ModeHunter: A Package for the Reductionist Analysis, Animation, and Application of Elastic Biomolecular Motion.

ModeHunter is a modular Python software package for the simulation of 3D biophysical motion across spatial resolution scales using modal analysis of elastic networks. It has been curated from our in-house Python scripts over the last 15 years, with a focus on detecting similarities of elastic motion between atomic structures, coarse-grained graphs, and volumetric data obtained from biophysical or biomedical imaging origins, such as electron microscopy or tomography. With ModeHunter, normal modes of biophysical motion can be analyzed with various static visualization techniques or brought to life by dynamics animation in terms of single or multimode trajectories or decoy ensembles.

Safety and Efficacy of Transsternal Core Biopsy of Anterior Mediastinal Masses.

Background: The study evaluated the safety and adequacy of percutaneous transsternal anterior mediastinal core biopsy.

Methods: All percutaneous computed tomography-guided transsternal mediastinal 18-gauge core biopsies performed at 2 academic centers were retrospectively reviewed. Procedural, clinical, and pathology data were recorded.

Benign Soft Tissue Lesions Responsible for Pain: When and How Should the IR Intervene.

In most of the cases Interventional Radiology techniques and therapies are proposed for the management of symptomatic soft tissue benign tumors responsible for pain and/or compression symptoms aiming to offer a curative intent by means of tumor necrosis with subsequent symptoms' management and improvement of life quality. The ablative therapies include chemical, thermal and non-thermal approaches while, trans-arterial (chemo)embolization also has a distinct role. Adjunct ancillary techniques should be performed whenever necessary to increase efficacy and safety and avoid or reduce complications.

The master male sex determinant Gdf6Y of the turquoise killifish arose through allelic neofunctionalization.

Although sex determination is a fundamental process in vertebrate development, it is very plastic. Diverse genes became major sex determinants in teleost fishes. Deciphering how individual sex-determining genes orchestrate sex determination can reveal new actors in sexual development.

Neoadjuvant or concurrent atezolizumab with chemoradiation for locally advanced cervical cancer: a randomized phase I trial.

Combined immune checkpoint blockade (ICB) and chemoradiation (CRT) is approved in patients with locally advanced cervical cancer (LACC) but optimal sequencing of CRT and ICB is unknown. NRG-GY017 (NCT03738228) was a randomized phase I trial of atezolizumab (anti-PD-L1) neoadjuvant and concurrent with CRT (Arm A) vs. concurrent with CRT (Arm B) in patients with high-risk node-positive LACC.

Correlation of Histologic Features with Gene Alterations in Pleural Mesothelioma.

Histologic features, including architectural patterns, cytologic features, and 2021 World Health Organization nuclear grade have been shown to have prognostic significance in epithelioid diffuse pleural mesothelioma (DPM). Biphasic and sarcomatoid DPM, regardless of morphology, have worse outcomes. These prognostic findings are well-established but correlation of architectural patterns, cytologic features, and nuclear grade with genetic alterations has not been well studied.

Evaluating the Accuracy of Relative Value Unit and Operative Time Changes in Breast Reconstruction.

Background: As part of the 2021 changes to breast reconstruction CPT codes, the Relative Value Scale Update Committee (RUC) recommended adjustments to work RVUs (wRVUs) based on newly surveyed intraoperative times. Our objective was to gauge the accuracy of operative time and wRVU adjustments using national data as a benchmark.

Methods: We queried the National Surgical Quality Improvement Program (NSQIP) database for operative times from 2005-2021 for reevaluated CPT codes.

Bile acid synthesis impedes tumor-specific T cell responses during liver cancer.

The metabolic landscape of cancer greatly influences antitumor immunity, yet it remains unclear how organ-specific metabolites in the tumor microenvironment influence immunosurveillance. We found that accumulation of primary conjugated and secondary bile acids (BAs) are metabolic features of human hepatocellular carcinoma and experimental liver cancer models. Inhibiting conjugated BA synthesis in hepatocytes through deletion of the BA-conjugating enzyme bile acid-CoA:amino acid -acyltransferase (BAAT) enhanced tumor-specific T cell responses, reduced tumor growth, and sensitized tumors to anti-programmed cell death protein 1 (anti-PD-1) immunotherapy.

Genetic Ancestry-Based Differences in Biomarker-Based Eligibility for Precision Oncology Therapies.

Importance: Although differences in the prevalence of key cancer-specific somatic mutations as a function of genetic ancestry among patients with cancer has been well-established, few studies have addressed the practical clinical implications of these differences for the growing number of biomarker-driven treatments.

Objective: To determine if the approval of precision oncology therapies has benefited patients with cancer from various ancestral backgrounds equally over time.

Design, Setting, And Participants: A retrospective analysis of samples from patients with solid cancers who underwent clinical sequencing using the integrated mutation profiling of actionable cancer targets (MSK-IMPACT) assay between January 2014 and December 2022 was carried out.

Contemporary prostate cancer radiation therapy trials may underestimate the risk of biochemical recurrence.

Background: Radiotherapy is often given with androgen deprivation therapy for prostate cancer which causes a reduction in testosterone levels, which when below castrate levels, can cause the prostate specific antigen (PSA) levels to be artificially low.

