Head and neck automatic multi-organ segmentation on Dual-Energy Computed Tomography.

Background And Purpose: Deep-learning-based automatic segmentation is widely used in radiation oncology to delineate organs-at-risk. Dual-energy CT (DECT) allows the reconstruction of enhanced contrast images that could help with manual and auto-delineation. This paper presents a performance evaluation of a commercial auto-segmentation software on image series generated by a DECT.

a comprehensive view of the proteome.

We describe a new release of the PeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively.

Pushing the boundaries of radiotherapy-immunotherapy combinations: highlights from the 7 immunorad conference.

Over the last decade, the annual Immunorad Conference, held under the joint auspicies of Gustave Roussy (Villejuif, France) and the Weill Cornell Medical College (New-York, USA) has aimed at exploring the latest advancements in the fields of tumor immunology and radiotherapy-immunotherapy combinations for the treatment of cancer. Gathering medical oncologists, radiation oncologists, physicians and researchers with esteemed expertise in these fields, the Immunorad Conference bridges the gap between preclinical outcomes and clinical opportunities. Thus, it paves a promising way toward optimizing radiotherapy-immunotherapy combinations and, from a broader perspective, improving therapeutic strategies for patients with cancer.

Heterogeneous intratumor irradiation: a new partner for immunotherapy.

We recently demonstrated that a heterogeneous tumor irradiation strategy, combining high-dose and low-dose radiotherapy (RT) within the same tumor volume, can synergize with immunotherapy in mice. Our findings indicate that heterogeneous RT doses may promote the spatial diversification of the antitumor immune response. Spatial fractionation of the RT dose has the potential to enhance the therapeutic index of RT/IO combinations, particularly in scenarios where irradiating the entire tumor volume is unfeasible or excessively harmful to the patient.

The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.

Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.

The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends.

Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the circulating proteome, as blood offers an accessible window into human health. However, every methodological innovation and analytical progress calls for reassessing our existing approaches and routines to ensure that the new data will add value to the greater biomedical research community and avoid previous errors.

Phosphorylation in the Proteome: A Meta-Analysis of Publicly Available Data Sets.

Malaria is a deadly disease caused by Apicomplexan parasites of the genus. Several species of the genus are known to be infectious to humans, of which is the most virulent. Post-translational modifications (PTMs) of proteins coordinate cell signaling and hence regulate many biological processes in homeostasis and host infection, of which the most highly studied is phosphorylation.

Deleting Trim33 in Myeloid Cells Improves the Efficiency of Radiotherapy through an IFNβ-Dependent Antitumor Immune Response.

Radiotherapy (RT) triggers an immune response that contributes to antitumor effects. Induction of IFNβ is a key event in this immunogenicity of RT. We have previously shown that TRIM33, a chromatin reader, restrains IFNβ expression in Toll-like receptor-activated myeloid cells.

Evidence of Alveolar Macrophage Metabolic Shift Following Stereotactic Body Radiation Therapy -Induced Lung Fibrosis in Mice.

Purpose: Radiation-induced pneumopathy is the main dose-limiting factor in cases of chest radiation therapy. Macrophage infiltration is frequently observed in irradiated lung tissues and may participate in lung damage development. Radiation-induced lung fibrosis can be reproduced in rodent models using whole thorax irradiation but suffers from limits concerning the role played by unexposed lung volumes in damage development.

SQUIRE-SIM (Standards for Quality Improvement Reporting Excellence for SIMulation): Publication Guidelines for Simulation-Based Quality Improvement Projects.

Introduction: With increased incorporation of simulation-based methodologies into quality improvement activities, standards for reporting on simulation-specific elements in healthcare improvement research are needed.

Methods: We followed established consensus process methodology to iteratively create simulation-based extensions for SQUIRE 2.0 reporting guidelines.

The PeptideAtlas: A New Maize Community Resource.

This study presents the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome.

Feasibility and Safety of the "One-Week Breast Radiation Therapy" Program.

Aims: FAST-Forward and UK-FAST-trials have demonstrated the safety and efficacy of five-fraction breast adjuvant radiation therapy (RT) and have become the standard of care for selected early breast cancer patients. In response to the additional burden caused by the COVID-19 pandemic, we implemented "One-Week Breast RT," an innovative program delivering five-fraction whole breast RT in a complete 5-day workflow. The primary objective of this study was to demonstrate the feasibility and safety of our program.

Baseline DSB repair prediction of chronic rare Grade ≥ 3 toxicities induced by radiotherapy using classification algorithms.

Small fractions of patients suffer from radiotherapy late severe adverse events (AEs Grade ≥ 3), which are usually irreversible and badly affect their quality of life. A novel functional DNA repair assay characterizing several steps of double-strand break (DSB) repair mechanisms was used. DNA repair activities of peripheral blood mononuclear cells were monitored for 1 week using NEXT-SPOT assay in 177 breast and prostate cancer patients.

Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.

Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins.

Nonpersistent Nanoarchitectures Enhance Concurrent Chemoradiotherapy in an Immunocompetent Orthotopic Model of HPV+ Head/Neck Carcinoma.

Cisplatin chemoradiotherapy (CRT) is the established standard of care for managing locally advanced human papillomavirus-positive head/neck carcinoma. The typically young patients may suffer serious and long-time side effects caused by the treatment, such as dysphagia, and hearing loss. Thus, ensuring a satisfactory post-treatment quality of life is paramount.

LymphoDose: a lymphocyte dose estimation framework-application to brain radiotherapy.

. Severe radiation-induced lymphopenia occurs in 40% of patients treated for primary brain tumors and is an independent risk factor of poor survival outcomes. We developed anframework that estimates the radiation doses received by lymphocytes during volumetric modulated arc therapy brain irradiation.