Dataset Information

Pofatu, a curated and open-access database for geochemical sourcing of archaeological materials.

ABSTRACT: Compositional analyses have long been used to determine the geological sources of artefacts. Geochemical "fingerprinting" of artefacts and sources is the most effective way to reconstruct strategies of raw material and artefact procurement, exchange or interaction systems, and mobility patterns during prehistory. The efficacy and popularity of geochemical sourcing has led to many projects using various analytical techniques to produce independent datasets. In order to facilitate access to this growing body of data and to promote comparability and reproducibility in provenance studies, we designed Pofatu, the first online and open-access database to present geochemical compositions and contextual information for archaeological sources and artefacts in a form that can be readily accessed by the scientific community. This relational database currently contains 7759 individual samples from archaeological sites and geological sources across the Pacific Islands. Each sample is comprehensively documented and includes elemental and isotopic compositions, detailed archaeological provenance, and supporting analytical metadata, such as sampling processes, analytical procedures, and quality control.

SUBMITTER: Hermann A

PROVIDER: S-EPMC7214434 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Pofatu, a curated and open-access database for geochemical sourcing of archaeological materials.

Hermann Aymeric A Forkel Robert R McAlister Andrew A Cruickshank Arden A Golitko Mark M Kneebone Brendan B McCoy Mark M Reepmeyer Christian C Sheppard Peter P Sinton John J Weisler Marshall M

Scientific data 20200511 1

Compositional analyses have long been used to determine the geological sources of artefacts. Geochemical "fingerprinting" of artefacts and sources is the most effective way to reconstruct strategies of raw material and artefact procurement, exchange or interaction systems, and mobility patterns during prehistory. The efficacy and popularity of geochemical sourcing has led to many projects using various analytical techniques to produce independent datasets. In order to facilitate access to this g ...[more]

PMID: 32393758

Similar Datasets

Project description:Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/.

Project description:BackgroundCardiotocography (CTG) is a monitoring of fetal heart rate and uterine contractions. Since 1960 it is routinely used by obstetricians to assess fetal well-being. Many attempts to introduce methods of automatic signal processing and evaluation have appeared during the last 20 years, however still no significant progress similar to that in the domain of adult heart rate variability, where open access databases are available (e.g. MIT-BIH), is visible. Based on a thorough review of the relevant publications, presented in this paper, the shortcomings of the current state are obvious. A lack of common ground for clinicians and technicians in the field hinders clinically usable progress. Our open access database of digital intrapartum cardiotocographic recordings aims to change that.DescriptionThe intrapartum CTG database consists in total of 552 intrapartum recordings, which were acquired between April 2010 and August 2012 at the obstetrics ward of the University Hospital in Brno, Czech Republic. All recordings were stored in electronic form in the OB TraceVue®;system. The recordings were selected from 9164 intrapartum recordings with clinical as well as technical considerations in mind. All recordings are at most 90 minutes long and start a maximum of 90 minutes before delivery. The time relation of CTG to delivery is known as well as the length of the second stage of labor which does not exceed 30 minutes. The majority of recordings (all but 46 cesarean sections) is - on purpose - from vaginal deliveries. All recordings have available biochemical markers as well as some more general clinical features. Full description of the database and reasoning behind selection of the parameters is presented in the paper.ConclusionA new open-access CTG database is introduced which should give the research community common ground for comparison of results on reasonably large database. We anticipate that after reading the paper, the reader will understand the context of the field from clinical and technical perspectives which will enable him/her to use the database and also understand its limitations.