Aim: To determine if high-level radiotherapy clinical trials are underestimating biochemical recurrence (BCR) rates due to inadequate measurement of testosterone levels.

Methods: The study plans for clinical trials performed by the Radiation Therapy Oncology Group (RTOG [now NRG]) on clinicaltrials.

Immune Checkpoint Blockade Delays Cancer Development and Extends Survival in DNA Polymerase Mutator Syndromes.

Mutations in the exonuclease domains of the replicative nuclear DNA polymerases POLD1 and POLE are associated with increased cancer incidence, elevated tumor mutation burden (TMB), and enhanced response to immune checkpoint blockade (ICB). Although ICB is approved for treatment of several cancers, not all tumors with elevated TMB respond, highlighting the need for a better understanding of how TMB affects tumor biology and subsequently immunotherapy response. To address this, we generated mice with germline and conditional mutations in the exonuclease domains of Pold1 and Pole.

Percutaneous transhepatic arterial access for coil embolization of hepatic artery infusion pump-associated bleeding.

Background: Hepatic artery infusion pump (HAIP) chemotherapy is a locoregional treatment for intrahepatic malignancies. HAIPs are surgically implanted, and the catheter tip is typically inserted into a ligated gastroduodenal artery stump. Potential complications at the catheter insertion site include dehiscence, pseudoaneurysm or extravasation, and adjacent hepatic arterial stenosis and thrombosis.

Breast Cancer Susceptibility Gene Sequence Variations and Development of Contralateral Breast Cancer.

Importance: Heterogeneity in development of estrogen receptor (ER)-specific first primary breast cancer exists due to deleterious germline variants in moderate- to high-penetrance breast cancer susceptibility genes, but it is unknown if these associations occur in ER-specific CBC.

Objective: To determine the association of deleterious germline variants in breast cancer susceptibility genes with ER-specific CBC development and whether ER status of the first primary breast cancer modifies these associations.

Design, Setting, And Participants: This case-control study included CBC cases and matched unilateral breast cancer controls from The Women's Environment, Cancer, and Radiation Epidemiology (WECARE) Study, a population-based case-control study.

Outcomes of Older Adults and Frail Patients Receiving Idecabtagene Vicleucel: A CIBMTR Study.

Idecabtagene vicleucel (ide-cel) is an anti-BCMA CAR-T cell therapy approved for patients with relapsed/refractory multiple myeloma (RRMM) after 2 prior lines of therapy. There is limited data on outcomes of CAR T in older adults and frail patients with RRMM. In this study, we utilized data from the Center for International Blood and Marrow Transplantation Registry to describe the safety and efficacy of ide-cel in these clinically important subgroups.

Host tissue factors predict immune surveillance and therapeutic outcomes in gastric cancer.

The immune composition of solid tumors is typically inferred from biomarkers, such as histologic and molecular classifications, somatic mutational burden, and PD-L1 expression. However, the extent to which these biomarkers predict the immune landscape in gastric adenocarcinoma-an aggressive cancer often linked to chronic inflammation-remains poorly understood. We leveraged high-dimensional spectral cytometry to generate a comprehensive single-cell immune landscape of tumors, normal tissue, and lymph nodes from patients in the Western Hemisphere with gastric adenocarcinoma.

Clinicopathological Characteristics and Long-Term Outcomes of Cystic vs. Solid Pancreatic Neuroendocrine Tumors: A Multi-Institutional Experience with 1727 Patients.

Objective: To investigate the clinicopathological features and long-term outcomes of cystic and solid pancreatic neuroendocrine tumors (PanNETs).

Summary Background Data: PanNETs uncommonly present as cystic lesions. Whether cystic PanNETs represent a distinct clinical entity compared to solid PanNETs is controversial.

Clinicopathologic and genomic features associated with brain metastasis after resection of lung adenocarcinoma.

Objective: To identify clinicopathologic and genomic features associated with brain metastasis after resection of lung adenocarcinoma (LUAD) and to evaluate survival after brain metastasis.

Methods: Patients who underwent complete resection of stage I-IIIA LUAD between 2011 and 2020 were included. A subset of patients had broad-based panel next-generation sequencing performed on their tumors.

FAP-Targeted SPECT/CT and PET/CT Imaging for Breast Cancer Patients.

Breast cancer presents a significant global health challenge, necessitating continued innovation in diagnostic and therapeutic approaches. Recent advances have led to the identification of cancer-associated fibroblasts, which are highly prevalent in breast cancers and express fibroblast activation proteins (FAPs), as critical targets. FAP-specific radiotracers, when used with PET/CT and SPECT/CT, have significant potential for improving early breast cancer detection, staging, treatment response monitoring, and therapeutic intervention.

Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing.

Single-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing identifies rare populations that express specific marker transcript combinations, traditional flow sorting requires cell surface markers with high-fidelity antibodies, limiting our ability to interrogate these populations. In addition, many single-cell studies require the isolation of nuclei from tissue, eliminating the ability to enrich learned rare cell states based on extranuclear protein markers.