nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares.

Summary: With the increased reliance on multi-omics data for bulk and single cell analyses, the availability of robust approaches to perform unsupervised learning for clustering, visualization, and feature selection is imperative. We introduce nipalsMCIA, an implementation of multiple co-inertia analysis (MCIA) for joint dimensionality reduction that solves the objective function using an extension to Non-linear Iterative Partial Least Squares (NIPALS). We applied nipalsMCIA to both bulk and single cell datasets and observed significant speed-up over other implementations for data with a large sample size and/or feature dimension.

Sex Differences in Melanoma Survival-a GEM study.

Sex differences in melanoma are prominent, with females having a significant survival advantage. However, it is unclear why we see this survival advantage. Here we investigate the relationship between sex, clinicopathologic variables, and melanoma specific survival in 1,753 single primary melanomas from patients in the GEM study.

5-FU Weakens Defensive Functions of the Junctional Epithelium.

Aim: To investigate additional factors contributing to the pathophysiology of chemotherapy-induced oral mucositis and periodontitis beyond the systemic immune suppression caused by the chemotherapeutic agent 5-Fluorouracil (5-FU).

Methods: 5-Fluorouracil was topically delivered to the non-keratinized, rapidly proliferating junctional epithelium (JE) surrounding the dentition, and acts as an immunologic and functional barrier to bacterial ingression. Various techniques, including EdU incorporation, quantitative immunohistochemistry (qIHC), histology, enzymatic activity assays, and micro-computed tomographic (μCT) imaging, were employed to analyze the JE at multiple time points following topical 5-FU treatment.

Psychotic-Spectrum Disorders With Comorbid Anxiety are Predisposing Factors for Parkinson's Disease in a Case-Control Study.

Background: Multiple studies have demonstrated associations between psychiatric conditions and Parkinson's disease (PD) development; fewer have examined psychotic-spectrum disorders and PD development.

Objective: The objective was to assess the prevalence of psychotic-spectrum disorders with and without depression and anxiety preceding a PD diagnosis.

Methods: In this retrospective, case-control study of adults > 60 years of age, cases were identified by PD diagnosis and controls were identified in a 3:1 ratio by ambulatory encounter from 2015 to 2020.

Comparative diversification analyses of Hydrangeaceae and Loasaceae reveal complex evolutionary history as species disperse out of Mesoamerica.

Premise: The movement of lineages into novel areas can promote ecological opportunity and adaptive radiation, leading to significant species diversity. Not all studies, however, have identified support for ecological opportunity associated with novel intercontinental colonizations. To gain key insights into the drivers of ecological opportunity, we tested whether intercontinental dispersals resulted in ecological opportunity using the Hydrangeaceae-Loasaceae clade, which has numerous centers of diversity across the globe.

Nebulized dexmedetomidine in the treatment of obstetric post-dural puncture headache: two case reports.

Post-dural puncture headache (PDPH) is a debilitating complication of neuraxial anesthesia, particularly prevalent in obstetric patients, usually characterized by a postural headache. PDPH is hypothesized to result from cerebrospinal fluid leakage through a dural puncture, triggering symptoms like neck stiffness and subjective hearing changes. While conservative measures are common for treatment, more refractory cases may require invasive interventions such as an epidural blood patch (EBP).

Classroom air quality in a randomized crossover trial with portable HEPA air cleaners.

Background: Children living in communities with lower socioeconomic status and higher minority populations are often disproportionately exposed to particulate matter (PM) compared to children living in other communities.

Objective: We assessed whether adding HEPA filter air cleaners to classrooms with existing HVAC systems reduces indoor air pollution exposure.

Methods: From July 2022 to June 2023, using a block randomized crossover trial of 17 Los Angeles Unified School District elementary schools, classroom PM concentrations were monitored and compared for 99 classrooms with HEPA filter air cleaners and 87 classrooms with non-HEPA filter air cleaners.

Unsupervised deep learning of electrocardiograms enables scalable human disease profiling.

The 12-lead electrocardiogram (ECG) is inexpensive and widely available. Whether conditions across the human disease landscape can be detected using the ECG is unclear. We developed a deep learning denoising autoencoder and systematically evaluated associations between ECG encodings and ~1,600 Phecode-based diseases in three datasets separate from model development, and meta-analyzed the results.

Small protein ERSP encoded by LINC02870 promotes triple negative breast cancer progression via IRE1α/XBP1s activation.

Clinical treatment options for triple-negative breast cancer (TNBC) are currently limited to chemotherapy because of a lack of effective therapeutic targets. Recent evidence suggests that long noncoding RNAs (lncRNAs) encode bioactive peptides or proteins, thereby playing noncanonical yet significant roles in regulating cellular processes. However, the potential of lncRNA-translated products in cancer progression remains largely unknown.

Comprehensive analysis of targetable mutations and tumor microenvironment in urachal cancer.

Urachal cancer, a rare malignancy, generally presents in the clinical setting with advanced stages of disease. Systemic treatment with chemotherapy is generally utilized in this setting. However, there remains a paucity of data on the effectiveness of immune checkpoint inhibitors or targeted therapies for urachal cancer.

Identification of cardiac wall motion abnormalities in diverse populations by deep learning of the electrocardiogram.

Cardiac wall motion abnormalities (WMA) are strong predictors of mortality, but current screening methods using Q waves from electrocardiograms (ECGs) have limited accuracy and vary across racial and ethnic groups. This study aimed to identify novel ECG features using deep learning to enhance WMA detection, referencing echocardiography as the gold standard. We collected ECG and echocardiogram data from 35,210 patients in California and labeled WMA using unstructured language parsing of echocardiographic reports.

