Data Hub Research Articles

DEVELOPMENT OF A WEB PLATFORM FOR AIR QUALITY MONITORING

Abstract. Access to information on the quality of the air we breathe is important as it has a huge impact on our health. Also, with the recent Covid pandemic, maintaining our respiratory health has been more important than ever. With knowledge on the air quality in our surroundings, we can make better-informed decisions concerning our health. While geospatial datasets are available, they are often not in an easily digestible format. The tools commonly used in the analysis of these datasets usually require technical knowledge, which limits their accessibility. The study hopes to address these issues by scoping currently available technologies to develop a framework for consolidating the datasets into a single data hub, and presenting the data in way that’s easily understandable without requiring a technical background. Easy-to-use processing and automation tools are also being developed to make performing analysis on the datasets simpler and more accessible. The work done in this project is also intended to serve as a template for future studies in similar fields.

Emergency Charging Service Information Exchange System Linked to Data Hubs

Emergency Charging Service Information Exchange System Linked to Data Hubs

Frontex as a hub for surveillance and data sharing: Challenges for data protection and privacy rights

The European Border and Coast Guard Agency, more commonly known as Frontex, was established in 2004 with “a view to improving the integrated management of the external borders of the Member States of the European Union.” It was tasked with the responsibility of providing technical support and expertise to Member States in the management of borders. Over the years its mandate has increased considerably through amendments to its legislative framework. This expansion has taken place against a background of serious allegations concerning Frontex's role in violating the fundamental rights of asylum seekers through its involvement in pushback operations – the practice of stopping asylum-seekers and migrants in need of protection at or before they reach the European Union's external border. While Frontex's complicity in pushbacks has been widely examined by academics, its transformation into a major surveillance and data processing hub and its compliance (or lack thereof) with the fundamental rights to privacy and protection of personal data have received limited academic attention.This paper traces the evolution of Frontex over the years and fundamental rights implications of the transformation of its role.

Integrated Poultry Care System (IPCS)

The Integrated Poultry Care System (IPCS) is an innovative IoT-based real-time monitoring and control system designed specifically for poultry farms. Leveraging the power of Internet of Things (IoT) technology, IPCS offers comprehensive monitoring capabilities, allowing farmers to remotely track with using individual tags for identifying the temperature, humidity in their poultry houses in real-time. Raspberry Pi 4 serves as the central processing unit and data hub, collection, processing, and transmission of sensor data from the poultry houses. The ESP8266 module is specifically utilized for its capability to connect to Wi-Fi networks, allowing seamless communication between sensors. These modules then transmit the collected data wirelessly to the central control unit, typically powered by a Raspberry Pi or a similar computing device, for processing, analysis, and monitoring. It also serves as the interface through which farmers can remotely access and monitor the conditions within their poultry houses via a user-friendly dashboard or mobile application.

The South Carolina Water Monitoring Portal - A Hub for South Carolina Water Quality Monitoring Data

The South Carolina (SC) Water Monitoring Portal is an ArcGIS-based, geospatial application that incorporates water quality data from a variety of sources and projects them onto an interactive map. This application will provide those interested in accessing and retrieving South Carolina water quality data with a free and easyto- use tool that allows for spatial visualization, interaction with, and direct download of data. At the time of this publication, the application accesses roughly four million water quality data records collected by seventeen different organizations. To allow users to seamlessly find and access the data they need, filters are available to query the data to match the user's needs. Once users find the data applicable to them, they can download and export it into various formats. The application also allows groups and organizations to indirectly upload their own water quality data to have it incorporated into the application. With these capabilities in a spatial format, this application has the potential to provide many benefits. For example, in academia it could be utilized in both classroom and research settings, and regulatory agencies could use this application to communicate water quality from a spatial viewpoint, potentially fostering a better understanding of water quality to stakeholders. The management and protection of our state’s waters are difficult to achieve when the data pertaining to water quality isn’t easily accessible or available in a user-friendly format. The SC Water Monitoring Portal has the potential to aid in the protection and management of our state’s waters as it makes water quality data more accessible and the retrieval of data more user-friendly. The SC Water Monitoring Portal is hosted on the South Carolina (SC) Sea Grant Consortium and the College of Charleston’s Lowcountry Hazards Center websites, making it available to anyone interested in water quality data in the State of South Carolina (available online: www.scseagrant.org/SCWMP).