Project description:While art is omnipresent in human history, the neural mechanisms of how we perceive, value and differentiate art has only begun to be explored. Functional magnetic resonance imaging (fMRI) studies suggested that art acts as secondary reward, involving brain activity in the ventral striatum and prefrontal cortices similar to primary rewards such as food. However, potential similarities or unique characteristics of art-related neuroscience (or neuroesthetics) remain elusive, also because of a lack of adequate experimental tools: the available collections of art stimuli often lack standard image definitions and normative ratings. Therefore, we here provide a large set of well-characterized, novel art images for use as visual stimuli in psychological and neuroimaging research. The stimuli were created using a deep learning algorithm that applied different styles of popular paintings (based on artists such as Klimt or Hundertwasser) on ordinary animal, plant and object images which were drawn from established visual stimuli databases. The novel stimuli represent mundane items with artistic properties with proposed reduced dimensionality and complexity compared to paintings. In total, 2,332 novel stimuli are available open access as "art.pics" database at https://osf.io/BTWNQ/ with standard image characteristics that are comparable to other common visual stimuli material in terms of size, variable color distribution, complexity, intensity and valence, measured by image software analysis and by ratings derived from a human experimental validation study [n = 1,296 (684f), age 30.2 ± 8.8 y.o.]. The experimental validation study further showed that the art.pics elicit a broad and significantly different variation in subjective value ratings (i.e., liking and wanting) as well as in recognizability, arousal and valence across different art styles and categories. Researchers are encouraged to study the perception, processing and valuation of art images based on the art.pics database which also enables real reward remuneration of the rated stimuli (as art prints) and a direct comparison to other rewards from e.g., food or money. Key Messages: We provide an open access, validated and large set of novel stimuli (n = 2,332) of standardized art images including normative rating data to be used for experimental research. Reward remuneration in experimental settings can be easily implemented for the art.pics by e.g., handing out the stimuli to the participants (as print on premium paper or in a digital format), as done in the presented validation task. Experimental validation showed that the art.pics' images elicit a broad and significantly different variation in subjective value ratings (i.e., liking, wanting) across different art styles and categories, while size, color and complexity characteristics remained comparable to other visual stimuli databases.

Project description:The number of genome-wide association studies (GWAS) is growing rapidly leading to the discovery and replication of many new disease loci. Combining results from multiple GWAS datasets may potentially strengthen previous conclusions and suggest new disease loci, pathways or pleiotropic genes. However, no database or centralized resource currently exists that contains anywhere near the full scope of GWAS results.We collected available results from 118 GWAS articles into a database of 56,411 significant SNP-phenotype associations and accompanying information, making this database freely available here. In doing so, we met and describe here a number of challenges to creating an open access database of GWAS results. Through preliminary analyses and characterization of available GWAS, we demonstrate the potential to gain new insights by querying a database across GWAS.Using a genomic bin-based density analysis to search for highly associated regions of the genome, positive control loci (e.g., MHC loci) were detected with high sensitivity. Likewise, an analysis of highly repeated SNPs across GWAS identified replicated loci (e.g., APOE, LPL). At the same time we identified novel, highly suggestive loci for a variety of traits that did not meet genome-wide significant thresholds in prior analyses, in some cases with strong support from the primary medical genetics literature (SLC16A7, CSMD1, OAS1), suggesting these genes merit further study. Additional adjustment for linkage disequilibrium within most regions with a high density of GWAS associations did not materially alter our findings. Having a centralized database with standardized gene annotation also allowed us to examine the representation of functional gene categories (gene ontologies) containing one or more associations among top GWAS results. Genes relating to cell adhesion functions were highly over-represented among significant associations (p < 4.6 x 10(-14)), a finding which was not perturbed by a sensitivity analysis.We provide access to a full gene-annotated GWAS database which could be used for further querying, analyses or integration with other genomic information. We make a number of general observations. Of reported associated SNPs, 40% lie within the boundaries of a RefSeq gene and 68% are within 60 kb of one, indicating a bias toward gene-centricity in the findings. We found considerable heterogeneity in information available from GWAS suggesting the wider community could benefit from standardization and centralization of results reporting.

Dataset Information

Pofatu, a curated and open-access database for geochemical sourcing of archaeological materials.

Publications

Pofatu, a curated and open-access database for geochemical sourcing of archaeological materials.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets