Recent Submissions

  • MaxEnt modelling as a tool to inform discovery of deep-sea coral ecosystems

    Nolan, Megan K. B.; Marchese, Fabio; Kheireddine, Malika; Chimienti, Giovanni; Purkis, Sam; Terraneo, Tullia Isotta; Rodrigue, Mattie; Eweida, Ameer A.; Jones, Burton; Benzoni, Francesca (Copernicus GmbH, 2022-06-20) [Presentation]
    Coral reefs are now one of the most threatened marine ecosystems, due to local anthropogenic pressures and global changes in ocean conditions. Until recently, research has focused on the vulnerability of shallow coral ecosystems, however effects on deeper coral-dominated ecosystems become more severe with climate change. Deep-sea corals form large bioconstructions, including dense frameworks and mounds, which can remain even when the organisms are dead. The presence of these ecosystems alters the local seafloor morphology. To understand the changes that deep-sea coral ecosystems are undergoing, and the impacts these changes may have on local seafloor morphology, we must first know where they are located. Exploration of deep-sea habitats is costly, challenging and time-consuming, reducing the geographic extent at which it is possible. Methods are also often difficult in remote areas. Therefore, as such ecosystems are relatively sparse, extensive resources may be used attempting to locate them. Species distribution models can be used to identify key areas of interest with much less information, focusing surveys to a smaller extent, and making it much more cost-effective to study. MaxEnt is a habitat suitability modelling software which uses a unique maximum entropy algorithm to find the most dispersed distribution. It requires only presence data, allowing accurate results with less input data. Here we present the first habitat suitability models for deep coral habitats, as deep as 720 m, in the Red Sea. During the OceanX-NEOM ‘Deep Blue’ expedition in the Northern Saudi Arabian Red Sea and the Gulf of Aqaba in 2020, deep-sea coral ecosystems were identified and characterised by ROV and submersible dives. Geomorphometric variables were derived from bathymetry, including measures of aspect, curvature and local-scale rugosity. These variables were used as input data for MaxEnt, along with backscatter, which can provide information about the seafloor substrate, and environmental data from CTD casts and current models. The potential of such models to identify areas of interest is clear, and could become an important tool in order to focus limited conservation funding.
  • A Baseline Assessment Of Seafloor Geomorphology And Benthic Habitat Distribution Along The Neom Coast (Northern Saudi Arabia, Red Sea)

    Marchese, Fabio; Purkis, Sam; Chimienti, Giovanni; Ouhssain, Mostapha; Shernisky, Hannah; Terraneo, Tullia Isotta; Peters, Colleen; Rodrigue, Matthie; Jones, Burton; Eweida, Ameer; Benzoni, Francesca (Copernicus GmbH, 2022-06-20) [Presentation]
    The Red Sea is an isolated active rift in the latest stages of continental rifting. The basin is close to the transition to the following stage of oceanic seafloor spreading. These peculiar characteristics make it one of the warmest, most saline, and most oligotrophic marine ecosystems currently on Earth, supporting high rate of endemism of marine life from shallow to deep waters. In this work, we present a baseline description of the mesophotic and deep-sea environment from the Saudi Arabian continental margin of the North Red Sea and the Gulf of Aqaba with emphasis on shelf-slope transitions and shelf-edge reefs. A high-resolution acoustics dataset with coverage of 34,000 km2 has been collected in the NEOM gigaproject area, from 30 to 1770 m water depth. More than 60 benthic transects have been performed using submersibles and Remote Operated Vehicle (ROV) coupled with high-resolution underwater positioning systems. Over 650 samples of sediment, benthos, and rocks were collected to characterize the benthic environment. Data from CTD casts were used to characterize the water column. Our results reveal a complex mosaic of benthic habitats, related to depth range, substrate type, continental slope morphology, water masses, and sediment delivery into the basin. Habitat composition varied along the depth gradient from the shelf break to the deep basin, with a high level of diversity in the lower mesophotic zone. Our findings allow us for the first time to characterize the diversity of benthic habitats in the NEOM area from shallow to deep waters. Here, we also provide a fundamental contribution to a better understanding of the key role of geomorphology with respect to the largerly uknown mesophotic and deep-sea habitats in the Red Sea. Finally, we propose a classification of benthic habitats valuable for management purposes, including the design of monitoring programs, for ecosystem-based management, and for documenting the effects of climate change on ecosystems in a region undergoing rapid economic development.
  • Repository Role in Transformative Agreement Implementation

    Alsaedi, Yasmeen; Tomic, Nevena; Grenz, Daryl M.; Baessa, Mohamed A. (2022-06-07) [Presentation]
    As the publishing landscape continues to evolve, libraries and publishers are experimenting with a wide range of new types of open access publishing agreements, and KAUST has been able to make transformative agreements with several STEM publishers. However, the related workflows are not yet mature, and differ greatly across publishers. Ideally, all available funds (free tokens / free article processing charges) covered by transformative agreements should be used and eligible articles should have immediate open access. What happens is that sometimes the author is not aware of the deal or did not properly follow the workflow, so eligible articles are published behind the paywall, or published as open access, but paid outside the deal. When this happens, the library tries to get the article published as open access retroactively or to get a refund if possible. To help address this, the repository team made several improvements to the existing publications tracking service, developing a mechanism to track and identify eligible articles, including an email alert and a dashboard page, to help the librarians managing transformative agreements monitor articles covered by the agreements.
  • Deep Learning Accelerated History Matching and Forecasting for Geologic CO2 Sequestration

