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Studies in Health Technology and... Sep 2019The German Center for Lung Research (DZL) is a research network with the aim of researching respiratory diseases. In order to enable consortium-wide retrospective...
The German Center for Lung Research (DZL) is a research network with the aim of researching respiratory diseases. In order to enable consortium-wide retrospective research and prospective patient recruitment, we perform data integration into a central data warehouse. The enhancements of the underlying ontology is an ongoing process for which we developed the Collaborative Metadata Repository (CoMetaR) tool. Its technical infrastructure is based on the Resource Description Framework (RDF) for ontology representation and the distributed version control system Git for storage and versioning. Ontology development involves a considerable amount of data curation. Data provenance improves its feasibility and quality. Especially in collaborative metadata development, a comprehensive annotation about "who contributed what, when and why" is essential. Although RDF and Git versioning repositories are commonly used, no existing solution captures metadata provenance information in sufficient detail. We propose an enhanced composition of standardized RDF statements for detailed provenance representation. Additionally, we developed an algorithm that extracts and translates provenance data from the repository into the proposed RDF statements.
Topics: Biological Ontologies; Data Warehousing; Humans; Metadata; Prospective Studies; Retrospective Studies
PubMed: 31483277
DOI: 10.3233/SHTI190832 -
IEEE Transactions on Visualization and... Sep 2023In domains, such as agronomy or manufacturing, experts need to consider trade-offs when making decisions that involve several, often competing, objectives. Such analysis...
In domains, such as agronomy or manufacturing, experts need to consider trade-offs when making decisions that involve several, often competing, objectives. Such analysis is complex and may be conducted over long periods of time, making it hard to revisit. In this paper, we consider the use of analytic provenance mechanisms to aid experts recall and keep track of trade-off analysis. We implemented VisProm, a web-based trade-off analysis system, that incorporates in-visualization provenance views, designed to help experts keep track of trade-offs and their objectives. We used VisProm as a technology probe to understand user needs and explore the potential role of provenance in this context. Through observation sessions with three groups of experts analyzing their own data, we make the following contributions. We first, identify eight high-level tasks that experts engaged in during trade-off analysis, such as locating and characterizing interest zones in the trade-off space, and show how these tasks can be supported by provenance visualization. Second, we refine findings from previous work on provenance purposes such as recall and reproduce, by identifying specific objects of these purposes related to trade-off analysis, such as interest zones, and exploration structure (e.g., exploration of alternatives and branches). Third, we discuss insights on how the identified provenance objects and our designs support these trade-off analysis tasks, both when revisiting past analysis and while actively exploring. And finally, we identify new opportunities for provenance-driven trade-off analysis, for example related to monitoring the coverage of the trade-off space, and tracking alternative trade-off scenarios.
PubMed: 35507619
DOI: 10.1109/TVCG.2022.3171074 -
Journal of Medical Internet Research Feb 2023Wearable devices have limited ability to store and process such data. Currently, individual users or data aggregators are unable to monetize or contribute such data to...
BACKGROUND
Wearable devices have limited ability to store and process such data. Currently, individual users or data aggregators are unable to monetize or contribute such data to wider analytics use cases. When combined with clinical health data, such data can improve the predictive power of data-driven analytics and can proffer many benefits to improve the quality of care. We propose and provide a marketplace mechanism to make these data available while benefiting data providers.
OBJECTIVE
We aimed to propose the concept of a decentralized marketplace for patient-generated health data that can improve provenance, data accuracy, security, and privacy. Using a proof-of-concept prototype with an interplanetary file system (IPFS) and Ethereum smart contracts, we aimed to demonstrate decentralized marketplace functionality with the blockchain. We also aimed to illustrate and demonstrate the benefits of such a marketplace.
METHODS
We used a design science research methodology to define and prototype our decentralized marketplace and used the Ethereum blockchain, solidity smart-contract programming language, the web3.js library, and node.js with the MetaMask application to prototype our system.
