DASH properties: Estimating atomic and molecular properties from a dynamic attention-based substructure hierarchy.

Recently, we presented a method to assign atomic partial charges based on the DASH (dynamic attention-based substructure hierarchy) tree with high efficiency and quantum mechanical (QM)-like accuracy. In addition, the approach can be considered "rule based"-where the rules are derived from the attention values of a graph neural network-and thus, each assignment is fully explainable by visualizing the underlying molecular substructures. In this work, we demonstrate that these hierarchically sorted substructures capture the key features of the local environment of an atom and allow us to predict different atomic properties with high accuracy without building a new DASH tree for each property.

lwreg: A Lightweight System for Chemical Registration and Data Storage.

Here, we present lwreg, a lightweight, yet flexible chemical registration system supporting the capture of both two-dimensional molecular structures (topologies) and three-dimensional conformers. lwreg is open source, with a simple Python API, and is designed to be easily integrated into computational workflows. In addition to lwreg itself, we also introduce a straightforward schema for storing experimental data and metadata in the registration database.

Unraveling motion in proteins by combining NMR relaxometry and molecular dynamics simulations: A case study on ubiquitin.

Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of molecular systems in the picosecond to millisecond timescales. As these methods cannot provide an atomically resolved view of the motion of atoms, functional groups, or domains giving rise to such signals, relaxation techniques have been combined with molecular dynamics (MD) simulations to obtain mechanistic descriptions and gain insights into the functional role of side chain or domain motion. In this work, we present a comparison of five computational methods that permit the joint analysis of MD simulations and NMR relaxation experiments.

DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment.

We present a robust and computationally efficient approach for assigning partial charges of atoms in molecules. The method is based on a hierarchical tree constructed from attention values extracted from a graph neural network (GNN), which was trained to predict atomic partial charges from accurate quantum-mechanical (QM) calculations. The resulting dynamic attention-based substructure hierarchy (DASH) approach provides fast assignment of partial charges with the same accuracy as the GNN itself, is software-independent, and can easily be integrated in existing parametrization pipelines, as shown for the Open force field (OpenFF).

How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation.

Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from N relaxation and side-chain dynamics from C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.

Oral Diagnostic Methods for the Detection of Periodontal Disease.

Periodontitis is a common immune-inflammatory oral disease. Early detection plays an important role in its prevention and progression. Saliva is a reliable medium that mirrors periodontal health and is easily obtainable for identifying periodontal biomarkers in point-of-care diagnostics.

Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations.

Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step).

[What influences end-of-life decisions? Results of a representative German survey].

Background: Because of demographic changes of an aging society, palliative care is becoming increasingly important. It is therefore necessary to evaluate preferences at the end of life at an early stage to meet the needs and requests of future patients.

Objectives: The aim of this study was to find out preferences in a theoretical scenario ("If you developed a serious medical condition such as cancer and you had less than a year to live…") regarding the desired involvement in decision-making at the end of life and the preferred place of death.

Interleukin 6 stimulates endothelial binding and transport of high-density lipoprotein through induction of endothelial lipase.

Objective: In the reverse cholesterol transport pathway, high-density lipoprotein (HDL) passes the endothelial cell barrier by mechanisms involving the scavenger receptor class B type I and the ATP-binding cassette G1. However, little is known on how inflammation influences this transendothelial transport.

Approach And Results: On stimulation with interleukin-6, cultivated primary endothelial cells showed increased binding and transport of (125)I-HDL without changing the expression of scavenger receptor class B type I and ATP-binding cassette G1.

Validity of the 3D VECTRA photogrammetric surface imaging system for cranio-maxillofacial anthropometric measurements.

Purpose: The use of three-dimensional (3D) photography for anthropometric measurements is of increasing interest, especially in the cranio-maxillofacial field. Before standard implementation, accurate determination of the precision and accuracy of each system is mandatory.

Methods: A mannequin head was labelled with 52 landmarks, and 28 three-dimensional images were taken using a commercially available five-pod 3D photosystem (3D VECTRA; Canfield, Fairfield, NJ) in different head positions.

Improving oral hygiene skills by computer-based training: a randomized controlled comparison of the modified Bass and the Fones techniques.

Background: Gingivitis and other plaque-associated diseases have a high prevalence in western communities even though the majority of adults report daily oral hygiene. This indicates a lack of oral hygiene skills. Currently, there is no clear evidence as to which brushing technique would bring about the best oral hygiene skills.

High-density lipoprotein transport through aortic endothelial cells involves scavenger receptor BI and ATP-binding cassette transporter G1.

Cholesterol efflux from macrophage foam cells is a rate-limiting step in reverse cholesterol transport. In this process cholesterol acceptors like high-density lipoproteins (HDL) and apolipoprotein (apo)A-I must cross the endothelium to get access to the donor cells in the arterial intima. Previously, we have shown that apoA-I passes a monolayer of aortic endothelial cells (ECs) from the apical to the basolateral side by transcytosis, which is modulated by the ATP-binding cassette transporter (ABC)A1.