Brain tumor segmentation using synthetic MR images - A comparison of GANs and diffusion models

Large annotated datasets are required for training deep learning models, but in medical imaging data sharing is often complicated due to ethics, anonymization and data protection legislation. Generative AI models, such as generative adversarial networks (GANs) and diffusion models, can today produce very realistic synthetic images, and can potentially facilitate data sharing. However, in order to share synthetic medical images it must first be demonstrated that they can be used for training different networks with acceptable performance. Here, we therefore comprehensively evaluate four GANs (progressive GAN, StyleGAN 1–3) and a diffusion model for the task of brain tumor segmentation (using two segmentation networks, U-Net and a Swin transformer). Our results show that segmentation networks trained on synthetic images reach Dice scores that are 80%–90% of Dice scores when training with real images, but that memorization of the training images can be a problem for diffusion models if the original dataset is too small. Our conclusion is that sharing synthetic medical images is a viable option to sharing real images, but that further work is required. The trained generative models and the generated synthetic images are shared on AIDA data hub.

Evolution of SARS-CoV-2 in the Rhine-Neckar/Heidelberg Region 01/2021 – 07/2023

In January 2021, the monitoring of circulating variants of SARS-CoV-2 was initiated in Germany under the Corona Surveillance Act, which was discontinued after July 2023. This initiative aimed to enhance pandemic containment, as specific amino acid changes, particularly in the spike protein, were associated with increased transmission and reduced vaccine efficacy.Our group conducted whole genome sequencing using the ARTIC protocol (currently V4) on Illumina's NextSeq 500 platform (and, starting in May 2023, on the MiSeq DX platform) for SARS-CoV-2 positive specimen from patients at Heidelberg University Hospital, associated hospitals, and the public health office in the Rhine-Neckar/Heidelberg region. In total, we sequenced 26,795 SARS-CoV-2-positive samples between January 2021 and July 2023. Valid sequences, meeting the requirements for upload to the German electronic sequencing data hub (DESH) operated by the Robert Koch Institute (RKI), were determined for 24,852 samples, and the lineage/clade could be identified for 25,912 samples.The year 2021 witnessed significant dynamics in the circulating variants in the Rhine-Neckar/Heidelberg region, including A.27.RN, followed by the emergence of B.1.1.7 (Alpha), subsequently displaced by B.1.617.2 (Delta), and the initial occurrences of B.1.1.529 (Omicron). By January 2022, B.1.1.529 had superseded B.1.617.2, dominating with over 90%. The years 2022 and 2023 were then characterized by the dominance of B.1.1.529 and its sublineages, particularly BA.5 and BA.2, and more recently, the emergence of recombinant variants like XBB.1.5.Since the global dominance of B.1.617.2, the identified variant distribution in our local study, apart from a time delay in the spread of new variants, can be considered largely representative of the global distribution.om a time delay in the spread of new variants, can be considered largely representative of the global distribution.

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.

Making the China Data Valley – The National Integrated Big Data Centre System and Local Governance

As a core part of the New Infrastructure Project, China officially launched the National Integrated Big Data Centre System (NIBDCS) in 2022. As part of the “West Computes Data for East” initiative, the NBDCS is a national digital governing infrastructure that includes eight National Data Hubs hosted by ten National Data Centre Clusters. This article examines the Guizhou Hub – one of the earliest established National Data Hubs and where China’s first National Big Data Pilot Zone is located. The research takes an infrastructural perspective and reveals how contingent alignments, including the central state’s initiatives, local government’s role, and corporations like Apple and Alibaba, have come to negotiate, collaborate, and compromise in sustainable arrangements, and eventually bring about Guizhou Hub. The research shows that the grand strategies envisioned and supported by the central state are not enough; localising technological infrastructures requires key local leaders with business and political networks, and mechanisms of state–commercial complexes where intimate partnerships among governmental entities, state-owned enterprises, and private corporations are established, and mutual interests are achieved. This process is conditioned by a “frame of locality” and requires scholarly attention to a local perspective of infrastructural developments.