RESULTS
We designed and implemented a prototype of a decentralized health care marketplace catering to health data. We used an IPFS to store data, provide an encryption scheme for the data, and provide smart contracts to communicate with users on the Ethereum blockchain. We met the design goals we set out to accomplish in this study.
CONCLUSIONS
A decentralized marketplace for trading patient-generated health data can be created using smart-contract technology and IPFS-based data storage. Such a marketplace can improve quality, availability, and provenance and satisfy data privacy, access, auditability, and security needs for such data when compared with centralized systems.
Topics: Humans; Blockchain; Data Accuracy; Patients; Privacy; Programming Languages
PubMed: 36848185
DOI: 10.2196/42743 -
Briefings in Bioinformatics Mar 2024The 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. 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.
Topics: Humans; Genome; Genomics; Information Dissemination; Software
PubMed: 38555475
DOI: 10.1093/bib/bbae122 -
PloS One 2024This study, conducted in China in November 2020, was aimed at exploring the variations in growth traits among different provenances and families as well as to select...
This study, conducted in China in November 2020, was aimed at exploring the variations in growth traits among different provenances and families as well as to select elite materials of Juglans mandshurica. Thus, seeds of 44 families from six J. mandshurica provenances in Heilongjiang and Jilin provinces were sown in the nursery and then transplanted out in the field. At the age of 5 years, seven growth traits were assessed, and a comprehensive analysis was conducted as well as selection of provenance and families. Analysis of variance revealed statistically significant (P < 0.01) differences in seven growth traits among different provenances and families, thereby justifying the pursuit of further breeding endeavors. The genetic coefficient of variation (GCV) for all traits ranged from 5.44% (branch angle) to 21.95% (tree height) whereas the phenotypic coefficient of variation (PCV) ranged from 13.74% (tapering) to 38.50% (branch number per node), indicating considerable variability across the traits. Further, all the studied traits except stem straightness degree, branch angle and branch number per node, showed high heritability (Tree height, ground diameter, mean crown width and tapering, over 0.7±0.073), indicating that the variation in these traits is primarily driven by genetic factors. Correlation analysis revealed a strong positive correlation (r > 0.8) between tree height and ground diameter (r = 0.86), tree height and mean crown width (r = 0.82), and ground diameter and mean crown width (r = 0.83). This suggests that these relationships can be employed for more precise predictions of the growth and morphological characteristics of trees, as well as the selection of superior materials. There was a strong correlation between temperature factors and growth traits. Based on the comprehensive scores in this study, Sanchazi was selected as elite provenance. Using the top-percentile selection criteria, SC1, SC8, DJC15, and DQ18 were selected as elite families. These selected families exhibit genetic gains of over 10% in tree height, ground diameter and mean crown width, signifying their significant potential in forestry for enhancing timber production and reducing production cycles, thereby contributing to sustainable forest management. In this study, the growth traits of J. mandshurica were found to exhibit stable variation, and there were correlations between these traits. The selected elite provenance and families of J. mandshurica showed faster growth, which is advantageous for the subsequent breeding and promotion of improved J. mandshurica varieties.
Topics: Juglans; Plant Breeding; Trees; Forests; China
PubMed: 38451964
DOI: 10.1371/journal.pone.0298918 -
Heliyon Sep 2022The Cretaceous and Neogene deposits from the Mamfe Basin consisting of sandstone, shale and claystone were studied using petrography, and major, traces and REEs analyses...
