InPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data.

Background: Alternative cleavage and polyadenylation (APA) is a crucial post-transcriptional gene regulation mechanism that regulates gene expression in eukaryotes by increasing the diversity and complexity of both the transcriptome and proteome. Despite the development of more than a dozen experimental methods over the last decade to identify and quantify APA events, widespread adoption of these methods has been limited by technical, financial, and time constraints. Consequently, APA remains poorly understood in most eukaryotes.

Effects of Extracellular Matrix Changes Induced by a High-Fat Diet on Gallbladder Smooth Muscle Dysfunction.

Background: Gallstone formation is a common digestive ailment, with unclear mechanisms underlying its development. Dysfunction of the gallbladder smooth muscle (GSM) may play a crucial role, particularly with a high-fat diet (HFD). This study aimed to investigate the effects of an HFD on GSM and assess how it alters contractility through changes in the extracellular matrix (ECM).

High-Affinity Lectin Ligands Enable the Detection of Pathogenic Biofilms: Implications for Diagnostics and Therapy.

is a critical priority pathogen and causes life-threatening acute and biofilm-associated chronic infections. The choice of suitable treatment for complicated infections requires lengthy culturing for species identification from swabs or an invasive biopsy. To date, no fast, pathogen-specific diagnostic tools for infections are available.

Proximity to Practice: The Role of Technology in the Next Era of Assessment.

The integration of technology into health professions assessment has created multiple possibilities. In this paper, we focus on the challenges and opportunities of integrating technologies that are used during clinical activities or that are completed by raters after a clinical encounter. In focusing on technologies that are more proximal to practice, we identify tradeoffs with different data collection approaches.

Dysregulated transfer RNA-derived small RNAs as potential gastric cancer biomarkers.

Gastric cancer (GC) is the kind of carcinoma that has the highest rates of morbidity and death worldwide. In the early stages of GC, there is currently an absence of sensitive and specific biomarkers. The newly-discovered class of non-coding RNAs (ncRNAs) known as transfer RNA-derived small RNAs (tsRNAs) is highly expressed in bodily fluids and neoplastic cells.

Acute Decompensated Valvular Disease in the Intensive Care Unit.

Acute decompensated valvular disease encompasses a group of complex and challenging conditions, which are often the primary reason for admission to the cardiac intensive care unit and can also complicate the management of other primary cardiac disorders. Critically ill patients with valvular disease also present unique diagnostic and management challenges. Historically, medical and percutaneous interventional therapies have been limited and surgery was the only definitive treatment; however, surgical risk can at times be prohibitive.

A Magnetic-Responsive Biomimetic Nanosystem Coated with Glioma Stem Cell Membranes Effectively Targets and Eliminates Malignant Gliomas.

Glioblastoma multiforme (GBM) is among the most challenging malignant brain tumors, making the development of new treatment strategies highly necessary. Glioma stem cells (GSCs) markedly contribute to drug resistance, radiation resistance, and tumor recurrence in GBM. The therapeutic potential of nanomaterials targeting GSCs in GBM urgently needs to be explored.

Diversity-Related, Student-Led National Medical Organizations: Leadership Opportunities for Learners.

Introduction: In light of the lack of diversity in academic medicine leadership, diversity-related, student-led national medical organizations (NMOs) provide a space for solace and reprieve among common peers while providing an opportunity to develop leadership competencies in a supportive environment. Despite the impact NMOs have had on cultivating generations of leaders in medicine, trainees may not identify opportunities for leadership development that are transferable to future careers in academic medicine.

Methods: We designed and implemented a dynamic 60-minute workshop with an interactive PowerPoint presentation, author-owned video testimonials (from past student leaders of NMOs), two case presentations, and reflection exercises.

CAF-derived exosome-miR-3124-5p promotes malignant biological processes in NSCLC via the TOLLIP/TLR4-MyD88-NF-κB pathway.

Background: Lung cancer is a life-threatening disease that occurs worldwide, but is especially common in China. The crucial role of the tumour microenvironment (TME) in non-small cell lung cancer (NSCLC) has attracted recent attention. Cancer-associated fibroblasts (CAFs) are the main factors that contribute to the TME function, and CAF exosomes are closely linked to NSCLC.

lncRNA SNHG4 enhanced gastric cancer progression by modulating miR-409-3p/CREB1 axis.

