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PNAS Nexus Feb 2024Storms can have devasting effects on shorelines, causing flooding and the destruction of property and infrastructure. As global warming and the frequency and magnitude...
Storms can have devasting effects on shorelines, causing flooding and the destruction of property and infrastructure. As global warming and the frequency and magnitude of tropical storms increase, barrier islands comprising 10% of the world's coast may undergo significant change caused by beach erosion, loss of dunes, and formation of washovers and tidal inlets. Understanding how storms affect sediment transport at tidal inlets is an understudied subject that directly influences barrier island erosional-depositional processes and long-term sediment budgets. This study models hydrodynamics and sediment transport at a conceptualized mixed-energy, mesotidal inlet system using 10 synthetic storm tracks. We investigate the provenance and the role of various storm characteristics and timing between the peak storm surge and high tide on sediment fluxes for different grain sizes. We find that most storms (38 of 40) cause a net import of sediment into the basin that is sourced primarily from the updrift and downdrift nearshore and secondly from the ebb-delta. Very little sediment comes from inlet channel scour. Cumulative (net) transport correlates well with peak significant wave height because wave height influences bottom shear stresses and sediment suspension on the ebb-tidal delta and in the nearshore. The duration of the storm surge also correlates with net transport because it controls the period of flood-directed currents. Our findings help explain the formation of flood deltas inside tidal inlets and the formation of sand shoals in backbarrier regions. Storm-induced enlargement of these deposits represents a permanent long-term loss of sand from barrier islands that will lead to erosion.
PubMed: 38415221
DOI: 10.1093/pnasnexus/pgae042 -
Biology Oct 2023In the global migration crisis, one of the challenges in the effort to identify deceased migrants is establishing their region of origin, which facilitates the search...
In the global migration crisis, one of the challenges in the effort to identify deceased migrants is establishing their region of origin, which facilitates the search for ante mortem data to be compared with the post mortem information. This pilot study explores the potential of using stable isotope analysis to distinguish between individuals coming from West Africa and the Horn of Africa. Six individuals (four of known origin and two of unknown origin) were sampled. δC, δN and δO of hair were analysed using Elemental Analyzers coupled with Isotope Ratio Mass Spectrometry (IRMS). δO and δC of bone were analysed using GasBench II with IRMS, while Sr/Sr composition was determined in bone and dental enamel using laser ablation multi-collector inductively coupled plasma mass spectrometry. The stable isotope compositions of the individual from the Horn of Africa differed from the other individuals. The differences found between Sr/Sr of enamel and bone and between δO and δC in bone and hair reflect changes in sources of food and water in accordance with regionally typical migration journeys. The analysis of multiple stable isotopes delivered promising results, allowing us to narrow down the region of origin of deceased migrants and corroborate the information about the migration journey.
PubMed: 37997970
DOI: 10.3390/biology12111371 -
Heliyon Jul 2023Over the last decade, pharmaceutical businesses have battled to standardize product traceability across the supply chain process, enabling counterfeiters to enter the...
Over the last decade, pharmaceutical businesses have battled to standardize product traceability across the supply chain process, enabling counterfeiters to enter the market with counterfeit pharmaceuticals. As a result, an end-to-end product tracking system is crucial for ensuring product safety and eliminating counterfeit products across the pharmaceutical supply chain. In this paper, we introduce PharmaChain, a decentralized hyperledger fabric framework that leverages confidentiality, accountability, and interoperability. This system enables on-chain and off-chain storage for secured, rapid transactions, along with smart contracts establishing data provenance. To demonstrate security, we have provided double signing through the elliptic curve digital signature algorithm, hash data encryption, and 33% node attack. The purpose of this suggested framework is to engage particular governance disciplines to assess its effectiveness in improving drug traceability across the pharmaceutical supply chain to preserve public health by preventing counterfeit pharmaceuticals.
PubMed: 37483827
DOI: 10.1016/j.heliyon.2023.e17957 -
Viruses Jul 2023The moon jellyfish is associated with a highly diverse microbiota changing with provenance, tissue, and life stage. While the crucial relevance of bacteria to host...