IOWN Data Hub to Become a Reality

IOWN Data Hub to Become a Reality

Australian Ocean surface waves dataset from SAR

AbstractIn this article, a regional ocean surface waves dataset from Sentinel‐1 A and B Synthetic Aperture Radar (SAR) satellites has been described. The ocean wave data have been extracted from the Sentinel‐1 level‐2 OCN (ocean) product as provided by the European Space Agency and downloadable for this region from the Copernicus Australasia regional data hub. The source OCN data have been produced by evolving versions of Sentinel‐1 Instrument Processing Facility (IPF). The structure of the source OCN NetCDF files changes over time and presents a challenge in performing long duration, time series analyses, including the examination of potential inconsistencies in OCN wave data, due to employment of different IPF versions over the duration of the satellite missions. Here, the input OCN wave data have been homogenized to a single, easily usable standard format after applying a quality assurance and control procedure that removes various inconsistencies in variables, coordinates, dimensions and land flag, and through the addition of new auxiliary variables. The new format has the desirable properties of being compact in size, consistent in structure, and scalable in temporal and spatial coverage. It is also convenient to use and offers opportunities to perform fast, multi‐year regional processing and analysis for calibration and validation studies and scientific applications. No re‐processing of Sentinel‐1 level‐1 data has been carried out in this work.

Real-life study to assess effectiveness and safety of eculizumab in patients with neuromyelitis optica spectrum disorders in France: protocol for ECUP4, an observational study.

Eculizumab, a humanized monoclonal antibody targeting the C5 complement protein, has been approved for the treatment of neuromyelitis optica spectrum disorders (NMOSD) in adult patients who are anti-aquaporin-4 (AQP4) antibody positive (Ab+). The aim of this study is to evaluate the long-term effectiveness and safety of eculizumab in French adults with NMOSD and to describe patients' characteristics, disability, and quality of life using data collected in a real-world setting. This is the protocol for ECUP4, an ongoing prospective, observational, non-comparative, multicenter study conducted in 32 reference centers in France. Eligible patients must also be enrolled in NOMADMUS, a nested cohort of the French national multiple sclerosis registry (OFSEP). The primary endpoint is the annualized relapse rate. Secondary endpoints include the long-term safety of eculizumab, as well as patients' characteristics, treatment outcomes, disability, pain, visual acuity, and quality of life. Visits and treatments follow routine clinical practice. The case report forms (CRF) comprise data recorded in the context of the NOMADMUS cohort, collected during routine visits. The inclusion period is planned for 3 years, with no limitation on the number of patients enrolled. The maximum follow-up duration will be 5.5 years. The efficacy and safety of eculizumab in patients with AQP4+ NMOSD have been demonstrated in randomized clinical trials that showed a significant reduction in the risk of relapse, with a safety profile consistent with other indications. This study will provide clinical and patient-reported evidence of the benefits of eculizumab, using data from a real-world setting in France. This study is registered at the French public repertory Health data Hub, N° F20211228123801. All information can be accessed at: https://www.health-data-hub.fr/.

UNCAN.eu: Toward a European Federated Cancer Research Data Hub.

To enable a collective effort that generates a new level of UNderstanding CANcer (UNCAN.eu) [Cancer Discov (2022) 12 (11): OF1], the European Union supports the creation of a sustainable platform that connects cancer research across Member States. A workshop hosted in Heidelberg gathered European cancer experts to identify ongoing initiatives that may contribute to building this platform and discuss the governance and long-term evolution of a European Federated Cancer Data Hub.

