A versatile Cloud Computing environment to facilitate African-European partnership in research: EO AFRICA R&D Innovation Lab

The African Framework for Research, Innovation, Communities and Applications (EO AFRICA) is an ESA initiative in collaboration with the African Union Commission that aims to foster an African-European R&D partnership facilitating the sustainable adoption of Earth Observation and related space technologies in Africa. EO AFRICA R&D Facility is the flagship of EO AFRICA with the overarching goals of enabling an active research community and promoting creative and collaborative innovation processes by providing funding, advanced training, and computing resources. The Innovation Lab is a state-of-the-art Cloud Computing infrastructure provided by the Facility to 30 research projects of African-European research tandems and participants of the capacity development activities of the Space Academy. The Innovation Lab creates new opportunities for innovative research to develop EO algorithms and applications adapted to African challenges and needs, through interactive Virtual Research Environments (VREs) with ready-to-use research and EO analysis software, and facilitated access to a wide range of analysis-ready EO datasets by leveraging the host DIAS infrastructure. The Innovation Lab is a cloud-based, user-friendly, and versatile Platform as a service (PaaS) that allows the users to develop, test, run, and optimize their research code making full use of the Copernicus DIAS infrastructure and a tailor-made interactive computing environment for geospatial analysis. Co-located data and computing services enable fast data exploitation and analysis, which in turn facilitates the utilization of multi-spectral spatiotemporal big data and machine learning methods. Each user has direct access to all online EO data available on the host DIAS (CreoDIAS), especially for Africa, and if required, can also request archived data, which is automatically retrieved and made available within a short delay. The Innovation Lab also supports user-provided in-situ data and allows access to EO data on the Cloud (e.g., other DIASes, CNES PEPS, Copernicus Hub, etc.) through a unified and easy-to-use and open-source data access API (EODAG). Because all data access and analysis are performed on the server-side, the platform does not require a fast Internet connection, and it is adapted for low bandwidth access to enable active collaboration of African – European research tandems. As a minimum configuration, each user has access to computing units with four virtual CPUs, 32 GB RAM, 100 GB local SSD storage, and 1 TB network storage. To a limited extent and for specific needs (e.g., AI applications like Deep Learning), GPU-enabled computing units are also provided. The user interface of the Innovation Lab allows the use of interactive Jupyter notebooks through the JupyterLab environment, which is served by a JupyterHub deployment with improved security and scalability features. For advanced research code development purposes, the Innovation Lab features a web-based VS Code integrated development environment, which provides specialized tools for programming in different languages, such as Python and R. Code analytics tools are also available for benchmarking, code profiling, and memory/performance monitoring. For specific EO workflows that require exploiting desktop applications (e.g., ESA SNAP, QGIS) for pre-processing, analysis, or visualization purposes, the Innovation Lab provides a web-based remote desktop with ready-to-use EO desktop applications. The users can also customize their working environment by using standard package managers. As endorsed by the European Commission Open Science approach, data and code sharing and versioning are crucial to allow reuse and reproduction of the algorithms, workflows, and results. In this context, the Innovation Lab has tools integrated into its interactive development environment that provide direct access to code repositories and allow easy version control. Although public code repositories (e.g., Github) are advised for better visibility, the Innovation Lab also includes a dedicated code repository to support the users' particular needs (e.g., storage of sensitive information). The assets (e.g., files, folders) stored on the platform can be easily accessed and shared externally through the FileBrowser tool. Besides providing a state-of-the-art computing infrastructure, the Innovation Lab also includes other necessary services to ensure a comfortable virtual research experience. All research projects granted by the EO AFRICA R&D Facility receive dedicated technical support for the Innovation Lab facilities. Scientific support and advice from senior researchers and experts for developing geospatial computing workflows are also provided. Users are able to request support contacting a helpdesk via a dedicated ticketing and chat system. After a 6-month development and testing period, the Innovation Lab became operational in September 2021. The first field testing of the platform took place in November 2021 during a 3-day hackathon jointly organized by EO AFRICA R&D, GMES & Africa, and CURAT as part of the AfricaGIS 2021 conference. Forty participants utilized the platform to develop innovative solutions to food security and water resources challenges, such as the impact of the COVID-19 pandemic on agricultural production or linking the decrease in agricultural production to armed conflicts. The activity was successful and similar ones are expected to be organized during major GIS and EO conferences in Africa during the lifetime of the project. Thirty research projects of African-European research tandems granted by the Facility will utilize the Innovation Lab to develop innovative and open-source EO algorithms and applications, preferably as interactive notebooks, adapted to African solutions to African challenges in food security and water scarcity by leveraging cutting-edge cloud-based data access and computing infrastructure. The call for the first 15 research projects was published in November 2021, and the projects are expected to start using the Innovation Lab in February 2022. In parallel, the Innovation Lab provides the computing environment for the capacity development activities of the EO AFRICA R&D Facility, which are organized under the umbrella of EO AFRICA Space Academy. These capacity development activities include several MOOCs, webinars, online and face-to-face courses designed and tailored to improve the knowledge and skills of African researchers in the utilization of Cloud Computing technology to work with EO data. Selected participants of the capacity development activities will use the Innovation Lab during their training. Moreover, the instructors in the Facility use the Innovation Lab to develop the training materials for the Space Academy. Access to the Innovation Lab will also be granted to individual researchers and EO experts depending on the use case and resource availability. Application for access can be made easily through the EO AFRICA R&D web portal after becoming a member of the EO AFRICA Community.This study is funded by ESA Contract No. 4000133905/21/I-EF