The moon jellyfish is associated with a highly diverse microbiota changing with provenance, tissue, and life stage. While the crucial relevance of bacteria to host fitness is well known, bacteriophages have often been neglected. Here, we aimed to isolate virulent phages targeting bacteria that are part of the -associated microbiota. Four phages ( phage BSwM KMM1, phages BSwM KMM2-BSwM KMM4) were isolated from the Baltic Sea water column and characterized. Phages KMM2/3/4 infected representatives of , , and (), whereas KMM1 showed a remarkably broad host range, infecting Gram-negative as well as Gram-positive . All phages showed an up to 99% adsorption to host cells within 5 min, short latent periods (around 30 min), large burst sizes (mean of 128 pfu/cell), and high efficiency of plating (EOP > 0.5), demonstrating decent virulence, efficiency, and infectivity. Transmission electron microscopy and viral genome analysis revealed that all phages are novel species and belong to the class of Caudoviricetes harboring a tail and linear double-stranded DNA (formerly known as -like (KMM3) and -like (KMM1/2/4) bacteriophages) with genome sizes between 50 and 138 kbp. In the future, these isolates will allow manipulation of the -associated microbiota and provide new insights into phage impact on the multicellular host.
Topics: Bacteriophages; Enterobacteriaceae; Pseudomonas Phages; DNA; Bacteria; Seawater; Genome, Viral
PubMed: 37515211
DOI: 10.3390/v15071525 -
JMIR Formative Research Jul 2023To fulfill their epidemiological vigilance function, authorities require valid, complete, timely, precise, and reliable information. Advancements in new technologies...
BACKGROUND
To fulfill their epidemiological vigilance function, authorities require valid, complete, timely, precise, and reliable information. Advancements in new technologies have facilitated public health control through vigilance systems for notifiable diseases; these systems can gather large numbers of simultaneous notifications, process a wide array of data, and deliver updated information in real time to relevant decision-makers. A large worldwide deployment of new information technologies was seen during the COVID-19 pandemic; these technologies proved to be efficient, resourceful tools . Platform developers should seek self-evaluation strategies to optimize functionality or improve the capacity of national vigilance systems. These tools exist in the Latin American region at various development stages, although publications reporting architectural characteristics of these tools are scarce. International publications are more abundant a nd serve as a basis for comparing the standards that need to be met.
OBJECTIVE
This study aimed to assess the architecture of the Chilean epidemiological surveillance system for notifiable diseases (EPIVIGILA), as compared to that of the international systems reported in scientific publications.
METHODS
A search for scientific publications was conducted to identify systematic reviews that documented the architectural characteristics of disease notification and vigilance systems. EPIVIGILA was compared to other systems from countries in Africa, the Americas, Asia, Europe, and Oceania.
RESULTS
The following aspects of the architecture were identified: (1) notification provenance, (2) minimum data set, (3) database users, and (4) data quality control. The notifying organizations, including hospitals, clinics, laboratories, and medical consultation offices, were similar among the 13 countries analyzed; this contrasted with Chile, where the reporting agent is the physician who can belong to an organization. The minimum data set include patient identification, disease data, and general codifications. EPIVIGILA includes all these elements, in addition to symptomatology, hospitalization data, type of medicine and treatment result, and laboratory test types. The database users or data analyzers include public health organizations, research organizations, epidemiological organizations, health organizations or departments, and the Centers for Disease Control and Prevention. Finally, for data quality control, the criteria most often used were completeness, consistency, validity, timeliness, accuracy, and competencies.
CONCLUSIONS
An efficient notification and vigilance system must be capable of promptly identifying probable risks as well as incidence and prevalence of the diseases under surveillance. EPIVIGILA has been shown to comply with high quality and functionality standards, at the level of developed countries, by achieving total national coverage and by providing timely, trustworthy, and complete information at high-security levels, thus obtaining positive assessment from national and international authorities.
PubMed: 37418297
DOI: 10.2196/34387 -
Foods (Basel, Switzerland) Jul 2023As the demand for seafood increases, so does the incidence of seafood fraud. Confirming provenance of seafood is important to combat fraudulent labelling but requires a...
