An explorable model of an adverse outcome pathway of cytokine release syndrome related to the administration of immunomodulatory biotherapeutics and cellular therapies.

Introduction: Cytokine release syndrome (CRS) is a potentially severe systemic inflammatory condition triggered by various immunomodulatory therapies, making understanding its pathogenesis critical for improving patient outcomes.

Results/methods: By combining immunotoxicology and systems biology approaches, we offer a novel and integrative conceptual model of CRS as an adverse outcome (AO), induced by five different immunomodulatory biotherapies: 1) chimeric antigen receptor (CAR) T cells, 2) checkpoint inhibitors, 3) T cell engaging bispecific modalities, 4) monoclonal antibodies targeting and activating T cell receptors, and 5) FcγR activating monoclonal antibodies. This model uniquely integrates multiple CRS-inducing therapies into a unified framework, offering a comprehensive mechanistic representation of CRS pathophysiology.

Caffeine Intoxication: An Analysis of Published Case Reports, 1883–2023.

Background: Many case reports of acute caffeine intoxication have been published, but there have been hardly any systematic data analyses, nor have there been any prospective studies, representative epidemiologic studies, or guideline recommendations. In this review, we aim to describe the clinical entity of acute caffeine intoxication and its treatments to date on the basis of published case reports.

Methods: This review is based on pertinent case reports retrieved by a search in the PubMed, Google Scholar, and Semantic Scholar databases covering the period 1851-2023 and employing the keywords "caffeine intoxication," "caffeine poisoning," and "caffeine overdose.

FAIR assessment of Disease Maps fosters open science and scientific crowdsourcing in systems biomedicine.

The Disease Maps Project focuses on the development of disease-specific comprehensive structured knowledge repositories supporting translational medicine research. These disease maps require continuous interdisciplinary collaboration and should be reusable and interoperable. Adhering to the Findable, Accessible, Interoperable and Reusable (FAIR) principles enhances the utility of such digital assets.

Repurposing Amiodarone for Bladder Cancer Treatment.

Unlabelled: Cisplatin-based neoadjuvant chemotherapy followed by radical cystectomy is the main treatment for muscle-invasive bladder cancer (MIBC). However, low survival rates highlight the necessity for new therapeutic strategies. Drug repurposing has emerged as a promising approach in cancer treatment, with various studies proposing the use of existing drugs for the treatment of bladder cancer.

Protocol to identify regulatory modules in Parkinson's disease progression using miRNA data and Boolean modeling.

Regulatory modules are molecules that interact functionally, driving disease processes. Here, we present a protocol for identifying regulatory modules in Parkinson's disease (PD) using cohort-specific microRNA (miRNA) data and Boolean modeling. We describe steps for omics data collection, biomolecule and miRNA target analysis, and Boolean model construction and simulation.

FAIRification of computational models in biology.

Computational models are essential for studying complex systems which, particularly in clinical settings, need to be quality-approved and transparent. To enhance the communication of a model's features and capabilities, we propose an adaptation of the Findability, Accessibility, Interoperability and Reusability (FAIR) indicators published by the Research Data Alliance to assess models encoded in domain-specific standards, such as those established by COMBINE. The assessments guide FAIRification and add value to models.

COBREXA 2: tidy and scalable construction of complex metabolic models.

Summary: Constraint-based metabolic models offer a scalable framework to investigate biological systems using optimality principles. Construction and simulation of detailed models that utilize multiple kinds of constraint systems pose a significant coding overhead, complicating implementation of new types of analyses. We present an improved version of the constraint-based metabolic modeling package COBREXA, which utilizes a hierarchical model construction framework that decouples the implemented analysis algorithms into independent, yet re-combinable, building blocks.

Using interactive platforms to encode, manage and explore immune-related adverse outcome pathways.

This work focuses on the need for modeling and predicting adverse outcomes in immunotoxicology to improve nonclinical assessments of the safety of immunomodulatory therapies. The integrated approach includes, first, the adverse outcome pathway concept established in the toxicology field, and, second, the systems medicine disease map approach for describing molecular mechanisms involved in a particular pathology. The proposed systems immunotoxicology workflow is illustrated with chimeric antigen receptor (CAR) T cell treatment as a use case.

Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study.

Allergen-specific immunotherapy (AIT) induces immune tolerance, showing the highest success rate (>95%) for insect venom while a much lower chance for pollen allergy. However, the molecular switches leading to successful durable tolerance restoration remain elusive. The primary outcome of this observational study is the comprehensive immunological cellular characterization during the AIT initiation phase, whereas the secondary outcomes are the serological and Th2-cell-type-specific transcriptomic analyses.

Graph databases in systems biology: a systematic review.

Graph databases are becoming increasingly popular across scientific disciplines, being highly suitable for storing and connecting complex heterogeneous data. In systems biology, they are used as a backend solution for biological data repositories, ontologies, networks, pathways, and knowledge graph databases. In this review, we analyse all publications using or mentioning graph databases retrieved from PubMed and PubMed Central full-text search, focusing on the top 16 available graph databases, Publications are categorized according to their domain and application, focusing on pathway and network biology and relevant ontologies and tools.

Isotopic labeling of nanoparticles for the evaluation of their environmental fate in mesocosm experiments.

Mesocosm systems simulating floodplain areas are essential for the understanding of the environmental fate and effects of engineered nanoparticles (ENPs). In such mesocosm studies, the quantification of different types of nanoparticles coexisting in natural systems and containing the same element is often challenging. Such coexistence is expected e.

