Expansion of the MutS gene family in plants.

The widely distributed MutS gene family functions in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded this gene family in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes.

Parents' Experiences With and Preferences for Receiving Information About Tumor Genomic Sequencing: Findings From a Qualitative Study and Implications for Practice.

Purpose: The use of up-front tumor genomic sequencing (TGS) is becoming increasingly common in pediatric oncology. Despite this, little is known about how parents receive information about TGS at the time of their child's cancer diagnosis. We aimed to describe parents' experiences with and preferences for receiving information about TGS and to use these findings to inform practical guidance for pediatric oncology clinicians.

A patient-led survey on information and communication needs of patients with metastatic breast cancer in Ireland and Northern Ireland (CTRIAL-IE 23-05).

Introduction: Although treatment advances have improved survival rates for patients with metastatic breast cancer (MBC), patient expressed needs have not been evaluated in Ireland to date.

Methods: A 76 item questionnaire was designed by the lead author and a cohort of 41 other MBC patients in collaboration with a multidisciplinary team. The online survey was publicised nationally on all media platforms.

Prognosis-Based Definitions for Potentially Inappropriate Treatment: Still Flawed, If Not Futile.

AbstractThis analysis of professional organizational policies regarding potentially inappropriate life-sustaining medical treatment (LSMT) focuses on the specific threshold criteria that policies apply for limiting LSMT, as well as when (if ever) override of patient/surrogate preferences may be reasonable. Our article offers a critical analysis of one influential approach, proffered by the Society of Critical Care Medicine, that applies a prognosis-based definition of nonbeneficial/inappropriate treatment to determine that ethical threshold. We observe that this prognosis-based threshold resembles rationing in important ways, though it pertains to settings where resources may not be limited.

Investigating the relationship between radiographic joint space width loss and deep learning-derived magnetic resonance imaging-based cartilage thickness loss in the medial weight-bearing region of the tibiofemoral joint.

Objective: To investigate the relationship between measures of radiographic joint space width (JSW) loss and magnetic resonance imaging (MRI)-based cartilage thickness loss in the medial weight-bearing region of the tibiofemoral joint over 12-24 months. To stratify this relationship by clinically meaningful subgroups (sex and pain status).

Design: We analyzed a subset of knees (n ​= ​256) from the Osteoarthritis Initiative (OAI) likely in early stage OA based on joint space narrowing (JSN) measurements.

Measure of Strength of Evidence for Visually Observed Differences between Subpopulations.

For measuring the strength of visually-observed subpopulation differences, the Population Difference Criterion is proposed to assess the statistical significance of visually observed subpopulation differences. It addresses the following challenges: in high-dimensional contexts, distributional models can be dubious; in high-signal contexts, conventional permutation tests give poor pairwise comparisons. We also make two other contributions: Based on a careful analysis we find that a balanced permutation approach is more powerful in high-signal contexts than conventional permutations.

Region of Interest Detection in Melanocytic Skin Tumor Whole Slide Images-Nevus and Melanoma.

Automated region of interest detection in histopathological image analysis is a challenging and important topic with tremendous potential impact on clinical practice. The deep learning methods used in computational pathology may help us to reduce costs and increase the speed and accuracy of cancer diagnosis. We started with the UNC Melanocytic Tumor Dataset cohort which contains 160 hematoxylin and eosin whole slide images of primary melanoma (86) and nevi (74).

Perspectives of pediatric oncologists on referral for CAR-T therapy: a mixed methods pilot study.

Background: Receipt of chimeric antigen receptor T-cell (CAR-T) therapy at an institution different from the primary oncologist's institution is a complex, multistep process. Referral by oncologists plays an important role in the process but may be susceptible to bias.

Methods: Oncologists who previously referred patients for CAR-T therapy at 5 pediatric hospitals were sent surveys by email exploring their CAR-T referral practices.

Expansion of the MutS Gene Family in Plants.

The gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes.

Clinical ethics consultation services: public-facing information on NCI-designated cancer center websites.

Clinical ethics consultation services (CECS) can be particularly complex in oncology, and widespread misconceptions exist about their nature. As a result, visibility and accessibility of information regarding CECS is critical. We investigated the availability and content of information regarding CECS on websites of NCI-designated comprehensive cancer centers and cancer centers (CCs).

Visual Intratumor Heterogeneity and Breast Tumor Progression.