As the demand for seafood increases, so does the incidence of seafood fraud. Confirming provenance of seafood is important to combat fraudulent labelling but requires a database that contains the isotopic and elemental "fingerprints" of authentic seafood samples. Local isotopic and elemental databases can be scaled up or combined with other databases to increase the spatial and species coverage to create a larger database. This study showcases the use of isotopic and elemental fingerprints of the black tiger prawn () to develop a database that can be used to securely store the data necessary for determining provenance. The utility of this database was tested through querying and building seven different datasets that were used to develop models to determine the provenance of . The models built using the data retrieved from the database demonstrated that the provenance of could be determined with >80% accuracy. As the database was developed using MySQL, it can be scaled up to include additional regions, species, or methodologies depending on the needs of the users. Combining the database with methods of determining provenance will provide regulatory bodies and the seafood industry with another provenance tool to combat fraudulent seafood labelling.
PubMed: 37509769
DOI: 10.3390/foods12142677 -
In-situ δO and Sr/Sr proxies in an unconformable clastic unit at the Ordovician-Silurian transition.Scientific Reports Sep 2023Clastic successions found in the carbonate platform of continental margin during the Ordovician-Silurian Transition (OST) period are archives for interpreting...
Clastic successions found in the carbonate platform of continental margin during the Ordovician-Silurian Transition (OST) period are archives for interpreting paleo-depositional systems. Here, we report in-situ δO and Sr/Sr isotope chemo-stratigraphy for an unconformable clastic unit from the Cathaysia terrane that rifted off the Gondwana Supercontinent in the Early Paleozoic Era. Our results suggest a depositional proxy and model for geological events attributed to rapid changes in the sedimentary environment during the OST period. Importantly, these results present crucial clues that infer the influence of Paleo-Tethys Sea opening, global eustatic regression, and rapid sedimentary provenance change. Our study provides insight into paleo-tracer that could be a key method for interpreting depositional system of carbonate platform based on in-situ mineral isotope chemo-stratigraphy that preserves the original value of provenance and geochemical condition.
PubMed: 37704744
DOI: 10.1038/s41598-023-42200-3 -
Frontiers in Digital Health 2024In the big data era, where corporations commodify health data, non-fungible tokens (NFTs) present a transformative avenue for patient empowerment and control. NFTs are...
INTRODUCTION
In the big data era, where corporations commodify health data, non-fungible tokens (NFTs) present a transformative avenue for patient empowerment and control. NFTs are unique digital assets on the blockchain, representing ownership of digital objects, including health data. By minting their data as NFTs, patients can track access, monetize its use, and build secure, private health information systems. However, research on NFTs in healthcare is in its infancy, warranting a comprehensive review.
METHODS
This study conducted a systematic literature review and thematic analysis of NFTs in healthcare to identify use cases, design models, and key challenges. Five multidisciplinary research databases (Scopus, Web of Science, Google Scholar, IEEE Explore, Elsevier Science Direct) were searched. The approach involved four stages: paper collection, inclusion/exclusion criteria application, screening, full-text reading, and quality assessment. A classification and coding framework was employed. Thematic analysis followed six steps: data familiarization, initial code generation, theme searching, theme review, theme definition/naming, and report production.
RESULTS
Analysis of 19 selected papers revealed three primary use cases: patient-centric data management, supply chain management for data provenance, and digital twin development. Notably, most solutions were prototypes or frameworks without real-world implementations. Four overarching themes emerged: data governance (ownership, tracking, privacy), data monetization (commercialization, incentivization, sharing), data protection, and data storage. The focus lies on user-controlled, private, and secure health data solutions. Additionally, data commodification is explored, with mechanisms proposed to incentivize data maintenance and sharing. NFTs are also suggested for tracking medical products in supply chains, ensuring data integrity and provenance. Ethereum and similar platforms dominate NFT minting, while compact NFT storage options are being explored for faster data access.
CONCLUSION
NFTs offer significant potential for secure, traceable, decentralized healthcare data exchange systems. However, challenges exist, including dependence on blockchain, interoperability issues, and associated costs. The review identified research gaps, such as developing dual ownership models and data pricing strategies. Building an open standard for interoperability and adoption is crucial. The scalability, security, and privacy of NFT-backed healthcare applications require further investigation. Thus, this study proposes a research agenda for adopting NFTs in healthcare, focusing on governance, storage models, and perceptions.
PubMed: 38919876
DOI: 10.3389/fdgth.2024.1377531 -
JCO Clinical Cancer Informatics Jan 2024Electronic health record (EHR)-based real-world data (RWD) are integral to oncology research, and understanding fitness for use is critical for data users. Complexity of...
