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PloS One 2022In 2016, a Stollhof-type copper hoard was found during an excavation in Magyaregres, Hungary. It was placed in a cooking pot, and deposited upside down within the...
In 2016, a Stollhof-type copper hoard was found during an excavation in Magyaregres, Hungary. It was placed in a cooking pot, and deposited upside down within the boundaries of an Early Copper Age settlement. Similar hoards dating to the end of the 5th millennium BCE are well-known from Central Europe, however, this hoard represents the only one so far with thoroughly documented finding circumstances. The hoard contained 681 pieces of copper, 264 pieces of stone and a single Spondylus bead, along with 19 pieces of small tubular spiral copper coils, three spiral copper bracelets, and two large, spectacle spiral copper pendants. Until now, information on the provenance of raw materials and how such copper artefacts were manufactured has not been available. The artefacts were studied under optical microscopes to reveal the manufacturing process. Trace elemental composition (HR-ICP-MS) and lead isotope ratios (MC-ICP-MS) were measured to explore the provenance of raw materials. The ornaments were rolled or folded and coiled from thin sheets of copper using fahlore copper probably originating from the Northwestern Carpathians. A complex archaeological approach was employed to reveal the provenance, distribution and the social roles the ornaments could have played in the life of a Copper Age community. Evidence for local metallurgy was lacking in contemporaneous Transdanubian sites, therefore it is likely that the items of the hoard were manufactured closer to the raw material source, prior to being transported to Transdanubia as finished products. The method of deposition implies that such items were associated with special social contexts, represented exceptional values, and the context of deposition was also highly prescribed. The Magyaregres hoard serves as the first firm piece of evidence for the existence of a typologically independent Central European metallurgical circle which exploited the raw material sources located within its distribution.
Topics: Hungary; Technology; Archaeology; Artifacts; Metallurgy
PubMed: 36417420
DOI: 10.1371/journal.pone.0278116 -
F1000Research 2021Knowledge graph (KG) publishes machine-readable representation of knowledge on the Web. Structured data in the knowledge graph is published using Resource Description...
Knowledge graph (KG) publishes machine-readable representation of knowledge on the Web. Structured data in the knowledge graph is published using Resource Description Framework (RDF) where knowledge is represented as a triple (subject, predicate, object). Due to the presence of erroneous, outdated or conflicting data in the knowledge graph, the quality of facts cannot be guaranteed. Trustworthiness of facts in knowledge graph can be enhanced by the addition of metadata like the source of information, location and time of the fact occurrence. Since RDF does not support metadata for providing provenance and contextualization, an alternate method, RDF reification is employed by most of the knowledge graphs. RDF reification increases the magnitude of data as several statements are required to represent a single fact. Another limitation for applications that uses provenance data like in the medical domain and in cyber security is that not all facts in these knowledge graphs are annotated with provenance data. In this paper, we have provided an overview of prominent reification approaches together with the analysis of popular, general knowledge graphs Wikidata and YAGO4 with regard to the representation of provenance and context data. Wikidata employs qualifiers to include metadata to facts, while YAGO4 collects metadata from Wikidata qualifiers. However, facts in Wikidata and YAGO4 can be fetched without using reification to cater for applications that do not require metadata. To the best of our knowledge, this is the first paper that investigates the method and the extent of metadata covered by two prominent KGs, Wikidata and YAGO4.
Topics: Empirical Research; Metadata; Pattern Recognition, Automated; Research Design
PubMed: 34900233
DOI: 10.12688/f1000research.72843.2 -
PeerJ. Computer Science 2022Scientific data management plays a key role in the reproducibility of scientific results. To reproduce results, not only the results but also the data and steps of...
Scientific data management plays a key role in the reproducibility of scientific results. To reproduce results, not only the results but also the data and steps of scientific experiments must be made findable, accessible, interoperable, and reusable. Tracking, managing, describing, and visualizing provenance helps in the understandability, reproducibility, and reuse of experiments for the scientific community. Current systems lack a link between the data, steps, and results from the computational and non-computational processes of an experiment. Such a link, however, is vital for the reproducibility of results. We present a novel solution for the end-to-end provenance management of scientific experiments. We provide a framework, CAESAR (CollAborative Environment for Scientific Analysis with Reproducibility), which allows scientists to capture, manage, query and visualize the complete path of a scientific experiment consisting of computational and non-computational data and steps in an interoperable way. CAESAR integrates the REPRODUCE-ME provenance model, extended from existing semantic web standards, to represent the whole picture of an experiment describing the path it took from its design to its result. ProvBook, an extension for Jupyter Notebooks, is developed and integrated into CAESAR to support computational reproducibility. We have applied and evaluated our contributions to a set of scientific experiments in microscopy research projects.
