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Scientific Data Aug 2022Provenance is information describing the lineage of an object, such as a dataset or biological material. Since these objects can be passed between organizations, each...
Provenance is information describing the lineage of an object, such as a dataset or biological material. Since these objects can be passed between organizations, each organization can document only parts of the objects life cycle. As a result, interconnection of distributed provenance parts forms distributed provenance chains. Dependant on the actual provenance content, complete provenance chains can provide traceability and contribute to reproducibility and FAIRness of research objects. In this paper, we define a lightweight provenance model based on W3C PROV that enables generation of distributed provenance chains in complex, multi-organizational environments. The application of the model is demonstrated with a use case spanning several steps of a real-world research pipeline - starting with the acquisition of a specimen, its processing and storage, histological examination, and the generation/collection of associated data (images, annotations, clinical data), ending with training an AI model for the detection of tumor in the images. The proposed model has become an open conceptual foundation of the currently developed ISO 23494 standard on provenance for biotechnology domain.
PubMed: 35977957
DOI: 10.1038/s41597-022-01537-6 -
Environmental Pollution (Barking, Essex... Nov 2023This study aims to improve the current method of studying potentially toxic elements (PTEs) in urban dust using direct chemical evidence (from dust, rock, and emission...
This study aims to improve the current method of studying potentially toxic elements (PTEs) in urban dust using direct chemical evidence (from dust, rock, and emission source samples) and robust geochemical methods. The provenance of urban dust was determined using rare earth elements (REEs) and geochemical diagrams (V-Ni-Th*10, TiO vs. Zr, and Zr/Ti vs. Nb/Y). The geogenic or anthropogenic source of PTEs was determined using the enrichment factor (EF) and compositional data analysis (CoDA), while a PTE's point emission source was identified using a 3.1*La-1.54*Ce-Zn diagram, mineralogy, and morphology analyses. The spatiotemporal distribution of PTEs was determined using a geographic information system, and their health risk (by inhalation) was estimated using a lung bioaccessibility test and particle size distribution. We collected urban dust (n = 38), rock (n = 4), and zinc concentrate (n = 2) samples and determined PTEs and REEs in a city of 1.25 million inhabitants in central Mexico. Results showed that urban dust derived from the San Miguelito Range. REEs, Sc, and Zr were geogenic, while Mn, Cu, Zn, As, and Pb were anthropogenic. Due to the presente of sphalerite particles, a zinc refinery was identified as the point emission source of Zn, As, and Pb. High concentrations of Zn (5000-20,008 mg/kg), As (120-284 mg/kg), and Pb (350-776 mg/kg) were found in urban dust near the zinc refinery. Additionally, particles of PM (66-84%), PM (13-27%), PM (3-8%), and PM (0-2%) and lung bioaccessibility of Sr (48.5-72.4%), Zn (9.6-28.4%), Cu (10.5-27.0%), Fe (4.5-8.6%), Mn (2.9-9.2%), Cr (38.3%) and Pb (30.6%) demonstrated a latent risk to human health. These approaches improve our understanding of the provenance of urban dust and its PTE emission sources in urban areas.
Topics: Humans; Metals, Heavy; Environmental Monitoring; Dust; Lead; Mexico; Metals, Rare Earth; Cities; Zinc; Risk Assessment
PubMed: 37683756
DOI: 10.1016/j.envpol.2023.122525 -
PloS One 2023The southern third of Africa is unusually rich in copper ore deposits. These were exploited by precolonial populations to manufacture wound-wire bangles, other forms of...
The southern third of Africa is unusually rich in copper ore deposits. These were exploited by precolonial populations to manufacture wound-wire bangles, other forms of jewelry, and large copper ingots that were used as stores of copper or as forms of prestige. Rectangular, fishtail, and croisette ingots dating between the 5th and 20th centuries CE have been found in many locations in the Democratic Republic of the Congo (DRC), Zambia, and Zimbabwe, with isolated finds in Malawi and Mozambique. Molds for casting these ingots have been found mostly in the Central African Copperbelt, but also around the Magondi Belt copper deposits in northern Zimbabwe. For years, scholars have debated whether these ingots were exclusively made in the Copperbelt or if the molds found in Zimbabwe indicate that local copies were produced from Magondi Belt copper ore (Garlake 1970; Bisson 1976). Before the recent application of lead isotopic and chemical methods to provenance copper in central and southern Africa, there was no way to discern between these hypotheses. Rademakers et al. (2019) and Stephens et al. (2020) showed that copper artifacts from southern DRC (mostly from Upemba) and from northwestern Botswana (Tsodilo Hills) match the lead isotope ratios of ores from the Copperbelt. Building upon these previous studies, we present here the first results from a copper provenance project across the southern third of Africa, from the Copperbelt to northern South Africa. We apply lead isotopic analysis (LIA) and chemical analyses to establish the provenance of 29 croisette ingots recovered in Zimbabwe, 2 fishtail and 1 rectangular ingot recovered from sites in Zambia, and an "X" shaped ingot smelted in an experiment in Zambia in the 1970's. Our chemistry and lead isotopic results indicate that 16 of these objects were smelted with copper from the Copperbelt, 16 objects source more specifically to the Kipushi deposit within this geological district, and only one HXR ingot sources to the Magondi Belt in Zimbabwe. Taken together, we clearly illustrate that croisette ingots were traveling significant distances to reach their eventual sites of deposition, and that there was also local production of these objects in Zimbabwe.