    Bailian, Chen; Bicheng, Yan; Qinjun, Kang; Rajesh, Pawar (2022-06-01) [Presentation]
    Traditional physics-simulation based approaches for inverse modeling and forecasting in large-scale subsurface flow and transport problems, e.g., geologic CO2 sequestration, is a very time consuming process. In this work, we developed a deep learning assisted workflow to speed up this process. First, we developed a deep learning model to predict the pressure/saturation evolution in large-scale storage reservoir. A feature coarsening technique was applied to extract the most representative information and perform the training and prediction at the coarse scale, and further recover the resolution at the fine scale by 2D piecewise cubic interpolation. Thereafter, the feature coarsening based deep learning model was utilized as forward model in the inverse modeling process where a classical data assimilation approach, ES-MDA-GEO, was applied. The efficiency and effectiveness of the proposed deep learning assisted workflow for large-scale inverse modeling and forecasting was demonstrated with a reservoir model (~1.34 million grid cells) built upon Clastic Shelf storage site.
  • The unique and varied roles of glycogen in brain

    Swanson, Raymond; Yemisci, Muge; Magistretti, Pierre J.; Duran, Jordi (SAGE PUBLICATIONS INC, 2022-06) [Presentation]
  • Late Pleistocene to Holocene Architecture of a Land-attached Carbonate Platform Lagoon in the African-Arabian Desert Belt (Al Wajh platform, N Red Sea, Saudi Arabia).

    Putri, Indah; Petrovic, Alexander; Sifontes, Rangelys; Vahrenkamp, Volker (Copernicus GmbH, 2022-05-12) [Presentation]
    Investigation of carbonate platform architecture is a crucial element to understanding the evolution of a platform. Extensive studies have been done on the architectures of various modern carbonate platforms. However, compared to humid climates, detailed studies in arid climates are rare, although many ancient carbonate reservoirs are developed under these conditions. This study investigates the Late Pleistocene architecture of the land-attached Al Wajh carbonate platform in the Northeastern Red Sea, Saudi Arabia. The platform is enclosed by a coral reef belt and characterized by a large lagoon (1,100 km2). The lagoon reaches 43 meters in depth and hosts more than 90 carbonate islands and numerous pinnacle and patch reefs. We utilize 700 km hydroacoustic data acquired using EdgeTech sub-bottom profiler during two research cruises with KAUST RV EXPLORER. An age model was established by utilizing a recently published Red Sea sea-level curve. Available climate data were used for the reconstructions of depositional environments. Data analysis reveals five depositional units: U1(Holocene) to U5(Late Pleistocene). Nine hydroacoustic facies are identified to describe the internal architecture, from homogenous reflection-free to wavy laminated facies. The oldest unit (U5) consists of homogeneous facies and reef facies. The unit is overlain by units 4 and 3, with up to five meters thick homogeneous facies and stratified facies. Unit 2 has a maximum thickness of 3 meters and consists of wavy laminated facies. Unit 1 is the youngest unit and consists of several facies, including heterogeneous, homogeneous, stratified, drift, reef, and reef debris facies. During MIS5e (U5), the Red Sea was experiencing a pluvial period, while the sea level was 10 meters higher than the present, leading to total flooding of the lagoon. Most of today's exposed carbonate islands in the lagoon correspond to carbonate accumulation during MIS5e. The depositional environment is interpreted as carbonate-dominated with the frequent siliciclastic influx in the coastal region during heavy rain. In the subsequent periods (MIS 5d to 5a), sea level dropped stepwise and exposed the platform partly. Stratified facies indicate terrestrial sediment input introduced during short pluvial periods. In the following glacial period (MIS 4 to 2), the platform was fully exposed for over 70,000 years. Due to the hyper-arid climate, we interpret unit 2 as an aeolian deposit likely reworked during Holocene transgression. During the platform's flooding in the Holocene, carbonate sedimentation restarted while coastal near stratified facies indicate an increased terrestrial influx during the short Holocene pluvial period (10,000-6000 years ago). The modern Al Wajh lagoon experiences an arid climate, with active carbonate sedimentations and minimal terrestrial input. Although the Red Sea has experienced several humid periods during the last 125,000 years, and extensive diagenetic alteration is recognized in the island's drill cores, no karst morphology has been identified. Results indicate that climate highly influences Al Wajh lagoon architecture, shown by its unique characteristics, including extensive carbonate deposition, intermittent terrestrial influx including aeolian deposits, and minimum karstification. Insights of this study will improve our understanding of the architecture of carbonate platforms in the subsurface deposited under similar conditions.
  • Acoustics of Drop Impact on Hydrophobic Surfaces and Liquid Pools