PURPOSE
Electronic health record (EHR)-based real-world data (RWD) are integral to oncology research, and understanding fitness for use is critical for data users. Complexity of data sources and curation methods necessitate transparency into how quality is approached. We describe the application of data quality dimensions in curating EHR-derived oncology RWD.
METHODS
A targeted review was conducted to summarize data quality dimensions in frameworks published by the European Medicines Agency, The National Institute for Healthcare and Excellence, US Food and Drug Administration, Duke-Margolis Center for Health Policy, and Patient-Centered Outcomes Research Institute. We then characterized quality processes applied to curation of Flatiron Health RWD, which originate from EHRs of a nationwide network of academic and community cancer clinics, across the summarized quality dimensions.
RESULTS
The primary quality dimensions across frameworks were (including subdimensions of availability, sufficiency, and representativeness) and (including subdimensions of accuracy, completeness, provenance, and timeliness). Flatiron Health RWD quality processes were aligned to each dimension. Relevancy to broad or specific use cases is optimized through data set size and variable breadth and depth. Accuracy is addressed using validation approaches, such as comparison with external or internal reference standards or indirect benchmarking, and verification checks for conformance, consistency, and plausibility, selected on the basis of feasibility and criticality of the variable to the intended use case. Completeness is assessed against expected source documentation; provenance by recording data transformation, management procedures, and auditable metadata; and timeliness by setting refresh frequency to minimize data lags.
CONCLUSION
Development of high-quality, scaled, EHR-based RWD requires integration of systematic processes across the data lifecycle. Approaches to quality are optimized through knowledge of data sources, curation processes, and use case needs. By addressing quality dimensions from published frameworks, Flatiron Health RWD enable transparency in determining fitness for real-world evidence generation.
Topics: Humans; Reproducibility of Results; Medical Oncology; Neoplasms; Data Accuracy; Health Policy
PubMed: 38241599
DOI: 10.1200/CCI.23.00046 -
Frontiers in Digital Health 2024Population health data integration remains a critical challenge in low- and middle-income countries (LMIC), hindering the generation of actionable insights to inform... (Review)
Review
INTRODUCTION
Population health data integration remains a critical challenge in low- and middle-income countries (LMIC), hindering the generation of actionable insights to inform policy and decision-making. This paper proposes a pan-African, Findable, Accessible, Interoperable, and Reusable (FAIR) research architecture and infrastructure named the INSPIRE datahub. This cloud-based Platform-as-a-Service (PaaS) and on-premises setup aims to enhance the discovery, integration, and analysis of clinical, population-based surveys, and other health data sources.
METHODS
The INSPIRE datahub, part of the Implementation Network for Sharing Population Information from Research Entities (INSPIRE), employs the Observational Health Data Sciences and Informatics (OHDSI) open-source stack of tools and the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to harmonise data from African longitudinal population studies. Operating on Microsoft Azure and Amazon Web Services cloud platforms, and on on-premises servers, the architecture offers adaptability and scalability for other cloud providers and technology infrastructure. The OHDSI-based tools enable a comprehensive suite of services for data pipeline development, profiling, mapping, extraction, transformation, loading, documentation, anonymization, and analysis.
RESULTS
The INSPIRE datahub's "On-ramp" services facilitate the integration of data and metadata from diverse sources into the OMOP CDM. The datahub supports the implementation of OMOP CDM across data producers, harmonizing source data semantically with standard vocabularies and structurally conforming to OMOP table structures. Leveraging OHDSI tools, the datahub performs quality assessment and analysis of the transformed data. It ensures FAIR data by establishing metadata flows, capturing provenance throughout the ETL processes, and providing accessible metadata for potential users. The ETL provenance is documented in a machine- and human-readable Implementation Guide (IG), enhancing transparency and usability.
CONCLUSION
The pan-African INSPIRE datahub presents a scalable and systematic solution for integrating health data in LMICs. By adhering to FAIR principles and leveraging established standards like OMOP CDM, this architecture addresses the current gap in generating evidence to support policy and decision-making for improving the well-being of LMIC populations. The federated research network provisions allow data producers to maintain control over their data, fostering collaboration while respecting data privacy and security concerns. A use-case demonstrated the pipeline using OHDSI and other open-source tools.
PubMed: 38347885
DOI: 10.3389/fdgth.2024.1329630