Objective: Gastric cancer (GC) is a globally common cancer characterized by high incidence and mortality worldwide. Advances in the molecular understanding of GC provide promising targets for GC diagnosis and therapy. Long non-coding RNAs (lncRNAs) and their downstream regulators are regarded to be implicated in the progression of multiple types of malignancies.

Predicting epidermal growth factor receptor mutation status of lung adenocarcinoma based on PET/CT images using deep learning.

Background: The aim of this study is to develop deep learning models based on F-fluorodeoxyglucose positron emission tomography/computed tomographic (F-FDG PET/CT) images for predicting individual epidermal growth factor receptor () mutation status in lung adenocarcinoma (LUAD).

Methods: We enrolled 430 patients with non-small-cell lung cancer from two institutions in this study. The advanced Inception V3 model to predict EGFR mutations based on PET/CT images and developed CT, PET, and PET + CT models was used.

Frequency, characteristics, and immunological accompaniments of ataxia in anti-NMDAR antibody-associated encephalitis.

Introduction: Very rarely, adult NMDAR antibody-associated encephalitis (NMDAR-E) leads to persistent cerebellar atrophy and ataxia. Transient cerebellar ataxia is common in pediatric NMDAR-E. Immune-mediated cerebellar ataxia may be associated with myelin oligodendrocyte glycoprotein (MOG), aquaporin-4 (AQP-4), kelch-like family member 11 (KLHL11), and glutamate kainate receptor subunit 2 (GluK2) antibodies, all of which may co-occur in NMDAR-E.

Virtual versus in-person didactic modalities: A national survey of emergency medicine residencies.

Background: Following the widespread shift from in-person to virtual delivery of didactics during the COVID-19 pandemic, some emergency medicine (EM) residency programs have retained virtual didactic time while others have returned exclusively to in-person didactics. In this national survey of EM residency programs, we explored the current national distribution of virtual versus in-person didactic time and the circumstances and motivators for use of each.

Methods: A cross-sectional survey with branched logic was designed via Qualtrics.

Comparison of different group-level templates in gradient-based multimodal connectivity analysis.

The study of large-scale brain connectivity is increasingly adopting unsupervised approaches that derive low-dimensional spatial representations from high-dimensional connectomes, referred to as gradient analysis. When translating this approach to study interindividual variations in connectivity, one technical issue pertains to the selection of an appropriate group-level template to which individual gradients are aligned. Here, we compared different group-level template construction strategies using functional and structural connectome data from neurotypical controls and individuals with autism spectrum disorder (ASD) to identify between-group differences.

A generative model of the connectome with dynamic axon growth.

Connectome generative models, otherwise known as generative network models, provide insight into the wiring principles underpinning brain network organization. While these models can approximate numerous statistical properties of empirical networks, they typically fail to explicitly characterize an important contributor to brain organization-axonal growth. Emulating the chemoaffinity-guided axonal growth, we provide a novel generative model in which axons dynamically steer the direction of propagation based on distance-dependent chemoattractive forces acting on their growth cones.

Increasing hub disruption parallels dementia severity in autosomal dominant Alzheimer's disease.

Hub regions in the brain, recognized for their roles in ensuring efficient information transfer, are vulnerable to pathological alterations in neurodegenerative conditions, including Alzheimer's disease (AD). Computational simulations and animal experiments have hinted at the theory of activity-dependent degeneration as the cause of this hub vulnerability. However, two critical issues remain unresolved.

Age-related unstable transient states and imbalanced activation proportion of brain networks in people with autism spectrum disorder: A resting-state fMRI study using coactivation pattern analyses.

The atypical static brain functions related to the executive control network (ECN), default mode network (DMN), and salience network (SN) in people with autism spectrum disorder (ASD) has been widely reported. However, their transient functions in ASD are not clear. We aim to identify transient network states (TNSs) using coactivation pattern (CAP) analysis to characterize the age-related atypical transient functions in ASD.