    Allen, John S.; Rabbi, Rafsan; Kiyama, Akihito; Truscott, Tadd (The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), 2022-05-09) [Presentation]
    Drop impact on surfaces has been studied comprehensively as it has a wide range of fundamental and practical implications. The splash, spreading, and rebound have been investigated with respect to substrate interfaces with hydrophobic surfaces being of particular interest. However, impact on wetted substrates is less understood for the hydrophobic surfaces. Also the associated acoustics of the drop impact has not be explored in terms of air entrainment and substrate vibrations. We investigate the impact of water drops (∼2–10 mm diameter) from heights 100–400 cm upon hydrophilic– and hydrophobic–coated solid surfaces as well as free floating liquid pools (0.15–0.45 ml). A contact microphone coated with the Glaxco water repellant provides a hydrophobic surface upon which impact vibrations can be quantified. An air microphone is synchronized to a high-speed Phantom camera for sound recording and optical visualization of the impact and rebound phases. Cross-correlation of the two microphones reveals distinct differences between the two solid substrates. The initial rebound and subsequent jet break-up are found in an analysis of the signal’s amplitude and phase. These results are compared to those from gel spheres and discussed for applications of non-contact coating monitoring.
  • Optimization of PCDTBT Metal-Insulator-Metal Hole-Only Photodiodes

    Petoukhoff, Christopher; O'Carroll, Deirdre (Fundació Scito, 2022-04-20) [Presentation]
    While there have been significant strides in improvements to organic solar cell (OSC) power conversion efficiencies using non-fullerene acceptors and novel benzodithophene and benzodithiophene-dione co-polymers, many of these new polymers still suffer from intrinsic degradation via photooxidation or light-induced cross-linking [1]. PCDTBT, a co-polymer of carbazole and dithienyl-benzothiadiazole, has remained among one of the most stable donor polymers to-date [2,3]. PCDTBT has recently been employed as a donor component in ternary blend OSCs [4], and as a hole transport layer in perovskite solar cells, resulting in improvements to device efficiency and stability [5]. Thus, understanding properties of neat PCDTBT thin-films is of great importance for determining how to best employ this stable co-polymer in highly efficient and stable OSC devices. In this work, we fabricated PCDTBT unipolar hole-only devices in a metal-insulator-metal Schottky photodiode geometry. Neat PCDTBT thin-films are challenging to prepare due to their poor solubility in typical organic solvents and ease of aggregation. We optimized PCDTBT thin-films by varying the solvent, molecular weight, heating times and temperatures, and filtering conditions. To evaluate the quality of PCDTBT thin-films with low degree of aggregation, we used a relatively unexplored technique of polarized light microscopy (PLM) [6]. PLM is a non-destructive, wide-field technique that allows elucidation of birefringent materials, such as conjugated polymers, giving enhanced contrast compared to standard bright-field light microscopy (BFM). We used PLM to rapidly evaluate the quality of PCDTBT thin-films in order to find optimal conditions for uniform thin-films with low aggregation. By using optical transfer matrix methods (TMM) simulations and experimental measurements of transmission and sheet resistivity, we further optimized conditions for transparent Au electrodes. TMM simulations revealed the optimal thickness of each layer to maximize photocurrent generation. Finally, using optimized conditions, we fabricated PCDTBT photodiodes in a Au/MoOx/PCDTBT/Ag geometry for thick (200 nm) and thin (80 nm) PCDTBT layers. We extracted the Schottky barrier height and hole mobility of PCDTBT from current-voltage measurements and drift-diffusion simulations, respectively.
  • Bi-allelic variants in HOPS subunit VPS41 cause cerebellar ataxia and point to differential lysosomal dysregulation in brain cell types

    Sanderson, Leslie E.; Lanko, Kristina; Alsagob, Maysoon; AlMass, Rawan; Al-Ahmady, Nada; Najafi, Maryam; Al-Muhaizea, Mohammad; Alzaidan, Hamad; Aldhalaan, Hesham; Perenthaler, Elena; van der Linde, Herma C.; Nikoncuk, Anita; Kuhn, Nikolas; Antony, Dinu; Owaidah, Tarek; Raskin, Salmo; Vieira, Luana; Mombach, Romulo; Ahangari, Najmeh; Silveira, Taina; Ameziane, Najim; Rolfs, Arndt; Alharbi, Aljohara; Sabbagh, Raghda; AlAhmadi, Khalid; Alawam, Bashayer; Ghebeh, Hazem; AlHargan, Aljouhra; Albader, Anoud; Binhumaid, Faisal; Almutairi, Faten; Al-Odaib, Ali; Aksoy, Durdane; Basak, Nazli A.; Palvadeau, Robin; Rosenfeld, Jill; Trabzuni, Daniah; Karimiani, Ehsan; Meyer, Brian; Karakac, Bedri; Al-Mohanna, Futwan; Arold, Stefan T.; Colak, Dilek; Maroofian, Reza; Houlden, Henry; Bertoli-Avella, Aida; Schmidts, Miriam; Barakat, Tahsin S.; van Ham, Tjakko; Kaya, Namik (Springer Nature, 2022-04) [Presentation]
  • Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome

    Weerts, Marjolein J. A.; Lanko, Kristina; Guzman-Vega, Francisco J.; Jackson, Adam; Ramakrishnan, Reshmi; Cardona-Londono, Kelly J.; Pena-Guerra, Karla A.; van Bever, Yolande; van Paassen, Barbara W.; Kievit, Anneke; van Slegtenhorst, Marjon; Allen, Nicholas M.; Kehoe, Caroline M.; Robinson, Hannah K.; Pang, Lewis; Banu, Selina H.; Zaman, Mashaya; Efthymiou, Stephanie; Houlden, Henry; Jarvela, Irma; Lauronen, Leena; Maatta, Tuomo; Schrauwen, Isabelle; Leal, Suzanne M.; Ruivenkamp, Claudia A. L.; Barge-Schaapveld, Daniela Q. C. M.; Peeters-Scholte, Cacha M. P. C.; Galehdari, Hamid; Mazaheri, Neda; Sisodiya, Sanjay M.; Harrison, Victoria; Maroofian, Reza; Banka, Siddharth; Sadikovic, Bekim; Arold, Stefan T.; Barakat, Tahsin Stefan (Springer Nature, 2022-04) [Presentation]
  • Paragenesis of a Pleistocene Carbonate Island in the African-Arabian Desert Belt (Al-Wajh Carbonate Platform Lagoon, NE Red Sea, Saudi-Arabia)

    Chirakal, Tojo; Petrovic, Alexander; Oyinloye, Michael; Vahrenkamp, Volker (Copernicus GmbH, 2022-03-28) [Presentation]
    Quaternary carbonate islands have contributed significantly to the fundamental understanding of the interplay between climate and early diagenetic processes in carbonates. However, most of the studied islands, such as the carbonate islands on the Great Bahamas Bank, are situated in humid climate zones. Contrary to this, the Al-Wajh carbonate platform, situated within the arid African-Arabian desert belt on the NE Red Sea shelf (Saudi-Arabia), hosts a plethora of poorly studied carbonate islands. These islands were likely formed during the Last Interglacial (LIG) sea level highstand, commonly defined by Marine Isotope Stage 5e (MIS 5e: 124 – 119 ka). As such, these islands provide an excellent opportunity to give new insights into the paragenesis of carbonate islands within an arid climatic setting and an overall regressive/transgressive sequence. This study investigates Shurayrah Island, located in the southern part of the Al-Wajh platform lagoon. Shaped by the prevailing NW wind direction, Shurayrah Island has an elongated shape, while a reef belt is established on the upwind NW side and carbonate sand spits accumulate on the leeward SE side. The main data base consisted of five drill cores with a total recovered length of 61 m and 150 thin sections. Eight lithofacies (LFT) and 17 microfacies types (MFT) were differentiated, including, amongst others, coral framestones, coral float- & rudstones and ooid-bioclast grainstones. Diagenetic analysis was based on a detailed petrographic investigation, while porosities (Φ) were measured from thin sections with digital image analysis (n = 150) and core plugs using a helium porosimeter (n = 102). Results reveal generally high porosities (mean Φ from thin sections = 29 %; mean Φ from core plugs = 45 %). Pore types are dominated by primary pores in the growth framework of coral framestones and secondary moldic & vuggy pores. Dissolution features are most pronounced in coral framestones, which show almost complete dissolution of original aragonite microstructures. Cement types include dog tooth, pore-filling and bladed cements, with a dominance of dog tooth cements in terms of frequency. Aragonite fibrous cements only occur scarcely and can be overgrown by dog tooth cements. Additionally, dog tooth and bladed cements are frequently observed to grow inside moldic pores. The diagenetic analysis clearly reveals a dominance of porosity creating processes (dissolution) vs. porosity reducing processes (cementation) during paragenesis. In addition, results emphasize the importance of facies-controlled diagenesis: high primary porosities combined with metastable mineral composition of aragonite in coral framestones, result in a high meteoric diagenetic potential. Cement stratigraphy indicates a shift in the diagenetic realm, transitioning from marine (MIS 5e) to meteoric (MIS 5d – MIS 2) conditions, followed by a return to a marine setting with the Holocene Transgression (MIS 1). The overall strong meteoric diagenetic overprint suggests the influence of temporary humid phases (MIS 5c & a), during the overall >100 ka long subaerial exposure period. The observations highlight the significance of short-term climate fluctuations introducing meteoric waters for the diagenesis of carbonate islands in arid climate belts.
  • Micritization and Microbial-related Diagenetic Features in Modern Shallow Marine Carbonates (Red Sea, Arabian Sea and Arabian Gulf)

