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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Vieira, Márcia; Nabais, Paula; Hidalgo, Rafael Javier Díaz; Melo, Maria J.; +1 Authors

    Abstract The Ajuda Songbook is an exceptional illuminated manuscript being the only surviving codex of Galician-Portuguese secular poetry; it was produced in the end of the thirteenth century, beginning of the fourteenth century. The diversity of colors accentuated by the presence of lapis lazuli blue and brazilwood pink, demonstrates the desire to produce a sumptuous manuscript. Pink is, in this context, a luxury color and its identification attests to one of the earliest known occurrences of brazilwood in artworks. Scientific analysis showed, for the light pinks, a different formulation from that found in fifteenth-century books of hours and from all historical reconstructions of these colors prepared to date. This knowledge was used to further expand a database previously built in our laboratory and applied to the characterization of pink shades in the Ajuda Songbook. Thirteen brazilwood recipes were selected from seven Medieval treatises and reference materials were prepared based on such historical information. Three types of colors were achieved, defined as translucent rose, rose, and red. The translucent rose was obtained from recipes where egg white is used for extraction, and no other additives are present; rose from recipes with calcium carbonate; and red from a wider range of recipes, in which these ingredients are not mentioned. These colors were then prepared as paints, and analytical results were thus compared with data from the light pinks seen in the Ajuda Songbook’s architectural backgrounds. We were able to reproduce the pink very well using infrared spectroscopy, identifying its main ingredients: calcium carbonate as filler; lead white as the pigment that produces light pink; and the binder as a polysaccharide with a fingerprint similar to mesquite gum. For the chromophore color, the application of chemometrics approaches to molecular fluorescence spectra highlighted a high degree of similarity with the paint reconstructions.

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    Collection . 2023
    License: CC BY
    Data sources: Datacite
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    Collection . 2023
    License: CC BY
    Data sources: Datacite
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      Collection . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Welle, Alexander;
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    RADAR
    Dataset . 2023
    Data sources: B2FIND
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    https://doi.org/10.35097/867...
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ RADARarrow_drop_down
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      RADAR
      Dataset . 2023
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      https://doi.org/10.35097/867...
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Abstract Background DNA methylation profiling of circulating cell-free DNA (cfDNA) has rapidly become a promising strategy for biomarker identification and development. The cell-type-specific nature of DNA methylation patterns and the direct relationship between cfDNA and apoptosis can potentially be used non-invasively to predict local alterations. In addition, direct detection of altered DNA methylation patterns performs well as a biomarker. In a previous study, we demonstrated marked DNA methylation alterations in brain tissue from patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE–HS). Results We performed DNA methylation profiling in cfDNA isolated from the serum of MTLE patients and healthy controls using BeadChip arrays followed by systematic bioinformatic analysis including deconvolution analysis and integration with DNase accessibility data sets. Differential cfDNA methylation analysis showed an overrepresentation of gene ontology terms and transcription factors related to central nervous system function and regulation. Deconvolution analysis of the DNA methylation data sets ruled out the possibility that the observed differences were due to changes in the proportional contribution of cortical neurons in cfDNA. Moreover, we found no overrepresentation of neuron- or glia-specific patterns in the described cfDNA methylation patterns. However, the MTLE–HS cfDNA methylation patterns featured a significant overrepresentation of the epileptic DNA methylation alterations previously observed in the hippocampus. Conclusions Our results support the use of cfDNA methylation profiling as a rational approach to seeking non-invasive and reproducible epilepsy biomarkers.