O-HEALTH-EDU: A viewpoint into the current state of Oral Health Professional education in Europe: Part 1: Programme-level data.

Current legislation leaves Oral Health Professional (OHP) education open to wide interpretation and may result in significant variation in educational practice and resultant professional attributes across Europe. Data regarding the current state of OHP education across Europe is limited. The aim of Part 1 of this series is to provide programme-level data for Primary Dental Degree Programmes, Dental Hygiene and Postgraduate Education. A 91-item questionnaire was developed following the Delphi method. The questionnaire and the Articulate glossary of OHP education terms were developed concurrently to facilitate a common understanding of language. Piloting was performed in multiple stages and included institutions internal and external to the research group. The questionnaire was uploaded online and converted to a data hub, allowing dental schools to control their own data and update the data provided whenever they wish. All ADEE member schools (n = 144) were invited to provide data. Forty questions relating to school details, Primary Dental Degree Programmes, Dental Hygiene and Postgraduate Education were included in this part of the series. Seventy-one institutions from 25 European countries provided data between June 2021 and April 2023, which represents a response rate of 49.3% of ADEE members. Programme-level data for Primary Dental Degree Programmes, Dental Hygiene and Postgraduate Education is presented including programme length, funding, languages and fees, student numbers and demographics, student admission and selection processes and permission to practice after graduation. This series of papers, as far as the authors are aware, are the first attempts to build a comprehensive picture of the current state of OHP education in Europe. A comprehensive view of the state of OHP education in Europe is not yet available but the O-Health-Edu data hub provides a means for all education providers in Europe to contribute data to reach this goal. It is anticipated that the data hub will be updated and built upon over time to continually establish a clearer picture of the state of OHP education in Europe.

Low expression of GRM4 is associated with poor prognosis and tumor immune infiltration in glioma

Introduction The metabotropic glutamate receptor 4 (mGlu4, GRM4) exhibits significant expression within the central nervous system (CNS) and has been implicated to be correlated with a poor prognosis. Objective This study was aimed to elucidate the relationship between the expression profile of GRM4 and the prognosis of glioma patients. Methods RNA-sequencing datasets from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and China Glioma Genome Atlas (CGGA) repositories were used to evaluate the potential relationship. The value of clinical prognostic about GRM4 was assessed using clinical survival data from CGGA and TCGA. The GEPIA database was used to select genes like GRM4. PPI network was constructed by the database of (STRING), GO and KEGG analyses were performed. TargetScan, TarBase, miRDB, and starBase were used to explore miRNAs that could regulate GRM4 expression. EWAS Data Hub, MethSurv, and MEXPRESS were used for the analysis and relationship between DNA methylation and GRM4 expression and prognosis in glioma. TIMER2.0 and CAMOIP databases were used to assess the association between immune cell infiltration and GRM4. Human GBM cell lines were used to validate the function of GRM4. Results Our study shows that GRM4 is under expressed among gliomas and accompanied by poorer OS. Multivariate analysis showed that low mRNA expression of GRM4 was an independent factor of prognostic for shorter OS in all glioma patients. MiR-1262 affects the malignant phenotype of gliomas through GRM4. Methylation of DNA plays an important role in the instruction of GRM4 expression, the methylation level of GRM4 in glioma tissue is higher in comparison to normal tissue, and the higher methylation level was accompanied with the worse prognosis. Further analysis showed that GRM4 mRNA expression in GBM linked negatively with common lymphoid progenitor, Macrophage M1, Macrophage, and T cell CD4+ Th2, but not with the tumor purity. Overexpression of GRM4 prevents the migration of human GBM cell lines in vitro. Conclusion GRM4 may have a substantial impact on the infiltration of immune cells and serve as a valuable prognostic biomarker in gliomas.