    Teillet, Thomas; Hachmann, Kai; Chandra, Viswasanthi; Garuglieri, Elisa; Odobel, Charlene; Areias, Camila; Sánchez-Román, Mónica; Vahrenkamp, Volker (Copernicus GmbH, 2022-03-28) [Presentation]
    Pores smaller than 10 microns in diameter (microporosity) can make up more than 90% of the total porosity in giant Arabian carbonate reservoirs. While a lot of research has been done to understand the distribution of microporosity, the diagenetic processes initiating its development are still debated. Since microporosity occurs in highly diagenetically overprinted rocks the involvement of early syn-sedimentary processes are generally overlooked. Micritization is a process happening during early diagenesis in the first centimeters of depth in which parts of carbonate grains are reworked to cryptocrystalline textures. The fundamental drivers of micritization are still somewhat debated, however, more and more evidence points to the involvement of microbes such as cyanobacteria, algae, or fungi. So, how can we decipher the diagenetic sequence that ancient limestones have experienced and predict microporosity distribution if the initial steps are poorly understood? The hypothesis driving this research places microbial micritization as the first step toward the creation of microporosity in limestones. Here, we present the first results undertaken as part of a multidisciplinary research project, at the interface of geology and microbiology and coupling field sampling and laboratory experiments. We compare the rates of micritization and the variety of microbial-related diagenetic features encountered between different carefully selected intertidal locations from the Red Sea and Arabian Sea (Saudi Arabia), and the Arabian Gulf (United Arab Emirates). A series of 1 m long sediment cores has been collected at low tide, and subsamples were extracted from every 10 cm for systematic petrographic and geochemical analyses. Thin section petrography revealed extensive microborings and associated micritization in the sediments. XRD analysis has been carried out to establish the mineral variations through the locations and depth, and SEM imagery further confirmed the presence of organic biofilms and mucous. The results from the metagenomic analysis revealed the microbial diversities and provide further understanding of the specific microbial drivers that play a key role in micritization processes. The work presented here hence aims to enhance the fundamental understanding of micritization in shallow marine carbonate sediment, the role of microbes in early diagenetic processes and their potential impact on microporosity development.
  • CO2 injection and storage for geothermal power generation in hydrothermal reservoirs along the Red Sea of Western Saudi Arabia

    Yalcin, Bora; Ezekiel, Justin; Arifianto, Indra; Mai, Paul Martin (Copernicus GmbH, 2022-03-27) [Presentation]
    As an alternative to water, CO2 can be used for heat mining from geothermal reservoirs, while also trapping most of the injected CO2 underground. In addition, supercritical CO2 has higher mobility and heat capacity than water, rendering CO2 capture, utilization and storage (CCUS) in geothermal reservoirs a very attractive option in a circular carbon economy. CCUS is also in line with Saudi Vision 2030, which includes the strategic framework to reduce Saudi Arabia’s dependence on hydrocarbons and diversify its economy. The western coast of Saudi Arabia, where the young and high-heat-flow Red Sea rift basins are located, are considered suitable for geothermal heat extraction and CO2 storage. In this study, we explore the potential of CCUS for geothermal power generation and CO2 storage in the hydrothermal reservoirs of Al Wajh basin located on the Red Sea coast. Geological studies in Al Wajh basin report that the hot fluid bearing, thick, porous, siliciclastic formations, such as Al Wajh (formation’s top depth, TD= 3900 meters), Burqan (TD = 2880 m) and Jebel Kibrit (Umluj member with TD = 1930 m) are sealed by the overlying anhydrite (Kial) and salt formations (Mansiyah). We combine publicly available data with different resolution scales, such as satellite gravity, seismic sections and well-log information to build a 3D geologic model, which enables us to constrain the 3D gross rock volume and the Net-to-Gross ratio/distribution of the target hydrothermal reservoirs. A 3D temperature model shows that the average surface temperature in the region and the subsurface temperature gradient create formation fluid temperature of over 120o C at 3 km depth. We conduct reservoir simulation of coupled transport of formation fluid, injected non-condensable gas (CO2) and heat in heterogeneous 3D reservoir model, using CMG STARS. We then estimate the geothermal energy extracting capacity and storage efficiency of CO2 in the prospective hydrothermal reservoirs in the Al Wajh basin. Our study provides the first semi-realistic reservoir model and simulation study in Saudi Arabia for combined CO2-based geothermal power generation and CO2 storage potential at a designated target site. The work-flow we propose is transferable to other suitable hydrothermal reservoirs in different locations in Saudi Arabia, thereby enabling CCUS technology implementation along the Red Sea.
  • Epistemic uncertainty in fault geometry effects earthquake rupture behavior