Erwinia phage Asesino is a nucleus-forming phage that lacks PhuZ.

As nucleus-forming phages become better characterized, understanding their unifying similarities and unique differences will help us understand how they occupy varied niches and infect diverse hosts. All identified nucleus-forming phages fall within the Chimalliviridae family and share a core genome of 68 unique genes including chimallin, the major nuclear shell protein. A well-studied but non-essential protein encoded by many nucleus-forming phages is PhuZ, a tubulin homolog which aids in capsid migration, nucleus rotation, and nucleus positioning.

Systematic Review and Meta-Analysis on the Accuracy of Artificial Intelligence Algorithms in Individuals Gender Detection Using Orthopantomograms.

The integration of artificial intelligence (AI) into dental imaging has led to significant advancements, particularly in the analysis of panoramic radiographs, also known as orthopantomograms (OPGs). One emerging application of AI is in determining gender from these radiographs, a task traditionally performed by forensic experts using manual methods. This systematic review and meta-analysis aim to evaluate the accuracy of AI algorithms in gender determination using OPGs, focusing on the reliability and potential clinical and forensic applications of these technologies.

Nicotine levels in flavoured hookah (waterpipe) tobacco products: discrepancies between labelled and measured levels.

Background: Hookah tobacco smoking is prevalent among youth and young adults. While health warning labels play a critical role in communicating the health risks of tobacco product use to consumers, compliance with US Federal Regulation's nicotine warning requirements on hookah tobacco packaging is low. Some labelling suggests that consumers are exposed to 'only 0.

Late-onset diseases and patient education: additional considerations for polygenic risk score regulation.

In a recent article, Haining outline several ethical and regulatory considerations for polygenic risk scores (PRSs), which may expand current embryonic screening to include polygenic diseases and non-disease traits. I argue in this response that the authors overlook a few crucial issues that nations should address. For adult-onset diseases, regulations must not only account for predictive accuracy of PRSs but also establish the precise circumstances that warrant testing-such as a disease's severity and the average age at which symptoms manifest.

GWAS of CRP response to statins further supports the role of APOE in Statin Response: a GIST consortium study.

Statins are first-line treatments in the primary and secondary prevention of cardiovascular disease. Clinical studies show statins act independently of lipid-lowering mechanisms to decrease C-reactive protein (CRP), an inflammation marker. We aim to elucidate genetic loci associated with CRP statin response.

Accurate evaluation of factor VIII activity of efanesoctocog alfa in the presence of emicizumab.

Background: Efanesoctocog is a B-domain-deleted, Fc-fusion FVIII linked to the D'D3 domain of VWF and two XTEN polypeptides, designed for an ultra-extended half-life for prophylaxis in hemophilia A, but also aiding in managing acute bleeding or surgery in patients on long-term emicizumab. However, no current laboratory method accurately measures FVIII levels in the presence of emicizumab. We hypothesized that the chromogenic (CSA) FVIII assay, specifically calibrated for efanesoctocog using bovine coagulation factors, could provide an accurate assessment of efanesoctocog activity.

Accuracy of Survey-Based Assessment of Eligibility for Medication Abortion Compared to Clinician Assessment.

Background: With increasingly restricted access to facility-based abortion in the United States, pregnant people are increasingly relying on models of care that utilize history-based or no-test approaches to eligibility assessment. Minimal research has examined the accuracy of abortion patients' self-assessment of eligibility for medication abortion using their health history, a necessary step towards ensuring optimal access to history-based or no-test models, as well as potential over-the-counter access.

Objective: To examine the accuracy of pregnant people's eligibility for medication abortion determined using their self-reported health history as compared to clinician assessment with ultrasound and other tests.

Transcatheter versus Surgical Aortic Valve Replacement in Patients Younger than 65 Years in the US.

Objective: To characterize trends and outcomes of aortic valve replacement in patients <65 with aortic stenosis between 2013 and 2021.

Methods: This retrospective analysis included 9,557 patients who underwent biological aortic valve replacement in California, New York, and New Jersey from 2013 through 2021. Patients were stratified by approach: transcatheter aortic valve replacement (TAVR) versus surgical aortic valve replacement (SAVR).

A novel viral infection in a Captive Colony of pelagic red crabs (Pleuroncodes planipes) from California.

Captive, pelagic red crabs (Pleuroncodes planipes) had shortened lifespans and cutaneous black spots. Histologically, epidermal and mesenchymal cells had 3-5 µm diameter intranuclear inclusions, necrosis, vacuolation, and/or hyperplasia. The remaining organs were histologically unremarkable.

Shoulder and Elbow Surgery Fellowship Applicants with Greater Research Productivity During Residency are Ranked Higher by Fellowship Programs.

Introduction: Shoulder and elbow surgery fellowships in the United States are recognized for their academic emphasis, yet the correlation between an applicant's research productivity and fellowship match results remains unclear. This study (1) analyzed temporal trends in research productivity among matched fellowship applicants, (2) evaluated the influence of quantity of publications and first authorships on match positions, and (3) investigated program variations in research productivity.

Methods: This is a retrospective analysis of data from the San Francisco (SF) Match Database for shoulder and elbow surgery applicants matched between 2017 and 2024.

Default mode network functional connectivity as a transdiagnostic biomarker of cognitive function.

The default mode network (DMN) is intricately linked with processes such as self-referential thinking, episodic memory recall, goal-directed cognition, self-projection, and theory of mind. Over recent years, there has been a surge in examining its functional connectivity, particularly its relationship with frontoparietal networks (FPN) involved in top-down attention, executive function, and cognitive control. The fluidity in switching between these internal and external modes of processing-highlighted by anti-correlated functional connectivity-has been proposed as an indicator of cognitive health.