DAS Preprocessing Workflow

This report addresses deliverable D1.4 of the DigiMon project, which covers the preprocessing workflow for datasets acquired by Distributed Acoustic Systems (DAS). The workflow seeks to capture the key stages required to prepare the raw seismic data for the main processing stages and demonstrates their application using both synthetic and real-world data. A description of the synthetic datasets can be found in DigiMon deliverable D1.3 report, while details of the real-world datasets are included in DigiMon reports D1.1 and D1.2

DAS dataset suitable for microseismic and ANI analysis

Deliverable 1.2 concerns a DAS dataset suitable for microseismic and ambient noise interferometry (ANI). For this deliverable the DAS field dataset of FORGE is recommended. FORGE is the Frontier Organization For Research in Geothermal Energy, and is a field laboratory for developing an enhanced geothermal system in hot crystalline rock situated near the town of Milford in Utah, USA (https://utahforge.com/). The FORGE team is led by Joe Moore of Utah (and funded by the US Department of Energy) and is credited for this dataset. The dataset is completely open access, but obviously attribution would be appreciated in any publications. The FORGE dataset applies for deliverable 1.2, because it provides downhole DAS and geophone recordings of microseismic events, and covers approximately two weeks of continuous DAS recordings that can be used to test the potential of DAS for the ANI method. In addition to the FORGE dataset, various other DAS datasets have recently become publicly available that are recommended to consider as well for further work in task 1.3 and associated tasks, since they can be valuable in addressing different research aspects of the application of DAS. Table 1.1 gives a summary of the different open access datasets considered for this deliverable. This table also shows whether the datasets are suitable to be used for microseismic and ANI analysis. With this application in mind for deliverable 1.2, and when compared against alternative datasets (see Table 1.1), the FORGE dataset is considered to be especially relevant for this deliverable, since it provides both microseismic event data and continuous DAS recordings from a borehole configuration spanning a relatively long duration (17 days). The borehole configuration is preferable for the purpose of detecting micro-seismicity since it allows measurements close to the reservoir and therefore able to detect weaker events compared to a trenched deployment at the surface. FORGE concerns an enhanced geothermal system and in this setting the mechanism driving seismicity is different compared to the case of CO2 injection and storage (DIGIMON). However, the performance of the DAS cable with respect to detected seismicity is expected to be similar for the case of monitoring CO2 injection and storage as in a geothermal setting and therefore the FORGE dataset is expected to be suited for this purpose

DAS synthetic dataset

Deliverable D1.3 of the ACT DigiMon project is a synthetic microseismic distributed acoustic sensins (DAS) dataset. There are a number of possible uses for such a dataset; for example supporting the development and testing of DAS processing algorithms, testing the efficacy of different array geometries in detecting and characterising events, or simulating a field experiment to better understand observed processes. Given the large number of possible uses it was decided that rather than simply delivering a collection of files of synthetic seismic events, it would be more valuable to deliver a modelling framework from which synthetic data can be generated as the need arises, combined with a small example dataset of a few events to demonstrate the capabilities. DAS systems record seismic wavefields and ground motion due to their sensitivity to strain along the axis of the fibre. To understand the response of DAS it is necessary to understand (1) the seismic source, (2) the path effects and (3) the site and instrument effects. In this report we discuss the modelling of the first two contributions of the DAS response; the source and path effects. We simulate the resulting particle motion and strain at the fibre location, resulting from realistic microseismic sources in geological models representative of the North Sea. The third contribution; site and instrument effects, is contained in the transfer function, which describes the mathematical relationship between the wavefield properties at the cable location to the recorded DAS output. The form of the transfer function is a key unanswered question which will be addressed in Task 1.2 of the DigiMon project

Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies

Infectious disease treatments, both pharmaceutical and vaccine, face three universal challenges: the difficulty of targeting treatments to high-risk ‘superspreader’ populations who drive the great majority of disease spread, behavioral barriers in the host population (such as poor compliance and risk disinhibition), and the evolution of pathogen resistance. Here, we describe a proposed intervention that would overcome these challenges by capitalizing upon Therapeutic Interfering Particles (TIPs) that are engineered to replicate conditionally in the presence of the pathogen and spread between individuals — analogous to ‘transmissible immunization’ that occurs with live-attenuated vaccines (but without the potential for reversion to virulence). Building on analyses of HIV field data from sub-Saharan Africa, we construct a multi-scale model, beginning at the single-cell level, to predict the effect of TIPs on individual patient viral loads and ultimately population-level disease prevalence. Our results show that a TIP, engineered with properties based on a recent HIV gene-therapy trial, could stably lower HIV/AIDS prevalence by ∼30-fold within 50 years and could complement current therapies. In contrast, optimistic antiretroviral therapy or vaccination campaigns alone could only lower HIV/AIDS prevalence by <2-fold over 50 years. The TIP's efficacy arises from its exploitation of the same risk factors as the pathogen, allowing it to autonomously penetrate superspreader populations, maintain efficacy despite behavioral disinhibition, and limit viral resistance. While demonstrated here for HIV, the TIP concept could apply broadly to many viral infectious diseases and would represent a new paradigm for disease control, away from pathogen eradication but toward robust disease suppression

Modelling the Spread of HIV Immune Escape Mutants in a Vaccinated Population

Because cytotoxic T-lymphocytes (CTLs) have been shown to play a role in controlling human immunodeficiency virus (HIV) infection and because CTL-based simian immunodeficiency virus (SIV) vaccines have proved effective in non-human primates, one goal of HIV vaccine design is to elicit effective CTL responses in humans. Such a vaccine could improve viral control in patients who later become infected, thereby reducing onwards transmission and enhancing life expectancy in the absence of treatment. The ability of HIV to evolve mutations that evade CTLs and the ability of these ‘escape mutants’ to spread amongst the population poses a challenge to the development of an effective and robust vaccine. We present a mathematical model of within-host evolution and between-host transmission of CTL escape mutants amongst a population receiving a vaccine that elicits CTL responses to multiple epitopes. Within-host evolution at each epitope is represented by the outgrowth of escape mutants in hosts who restrict the epitope and their reversion in hosts who do not restrict the epitope. We use this model to investigate how the evolution and spread of escape mutants could affect the impact of a vaccine. We show that in the absence of escape, such a vaccine could markedly reduce the prevalence of both infection and disease in the population. However the impact of such a vaccine could be significantly abated by CTL escape mutants, especially if their selection in hosts who restrict the epitope is rapid and their reversion in hosts who do not restrict the epitope is slow. We also use the model to address whether a vaccine should span a broad or narrow range of CTL epitopes and target epitopes restricted by rare or common HLA types. We discuss the implications and limitations of our findings

Implications of CTL-Mediated Killing of HIV-Infected Cells during the Non-Productive Stage of Infection

Patients infected with HIV exhibit orders of magnitude differences in their set-point levels of the plasma viral load. As to what extent this variation is due to differences in the efficacy of the cytotoxic T lymphocyte (CTL) response in these patients is unclear. Several studies have shown that HIV-infected CD4+ T cells also present viral epitopes that are recognized by CTLs before the productive stage of infection, i.e., during the intracellular eclipse phase before the infected cell starts to produce new viral particles. Here, we use mathematical modeling to investigate the potential impact of early killing of HIV-infected cells on viral replication. We suggest that the majority of CTL-mediated killing could occur during the viral eclipse phase, and that the killing of virus-producing cells could be substantially lower at later stages due to MHC-I-down-regulation. Such a mechanism is in agreement with several experimental observations that include CD8+ T cell depletion and antiretroviral drug treatment. This indicates a potentially important role of CTL-mediated killing during the non-productive stage of HIV-infected cells

Quantifying the impact of human immunodeficiency virus-1 escape from cytotoxic T-lymphocytes.

Published versio

GMTSAR: An InSAR Processing System Based on Generic Mapping Tools

GMTSAR is an open source (GNU General Public License) InSAR processing system designed for users familiar with Generic Mapping Tools (GMT). The code is written in C and will compile on any computer where GMT and NETCDF are installed. The system has three main components: 1) a preprocessor for each satellite data type (e.g., ERS, Envisat, and ALOS) to convert the native format and orbital information into a generic format; 2) an InSAR processor to focus and align stacks of images, map topography into phase, and form the complex interferogram; 3) a postprocessor, mostly based on GMT, to filter the interferogram and construct interferometric products of phase, coherence, phase gradient, and line-of-sight displacement in both radar and geographic coordinates. GMT is used to display all the products as postscript files and kml-images for Google Earth. A set of C-shell scripts has been developed for standard 2- pass processing as well as image alignment for stacking and time series. ScanSAR processing is also possible but requires a knowledgeable user. Users are welcome to contribute to this effort