Topics: Zambia; Zimbabwe; Copper; Africa, Southern; Botswana
PubMed: 36947492
DOI: 10.1371/journal.pone.0282660 -
Neuroinformatics Jan 2023We present here an online platform for sharing resources underlying publications in neuroscience. It enables authors to easily upload and distribute digital resources,...
We present here an online platform for sharing resources underlying publications in neuroscience. It enables authors to easily upload and distribute digital resources, such as data, code, and notebooks, in a structured and systematic way. Interactivity is a prominent feature of the Live Papers, with features to download, visualise or simulate data, models and results presented in the corresponding publications. The resources are hosted on reliable data storage servers to ensure long term availability and easy accessibility. All data are managed via the EBRAINS Knowledge Graph, thereby helping maintain data provenance, and enabling tight integration with tools and services offered under the EBRAINS ecosystem.
Topics: Ecosystem; Computational Biology; Neurosciences; Information Storage and Retrieval
PubMed: 35986836
DOI: 10.1007/s12021-022-09598-z -
Ecology and Evolution Jul 2021Accurate identification of the botanical components of honey can be used to establish its geographical provenance, while also providing insights into honeybee ( L.) diet...
Accurate identification of the botanical components of honey can be used to establish its geographical provenance, while also providing insights into honeybee ( L.) diet and foraging preferences. DNA metabarcoding has been demonstrated as a robust method to identify plant species from pollen and pollen-based products, including honey. We investigated the use of pollen metabarcoding to identify the floral sources and local foraging preferences of honeybees using 15 honey samples from six bioregions from eastern and western Australia. We used two plant metabarcoding markers, ITS2 and the trnL P6 loop. Both markers combined identified a total of 55 plant families, 67 genera, and 43 species. The trnL P6 loop marker provided significantly higher detection of taxa, detecting an average of 15.6 taxa per sample, compared to 4.6 with ITS2. Most honeys were dominated by and other Myrtaceae species, with a few honeys dominated by (Proteaceae) and Fabaceae. Metabarcoding detected the nominal primary source provided by beekeepers among the top five most abundant taxa for 85% of samples. We found that eastern and western honeys could be clearly differentiated by their floral composition, and clustered into bioregions with the trnL marker. Comparison with previous results obtained from melissopalynology shows that metabarcoding can detect similar numbers of plant families and genera, but provides significantly higher resolution at species level. Our results show that pollen DNA metabarcoding is a powerful and robust method for detecting honey provenance and examining the diet of honeybees. This is particularly relevant for hives foraging on the unique and diverse flora of the Australian continent, with the potential to be used as a novel monitoring tool for honeybee floral resources.
PubMed: 34257922
DOI: 10.1002/ece3.7679 -
Studies in Health Technology and... Nov 2022Medical data describe patient health information, both in healthy and disease conditions. In any case, health institutions need to ask for patient consent in order to...
Medical data describe patient health information, both in healthy and disease conditions. In any case, health institutions need to ask for patient consent in order to provide their services. Patients usually give consent on a one-time basis, for a specific usage. Afterwards, if medical data usage is research, original patient consent does not apply and further consents should be required. On the other hand, provenance of medical data to verify the origin of health procedures is desirable, as digital health is increasing. We propose HIPAMS modular architecture to provide both provenance and dynamic consents for medical data as described in this paper.
Topics: Humans; Informed Consent
PubMed: 36325859
DOI: 10.3233/SHTI220978 -
Metabolites Mar 2021The red meat supply chain is a complex network transferring product from producers to consumers in a safe and secure way. There can be times when fragmentation can arise... (Review)
Review
The red meat supply chain is a complex network transferring product from producers to consumers in a safe and secure way. There can be times when fragmentation can arise within the supply chain, which could be exploited. This risk needs reduction so that meat products enter the market with the desired attributes. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) is a novel ambient mass spectrometry technique originally developed for rapid and accurate classification of biological tissue which is now being considered for use in a range of additional applications. It has subsequently shown promise for a range of food provenance, quality and safety applications with its ability to conduct ex vivo and in situ analysis. These are regarded as critical characteristics for technologies which can enable real-time decision making in meat processing plants and more broadly throughout the sector. This review presents an overview of the REIMS technology, and its application to the areas of provenance, quality and safety to the red meat industry, particularly in an Australian context.
PubMed: 33804276
DOI: 10.3390/metabo11030171 -
PLoS Computational Biology Aug 2021For many biological systems, a variety of simulation models exist. A new simulation model is rarely developed from scratch, but rather revises and extends an existing...