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    Collection . 2023
    License: CC BY
    Data sources: Datacite
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    Collection . 2023
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    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      Collection . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Yang, Xun; Becker, Fabian; Nykamp, Moritz; Schütt, Brigitta;

    The data contains 34 files, including 1 excel file of meta information, 1 R code for data calculation and illustration, 1 excel file of calculated/summarized data, 1 excel file of field description guide, 7 csv files of sediment profile raw data, 7 csv files of simplified data, 7 csv files of sediment unit boundary, 4 csv files of raw elemental components data from pXRF device, and 5 field photos.1. includes the information of event level, study area coverage, parameters.2. is the code used in R studio for calculation and illustration of the sediment parameters. Some values in the code may need to change manually according to the profile characters.3. is the results calculated and summarized from the above-mentioned R code. Simplified sediment parameter data and sediment unit boundary data are used in the code.4. summarizes the classes and details that are used during the field work, including the unit contact, fabric, clast feature, sorting, grain size, textural classification, mottling, concertation, carbonate/gypsum content, beds, erosional/post-depositional structures, soil features, biological modifications and archaeological findings and pH terms.5. includes the raw data of 14 samples from Tek-1 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, and 3 times of low frequency of magnetic susceptibility.6. includes the raw data of 11 samples from Tek-2 with the sampling range (upper and lower boundary), 2 times of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, and 3 times of low frequency of magnetic susceptibility.7. includes the raw data of 19 samples from Tek-3 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, and 3 times of low frequency of magnetic susceptibility.8. includes the raw data of 32 samples from Tek-4-2 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition.9. includes the raw data of 48 samples from Tek-5 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, 7 times of low frequency of magnetic susceptibility measured by MS2B sensor, and the element ratios of Ca/Ti and Zr/Rb.10. includes the raw data of 17 samples from Tek-5-2 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, and the element ratios of Ca/Ti and Zr/Rb.11. includes the raw data of 50 samples from Tek-6 with the sampling range (upper and lower boundary), 2 times of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, 3 times of low frequency of magnetic susceptibility (only 41 samples), and the element ratios of Ca/Ti and Zr/Rb.12-18 files are the simplified data which are calculated from the raw data according to the corresponding equations.19-25 files are the sediment unit boundary based on the sediment features.26. is the raw data of sediment profile of Tek-5 exported from a portable energy-dispersive X-ray fluorescence spectrometer (p-ED-XRF; Thermo Fisher Scientific NITON XL3t) in the manufacture's "Mining Cu/Zn" mode with main, high, low, and light filters (50, 50, 15/20, and 8 kV, respectively) in a total of 120 seconds. A certified reference material (LKSD‐4) {Lynch, 1990 #1283} and an acid-purified silica sand were measured regularly to ensure the measurement quality.27. is the raw data of sediment profile of Tek-5-2 exported from the same p-ED-XRF device (Thermo Fisher Scientific NITON XL3t).28. is the raw data of sediment profile of Tek-6 exported from the same p-ED-XRF device (Thermo Fisher Scientific NITON XL3t).29. is the raw data of reference samples (a certified reference material (LKSD‐4, rf-2) {Lynch, 1990 #1283} and an acid-purified silica sand, si) exported from the same p-ED-XRF device (Thermo Fisher Scientific NITON XL3t).30-34 files are the 5 field photos from Tek-4, Tek-4-2, Tek-5, Tek-5-2 and Tek-6. The data support the interpretation of varying sediment facies and the reconstruction of the Mid-Late Holocene alluvial dynamics on the Tekkedere valley and the alluvial fan in the micro-region of an ancient city Pergamon, west Turkey (Yang et al. 2023). This dataset of sediment analyses was collected through the field work and laboratory measurements in the Bergama excavation house in 2019–2020. It comprises the geochemical and element composition of the sediment samples from seven sediment sequences (Tek-1, Tek-2, Tek-3, Tek-4-2, Tek-5, Tek-5-2 and Tek-6). Bulk geochemical sediment analyses include pH and electrical conductivity (EC) by a TDS/EC/pH/TEMP meter, mass magnetic susceptibility of low frequency (XLF) by Bartington magnetic susceptibility system (MS2B or MS3 sensor), and loss on ignition on 550 °C (LOI550) by temperature-controlled furnace. The element composition was analyzed using the p-XRF device. The data of sediment samples were recorded in Excel, calculated and illustrated in R software (version 3.6) (R Core Team, 2020) and imported into Inkscape software. The sample's depth is simplified by its middle depth. For the XLF measurement, the confidence intervals of the median are estimated by simple quantile bootstrapping (B = 1,000) in R. The sediment parameters of each sediment unit in this study are summarized in median and median absolute deviation (MAD, in brackets) which was calculated in R and they are descripted into 5 classes using the equal interval classification of the sediment parameters. Besides, we also summarize the sediment description guide during the field work and include the field photos of the sediment profiles from the alluvial fan.