Establish a Data Hub to Enhance the Projects Feasibility of BRI

Establish a Data Hub to Enhance the Projects Feasibility of BRI

ZNF471 Interacts with BANP to Reduce Tumour Malignancy by Inactivating PI3K/AKT/mTOR Signalling but is Frequently Silenced by Aberrant Promoter Methylation in Renal Cell Carcinoma.

Background: Renal cell carcinoma (RCC) is one of the most common malignant tumours of the urinary system. However, the aetiology and pathogenesis of RCC remain unclear. The C2H2 zinc finger protein (ZNF) family is the largest transcriptional regulatory factor family found in mammals, and Krüppel-associated box domain-containing zinc finger proteins (KRAB-ZFPs) constitute the largest subfamily of the C2H2 zinc finger protein family and play an important role in the occurrence and development of tumours. The aim of this study was to explore the role of abnormal methylation of ZNF471 in the development of renal carcinoma. Methods: In this study, we first used the TCGA and EWAS Data Hub databases to analyse the expression and methylation levels of ZNF471 in renal carcinoma tissues and adjacent normal tissues. Second, we collected samples of renal cancer and adjacent normal tissues at Peking University First Hospital to investigate the expression and methylation level of ZNF471 in renal cancer tissues and the relationships between these levels and the clinicopathological features and prognosis of patients with renal cancer. Next, we investigated the effects of ZNF471 on the proliferation, metastasis, cell cycle progression, and apoptosis of renal cell carcinoma cells by cell biology experiments. Finally, we elucidated the underlying molecular mechanisms of ZNF471 in renal cell carcinoma by transcriptome sequencing, bioinformatics analysis and molecular biology experiments. Results: The expression of ZNF471 in renal carcinoma tissues and cell lines was significantly lower than that in adjacent normal tissues and cell lines due to abnormal promoter CpG methylation. Furthermore, the expression of ZNF471 in renal carcinoma tissues was negatively correlated with tumour stage and grade in patients with renal carcinoma. The results of the cell biology experiments showed that ZNF471 could significantly inhibit the proliferation, migration and cell cycle progression of renal cell carcinoma cells and promote apoptosis in these cells. In addition, ZNF471 could interact with BANP and suppress the malignant phenotype of RCC by inactivating the PI3K/AKT/mTOR signalling pathway. Conclusions: As an important tumour suppressor, ZNF471 can interact with BANP in renal cancer cells and inhibit the activation of the PI3K/AKT/mTOR signalling pathway, thereby inhibiting the occurrence and development of renal cancer.

Year-long buoy-based observations of the air–sea transition zone off the US west coast

Abstract. Two buoys equipped with Doppler lidars owned by the US Department of Energy (DOE) were deployed off the coast of California in autumn of 2020 by Pacific Northwest National Laboratory. The buoys collected data for an entire annual cycle at two offshore locations proposed for offshore wind development by the Bureau of Ocean Energy Management. One of the buoys was deployed approximately 50 km off the coast near Morro Bay in central California in 1100 m of water. The second buoy was deployed approximately 40 km off Humboldt County in northern California in 625 m of water. The buoys provided the first-ever continuous measurements of the air–sea transition zone off the coast of California. The atmospheric and oceanographic characteristics of the area and estimates of annual energy production at both the Morro Bay and Humboldt wind energy areas show that both locations have a high wind energy yield and are prime locations for future floating offshore wind turbines. This article provides a description and comprehensive analysis of the data collected by the buoys, and a final post-processed dataset is uploaded to a data archive maintained by the DOE. Additional analysis was conducted to show the value of the data collected by the DOE buoys. All post-processed data from this study are available on the Wind Data Hub website: https://a2e.energy.gov/data# (last access: 14 September 2023). Near-surface, wave, current, and cloud datasets for Humboldt and Morro Bay are provided at https://doi.org/10.21947/1783807 (Krishnamurthy and Sheridan, 2023b) and https://doi.org/10.21947/1959715 (Krishnamurthy and Sheridan, 2023a), respectively. Lidar datasets for Humboldt and Morro Bay are provided at https://doi.org/10.21947/1783809 (Krishnamurthy and Sheridan, 2023d) and https://doi.org/10.21947/1959721 (Krishnamurthy and Sheridan, 2023c), respectively.