PubMed: 35494870
DOI: 10.7717/peerj-cs.921 -
GigaScience Dec 2021Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By...
BACKGROUND
Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level.
FINDINGS
We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics.
CONCLUSIONS
The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.
Topics: Base Sequence; Data Mining; Databases, Nucleic Acid; Europe; Nucleotides
PubMed: 34966925
DOI: 10.1093/gigascience/giab084 -
International Journal of Medical... Dec 2021An image sharing framework is important to support downstream data analysis especially for pandemics like Coronavirus Disease 2019 (COVID-19). Current centralized image...
BACKGROUND
An image sharing framework is important to support downstream data analysis especially for pandemics like Coronavirus Disease 2019 (COVID-19). Current centralized image sharing frameworks become dysfunctional if any part of the framework fails. Existing decentralized image sharing frameworks do not store the images on the blockchain, thus the data themselves are not highly available, immutable, and provable. Meanwhile, storing images on the blockchain provides availability/immutability/provenance to the images, yet produces challenges such as large-image handling, high viewing latency while viewing images, and software inconsistency while storing/loading images.
OBJECTIVE
This study aims to store chest x-ray images using a blockchain-based framework to handle large images, improve viewing latency, and enhance software consistency.
BASIC PROCEDURES
We developed a splitting and merging function to handle large images, a feature that allows previewing an image earlier to improve viewing latency, and a smart contract to enhance software consistency. We used 920 publicly available images to evaluate the storing and loading methods through time measurements.
MAIN FINDINGS
The blockchain network successfully shares large images up to 18 MB and supports smart contracts to provide code immutability, availability, and provenance. Applying the preview feature successfully shared images 93% faster than sharing images without the preview feature.
PRINCIPAL CONCLUSIONS
The findings of this study can guide future studies to generalize our framework to other forms of data to improve sharing and interoperability.
Topics: Blockchain; Diagnostic Imaging; Humans; Software; X-Rays
PubMed: 34628257
DOI: 10.1016/j.ijmedinf.2021.104599 -
Foods (Basel, Switzerland) Feb 2022Consumers' food preferences increasingly meet concerns of authenticity, health, origin, and sustainability, altogether attributes embodied in rural provenance food...
Consumers' food preferences increasingly meet concerns of authenticity, health, origin, and sustainability, altogether attributes embodied in rural provenance food products. The dynamics of production, commercialization, and availability of these products in urban centers are growing stronger. This study aims to explore rural provenance food consumption and underlying motivations, the consumers' images of products and provenance areas, and the influence of rural ties in consumption. Data from a survey directed to 1554 consumers of 24 urban specialty stores located in three Portuguese cities were analyzed. The analysis is based on the differences between frequent and sporadic consumers of Portuguese rural provenance food products. The two groups significantly differ in the reasons provided to acquire the products. Those who buy and consume these products more frequently especially value sensorial features, convenience, national provenance, and the impacts on rural development. Additionally, the motivations to choose rural provenance foods tend to pair with positive images of those products and of their territories of origin. This is intrinsically connected with familiarity, a nuclear notion that encompasses the symbolic images of the products and their origins as actual connections (familiar and otherwise) to rural contexts.
PubMed: 35206024
DOI: 10.3390/foods11040547 -
BioRxiv : the Preprint Server For... Dec 2023The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance...
The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
PubMed: 38076838
DOI: 10.1101/2023.11.29.569306 -
BioRxiv : the Preprint Server For... Mar 2023A large number of genomic and imaging datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While...
A large number of genomic and imaging datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While much effort has been devoted to capturing information related to biospecimen information and experimental procedures, the metadata standards that describe data matrices and the analysis workflows that produced them are relatively lacking. Detailed metadata schema related to data analysis are needed to facilitate sharing and interoperability across groups and to promote data provenance for reproducibility. To address this need, we developed the Matrix and Analysis Metadata Standards (MAMS) to serve as a resource for data coordinating centers and tool developers. We first curated several simple and complex "use cases" to characterize the types of feature-observation matrices (FOMs), annotations, and analysis metadata produced in different workflows. Based on these use cases, metadata fields were defined to describe the data contained within each matrix including those related to processing, modality, and subsets. Suggested terms were created for the majority of fields to aid in harmonization of metadata terms across groups. Additional provenance metadata fields were also defined to describe the software and workflows that produced each FOM. Finally, we developed a simple list-like schema that can be used to store MAMS information and implemented in multiple formats. Overall, MAMS can be used as a guide to harmonize analysis-related metadata which will ultimately facilitate integration of datasets across tools and consortia. MAMS specifications, use cases, and examples can be found at https://github.com/single-cell-mams/mams/.