For many biological systems, a variety of simulation models exist. A new simulation model is rarely developed from scratch, but rather revises and extends an existing one. A key challenge, however, is to decide which model might be an appropriate starting point for a particular problem and why. To answer this question, we need to identify entities and activities that contributed to the development of a simulation model. Therefore, we exploit the provenance data model, PROV-DM, of the World Wide Web Consortium and, building on previous work, continue developing a PROV ontology for simulation studies. Based on a case study of 19 Wnt/β-catenin signaling models, we identify crucial entities and activities as well as useful metadata to both capture the provenance information from individual simulation studies and relate these forming a family of models. The approach is implemented in WebProv, a web application for inserting and querying provenance information. Our specialization of PROV-DM contains the entities Research Question, Assumption, Requirement, Qualitative Model, Simulation Model, Simulation Experiment, Simulation Data, and Wet-lab Data as well as activities referring to building, calibrating, validating, and analyzing a simulation model. We show that most Wnt simulation models are connected to other Wnt models by using (parts of) these models. However, the overlap, especially regarding the Wet-lab Data used for calibration or validation of the models is small. Making these aspects of developing a model explicit and queryable is an important step for assessing and reusing simulation models more effectively. Exposing this information helps to integrate a new simulation model within a family of existing ones and may lead to the development of more robust and valid simulation models. We hope that our approach becomes part of a standardization effort and that modelers adopt the benefits of provenance when considering or creating simulation models.
Topics: Animals; Biochemical Phenomena; Computational Biology; Computer Graphics; Computer Simulation; Humans; Models, Biological; Software; Systems Biology; Wnt Signaling Pathway
PubMed: 34351901
DOI: 10.1371/journal.pcbi.1009227 -
IEEE Transactions on Visualization and... Jun 2024The study of cultural artifact provenance, tracing ownership and preservation, holds significant importance in archaeology and art history. Modern technology has...
The study of cultural artifact provenance, tracing ownership and preservation, holds significant importance in archaeology and art history. Modern technology has advanced this field, yet challenges persist, including recognizing evidence from diverse sources, integrating sociocultural context, and enhancing interactive automation for comprehensive provenance analysis. In collaboration with art historians, we examined the handscroll, a traditional Chinese painting form that provides a rich source of historical data and a unique opportunity to explore history through cultural artifacts. We present a three-tiered methodology encompassing artifact, contextual, and provenance levels, designed to create a "Biography" for handscroll. Our approach incorporates the application of image processing techniques and language models to extract, validate, and augment elements within handscroll using various cultural heritage databases. To facilitate efficient analysis of non-contiguous extracted elements, we have developed a distinctive layout. Additionally, we introduce ScrollTimes, a visual analysis system tailored to support the three-tiered analysis of handscroll, allowing art historians to interactively create biographies tailored to their interests. Validated through case studies and expert interviews, our approach offers a window into history, fostering a holistic understanding of handscroll provenance and historical significance.
PubMed: 38625782
DOI: 10.1109/TVCG.2024.3388523 -
Global Change Biology Nov 2022Climate change is altering temperature and precipitation, resulting in widespread plant mortality and shifts in plant distributions. Plants growing in soil types with...
Climate change is altering temperature and precipitation, resulting in widespread plant mortality and shifts in plant distributions. Plants growing in soil types with low water holding capacity may experience intensified effects of reduced water availability as a result of climate change. Furthermore, complex biotic interactions between plants and soil organisms may mitigate or exacerbate the effects of climate change. This 3-year field experiment observed the performance of Bouteloua gracilis ecotypes that were transplanted across an environmental gradient with either sympatric soil from the seed source location or allopatric soil from the location that plants were transplanted into. We also inoculated plants with either sympatric or allopatric soil biotic communities to test: (1) how changes in climate alone influence plant growth, (2) how soil types interact with climate to influence plant growth, and (3) the role of soil biota in mitigating plant migration to novel environments. As expected, plants moved to cooler-wetter sites exhibited enhanced growth; however, plants moved to warmer-drier sites responded variably depending on the provenance of their soil and inoculum. Soil and inoculum provenance had little influence on the performance of plants moved to cooler-wetter sites, but at warmer-drier sites they were important predictors of plant biomass, seed set, and specific leaf area. Specifically, transplants inoculated with their sympatric soil biota and grown in their sympatric soil were as large as or larger than reference plants grown at the seed source locations; however, individuals inoculated with allopatric soil biota were smaller than reference site individuals at warmer, drier sites. These findings demonstrate complicated plant responses to various aspects of environmental novelty where communities of soil organisms may help ameliorate stress. The belowground microbiome of plants should be considered to predict the responses of vegetation more accurately to climate change.
Topics: Biota; Climate Change; Humans; Plants; Poaceae; Soil; Water
PubMed: 36038989
DOI: 10.1111/gcb.16369