    Zielke, Olaf; Aspiotis, Theodoros; Mai, Paul Martin (Copernicus GmbH, 2022-03-27) [Presentation]
    It is well established in the seismology community that geometric complexity plays an important role for a fault’s seismotectonic behavior. It affects the initiation, propagation and termination of an earthquake as well as influencing the stress-slip relationship, the size of fault segments, and the probability of multi-segment rupture. Consequently, fault geometric complexity is studied intensively and increasingly incorporated into computational earthquake rupture simulations. These efforts reveal a problem: While we may be able to constrain a natural fault’s geometry with a high level of detail at the surface (i.e., the fault trace), we cannot do the same for the buried portion of the fault -where most of the rupture takes place. How much does a fault’s seismotectonic behavior vary as a result of this epistemic uncertainty? We address this question computationally with a physics-based multi-cycle earthquake rupture simulator (MCQsim), enabling us to investigate how (for example) earthquake recurrence, slip accumulation, magnitude-frequency distribution, and fault segmentation vary (looking at the entire fault as well as individual locations on the fault) as function of our insufficient knowledge about the fault’s geometric complexity. To simulate fault geometric complexity, we generate 2-D random fields, using the “random midpoint displacement” method (RMD), representing the fault’s non-planar, self-similar geometry. The advantage of using RMD is that it allows us to create a 2-D random field while also keeping one or more of the field’s edges at a prescribed value. Hence, this approach allows us to generate a random field to represent fault roughness while also allowing us to incorporate what is known about the fault geometry (i.e., the fault surface trace, representing one of the random field’s edges). In doing so, we can investigate how the aforementioned seismo-tectonic parameters vary as a function of fault roughness uncertainty. For this purpose, we create 5000-year long earthquake catalogs for a 150x18km large strike slip fault that is parameterized by more than 40k fault cells (average cell size 0.07km^2), containing earthquakes with 3.5 < M < 7.8. We create these catalogs for 100 roughness realizations while keeping the simulated fault’s surface trace constant for all realizations. The results of these simulations will be presented in our presentation.
  • Partially interpretable neural networks for high-dimensional extreme quantile regression: With application to wildfires within the Mediterranean Basin

    Richards, Jordan; Huser, Raphaël; Bevacqua, Emanuele; Zscheischler, Jakob (Copernicus GmbH, 2022-03-27) [Presentation]
    Quantile regression is a particularly powerful tool for modelling environmental data which exhibits spatio-temporal non-stationarity in its marginal behaviour. If our interest lies in quantifying risk associated with particularly extreme or rare weather events, we may want to estimate conditional quantiles that are outside the range of observable data; in these cases, it is practical to describe the data using some parametric extreme value model with its parameters represented as functions of predictor variables. Classical approaches for parametric extreme quantile regression use linear or additive relationships, and such approaches suffer in either their predictive capabilities or computational efficiency in high-dimensions. Neural networks can capture complex non-linear relationships between variables and scale well to high-dimensional predictor sets. Whilst they have been successfully applied in the context of fitting extreme value models, statisticians may choose to forego the use of neural networks as a result of their “black box" nature; although they facilitate highly accurate prediction, it is difficult to do statistical inference with neural networks as their outputs cannot readily be interpreted. Inspired by the recent focus in machine learning literature on “explainable AI”, we propose a framework for performing extreme quantile regression using partially interpretable neural networks. Distribution parameters are represented as functions of predictors with three main components; a linear function, an additive function and a neural network that are applied separately to complementary subsets of predictors. The output from the linear and additive components is interpreted, whilst the neural network component contributes to the high prediction accuracy of our method. We use our approach to estimate extreme quantiles and occurrence probabilities for wildfires occurring within a large spatial domain that encompasses the entirety of the Mediterranean Basin.
  • Giant polygonal Tepee structures discovered in the NE Red Sea - AL Wajh carbonate platform, KSA

    Vahrenkamp, Sarima; Panagiotou, Marika; Petrovic, Alexander; Khanna, Pankaj; Chandra, Viswasanthi; Vahrenkamp, Volker (Copernicus GmbH, 2022-03-27) [Presentation]
    Carbonate tepee structures are believed to initiate through cement growth in shallow marine hardgrounds causing lateral expansion and leading to upward buckling of cemented layers commonly along polygonal boundaries. They reportedly form in subtidal to supratidal marine settings and are stratigraphically important markers for exposure and cycle boundaries in ancient rock sequences. Yet in modern carbonate settings only minor occurrences have been reported from the Arabian Gulf in Abu Dhabi and Qatar as well as in Australia. We have discovered two spectacular fields of giant polygonal tepee structures on Sheybara Island, a part of the Al Wajh carbonate platform in the NE Red Sea, KSA. Satellite and drone data were used to measure the dimensions of polygons. Samples have been collected from three transects and two boreholes for age dating, petrographic and geochemical analysis. The tepee fields cover an area of 420,000 m2 and 130,000 m2, respectively, in the supratidal to intertidal environment on the ocean facing side of the island. Individual tepees are composed of chaotically superimposed rugged slabs reaching 3-10 cm in thickness. Tepee ridges range in height from 10-50 cm. Tepees are aligned along larger structures of well-defined polygonal shapes. Their diameters range from 5m to 55m (n =100) with the majority having a diameter of 10-25 m (n=69). Peculiar to many polygons is a central domal buckle with extensional fracture patterns. The tepees have formed in a well-cemented layer of shallow marine bioclastic sand to gravel-sized sediments composed predominantly of coral, red algae, benthic foraminfera, bivalve and gastropod debris that overlie a paleo-reef flat. Grains are heavily micritized, cemented by clotted micrite and fibrous to acicular rim cements and occasionally covered by lace-like meshes of organic matter, likely indicating microbial activity. SEM images from tepee samples show evidence for the presence of microbial activity - biofilms, morphologies that strongly resembles filamentous and coccoidal cyanobacteria, and mineralized cyanobacterial mats. Environmentally corrected C14 age data indicate that polygons formed between 3000 to 1000 years before present (b.p.) correlating with a sealevel regression from a mid-Holocene sealevel highstand some 4000 to 5000 years b.p. Dead and blackened finger corals commonly encrust tepees indicating that the elevated tepee crusts provide preferential seeding for coral colonialization upon re-submergence.
  • Realistic and Fast Modeling of Spatial Extremes over Large Geographical Domains