PubMed: 36945543
DOI: 10.1101/2023.03.06.531314 -
PloS One 2020The presence of glass beads in West African archaeological sites provides important evidence of long-distance trade between this part of the continent and the rest of...
The presence of glass beads in West African archaeological sites provides important evidence of long-distance trade between this part of the continent and the rest of the world. Until recently, most of these items came from historical Sub-Saharan urban centers, well known for their role in the medieval trans-Saharan trade. We present here the chemical analysis by Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) of 16 glass beads found in three rural sites excavated during the past decade: the funerary site of Dourou-Boro and settlement sites of Sadia, in central Mali, as well as the settlement site of Djoutoubaya, in eastern Senegal, in contexts dated between the 7th-9th and the 11th-13th centuries CE. Results show that the raw materials used to manufacture the majority of the glass most probably originated in Egypt, the Levantine coast and the Middle East. One bead is of uncertain provenance and shows similarities with glass found in the Iberian Peninsula and in South Africa. One bead fragment found inside a tomb is a modern production, probably linked to recent plundering. All of these ancient beads were exchanged along the trans-Saharan trade routes active during the rise of the first Sahelian states, such as the Ghana and the Gao kingdoms, and show strong similarities with the other West African bead assemblages that have been analysed. Despite the remoteness of their location in the Dogon Country and in the Falémé River valley, the beads studied were therefore included in the long-distance trade network, via contacts with the urban commercial centers located at the edge of the Sahara along the Niger River and in current southern Mauretania. These results bring a new light on the relationships between international and regional trade in Africa and highlight the complementarity between centres of political and economic power and their peripheries, important because of resources like gold for eastern Senegal.
Topics: Africa, Northern; Archaeology; Commerce; Demography; Egypt; Gas Chromatography-Mass Spectrometry; Ghana; Glass; History, Ancient; Humans; Mali; Middle East; Niger; Senegal; South Africa
PubMed: 33264318
DOI: 10.1371/journal.pone.0242027 -
ACS Omega Sep 2022To understand the geochemical characteristics of late Paleozoic coal in the Changzhi and Jincheng mining areas in the southeastern Qinshui Basin, major and rare earth...
To understand the geochemical characteristics of late Paleozoic coal in the Changzhi and Jincheng mining areas in the southeastern Qinshui Basin, major and rare earth element analyses were conducted through inductively coupled plasma-mass spectrometry (ICP-MS), X-ray fluorescence spectrometry (XRF), and proximate analysis. The results show that the study coals are bituminous A rank and anthracite C rank ( : 1.6-3.24%) with low-ash, low-moisture, low-volatile, and low- to medium-sulfur characteristics. The main forms of sulfur in the study coals are organic sulfur, followed by pyritic sulfur, only some coals with high sulfur contents in the Taiyuan Formation (SGJ, WTP, FHS) are mainly pyritic sulfur, and the contents of sulfate sulfur are extremely low. The major elements of the late Paleozoic coal in the southeastern Qinshui Basin are mainly SiO (4.77%) and AlO (3.64%), followed by FeO (1.22%), CaO (1.53%), FeO (0.48%), MgO (0.25%), NaO (0.21%), PO (0.18%), TiO (0.15%), and minor KO (0.04%) (on a whole-coal basis). Through correlation analysis and cluster analysis, the occurrence states of major elements in the Shanxi and Taiyuan Formations are different. The average rare earth elements and yttrium (REY) value in the study area is 88.68 μg/g (on a whole-coal basis). The mean light REY (LREY)-to-heavy REY (HREY) ratio is 26.33. The mean values of δEu, δCe, Y, and Gd are 0.60, 0.99, 1.07, and 1.02, respectively. The Shanxi Formation is dominated by the L-type REY enrichment, while the Taiyuan Formation is dominated by the M-H-type REY enrichment. The fractionation degree of REY in the Taiyuan Formation is lower than that in the Shanxi Formation. Rare earth elements in Shanxi coal mainly occur in clay minerals, and some rare earth elements are adsorbed and enriched by vitrinite. Rare earth elements in Taiyuan coal mainly occur in clay minerals and pyrite, and some rare earth elements occur in inertinite. A warm, humid, low-salinity, oxidizing, and acidic environment was favorable for REY enrichment. The coal-forming environment was weakly oxidizing and reducing, and the paleosalinity of the water was relatively high during late Paleozoic coal deposition in the southeastern Qinshui Basin. The paleotemperature of the Shanxi Formation is higher than that of the Taiyuan Formation. The provenance is mainly from an upper crustal felsic source region, the source rocks are mainly post-Archean sedimentary and calcareous mudstones mixed with some granite and alkaline basalt from the Yinshan Upland, and the tectonic setting of the source area mainly includes island arcs and active continental margins.
PubMed: 36092626
DOI: 10.1021/acsomega.2c02596