1. Home
  2. People Index
  3. Tim Johann

Tim Johann

About Tim Johann:
No description specified

SEEK ID: https://seek.lisym.org/people/106

Location:  Germany

Expertise: Not specified

Tools: Not specified

ORCID: https://orcid.org/0000-0001-5792-1562

help Their tags

This person has not yet tagged anything.

Related items

LiSyM network

This comprises the whole LiSyM network

Programme: LiSyM: Liver Systems Medicine

Public web page: http://www.lisym.org

Start date: 1st Jan 2016

LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP)

In one in five people with NAFLD, the functioning liver cells, the hepatocytes, are replaced by connective tissue. Eventually this fibrosis becomes irreversible. In this state the liver is like a ‘scar that never heals’. Through it, the liver loses many of its vital functions.
LiSyM-Pillar II wants to know more about which factors promote fibrosis and the conditions under which fibrosis becomes irreversible How can fibrosis be diagnosed as early as possible? Researchers in the pillar are also
...

Programme: LiSyM: Liver Systems Medicine

Public web page: http://www.lisym.org/our-work/pillar-research

Start date: 1st Jan 2016

LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF)

In chronic diseases, at some point the liver can suddenly stop functioning. This is called acute-on-chronic liver failure, or ACLF. This is the leading cause of death in liver patients and is often provoked by the use of transcription or freely available drugs or alcohol abuse. For this condition we need an effective treatment quickly.
LiSyM-Pillar III researches the factors that contribute significantly to ACLF. What exactly happens then? Are there any early signs that would enable ACLF to be
...

Programme: LiSyM: Liver Systems Medicine

Public web page: http://www.lisym.org/our-work/pillar-research

Start date: 1st Jan 2016

1 hidden item
Simulation of a detoxifying organ function: Focus on hemodynamics modeling and convection-reaction numerical simulation in microcirculatory networks.
LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF)

Abstract (Expand)

When modeling a detoxifying organ function, an important component is the impact of flow on the metabolism of a compound of interest carried by the blood. We here study the effects of red blood cells … (such as the Fahraeus-Lindqvist effect and plasma skimming) on blood flow in typical microcirculatory components such as tubes, bifurcations and entire networks, with particular emphasis on the liver as important representative of detoxifying organs. In one of the plasma skimming models, under certain conditions, oscillations between states are found and analyzed in a methodical study to identify their causes and influencing parameters. The flow solution obtained is then used to define the velocity at which a compound would be transported. A convection-reaction equation is studied to simulate the transport of a compound in blood and its uptake by the surrounding cells. Different types of signal sharpness have to be handled depending on the application to address different temporal compound concentration profiles. To permit executing the studied models numerically stable and accurate, we here extend existing transport schemes to handle converging bifurcations, and more generally multi-furcations. We study the accuracy of different numerical schemes as well as the effect of reactions and of the network itself on the bolus shape. Even though this study is guided by applications in liver micro-architecture, the proposed methodology is general and can readily be applied to other capillary network geometries, hence to other organs or to bioengineered network designs.

Authors: N. Boissier, D. Drasdo, I. E. Vignon-Clementel

Date Published: 29th Nov 2020

Publication Type: Journal

Guided interactive image segmentation using machine learning and color based data set clustering
LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI)

Abstract

Not specified

Authors: Adrian Friebel, Tim Johann, Dirk Drasdo, Stefan Hoehme

Date Published: 18th May 2020

Publication Type: Misc

A quantitative high-resolution computational mechanics cell model for growing and regenerating tissues
LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI)

Abstract

Not specified

Authors: Paul Van Liedekerke, Johannes Neitsch, Tim Johann, Enrico Warmt, Ismael Gonzàlez-Valverde, Stefan Hoehme, Steffen Grosser, Josef Kaes, Dirk Drasdo

Date Published: 1st Feb 2020

Publication Type: Journal

Quantitative analysis of hepatic macro- and microvascular alterations during cirrhogenesis in the rat.
LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI)

Abstract (Expand)

Cirrhosis represents the end-stage of any persistent chronically active liver disease. It is characterized by the complete replacement of normal liver tissue by fibrosis, regenerative nodules, and … complete fibrotic vascularized septa. The resulting angioarchitectural distortion contributes to an increasing intrahepatic vascular resistance, impeding liver perfusion and leading to portal hypertension. To date, knowledge on the dynamically evolving pathological changes of the hepatic vasculature during cirrhogenesis remains limited. More specifically, detailed anatomical data on the vascular adaptations during disease development is lacking. To address this need, we studied the 3D architecture of the hepatic vasculature during induction of cirrhogenesis in a rat model. Cirrhosis was chemically induced with thioacetamide (TAA). At predefined time points, the hepatic vasculature was fixed and visualized using a combination of vascular corrosion casting and deep tissue microscopy. Three-dimensional reconstruction and data-fitting enabled cirrhogenic features to extracted at multiple scales, portraying the impact of cirrhosis on the hepatic vasculature. At the macrolevel, we noticed that regenerative nodules severely compressed pliant venous vessels from 12 weeks of TAA intoxication onwards. Especially hepatic veins were highly affected by this compression, with collapsed vessel segments severely reducing perfusion capabilities. At the microlevel, we discovered zone-specific sinusoidal degeneration, with sinusoids located near the surface being more affected than those in the middle of a liver lobe. Our data shed light on and quantify the evolving angioarchitecture during cirrhogenesis. These findings may prove helpful for future targeted invasive interventions.