Abstract PR003: An examination of tobacco and alcohol outlet density in Boston to identify priority areas for cancer prevention efforts using environmental justice mapping

Abstract Background. Inequitable access to health-harming substances in the built environment can create and exacerbate race and SES-based disparities in cancer incidence and mortality. Availability and density of tobacco and alcohol outlets is associated with increased experimentation, initiation, and regular use of alcohol and tobacco products. Prior studies examining the sale of tobacco and alcohol indicate that these outlets tend to be concentrated in communities of color and low-income areas. Massachusetts has highlighted environmental justice (EJ), one’s right to be protected from hazards and live in clean, health-promoting environments, as a priority issue and identified block group populations who are at most risk of environmental burdens. The objective of this study was to (a) examine the distribution of tobacco and alcohol outlets in environmental justice block groups in Boston, and (b) compare outlet density in more deprived neighborhoods to more privileged neighborhoods. Methods. Publicly available licensing lists for tobacco and alcohol retailers with geocoded data were obtained from the City of Boston’s open data hub. Lists were de-duplicated so that retailers that sell both tobacco and alcohol products were only represented once. The environmental justice block group layer (2020) was downloaded from Mass.gov. EJ block groups meet one or more of the following criteria: ‘high minority’ (>40% non-white population), ‘low-income’, or ‘high English isolation.’ ArcGIS Pro software was used to spatially join retailer data to Boston block groups and calculate tobacco and alcohol outlet density (the number of retailers per 1,000 people). Sociodemographic and cancer mortality data from the Health of Boston Report was used to classify neighborhoods as ‘more privileged’ (Back Bay, Beacon Hill, North End, West End) or ‘more deprived’ (Dorchester, Hyde Park, Mattapan, Roslindale, Roxbury). Results. Of the 560 Boston block groups analyzed, 458 (81.8%) were considered environmental justice block groups with 60% of EJ block groups classified as ‘high minority’. There were 931 retailers that sell tobacco or alcohol products for off-premises consumption in Boston, with 86% of these retailers (n=811) located in EJ block groups. On average, tobacco and alcohol outlet density was greater in EJ block groups compared to non-EJ block groups (2.09 vs 1.25 retailers per 1,000 residents). Nearly half (48%) of environmental justice block groups in Boston are located in the most deprived neighborhoods compared to only 3.7% in the most privileged neighborhoods. Tobacco outlet density is significantly higher in deprived neighborhoods compared to privileged neighborhoods (1.25 vs 0.98, p < 0.01). However, alcohol density is lower in more deprived block groups compared to more privileged ones (0.35 vs 0.74, p < 0.01). Conclusion. Environmental justice mapping can be used as a tool to identify areas where cancer prevention efforts may be enhanced by modifying the built environment to reduce clusters of alcohol and tobacco outlets. Citation Format: Lindsay Kephart. An examination of tobacco and alcohol outlet density in Boston to identify priority areas for cancer prevention efforts using environmental justice mapping [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr PR003.

Proposals to Reform the EU Customs Union

On 17 May 2023 the European Commission published the most ambitious and comprehensive proposals to reform the EU Customs Union since the establishing of the Customs Union in 1968. The Commission’s proposals follow a series of studies and consultations and is intended as a response to tensions that have arisen in the customs world as a result of a huge increase in trade volumes, a rapidly rising number of EU standards to be checked at borders, the shifting geopolitical reality and various crises. This contribution provides an overview of and critical reflection on the highlights of the proposals, enabling readers with different levels of expertise in customs law to get familiar with what has been proposed by the European Commission and to pave the way for further, in-depth research on these proposals EU Customs Union, reform, European Commission, customs legislation, UCC, e-commerce, importer, sanctions, EU Customs Data Hub, Trust and Check traders