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    PANGAEA
    Dataset . 2023
    Data sources: B2FIND
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      PANGAEA
      Dataset . 2023
      Data sources: B2FIND
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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file. 4. Meth_atlas output. Estimated cell and tissue proportions of contribution for all samples.

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    figshare
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      figshare
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
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      Dataset . 2023
      License: CC BY
      Data sources: Datacite
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    Authors: Machado, Carla; Oujja, Mohamed; Cerqueira Alves, Luís; Martínez-Weinbaum, Marina; +5 Authors

    Abstract Grisaille was the first paint applied on stained-glass panels, used in Europe since the twelfth century. Historical written sources described the use of iron and copper together with a high lead-silica base glass in the grisailles production. This project aims to study the evolution of the grisaille paint composition throughout time and the changes in the raw materials used in their production using non-destructive and non-invasive techniques. To achieve this objective, 23 grisaille samples dated from the 13th to the twentieth centuries from nine different countries (Portugal, Poland, United Kingdom, Sweden, Norway, Belgium, Low Countries, Germany, and France) were studied by means of micro particle-induced X-ray emission (μ-PIXE), micro energy dispersive X-ray fluorescence (μ-EDXRF), laser-induced breakdown spectroscopy (LIBS), laser-induced fluorescence (LIF), non-linear optical microscopy (NLOM) in the modality of multiphoton excitation fluorescence (MPEF) and optical microscopy (OM). The results showed that it was possible to identify compositional differences and patterns throughout the samples when compared with literature results. The preference for using copper in central and south-central European countries and the addition of new compounds (CoO, Cr2O3, MnO) as colouring agents since the nineteenth century was verified. The LIBS analyses allow the identification of boron on two samples, confirming the change of base glass components since the seventeenth century. The NLOM-MPEF showed the capability of this technique to measure the grisaille paint layers’ thickness. This non-invasive multi-analytical and complementary approach proves itself efficient in identifying changes in the grisaille’s composition throughout time, which can be interpreted as changes in the raw materials and manufacture used in the production of these paint materials.

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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file 6. Differentially methylated regions (DMRs) in cfDNA of MTLE patients in comparison with controls.

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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file 2. A Heatmap representation of gene-expression values (nTPM) of the protein-coding genes associated with enriched TF motifs in cfDNA DMRs across CNS tissues, extracted from the HPA. B Heatmap representation of the level of confidence of the protein-coding genes associated with enriched TF motifs in cfDNA DMRs across the brain-related tissue clusters, extracted from the HPA. C Heatmap representation of the level of confidence of the protein-coding genes associated with enriched TF motifs in cfDNA DMRs across the brain-related single-cell clusters, extracted from the HPA.

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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file 1. Individual estimated percentages of contribution of each cell and tissue type from the meth_atlas deconvolution tool for the serum samples analysed (11 CTR and 12 MTLE–HS). A Distribution of all percentages of contributions of individual samples. B Boxplot comparison of the individual estimated proportion of cfDNA for the tissue and cell types within each study group. Vascular endothelial cell percentage contribution was significantly lower in MTLE–HS patients (n=12) than in CTR (n=11) (Wilcoxon test).*p < 0.05; **p < 0.01; ***p < 0.001.