Proximal aortic arch cannulation for proximal ascending aortic aneurysms

Introduction: Different arterial inflow sites have been reported to date for particularly challenging cardiac operations. The ascending aorta, femoral artery, and subclavian artery are the most commonly used sites. Although its use has been reported, the aortic arch has not gained popularity in the performance of cannulation. According to a search performed in the PubMed database, aortic arch cannulation for ascending aorta replacement has not been examined in a separate study before. In the present study, we report the treatment outcomes of patients with ascending aortic aneurysms in whom the aortic arch was cannulated for arterial inflow. Material and methods: Twenty-seven patients with aneurysmal dilatation of the ascending aorta underwent ascending aorta replacement from April 2010 to March 2013. The mean age of the patients was 64 years. All operations were carried out by cannulating the aortic arch distally from the origin of the innominate artery. Results: There was no mortality or cannulation-related morbidity. In 23 patients, only the supracoronary ascending aorta was replaced, whereas in 4 patients, the button modification of the Bentall procedure was performed to replace the root and the ascending aorta. Conclusions: The technique of aortic arch cannulation distal to the origin of the innominate artery is worthy of consideration in the treatment of aneurysms limited to the ascending aorta due to its safety, simplicity, and low morbidity

Tryptophan degradation in women with breast cancer: a pilot study

<p>Abstract</p> <p>Background</p> <p>Altered tryptophan metabolism and indoleamine 2,3-dioxygenase activity are linked to cancer development and progression. In addition, these biological factors have been associated with the development and severity of neuropsychiatric syndromes, including major depressive disorder. However, this biological mechanism associated with both poor disease outcomes and adverse neuropsychiatric symptoms has received little attention in women with breast cancer. Therefore, a pilot study was undertaken to compare levels of tryptophan and other proteins involved in tryptophan degradation in women with breast cancer to women without cancer, and secondarily, to examine levels in women with breast caner over the course of chemotherapy.</p> <p>Findings</p> <p>Blood samples were collected from women with a recent diagnosis of breast cancer (<it>n </it>= 33) before their first cycle of chemotherapy and after their last cycle of chemotherapy. The comparison group (<it>n </it>= 24) provided a blood sample prior to breast biopsy. Plasma concentrations of tryptophan, kynurenine, and tyrosine were determined. The kynurenine to tryptophan ratio (KYN/TRP) was used to estimate indoleamine 2,3-dioxygenase activity. On average, the women with breast cancer had lower levels of tryptophan, elevated levels of kynurenine and tyrosine and an increased KYN/TRP ratio compared to women without breast cancer. There was a statistically significant difference between the two groups in the KYN/TRP ratio (<it>p </it>= 0.036), which remained elevated in women with breast cancer throughout the treatment trajectory.</p> <p>Conclusions</p> <p>The findings of this pilot study suggest that increased tryptophan degradation may occur in women with early-stage breast cancer. Given the multifactorial consequences of increased tryptophan degradation in cancer outcomes and neuropsychiatric symptom manifestation, this biological mechanism deserves broader attention in women with breast cancer.</p

<i>Gastruloids</i> develop the three body axes in the absence of extraembryonic tissues and spatially localised signalling