Brain signaling becomes less integrated and more segregated with age.

The integration-segregation framework is a popular first step to understand brain dynamics because it simplifies brain dynamics into two states based on global versus local signaling patterns. However, there is no consensus for how to best define the two states. Here, we map integration and segregation to order and disorder states from the Ising model in physics to calculate state probabilities, and , from functional MRI data.

TDERS, an exosome RNA-derived signature predicts prognosis and immunotherapeutic response in clear cell renal cell cancer: a multicohort study.

Background: Tumor-derived exosomes are involved in tumor progression and immune invasion and might function as promising noninvasive approaches for clinical management. However, there are few reports on exosom-based markers for predicting the progression and adjuvant therapy response rate among patients with clear cell renal cell carcinoma (ccRCC).

Methods: The signatures differentially expressed in exosomes from tumor and normal tissues from ccRCC patients were correspondingly deregulated in ccRCC tissues.

Revisiting Injectable Estrogen Dosing Recommendations for Gender-Affirming Hormone Therapy.

Injectable estrogens are options for gender-affirming hormone therapy per guidelines, which suggest intramuscular dosages of 5-30 mg every 2 weeks or 2-10 mg weekly with estradiol cypionate or valerate interchangeably. Data among transgender and gender-diverse patients are limited due to local unavailability and concerns around laboratory assay variability and estradiol (E2) level fluctuation. We note a concerning trend where patients are prescribed high-dose injections based on the guidelines leading to serum E2 levels well above the range recommended in the same guidelines.

Transgender and Gender Diverse Patients Are Diagnosed with Borderline Personality Disorder More Frequently Than Cisgender Patients Regardless of Personality Pathology.

Purpose: Borderline personality disorder (BPD) is a severe form of psychopathology associated with a host of negative outcomes. Some literature suggests elevated prevalence among transgender and gender diverse (TGD) samples. Elevated BPD prevalence among TGD populations could be due to factors other than BPD-specific psychopathology.

Gender-Affirming Hormone Therapy Is Associated with Increased Odds of Screening for Sexually Transmitted Infections in a Clinical Cohort of Transgender and Nonbinary Adults.

Purpose: Transgender and nonbinary adults (TNB) are disproportionately burdened by sexually transmitted infections (STI) and the human immunodeficiency virus (HIV). This study investigated whether gender-affirming hormone therapy was associated with TNB adults' odds of screening for STI and HIV.

Methods: Longitudinal data came from the electronic medical records of TNB primary care patients receiving care at two community health centers located in Boston, Massachusetts, and New York City, New York, between January 2013 and December 2019.

Racial Disparities in Clinical Trial Enrollment Among Patients Diagnosed With Prostate Cancer: A Population-Based Cohort of Oncology Practices.

Although clinical trials should be accessible to all patients, persistent racial and ethnic disparities in clinical trial enrollment exist. Herein, we examine racial disparities in clinical trial enrollment among prostate cancer patients from a large population-based cohort of oncology practices in the United States. Using CancerLinQ Discovery, we identified men with regional (N1+) and/or metastatic (M1) prostate cancer diagnosed from 2011 to 2023.

Leveraging anatomical constraints with uncertainty for pneumothorax segmentation.

Background: Pneumothorax is a medical emergency caused by the abnormal accumulation of air in the pleural space-the potential space between the lungs and chest wall. On 2D chest radiographs, pneumothorax occurs within the thoracic cavity and outside of the mediastinum, and we refer to this area as "lung + space." While deep learning (DL) has increasingly been utilized to segment pneumothorax lesions in chest radiographs, many existing DL models employ an end-to-end approach.

Study protocol: A national cross-sectional study on psychology and behavior investigation of Chinese residents in 2023.

Introduction: This study protocol specifies the primary research line and theoretical framework of the 2023 Survey of the Psychology and Behavior of the Chinese Population. It aims to establish a consistent database of Chinese residents' psychological and behavioral surveys through multi-center and large-sample cross-sectional surveys to provide robust data support for developing research in related fields. It will track the public's physical and psychological health more comprehensively and systematically.