Cohort-specific boolean models highlight different regulatory modules during Parkinson's disease progression.

Parkinson's disease (PD) involves complex molecular interactions and diverse comorbidities. To better understand its molecular mechanisms, we employed systems medicine approaches using the PD map, a detailed repository of PD-related interactions and applied Probabilistic Boolean Networks (PBNs) to capture the stochastic nature of molecular dynamics. By integrating cohort-level and real-world patient data, we modeled PD's subtype-specific pathway deregulations, providing a refined representation of its molecular landscape.

Relevance of Platinum Underlayer Crystal Quality for the Microstructure and Magnetic Properties of the Heterostructures YbFeO/Pt/YSZ(111).

The hexagonal ferrite h-YbFeO grown on YSZ(111) by pulsed laser deposition is foreseen as a promising single multiferroic candidate where ferroelectricity and antiferromagnetism coexist for future applications at low temperatures. We studied in detail the microstructure as well as the temperature dependence of the magnetic properties of the devices by comparing the heterostructures grown directly on YSZ(111) (i.e.

DS-PACK: Tool assembly for the end-to-end support of controlled access human data sharing.

The EU General Data Protection Regulation (GDPR) requirements have prompted a shift from centralised controlled access genome-phenome archives to federated models for sharing sensitive human data. In a data-sharing federation, a central node facilitates data discovery; meanwhile, distributed nodes are responsible for handling data access requests, concluding agreements with data users and providing secure access to the data. Research institutions that want to become part of such federations often lack the resources to set up the required controlled access processes.

Structural and Morphological Studies of Pt in the As-Grown and Encapsulated States and Dependency on Film Thickness.

The morphology and crystal structure of Pt films grown by pulsed laser deposition (PLD) on yttria-stabilized zirconia (YSZ)at high temperatures = 900 °C was studied for four different film thicknesses varying between 10 and 70 nm. During the subsequent growth of the capping layer, the thermal stability of the Pt was strongly influenced by the Pt film's thickness. Furthermore, these later affected the film morphology, the crystal structure and hillocks size, and distribution during subsequent growth at = 900 °C for a long duration.

Dependence of the Structural and Magnetic Properties on the Growth Sequence in Heterostructures Designed by YbFeO and BaFeO.

The structure and the chemical composition of individual layers as well as of interfaces belonging to the two heterostructures M1 (BaFeO/YbFeO/YSZ) and M2 (YbFeO/BaFeO/YSZ) grown by pulsed laser deposition on yttria-stabilized zirconia (YSZ) substrates are deeply characterized by using a combination of methods such as high-resolution X-ray diffraction, transmission electron microscopy (TEM), and atomic-resolution scanning TEM with energy-dispersive X-ray spectroscopy. The temperature-dependent magnetic properties demonstrate two distinct heterostructures with different coercivity, anisotropy fields, and first anisotropy constants, which are related to the defect concentrations within the individual layers and to the degree of intermixing at the interface. The heterostructure with the stacking order BaFeO/YbFeO, i.

Bending and reverse bending during the fabrication of novel GaAs/(In,Ga)As/GaAs core-shell nanowires monitored byx-ray diffraction.

We report on the fabrication of a novel design of GaAs/(In,Ga)As/GaAs radial nanowire heterostructures on a Si 111 substrate, where, for the first time, the growth of inhomogeneous shells on a lattice mismatched core results in straight nanowires instead of bent. Nanowire bending caused by axial tensile strain induced by the (In,Ga)As shell on the GaAs core is reversed by axial compressive strain caused by the GaAs outer shell on the (In,Ga)As shell. Progressive nanowire bending and reverse bending in addition to the axial strain evolution during the two processes are accessed byby x-ray diffraction.

BioKC: a collaborative platform for curation and annotation of molecular interactions.

Curation of biomedical knowledge into systems biology diagrammatic or computational models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever-increasing growth of domain literature. New findings demonstrating elaborate relationships between multiple molecules, pathways and cells have to be represented in a format suitable for systems biology applications.

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing.

Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms.

The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease.

Chronic inflammatory diseases (CIDs), including inflammatory bowel disease (IBD), rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) are thought to emerge from an impaired complex network of inter- and intracellular biochemical interactions among several proteins and small chemical compounds under strong influence of genetic and environmental factors. CIDs are characterised by shared and disease-specific processes, which is reflected by partially overlapping genetic risk maps and pathogenic cells (e.g.

Effect of Underlayer Quality on Microstructure, Stoichiometry, and Magnetic Properties of Hexaferrite BaFeO Grown on YSZ(111) by Pulsed Laser Deposition.

We have studied the effect of platinum underlayer for two deposited thicknesses on the microstructure, crystalline quality, morphology, chemical composition, and magnetic properties as well as magnetic domain formation of BaFeO (BaM) grown on YSZ(111) by pulsed laser deposition (PLD). We found that PLD platinum deposited with a thickness of 25 nm cannot withstand the dewetting phenomenon occurring during the subsequent BaM layer growth. A smooth and continuous Pt underlayer that possesses a sharp interface and omits the intermixing between the BaM and substrate was successfully achieved for a deposited Pt film thickness of 75 nm.

Visualization of automatically combined disease maps and pathway diagrams for rare diseases.

Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mechanisms, including disease-dedicated schematics in pathway databases and disease maps. However, collection of knowledge across them is challenging, especially for research projects with limited manpower.

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.

As a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular project. This rich environment together with requirements for high-quality network reconstruction makes it challenging for new curators and groups to be quickly introduced to the development methods.