High intratumoral heterogeneity is thought to be a poor prognostic indicator. However, the source of heterogeneity may also be important, as genomic heterogeneity is not always reflected in histologic or 'visual' heterogeneity. We aimed to develop a predictor of histologic heterogeneity and evaluate its association with outcomes and molecular heterogeneity.

Everyday Clinical Ethics: Essential Skills and Educational Case Scenarios.

Bioethics conjures images of dramatic healthcare challenges, yet everyday clinical ethics issues unfold regularly. Without sufficient ethical awareness and a relevant working skillset, clinicians can feel ill-equipped to respond to the ethical dimensions of everyday care. Bioethicists were interviewed to identify the essential skills associated with everyday clinical ethics and to identify educational case scenarios to illustrate everyday clinical ethics.

Region of Interest Detection in Melanocytic Skin Tumor Whole Slide Images - Nevus & Melanoma.

Automated region of interest detection in histopathological image analysis is a challenging and important topic with tremendous potential impact on clinical practice. The deep-learning methods used in computational pathology may help us to reduce costs and increase the speed and accuracy of cancer diagnosis. We started with the UNC Melanocytic Tumor Dataset cohort that contains 160 hematoxylin and eosin whole-slide images of primary melanomas (86) and nevi (74).

Establishing and Defining an Approach to Climate Conscious Clinical Medical Ethics.

An anthropocentric scope for clinical medical ethics (CME) has largely separated this area of bioethics from environmental concerns. In this article, we first identify and reconcile the ethical issues imposed on CME by climate change including the dispersion of related causes and effects, the transdisciplinary and transhuman nature of climate change, and the historic divorce of CME from the environment. We then establish how several moral theories undergirding modern CME, such as virtue ethics, feminist ethics, and several theories of justice, promote both a flourishing of human medical practice and the environment.

Perspectives of Oncologists on the Ethical Implications of Using Artificial Intelligence for Cancer Care.

Importance: Artificial intelligence (AI) tools are rapidly integrating into cancer care. Understanding stakeholder views on ethical issues associated with the implementation of AI in oncology is critical to optimal deployment.

Objective: To evaluate oncologists' views on the ethical domains of the use of AI in clinical care, including familiarity, predictions, explainability (the ability to explain how a result was determined), bias, deference, and responsibilities.

A Communication and Decision-Making Framework for Pediatric Precision Medicine.

Advances in genomic testing have been pivotal in moving childhood cancer care forward, with genomic testing now a standard diagnostic tool for many children, adolescents, and young adults with cancer. Beyond oncology, the role of genomic testing in pediatric research and clinical care is growing, including for children with developmental differences, cardiac abnormalities, and epilepsy. Despite more standard use in their patients, pediatricians have limited guidance on how to communicate this complex information or how to engage parents in decisions related to precision medicine.

Shifting from Equality toward Equity: Addressing Disparities in Research Participation for Clinical Cancer Research.

AbstractThere is societal consensus that cancer clinical trial participation is unjust because some sociodemographic groups have been systematically underrepresented. Despite this, neither a definition nor an ethical explication for the justice norm of equity has been clearly articulated in this setting, leading to confusion over its application and goals. Herein we define equity as acknowledging sociodemographic circumstances and apportioning resource and opportunity allocation to eliminate disparities in outcomes, and we explore the issues and tensions this norm generates through practical examples.

Neoadjuvant trastuzumab deruxtecan (T-DXd) with response-directed definitive therapy in early stage HER2-positive breast cancer: a phase II study protocol (SHAMROCK study).

Background: The current standard of care in the neoadjuvant setting for high-risk HER2-positive (HER2 +) breast cancer is to combine systemic chemotherapy with dual HER2 blockade, trastuzumab and pertuzumab. Targeted therapies have significantly improved outcomes for patients with HER2-positive breast cancer. To improve treatment-associated toxicity, chemotherapy-sparing approaches are currently being investigated.

PAIRWISE NONLINEAR DEPENDENCE ANALYSIS OF GENOMIC DATA.

In The Cancer Genome Atlas (TCGA) data set, there are many interesting nonlinear dependencies between pairs of genes that reveal important relationships and subtypes of cancer. Such genomic data analysis requires a rapid, powerful and interpretable detection process, especially in a high-dimensional environment. We study the nonlinear patterns among the expression of pairs of genes from TCGA using a powerful tool called Binary Expansion Testing.