Reproducible geoscientific modelling with hypergraphs

Reproducing the construction of a geoscientific model is a hard task. It requires the availability of all required data and an exact description how the construction was performed. In practice data availability and the exactness of the description is often lacking. As part of this thesis I introduce a conceptual framework how geoscientific model constructions can be described as directed acyclic hypergraphs, how such recorded construction graphs can be used to reconstruct the model, and how repetitive constructions can be used to verify the reproducibility of a geoscientific model construction process. In addition I present a software prototype, implementing these concepts. The prototype is tested with three different case studies, including a geophysical measurement analysis, a subsurface model construction and the calculation of a hydrological balance model.:1. Introduction 1.1. Survey on Reproducibility and Automation for Geoscientific Model Construction 1.2. Motivating Example 1.3. Previous Work 1.4. Problem Description 1.5. Structure of this Thesis 1.6. Results Accomplished by this Thesis 2. Terms, Definitions and Requirements 2.1. Terms and Definitions 2.1.1. Geoscientific model 2.1.2. Reproducibility 2.1.3. Realisation 2.2. Requirements 3. Related Work 3.1. Overview 3.2. Geoscientific Data Storage Systems 3.2.1. PostGIS and Similar Systems 3.2.2. Geoscience in Space and Time (GST) 3.3. Geoscientific Modelling Software 3.3.1. gOcad 3.3.2. GemPy 3.4. Experimentation Management Software 3.4.1. DataLad 3.4.2. Data Version Control (DVC) 3.5. Reproducible Software Builds 3.6. Summarised Releated Work 4. Concept 4.1. Construction Hypergraphs 4.1.1. Reproducibility Based on Construction Hypergraphs 4.1.2. Equality definitions 4.1.3. Design Constraints 4.2. Data Handling 5. Design 5.1. Application Structure 5.1.1. Choice of Application Architecture for GeoHub 5.2. Extension Mechanisms 5.2.1. Overview 5.2.2. A Shared Library Based Extension System 5.2.3. Inter-Process Communication Based Extension System 5.2.4. An Extension System Based on a Scripting Language 5.2.5. An Extension System Based on a WebAssembly Interface 5.2.6. Comparison 5.3. Data Storage 5.3.1. Overview 5.3.2. Stored Data 5.3.3. Potential Solutions 5.3.4. Model Versioning 5.3.5. Transactional security 6. Implementation 6.1. General Application Structure 6.2. Data Storage 6.2.1. Database 6.2.2. User-provided Data-processing Extensions 6.3. Operation Executor 6.3.1. Construction Step Descriptions 6.3.2. Construction Step Scheduling 6.3.3. Construction Step Execution 7. Case Studies 7.1. Overview 7.2. Geophysical Model of the BHMZ block 7.2.1. Provided Data and Initial Situation 7.2.2. Construction Process Description 7.2.3. Reproducibility 7.2.4. Identified Problems and Construction Process Improvements 7.2.5. Recommendations 7.3. Three-Dimensional Subsurface Model of the Kolhberg Region 7.3.1. Provided Data and Initial Situation 7.3.2. Construction Process Description 7.3.3. Reproducibility 7.3.4. Identified Problems and Construction Process Improvements 7.3.5. Recommendations 7.4. Hydrologic Balance Model of a Saxonian Stream 7.4.1. Provided Data and Initial Situation 7.4.2. Construction Process Description 7.4.3. Reproducibility 7.4.4. Identified Problems and Construction Process Improvements 7.4.5. Recommendations 7.5. Lessons Learned 8. Conclusions 8.1. Summary 8.2. Outlook 8.2.1. Parametric Model Construction Process 8.2.2. Pull and Push Nodes 8.2.3. Parallelize Single Construction Steps 8.2.4. Provable Model Construction Process Attestation References Appendi

Cerebral haemodynamics and carbon dioxide reactivity during sepsis syndrome

peer reviewed[en] BACKGROUND: Most patients with sepsis develop potentially irreversible cerebral dysfunctions. It is yet not clear whether cerebral haemodynamics are altered in these sepsis patients at all, and to what extent. We hypothesized that cerebral haemodynamics and carbon dioxide reactivity would be impaired in patients with sepsis syndrome and pathological electroencephalogram patterns. METHODS: After approval of the institutional ethics committee, 10 mechanically ventilated patients with sepsis syndrome and pathological electroencephalogram patterns underwent measurements of cerebral blood flow and jugular venous oxygen saturation before and after reduction of the arterial carbon dioxide partial pressure by 0.93 +/- 0.7 kPa iu by hyperventilation. The cerebral capillary closing pressure was determined from transcranial Doppler measurements of the arterial blood flow of the middle cerebral artery and the arterial pressure curve. A t test for matched pairs was used for statistical analysis (P < 0.05). RESULTS: During stable mean arterial pressure and cardiac index, reduction of the arterial carbon dioxide partial pressure led to a significant increase of the capillary closing pressure from 25 +/- 11 mmHg to 39 +/- 15 mmHg (P < 0.001), with a consecutive decrease of blood flow velocity in the middle cerebral artery of 21.8 +/- 4.8%/kPa (P < 0.001), of cerebral blood flow from 64 +/- 29 ml/100 g/min to 39 +/- 15 ml/100 g/min (P < 0.001) and of jugular venous oxygen saturation from 75 +/- 8% to 67 +/- 14% (P < 0.01). CONCLUSION: In contrast to other experimental and clinical data, we observed no pathological findings in the investigated parameters of cerebral perfusion and oxygenation

Characterization of a prothrombotic phenotype using thrombin generation and thrombin activity in cirrhosis and portal hypertension