Authors: G. Peeters, C. Debbaut, A. Friebel, P. Cornillie, W. H. De Vos, K. Favere, I. Vander Elst, T. Vandecasteele, T. Johann, L. Van Hoorebeke, D. Monbaliu, D. Drasdo, S. Hoehme, W. Laleman, P. Segers

Date Published: 4th Dec 2017

Publication Type: Not specified

A multilevel framework to reconstruct anatomical 3D models of the hepatic vasculature in rat livers
LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI)

Abstract (Expand)

The intricate (micro)vascular architecture of the liver has not yet been fully unravelled. Although current models are often idealized simplifications of the complex anatomical reality, correct … morphological information is instrumental for scientific and clinical purposes. Previously, both vascular corrosion casting (VCC) and immunohistochemistry (IHC) have been separately used to study the hepatic vasculature. Nevertheless, these techniques still face a number of challenges such as dual casting in VCC and limited imaging depths for IHC. We have optimized both techniques and combined their complementary strengths to develop a framework for multilevel reconstruction of the hepatic circulation in the rat. The VCC and micro-CT scanning protocol was improved by enabling dual casting, optimizing the contrast agent concentration, and adjusting the viscosity of the resin (PU4ii). IHC was improved with an optimized clearing technique (CUBIC) that extended the imaging depth for confocal microscopy more than five-fold. Using in-house developed software (DeLiver), the vascular network - in both VCC and IHC datasets - was automatically segmented and/or morphologically analysed. Our methodological framework allows 3D reconstruction and quantification of the hepatic circulation, ranging from the major blood vessels down to the intertwined and interconnected sinusoids. We believe that the presented framework will have value beyond studies of the liver, and will facilitate a better understanding of various parenchymal organs in general, in physiological and pathological circumstances.

Authors: Geert Peeters, Charlotte Debbaut, Wim Laleman, Adrian Friebel, Diethard Monbaliu, Ingrid Vander Elst, Jan R Detrez, Tim Vandecasteele, Tim Johann, Thomas De Schryver, Luc Van Hoorebeke, Kasper Favere, Jonas Verbeke, Dirk Drasdo, Stefan Hoehme, Patrick Segers, Pieter Cornillie, Winnok H De Vos

Date Published: 28th Dec 2016

Publication Type: Not specified

Quantifying Tissue Mechanics and Tissue Formation with High Resolution Models
LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP)
No description specified

Creators: Tim Johann, Dirk Drasdo, Stefan Hoehme, Paul Van Liedekerke, Johannes Neitsch

Submitter: Tim Johann

Download
TiSim - A Workbench and Framework for Biophysical Agent-Based Multi-Scale Multi-Cellular Models.
LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP)

Computational models complement experimental methods in the analysis of tissue organization processes, and play an increasingly important role in systems biology and systems medicine. Creating and parameterizing mathematical models for the simulation of biological tissue dynamics at multiple scales is still a complex and resource-consuming task, which necessitates skills in diverse scientific disciplines. The software TiSim was conceived to facilitate programming, integration and deployment of
...

Creators: Tim Johann, Jieling Zhao, Stefan Hoehme, Dirk Drasdo, Andreas Buttenschön, Noémie Boissier, Géraldine Cellière, Paul Van Liedekerke, Johannes Neitsch

Submitter: Tim Johann

Download
Poster 17 Mid-Term Evaluation - Drasdo - Pillar II & III
LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), LiSyM network
No description specified

Creators: Tim Johann, Dirk Drasdo, Ayham Zaza, Jieling Zhao, Paul Van Liedekerke

Submitter: Tim Johann

Download
Presentation Mid-Term Evaluation Drasdo Pillar II
LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM network
No description specified

Creators: Tim Johann, Dirk Drasdo

Submitter: Tim Johann

Download
Presentation Mid-Term Evaluation Drasdo/Hengstler Pillar III
LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), LiSyM network
No description specified

Creators: Tim Johann, Dirk Drasdo, Jan Hengstler

Submitter: Tim Johann

Download
Powered by
 (v.1.10.3)
About FAIRDOM | LiSyM | Funding and Programmes | Credits | Terms & Conditions | Imprint
Copyright © 2008 - 2020 The University of Manchester and HITS gGmbH