Establishment of the three body axes is a critical step during animal development. In mammals, genetic studies have shown that a combination of precisely deployed signals from extraembryonic tissues position the anteroposterior axis (AP) within the embryo and lead to the emergence of the dorsoventral (DV) and left-right (LR) axes. We have used Gastruloids , embryonic organoids, as a model system to understand this process and find that they are able to develop AP, DV and LR axes as well as to undergo axial elongation in a manner that mirror embryos. The Gastruloids can be grown for 160 hours and form derivatives from ectoderm, mesoderm and endoderm. We focus on the AP axis and show that in the Gastruloids this axis is registered in the expression of T/Bra at one pole that corresponds to the tip of the elongation. We find that localisation of T/Bra expression depends on the combined activities of Wnt/ β -Catenin and Nodal/Smad2,3 signalling, and that BMP signalling is dispensable for this process. Furthermore, AP axis specification occurs in the absence of both extraembryonic tissues and of localised sources of signalling. Our experiments show that Nodal, together with Wnt/ β -Catenin signalling, is essential for the expression of T/Bra but that Wnt signalling has a separable activity in the elongation of the axis. The results lead us to suggest that, in the embryo, the role of the extraembryonic tissues might not be to induce the axes but to bias an intrinsic ability of the embryo to break its initial symmetry and organise its axes. One sentence summary Culture of aggregates of defined number of Embryonic Stem cells leads to self-organised embryo-like structures which, in the absence of localised signalling from extra embryonic tissues and under the autonomous influence of Wnt and Nodal signalling, develop the three main axes of the body

Anteroposterior polarity and elongation in the absence of extraembryonic tissues and spatially localised signalling in Gastruloids, mammalian embryonic organoids

The establishment of the anteroposterior (AP) axis is a critical step during animal embryo development. In mammals, genetic studies have shown that this process relies on signals spatiotemporally deployed in the extraembryonic tissues that locate the position of the head and the onset of gastrulation, marked by T/Brachyury (T/Bra) at the posterior of the embryo. Here, we use Gastruloids, mESC-based organoids, as a model system to study this process. We find that Gastruloids localise T/Bra expression to one end and undergo elongation similar to the posterior region of the embryo suggesting that they develop an AP axis. This process relies on precisely timed interactions between Wnt/β-Catenin and Nodal signalling, whereas BMP signalling is dispensable. Additionally, polarised T/Bra expression occurs in the absence of extraembryonic tissues or localised sources of signals. We suggest that the role of extraembryonic tissues in the mammalian embryo might not be to induce the axes but to bias an intrinsic ability of the embryo to initially break symmetry. Furthermore, we suggest that Wnt signalling has a separable activity involved in the elongation of the axis.BBSRC (BB/M023370/1), European Commission FP7 ERC Advanced Investigator Grants (AIG) (250316), EPSRC (1359454), NC3Rs (NC/P001467/1

Global Assessment Report on Disaster Risk Reduction 2019

The Global Assessment Report on Disaster Risk Reduction (GAR) is the flagship report of the United Nations on worldwide efforts to reduce disaster risk

Fluid challenges in intensive care: the FENICE study A global inception cohort study

Fluid challenges (FCs) are one of the most commonly used therapies in critically ill patients and represent the cornerstone of hemodynamic management in intensive care units. There are clear benefits and harms from fluid therapy. Limited data on the indication, type, amount and rate of an FC in critically ill patients exist in the literature. The primary aim was to evaluate how physicians conduct FCs in terms of type, volume, and rate of given fluid; the secondary aim was to evaluate variables used to trigger an FC and to compare the proportion of patients receiving further fluid administration based on the response to the FC.This was an observational study conducted in ICUs around the world. Each participating unit entered a maximum of 20 patients with one FC.2213 patients were enrolled and analyzed in the study. The median [interquartile range] amount of fluid given during an FC was 500 ml (500-1000). The median time was 24 min (40-60 min), and the median rate of FC was 1000 [500-1333] ml/h. The main indication for FC was hypotension in 1211 (59 %, CI 57-61 %). In 43 % (CI 41-45 %) of the cases no hemodynamic variable was used. Static markers of preload were used in 785 of 2213 cases (36 %, CI 34-37 %). Dynamic indices of preload responsiveness were used in 483 of 2213 cases (22 %, CI 20-24 %). No safety variable for the FC was used in 72 % (CI 70-74 %) of the cases. There was no statistically significant difference in the proportion of patients who received further fluids after the FC between those with a positive, with an uncertain or with a negatively judged response.The current practice and evaluation of FC in critically ill patients are highly variable. Prediction of fluid responsiveness is not used routinely, safety limits are rarely used, and information from previous failed FCs is not always taken into account