    Huser, Raphaël; Hazra, Arnab; Bolin, David (Copernicus GmbH, 2022-03-27) [Presentation]
    Various natural phenomena, such as precipitation, generally exhibit spatial extremal dependence at short distances only, while the dependence usually fades away as the distance between sites increases arbitrarily. However, the available models proposed in the literature for spatial extremes, which are based on max-stable or Pareto processes or comparatively less computationally demanding "sub-asymptotic" models based on Gaussian location and/or scale mixtures, generally assume that spatial extremal dependence persists across the entire spatial domain. This is a clear limitation when modeling extremes over large geographical domains, but surprisingly, it has been mostly overlooked in the literature. In this paper, we develop a more realistic Bayesian framework based on a novel Gaussian scale mixture model, where the Gaussian process component is defined by a stochastic partial differential equation that yields a sparse precision matrix, and the random scale component is modeled as a low-rank Pareto-tailed or Weibull-tailed spatial process determined by compactly supported basis functions. We show that our proposed model is approximately tail-stationary despite its non-stationary construction in terms of basis functions, and we demonstrate that it can capture a wide range of extremal dependence structures as a function of distance. Furthermore, the inherently sparse structure of our spatial model allows fast Bayesian computations, even in high spatial dimensions, based on a customized Markov chain Monte Carlo algorithm, which prioritize calibration in the tail. In our application, we fit our model to analyze heavy monsoon rainfall data in Bangladesh. Our study indicates that the proposed model outperforms some natural alternatives, and that the model fits precipitation extremes satisfactorily well. Finally, we use the fitted model to draw inferences on long-term return levels for marginal precipitation at each site, and for spatial aggregates.
  • Identification of the EGF receptor extracellular domain as a cell-surface sensor for dioxins and structurally related persistent organic pollutants

    Vogeley, C.; Sondermann, N.; Woeste, S.; Momin, Afaque Ahmad Imtiyaz; Rossi, A.; Arold, Stefan T.; Haarmann-Stemmann, T. (2022-03) [Presentation]
    Background: Chloracne, a persistent acne-like skin eruption, is the hallmark of an acute intoxication with dioxins and related halogenated aromatic hydrocarbons. The underlying pathomechanisms are not well understood but may involve alterations in the proliferation and differentiation of sebocytes and epidermal keratinocytes. The fact that in contrast to dioxin-like compounds (DLCs) some chloracnegenic agents do not bind to the aryl hydrocarbon receptor (AHR) implies the involvement of other cellular effector molecules. Preliminary data of our group point to an involvement of the epidermal growth factor receptor (EGFR), an important regulator of keratinocyte biology. Objective: To investigate whether the EGFR serves as a cell-surface sensor for dioxins and polychlorinated biphenyls (PCBs). Material & methods: Human HaCaT keratinocytes, Western blot analyses, in silico docking analysis, EGFR internalization assay, site-directed mutagenesis, CRISPR/Cas-based AHR knockout, BrdU incorporation assay. Results: Western blot analyses revealed that a treatment of HaCaT keratinocytes with DLCs inhibits the growth factor-stimulated phosphorylation of EGFR. Results from EGFR internalization assays confirmed that DLCs, i.e. 2,3,7,8- tetrachlorodibenzo-p-dioxin and PCB126, interfere with the EGF-induced internalization of the receptor tyrosine kinase. In silico docking analyses predicted that DLCs interact with the extracellular domain (ECD) of EGFR in its extended conformation in close proximity to the EGF binding site. A mutational exchange of the ECD amino acid residues predicted to be essential for DLC-binding (Q8A, Q408A) and subsequent Western blot analyses confirmed that the EGFR ECD serves as a cell-surface receptor for DLCs. Further experiments assessing the effect of various DLCs as well as non-dioxin-like PCBs on EGFR ligand-induced DNA synthesis in genetically modified HaCaT keratinocytes revealed that the chloracnegens inhibit EGFR function independently of AHR. Conclusion: Dioxins and PCBs, including non-dioxin like congeners, are capable of binding to the EGFR ECD to attenuate growth factor-induced signal transduction and DNA synthesis in human keratinocytes. These data may enhance our understanding of the pathogenesis of chloracne and other diseases associated with an exposure to ubiquitous halogenated aromatic hydrocarbons.
  • Identification of the epidermal growth factor receptor (EGFR) as a target of ubiquitous organic pollutants

