify targets that can potentially improve T cell infiltration and enhance ICB efficacy.

The Role of the Human Microbiome in Epithelial Ovarian Cancer.

Ovarian cancer is the fifth-leading cause of cancer deaths among women due to the absence of available screening methods to identify early disease. Thus, prevention and early disease detection investigations are of high priority, surrounding a critical window of opportunity to better understand important pathogenic mechanisms of disease progression. Microorganisms modulate molecular interactions in humans that can influence states of health and disease, including ovarian cancer.

Algorithm Training and Testing for a Nonendoscopic Barrett's Esophagus Detection Test in Prospective Multicenter Cohorts.

Background & Aims: Endoscopic Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) detection is invasive and expensive. Nonendoscopic BE/EAC detection tools are guideline-endorsed alternatives. We previously described a 5-methylated DNA marker (MDM) panel assayed on encapsulated sponge cell collection device (CCD) specimens.

High-titer manufacturing of SARS-CoV-2 Spike-pseudotyped VSV in stirred-tank bioreactors.

The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic highlighted the importance of vaccine innovation in public health. Hundreds of vaccines built on numerous technology platforms have been rapidly developed against SARS-CoV-2 since 2020. Like all vaccine platforms, an important bottleneck to viral-vectored vaccine development is manufacturing.

ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97.

The t(X,17) chromosomal translocation, generating the ASPSCR1::TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCCs), frustrating efforts to identify therapeutic targets for these rare cancers. Here, proteomic analysis identifies VCP/p97, an AAA+ ATPase with known segregase function, as strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1::TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1::TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology.

One-pot DTECT enables rapid and efficient capture of genetic signatures for precision genome editing and clinical diagnostics.

The detection of genomic sequences and their alterations is crucial for basic research and clinical diagnostics. However, current methodologies are costly and time-consuming and require outsourcing sample preparation, processing, and analysis to genomic companies. Here, we establish One-pot DTECT, a platform that expedites the detection of genetic signatures, only requiring a short incubation of a PCR product in an optimized one-pot mixture.

Exploring hospital mealtime experiences of older inpatients, caregivers and staff using photovoice methods.

Aim: To gather and understand the experience of hospital mealtimes from the perspectives of those receiving and delivering mealtime care (older inpatients, caregivers and staff) using photovoice methods to identify touchpoints and themes to inform the co-design of new mealtime interventions.

Methods: This study was undertaken on acute care wards within a single metropolitan hospital in Brisbane, Australia in 2019. Photovoice methods involved a researcher accompanying 21 participants (10 older patients, 5 caregivers, 4 nurses and 2 food service officers) during a mealtime and documenting meaningful elements using photographs and field notes.

Next-generation Multi-target Stool DNA Panel Accurately Detects Colorectal Cancer and Advanced Precancerous Lesions.

Unlabelled: The multi-target stool DNA (mt-sDNA) test screens for colorectal cancer by analyzing DNA methylation/mutation and hemoglobin markers to algorithmically derive a qualitative result. A new panel of highly discriminant candidate methylated DNA markers (MDM) was recently developed. Performance of the novel MDM panel, with hemoglobin, was evaluated in a simulated screening population using archived stool samples weighted to early-stage colorectal cancer and prospectively collected advanced precancerous lesions (APL).

We've Got a New One-Exploring the Resident-Fellow New Admission Interaction and Opportunities for Enhancing Motivation.

Objective: To characterize the phases of a new admission interaction between collaborating pediatric residents and fellows; to explore trainee perspectives on motivating and demotivating qualities of that interaction; and to identify behaviors that lead to an optimal new admission interaction.

Methods: The authors used modified grounded theory with experiential learning theory and self-determination theory as sensitizing concepts to conduct 6 focus groups and journey mapping at Stanford Children's Health from January to March 2021. The sessions were audio-recorded and transcribed verbatim.