Catnip for MedCAT: Optimizing the Input for Automated SNOMED CT Mapping of Clinical Variables.

Introduction: Mapping local medical data assets to international data standards such as medical ontology SNOMED CT fosters data harmonization and, thereby, global progress in medical research. Since its intense resource requirements often hinder manual SNOMED CT mapping, automated mapping tools such as MedCAT have been developed. We investigated how the formulation of study variable names (VNs) influences the efficacy and accuracy of the SNOMED CT concepts identified by MedCAT.

Seeing the primary tumor because of all the trees: Cancer type prediction on low-dimensional data.

The Cancer of Unknown Primary (CUP) syndrome is characterized by identifiable metastases while the primary tumor remains hidden. In recent years, various data-driven approaches have been suggested to predict the location of the primary tumor (LOP) in CUP patients promising improved diagnosis and outcome. These LOP prediction approaches use high-dimensional input data like images or genetic data.

Early Multimodal Data Integration for Data-Driven Medical Research - A Scoping Review.

Introduction: Data-driven medical research (DDMR) needs multimodal data (MMD) to sufficiently capture the complexity of clinical cases. Methods for early multimodal data integration (MMDI), i.e.

Data Quality in Medical Real-World Data - An Oncological Use Case.

Data quality deficiencies significantly limit the applicability of real-world data in data-driven medical research. In this study, using an oncological use case, we report and discuss common quality deficiencies in real-world medical datasets, such as missing data, class imbalances, and timeliness issues. We compiled a multi-departmental real-world dataset comprising 13861 cancer cases diagnosed at University Hospital Cologne and examined data quality throughout the data integration process.

EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter.

Cell-cell communication is mediated by membrane receptors and their ligands, such as the Eph/ephrin system, orchestrating cell migration during development and in diverse cancer types. Epigenetic mechanisms are key for integrating external "signals", e.g.

What prevents us from reusing medical real-world data in research.

Medical real-world data stored in clinical systems represents a valuable knowledge source for medical research, but its usage is still challenged by various technical and cultural aspects. Analyzing these challenges and suggesting measures for future improvement are crucial to improve the situation. This comment paper represents such an analysis from the perspective of research.

Integrating Cross-Departmental Data.

Developing smart clinical decision support systems requires integrating data from several medical departments. This short paper outlines the challenges we faced in cross-departmental data integration for an oncological use case. Most severely, they have led to a significant reduction in case numbers.

RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data.

Background: Massive amounts of data are produced by combining next-generation sequencing with complex biochemistry techniques to characterize regulatory genomics profiles, such as protein-DNA interaction and chromatin accessibility. Interpretation of such high-throughput data typically requires different computation methods. However, existing tools are usually developed for a specific task, which makes it challenging to analyze the data in an integrative manner.

The Expression of the Cancer-Associated lncRNA Is Modulated by EphrinA5-Induced Signaling.

The Eph receptor tyrosine kinases and their respective ephrin-ligands are an important family of membrane receptors, being involved in developmental processes such as proliferation, migration, and in the formation of brain cancer such as glioma. Intracellular signaling pathways, which are activated by Eph receptor signaling, are well characterized. In contrast, it is unknown so far whether ephrins modulate the expression of lncRNAs, which would enable the transduction of environmental stimuli into our genome through a great gene regulatory spectrum.

SARS-CoV-2 infects and replicates in cells of the human endocrine and exocrine pancreas.

Infection-related diabetes can arise as a result of virus-associated β-cell destruction. Clinical data suggest that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19), impairs glucose homoeostasis, but experimental evidence that SARS-CoV-2 can infect pancreatic tissue has been lacking. In the present study, we show that SARS-CoV-2 infects cells of the human exocrine and endocrine pancreas ex vivo and in vivo.

DNA Methylation-Mediated Modulation of Endocytosis as Potential Mechanism for Synaptic Function Regulation in Murine Inhibitory Cortical Interneurons.

The balance of excitation and inhibition is essential for cortical information processing, relying on the tight orchestration of the underlying subcellular processes. Dynamic transcriptional control by DNA methylation, catalyzed by DNA methyltransferases (DNMTs), and DNA demethylation, achieved by ten-eleven translocation (TET)-dependent mechanisms, is proposed to regulate synaptic function in the adult brain with implications for learning and memory. However, focus so far is laid on excitatory neurons.

In Situ Monitoring of Membrane Protein Insertion into Block Copolymer Vesicle Membranes and Their Spreading via Potential-Assisted Approach.

Synthosomes are polymer vesicles with transmembrane proteins incorporated into block copolymer membranes. They have been used for selective transport in or out of the vesicles as well as catalysis inside the compartments. However, both the insertion process of the membrane protein, forming nanopores, and the spreading of the vesicles on planar substrates to form solid-supported biomimetic membranes have been rarely studied yet.

Chiral separation of d/l-arginine with whole cells through an engineered FhuA nanochannel.

Downstream processing to obtain enantiopure compounds from a racemic mixture relies mainly on crystallization. Natural transporters can specifically translocate enantiomers through membranes. Here a β-barrel transmembrane protein FhuA is re-engineered into a chiral channel protein (FhuAF4) to resolve racemic mixtures of d-/l-arginine.

Influences of luminance and accommodation stimuli on pupil size and pupil center location.

Purpose: We investigated effects of luminance and accommodation stimuli on pupil size and pupil center location, and their implications for progressive addition lens wear.

Methods: Participants were young and older adult groups (n = 20; 22 ± 2 years; age range, 18-25 years; and n = 19; 49 ± 4 years; age range, 45-58 years). A wave aberrometer included a relay system to allow a 12.

Pupil shape as viewed along the horizontal visual field.

Changes in pupil size and shape are relevant for peripheral imagery by affecting aberrations and how much light enters and/or exits the eye. The purpose of this study is to model the pattern of pupil shape across the complete horizontal visual field and to show how the pattern is influenced by refractive error. Right eyes of 30 participants were dilated with 1% cyclopentolate, and images were captured using a modified COAS-HD aberrometer alignment camera along the horizontal visual field to ±90°.