    Sondermann, N. C.; Vogely, C.; Woeste, S.; Momin, A. A.; Rossi, A.; Arold, Stefan T.; Haarmann-Stemmann, T. (EXPERIMENTAL DERMATOLOGY, 2022-02-21) [Presentation]
    Several organic pollutants ubiquitously occur in our environment, including dioxins like TCDD that can accumulate in adipose tissue. Due to their long half-life an accumulation can take place for several years, causing chronic illness. In higher concentrations, those chemicals can also cause acute toxic effects such as chloracne. Until now, the processes evoked by dioxins and other halogenated compounds in the skin leading to this chronic-inflammatory skin disease remain unknown. However, an inhibition of proliferative signaling advantaging differentiation of epidermal keratinocytes seems to be fundamental. A receptor known to be activated by dioxin-like compounds in keratinocytes is the Arylhydrocarbon receptor (AHR). Since chloracne is only provoked by an acute intoxication with dioxins and other chlorinated aromatic compounds, but not by AHR ligands with different chemical structures, an activation of other pathways could be a reasonable explanation. Renownedly, the Epidermal growth factor receptor (EGFR) plays an important role in proliferation and differentiation of keratinocytes. An inhibition of the EGFR, often medically induced for cancer treatment, leads to adverse dermal effects such as papulopustular rashes on the face and upper body. This is presumed to be precipitated by a switch of epidermal keratinocytes program from proliferation to differentiation. We recently found that dioxins and other halogenated compounds interfere with the growth factor induced phosphorylation and internalization of EGFR. In silico docking analysis predicted that the dioxin-like compounds TCDD and PCB126, but not the polycyclic aromatic hydrocarbon (PAH) B[a]P, bind the EGFRs extracellular domain. Generation of point mutated EGFR plasmids and subsequent western blot analysis confirmed that the residues Q8 and Q408 of the predicted binding site are vital for the compound's interference of EGFR phosphorylation. Investigation of EGFR ligand-induced proliferation in keratinocytes showed that several dioxin-like compounds inhibit this process, while also non-dioxin-like compounds such as PCB47, but not PAHs like B[a]P or B[k]F, depleted proliferation. These findings could contribute to better understanding of the processes behind the emergence of chloracne and other dioxin-induced skin diseases and therefore, hold potential to help developing novel preventive and therapeutic approaches. Furthermore, a yet undescribed mechanism concerning the extracellular domain of the EGFR as a binding site for several ubiquitous organic pollutants is introduced, expanding the already essential role of EGFR in skin diseases.
  • Influence of side chains on the n-type organic electrochemical transistor performance

    Ohayon, David; Savva, Achilleas; du, weiyuan; Paulsen, Bryan; Rivnay, Jonathan; McCulloch, Iain; Inal, Sahika (Fundació Scito, 2022-02-07) [Presentation]
    Organic bioelectronics has experienced tremendous growth over the past two decades thanks to the expansion of the library of organic electronic materials available. Electron conducting (n-type) polymers are particularly suitable to translate biological events that involve the generation of electrons. However, n-type polymers that are stable when addressed electrically in aqueous media are relatively scarce, and the performance of existing ones lags behind their hole conducting (p-type) counterparts. Here, we report a new family of donor-acceptor type polymers based on naphthalene-1,4,5,8-tetracarboxylic-diimide-bithiophene (NDI-T2) backbone where the NDI unit always bears an ethylene glycol (EG) side chain. We study how small variations in the side chains tethered to the acceptor as well as the donor unit affect the performance of the polymer films in the state-of-the-art bioelectronic device, the organic electrochemical transistor (OECT). First, we show that substitution of the T2 core with an electron-withdrawing group (i.e., methoxy) or an EG side chain leads to ambipolar charge transport properties and causes significant changes in film microstructure revealed by ex-situ X-ray scattering studies, which overall impairs the n-type OECT performance. We thus find that the best n-type OECT performer is the polymer that has no substitution on the T2 unit. Next, we evaluate the distance of the oxygen from the NDI unit as a design parameter by varying the length of the carbon spacer placed between the EG unit and the backbone. We find that the distance of the EG from the backbone affects the film order and crystallinity, and thus, the electron mobility. As such, we develop the best performing NDI-T2 based n-type OECT material to date. Our work provides new guidelines for the side chain architecture of n-type polymers for OECTs and insight on the structure-performance relationships for mixed ionic-electronic conductors, crucial for devices where the film operates at the aqueous electrolyte interface.

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