The impact of package selection and versioning on single-cell RNA-seq analysis.

Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including filtering, highly variable gene selection, dimensionality reduction, clustering, and differential expression analysis. Seurat and Scanpy are the most widely-used packages implementing such workflows, and are generally thought to implement individual steps similarly. We investigate in detail the algorithms and methods underlying Seurat and Scanpy and find that there are, in fact, considerable differences in the outputs of Seurat and Scanpy.

Assessing the agreement of chronic lung disease of prematurity diagnosis between radiologists and clinical criteria.

Background: Chronic lung disease of prematurity (CLD) is the most prevalent complication of preterm birth and indicates an increased likelihood of long-term pulmonary complications. The accurate diagnosis of this condition is critical for long-term health management. Numerous definitions define CLD with different clinical parameters and radiology findings, making diagnosis of the disease ambiguous and potentially inaccurate.

Artificial Intelligence in Pathomics and Genomics of Renal Cell Carcinoma.

The integration of artificial intelligence (AI) with histopathology images and gene expression patterns has led to the emergence of the dynamic fields of pathomics and genomics. These fields have revolutionized renal cell carcinoma (RCC) diagnosis and subtyping and improved survival prediction models. Machine learning has identified unique gene patterns across RCC subtypes and grades, providing insights into RCC origins and potential treatments, as targeted therapies.

Localized Multifocal Retroperitoneal Ganglioneuroma with an Infiltrative Appearance on Imaging: A Case Report.

Multifocal ganglioneuromas are characterized by the presence of multiple benign neuroepithelial tumor nodules and are less common than solitary tumors. A small percentage of ganglioneuromas present with a fatty appearance. Only a few cases of multifocal ganglioneuromas have been reported, due to both their rarity and minimal symptomatic presentation; therefore, generalizations about risk factors and predictive markers are very difficult.

Feminizing Adrenocortical Tumor with Multiple Recurrences: A Case Report.

Feminizing adrenocortical tumors (FATs) are exceptionally rare primary adrenal neoplasms that cause high estrogen and low testosterone levels. They are most common in adult males, typically presenting with gynecomastia, hypogonadism, and weight loss. They are almost always malignant, with a poor prognosis and a high recurrence rate.

Comprehensive Systematic Review of Biomarkers in Metastatic Renal Cell Carcinoma: Predictors, Prognostics, and Therapeutic Monitoring.

Background: Challenges remain in determining the most effective treatment strategies and identifying patients who would benefit from adjuvant or neoadjuvant therapy in renal cell carcinoma. The objective of this review is to provide a comprehensive overview of biomarkers in metastatic renal cell carcinoma (mRCC) and their utility in prediction of treatment response, prognosis, and therapeutic monitoring in patients receiving systemic therapy for metastatic disease.

Methods: A systematic literature search was conducted using the PubMed database for relevant studies published between January 2017 and December 2022.

Deep learning image segmentation approaches for malignant bone lesions: a systematic review and meta-analysis.

Introduction: Image segmentation is an important process for quantifying characteristics of malignant bone lesions, but this task is challenging and laborious for radiologists. Deep learning has shown promise in automating image segmentation in radiology, including for malignant bone lesions. The purpose of this review is to investigate deep learning-based image segmentation methods for malignant bone lesions on Computed Tomography (CT), Magnetic Resonance Imaging (MRI), and Positron-Emission Tomography/CT (PET/CT).