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Articles by DFG Cluster
Gut Analysis Toolbox: Training data and 2D models for segmenting enteric neurons, neuronal subtypes and ganglia
This upload is associated with the software, Gut Analysis Toolbox (GAT). If you use it please cite: Sorensen et al. Gut Analysis Toolbox: Automating quantitative analysis of enteric neurons. J Cell Sci 2024; jcs.261950. doi: https://doi.org/10.1242/jcs.261950 The upload contains StarDist models for segmenting enteric neurons in 2D, enteric neuronal subtypes in 2D and FPN+ResNet101 model for enteric ganglia in 2D in gut wholemount tissue.
Towards Explainable AI: Interpreting Soil Organic Carbon Prediction Models Using a Learning‐Based Explanation Method
The integration of machine learning in environmental and soil sciences advances research but lacks transparency in decision-making processes, necessitating model explainability. Framed as a supervised learning task, we aim to train an explanation model to quantify input influence on ML model outputs, supplemented with expert-based environmental interpretations. Different ML model classes rely on distinct environmental features to explain SOC variability.
One-day dual-tracer examination in neuroendocrine neoplasms: a real advantage of low activity LAFOV PET imaging - European Journal of Nuclear Medicine and Molecular Imaging
Abstract Somatostatin receptor (SSTR)-PET is crucial for effective treatment stratification of neuroendocrine neoplasms (NENs). In highly proliferating or poorly differentiated NENs, dual-tracer approaches using additional [18F]FDG PET can effectively identify SSTR-negative disease, usually requiring separate imaging sessions.
Guiding Transient Peptide Assemblies with Structural Elements Embedded in Abiotic Phosphate Fuels
Introduction Phosphates and phosphate esters are essential in diverse biological functions,1 such as encoding genetic information, regulating signal transduction mechanisms and providing chemical energy.
Correction: Completing the view – histologic insights from circular AAA specimen including 3D imaging - Diagnostic Pathology
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.
Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth
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Completing the view – histologic insights from circular AAA specimen including 3D imaging - Diagnostic Pathology
Patient identification and ethical statement Patient samples were acquired at two university hospitals during 2018 to 2020 from open aortic repair procedures, where anatomically and surgically feasible without posing additional threat to the respective patient. We aimed to take samples perpendicular to the aneurysm centerline axis (Fig. 1). In all cases the aneurysm sac was closed over the proximal anastomosis where possible to prevent direct contact of the duodenum and the prosthesis.
Challenges and opportunities for bioimage analysis core‐facilities
1 INTRODUCTION New scientific discoveries in the life sciences are increasingly driven by computational methods nowadays. Microscopy plays a key role in the life sciences and so does bioimage analysis, a computational part of the life sciences research field. Traditionally, computer science research groups collaborate with wet-lab experimentalists on the biology, biochemistry and biophysics side. Furthermore, some imaging core-facilities hired individuals with computational expertise.
A Hitchhiker's guide through the bio‐image analysis software universe
Aspects to consider when choosing bio-image analysis software for your research The choice of the right bio-image analysis software is closely related to the purpose of a given research project and more broadly to the field a research group is working in.
CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo - Nature Biotechnology
Abstract RNA base editing represents a promising alternative to genome editing. Recent approaches harness the endogenous RNA-editing enzyme adenosine deaminase acting on RNA (ADAR) to circumvent problems caused by ectopic expression of engineered editing enzymes, but suffer from sequence restriction, lack of efficiency and bystander editing.
SpookyNet: Learning force fields with electronic degrees of freedom and nonlocal effects - Nature Communications
Abstract Machine-learned force fields combine the accuracy of ab initio methods with the efficiency of conventional force fields. However, current machine-learned force fields typically ignore electronic degrees of freedom, such as the total charge or spin state, and assume chemical locality, which is problematic when molecules have inconsistent electronic states, or when nonlocal effects play a significant role.
Rho‐kinase inhibition by fasudil modulates pre‐synaptic vesicle dynamics
Abstract The Rho kinase (ROCK) signaling pathway is an attractive therapeutic target in neurodegeneration since it has been linked to the prevention of neuronal death and neurite regeneration. The isoquinoline derivative fasudil is a potent ROCK inhibitor, which is already approved for chronic clinical treatment in humans. However, the effects of chronic fasudil treatments on neuronal function are still unknown. We analyzed here chronic fasudil treatment in primary rat hippocampal cultures.
ATP-powered molecular recognition to engineer transient multivalency and self-sorting 4D hierarchical systems
Abstract Biological systems organize multiple hierarchical structures in parallel, and create dynamic assemblies and functions by energy dissipation. In contrast, emerging artificial non-equilibrium self-assembling systems have remained relatively simplistic concerning hierarchical design, and non-equilibrium multi-component systems are uncharted territory.
Multiple Light Control Mechanisms in ATP‐Fueled Non‐equilibrium DNA Systems
Abstract Fuel‐driven self‐assemblies are gaining ground for creating autonomous systems and materials, whose temporal behavior is preprogrammed by a reaction network. However, up to now there has been a lack of simple external control mechanisms of the transient behavior, at best using remote and benign light control. Even more challenging is to use different wavelengths to modulate the reactivity of different components of the system, for example, as fuel or building blocks.
Over-fed bacteria make people sick
Since the end of the Second World War, along with the growing prosperity and the associated changes in lifestyle, numerous new and civilisation-related disease patterns have developed in today's industrialised nations. Examples of the so-called "environmental diseases" are different bowel inflammations like Crohn's disease or ulcerative colitis. Common causes include disruptions to the human microbiome, i.e. the natural microbial colonisation of the body, and in particular of the intestine.
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