The Cretaceous and Neogene deposits from the Mamfe Basin consisting of sandstone, shale and claystone were studied using petrography, and major, traces and REEs analyses to address sediment source, environment setting, prevailing paleoclimate as well as tectonic regime of the basin. The angular to subangular shape of detrital grains reflects the mineralogical and textural immaturity of sediments and the proximity of the sediment supply source. Sedimentary rocks are composed of a significant number of lithic debris, organic matter, ostracods as well as subrounded heavy minerals referring to notable igneous and metamorphic rocks bordering the Mamfe Basin. The plots of major element ratios including iron oxide/potasium oxide (FeO/KO) against silicium oxide/aluminium oxide (SiO/AlO) combined with that of sodium oxide/potassium oxide (NaO/KO) compared to silicium oxide/aluminium oxide (SiO/AlO) are characteristic of greywacke and shale with few arkoses. The pronounced Eu negative anomaly of chondrite normalized REEs along with the plot of La/Th vs Hf and Co/Th vs La/Sc suggest that sediments are in general from felsic and intermediate source rock provenance, only subordinated contribution of mafic source. The negative anomaly of Yb suggests igneous fractionation under highly reducing conditions. The chemical index of alteration values of 47-70 combined with chemical index of weathering values of 0.6-84 suggest low to moderate weathering process of the sediment in the basin. This result is further confirmed by an index of chemical variability values of 0.6-100 and Zr/Sc ratio of 0.06-2.96. The REEs distribution displays a substantial content in LREE, low content in HREE and noticible proportion of (La/Yb) ratio (mean >9), poor (Gd/Yb) ratio in the Cross River Formation (mean <2) and slightly moderate (Gd/Yb) ratio in the other formations (mean >2). This result implies that sediments from the Ngeme, Nfaitok and Baso formations derived from post-Archean rocks. Geochemical paleoenvironmental proxies including Sr/Cu, Sr/Ba, Ga/Rb vs Sr/Cu and SiO vs KO + NaO+AlO are in favor of arid to semi-arid conditions during the deposition. Trace Elemental ratios such as Sr/Cu, Sr/Ba, V/Ni, U/Th, Ni/Co, V/Sc, and V/Cr values indicate a predominance of oxic conditions during deposition. In contrast, some authigenic pyrite, hematite, siderite and vivianite which are iron-rich minerals suggests episodic reducing conditions in the basin. The study provides a valuable information in evaluating sediments source, depositional environment, tectonic regime as well as the paleoclimatic conditions prevailing in the basin during the depositional period. The geochemistry of rocks of the Ngeme and Baso formations suggest passive continental margin setting and Ngeme, Nfaitok and Cross River formations suggest oceanic island Arc tectonic setting.
PubMed: 36097494
DOI: 10.1016/j.heliyon.2022.e10304 -
PloS One 2022To select elite Robinia pseudoacacia L. germplasm resources for production, 13 phenotypes and three physiological indicators of 214 seedlings from 20 provenances were...
To select elite Robinia pseudoacacia L. germplasm resources for production, 13 phenotypes and three physiological indicators of 214 seedlings from 20 provenances were systematically evaluated and analyzed. The leaf phenotypic and physiological coefficients of variation among the genotypes ranged from 3.741% to 19.599% and from 8.260% to 42.363%, respectively. The Kentucky provenance had the largest coefficient of variation (18.541%). The average differentiation coefficients between and within provenances were 34.161% and 38.756%, respectively. These close percentages showed that R. pseudoacacia presented high genetic variation among and within provenances, which can be useful for assisted migration and breeding programs. Furthermore, based on the results of correlations, principal component analysis and cluster analysis, breeding improvements targeting R. pseudoacacia's ornamental value, food value, and stress resistance of were performed. Forty and 30 excellent individuals, accounting for 18.692% and 14.019%, respectively, of the total resources. They were ultimately screened, after comprehensively taking into considering leaf phenotypic traits including compound leaf length, leaflet number and leaflet area and physiological characteristics including proline and soluble protein contents. These selected individuals could provide a base material for improved variety conservation and selection.