Background: Patients with advanced chronic liver disease (ACLD) may develop a prothrombotic phenotype that seems to be more pronounced with more severe liver dysfunction. An imbalance of endogenous pro- and anticoagulants is not fully captured by routine coagulation assays. Methods: In a cohort of ACLD patients undergoing hepatic venous pressure gradient (HVPG) measurement, we assessed thrombin generation (TGA) using two commercially available assays (Technothrombin and Thrombinoscope) with and without addition of soluble thrombomodulin (TM), as well as thrombin activity, alongside a panel of coagulation parameters. Results: The cohort encompassed 37 patients (median age 55.3 years, mean HVPG 16 ± 5 mm Hg). In the TM-modified Thrombinoscope TGA, the endogenous thrombin generation potential (ETP) was significantly increased in Child-Pugh-Score (CPS) B/C patients (N = 23, 62 %) compared to CPS A patients (N = 14, 38 %) (ETP: 546 nM∗min (443–696) vs. 404 nM∗min (289–573), p = 0.028). Using the Technothrombin TGA without TM, patients with CPS B/C had decreased ETP compared to CPS A patients (ETP: 2792 ± 1336 nM∗min vs. 5040 ± 816 nM∗min, p &lt; 0.001) and with addition of TM (final concentration: 5 nM; ETP: 2545 ± 1327 nM∗min vs. 4824 ± 929 nM∗min, p &lt; 0.001). Thrombin activity levels were 0.6pM in median (0.2–1.6pM) and above the level of detectability (0.10pM) in 94.6 % of patients but were not correlated to severity of cirrhosis (CPS A 0.7pM vs CPS B/C 0.4pM, p = 0.377) nor to parameters of TGA. Conclusion: Thrombin plasma levels are elevated in liver disease patients without apparent correlation to TGA or severity of cirrhosis. TGAs can be modified with TM to enable protein C-dependent anticoagulation, but result in differences with regard to severity of liver disease.</p

Characterization of a prothrombotic phenotype using thrombin generation and thrombin activity in cirrhosis and portal hypertension

Background: Patients with advanced chronic liver disease (ACLD) may develop a prothrombotic phenotype that seems to be more pronounced with more severe liver dysfunction. An imbalance of endogenous pro- and anticoagulants is not fully captured by routine coagulation assays. Methods: In a cohort of ACLD patients undergoing hepatic venous pressure gradient (HVPG) measurement, we assessed thrombin generation (TGA) using two commercially available assays (Technothrombin and Thrombinoscope) with and without addition of soluble thrombomodulin (TM), as well as thrombin activity, alongside a panel of coagulation parameters. Results: The cohort encompassed 37 patients (median age 55.3 years, mean HVPG 16 ± 5 mm Hg). In the TM-modified Thrombinoscope TGA, the endogenous thrombin generation potential (ETP) was significantly increased in Child-Pugh-Score (CPS) B/C patients (N = 23, 62 %) compared to CPS A patients (N = 14, 38 %) (ETP: 546 nM∗min (443–696) vs. 404 nM∗min (289–573), p = 0.028). Using the Technothrombin TGA without TM, patients with CPS B/C had decreased ETP compared to CPS A patients (ETP: 2792 ± 1336 nM∗min vs. 5040 ± 816 nM∗min, p &lt; 0.001) and with addition of TM (final concentration: 5 nM; ETP: 2545 ± 1327 nM∗min vs. 4824 ± 929 nM∗min, p &lt; 0.001). Thrombin activity levels were 0.6pM in median (0.2–1.6pM) and above the level of detectability (0.10pM) in 94.6 % of patients but were not correlated to severity of cirrhosis (CPS A 0.7pM vs CPS B/C 0.4pM, p = 0.377) nor to parameters of TGA. Conclusion: Thrombin plasma levels are elevated in liver disease patients without apparent correlation to TGA or severity of cirrhosis. TGAs can be modified with TM to enable protein C-dependent anticoagulation, but result in differences with regard to severity of liver disease.</p

The impact of ABO blood type on the prevalence of portal vein thrombosis in patients with advanced chronic liver disease

Background and aimsNon-O blood type (BT) is a risk factor for thromboses, which has been attributed to its effects on von Willebrand factor (VWF)/factor VIII (FVIII) levels. Although high VWF/FVIII may be risk factors for portal vein thrombosis (PVT) in patients with advanced chronic liver disease (ACLD), the impact of BT on PVT is unknown. We aimed to assess (I) whether non-O-BT is a risk factor for PVT and (II) whether non-O-BT impacts VWF/factor VIII in patients with ACLD. MethodsRetrospective analysis comprising two cohorts: (I) "US" including all adult liver transplantations in the US in the MELD era and (II) "Vienna" comprising patients with a hepatic venous pressure gradient (HVPG) >= 6 mmHg. Results(I) The "US cohort" included 84 947 patients (non-O: 55.43%). The prevalence of PVT at the time of listing (4.37% vs 4.56%; P = .1762) and at liver transplantation (9.56% vs 9.33%; P = .2546) was similar in patients with O- and non-O-BT. (II) 411 patients were included in the "Vienna cohort" (non-O: 64%). Mean HVPG was 18(9) mmHg and 90% had an HVPG >= 10 mmHg. Patients with non-O-BT had slightly increased VWF levels (318(164)% vs 309(176)%; P = .048; increase of 23.8%-23.9% in adjusted analyses), but this difference was driven by patients with less advanced disease. However, non-O-BT explained only 1% of the variation in VWF and had no effect on FVIII. ConclusionsAlthough non-O-BT impacts VWF in patients with early stage ACLD, its contribution to VWF variation is considerably smaller than in the general population. Moreover, non-O-BT had no impact on FVIII. These findings may explain the absence of an association between non-O-BT and PVT in patients with advanced cirrhosis