Topics: Kentucky; Phenotype; Plant Breeding; Plant Leaves; Robinia; Seedlings
PubMed: 34986177
DOI: 10.1371/journal.pone.0262278 -
Frontiers in Plant Science 2022In this review we summarize the current knowledge about the changes in secondary metabolism induced by biotic/abiotic stressors. It is known that the extreme... (Review)
Review
In this review we summarize the current knowledge about the changes in secondary metabolism induced by biotic/abiotic stressors. It is known that the extreme environmental conditions activate signaling pathways leading to triggering of enzymatic and non-enzymatic defense systems, which stimulate production of secondary metabolites with antioxidant and protective effects. Due to several groups of bioactive compounds including naphthodianthrones, acylphloroglucinols, flavonoids, and phenylpropanes, the world-wide represents a high-value medicinal crop of genus, which belongs to the most diverse genera within flowering plants. The summary of the up-to-date knowledge reveals a relationship between the level of defense-related phenolic compounds and interspecific differences in the stress tolerance. The chlorogenic acid, and flavonoids, namely the amentoflavone, quercetin or kaempferol glycosides have been reported as the most defense-related metabolites associated with plant tolerance against stressful environment including temperature, light, and drought, in association with the biotic stimuli resulting from plant-microbe interactions. As an example, the species-specific cold-induced phenolics profiles of 10 representatives of different provenances cultured are illustrated in the case-study. Principal component analysis revealed a relationship between the level of defense-related phenolic compounds and interspecific differences in the stress tolerance indicating a link between the provenance of species and inherent mechanisms of cold tolerance. The underlying metabolome alterations along with the changes in the activities of ROS-scavenging enzymes, and non-enzymatic physiological markers are discussed. Given these data it can be anticipated that some species native to divergent habitats, with interesting high-value secondary metabolite composition and predicted high tolerance to biotic/abiotic stresses would attract the attention as valuable sources of bioactive compounds for many medicinal purposes.
PubMed: 36531362
DOI: 10.3389/fpls.2022.1042375 -
Journal of Human Evolution Sep 2021The aspects of hominin behavior responsible for Oldowan stone tool variation are the focus of much debate. There is some consensus that this variation arises from a...
The aspects of hominin behavior responsible for Oldowan stone tool variation are the focus of much debate. There is some consensus that this variation arises from a combination of ecological and cultural factors. The diversity of raw material types and technological strategies present at Kanjera South, Kenya, provide an opportunity to examine the interacting influences of ecology and culture on Oldowan stone tool variation. Here, we combine previous analyses of raw material properties, provenance, and technology with quantitative measures of core reduction intensity and tool utilization to examine the influence of both ecological and technocultural factors on stone tool variation at Kanjera South. The results of this analysis reflect a dynamic relationship between raw material properties, provenance, and hominin mobility. Exotic raw materials are generally more resistant to edge attrition compared with those available locally, which may have incentivized their transport over long distances and more extensive reduction. Cores produced on raw materials from distant sources also exhibit more complex core reduction strategies than locally acquired materials. While this pattern is partially due to the differences in the quality of knappable stone, bifacial centripetal and multifacial core reduction strategies also arise due to the continuous transport and use of exotic raw materials. Moreover, the variation in stone tool reduction is not consistent with neutral models of stone tool transport and discard. These results demonstrate that ecological factors such as raw material provenance and physical properties have strong impacts on reduction intensity and the technological strategies used by hominins.
Topics: Animals; Archaeology; Ecology; History, Ancient; Hominidae; Kenya; Technology; Tool Use Behavior
PubMed: 34384939
DOI: 10.1016/j.jhevol.2021.103029 -
IEEE Transactions on Visualization and... Dec 2023Understanding user behavior patterns and visual analysis strategies is a long-standing challenge. Existing approaches rely largely on time-consuming manual processes...
Understanding user behavior patterns and visual analysis strategies is a long-standing challenge. Existing approaches rely largely on time-consuming manual processes such as interviews and the analysis of observational data. While it is technically possible to capture a history of user interactions and application states, it remains difficult to extract and describe analysis strategies based on interaction provenance. In this article, we propose a novel visual approach to the meta-analysis of interaction provenance. We capture single and multiple user sessions as graphs of high-dimensional application states. Our meta-analysis is based on two different types of two-dimensional embeddings of these high-dimensional states: layouts based on (i) topology and (ii) attribute similarity. We applied these visualization approaches to synthetic and real user provenance data captured in two user studies. From our visualizations, we were able to extract patterns for data types and analytical reasoning strategies.
PubMed: 34910635
DOI: 10.1109/TVCG.2021.3135697