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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file 3 A Heatmap representation of DNA methylation of promoter, gene and CGI-DMRs in hippocampus of MTLE–HS patients compared with the hippocampus of controls. The DNA methylation value of each DMR corresponds to the mean beta value across the single-nucleotide positions encompassed by the DMR. Each individual is annotated with respect to age and sex. B Heatmap representation of DNA methylation of promoter, gene and CGI-DMRs in neocortex of MTLE–HS patients compared with the neocortex of controls. C Heatmap representation of DNA methylation of promoter, gene and CGI-DMRs in NeuN+ fractions from the prefrontal cortex of healthy individuals (GSE112179) compared with blood cells (GSE110555) D Heatmap representation of DNA methylation of promoter, gene, and CGI-DMRs in glial fractions from white matter of healthy individuals (GSE166207) compared with blood cells (GSE110555). E Representation of the overlap between cfDNA DMRs in MTLE–HS and neuron-specific DMRs. The sets of DMRs overlapped separately in relation to the type of DMR (promoter, gene, CGI) and to methylation behaviour (hypermethylated and hypomethylated). Red bars and lines correspond to the overlap of DMRs with coincidence in the direction of change. F. Heatmap matrix representation of the p values associated with the Fisher’s exact test of the overlaps between DMRs in cfDNA and neuron-specific DMRs. G Representation of the overlap between cfDNA DMRs in MTLE–HS glia-specific DMRs. The sets of DMRs overlapped separately in relation to the type of DMR (promoter, gene, CGI) and the methylation behaviour (hypermethylated and hypomethylated). Red bars and lines correspond to the overlap of DMRs with coincidence in the direction of change. H Heatmap matrix representation of the p values associated with the Fisher’s exact test of the overlaps between DMRs in cfDNA and glia-specific DMRs.

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    Authors: Vieira, Márcia; Nabais, Paula; Hidalgo, Rafael Javier Díaz; Melo, Maria J.; +1 Authors

    Abstract The Ajuda Songbook is an exceptional illuminated manuscript being the only surviving codex of Galician-Portuguese secular poetry; it was produced in the end of the thirteenth century, beginning of the fourteenth century. The diversity of colors accentuated by the presence of lapis lazuli blue and brazilwood pink, demonstrates the desire to produce a sumptuous manuscript. Pink is, in this context, a luxury color and its identification attests to one of the earliest known occurrences of brazilwood in artworks. Scientific analysis showed, for the light pinks, a different formulation from that found in fifteenth-century books of hours and from all historical reconstructions of these colors prepared to date. This knowledge was used to further expand a database previously built in our laboratory and applied to the characterization of pink shades in the Ajuda Songbook. Thirteen brazilwood recipes were selected from seven Medieval treatises and reference materials were prepared based on such historical information. Three types of colors were achieved, defined as translucent rose, rose, and red. The translucent rose was obtained from recipes where egg white is used for extraction, and no other additives are present; rose from recipes with calcium carbonate; and red from a wider range of recipes, in which these ingredients are not mentioned. These colors were then prepared as paints, and analytical results were thus compared with data from the light pinks seen in the Ajuda Songbook’s architectural backgrounds. We were able to reproduce the pink very well using infrared spectroscopy, identifying its main ingredients: calcium carbonate as filler; lead white as the pigment that produces light pink; and the binder as a polysaccharide with a fingerprint similar to mesquite gum. For the chromophore color, the application of chemometrics approaches to molecular fluorescence spectra highlighted a high degree of similarity with the paint reconstructions.

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    Authors: Welle, Alexander;
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    RADAR
    Dataset . 2023
    Data sources: B2FIND
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    https://doi.org/10.35097/867...
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      RADAR
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      https://doi.org/10.35097/867...
      Dataset . 2023
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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Abstract Background DNA methylation profiling of circulating cell-free DNA (cfDNA) has rapidly become a promising strategy for biomarker identification and development. The cell-type-specific nature of DNA methylation patterns and the direct relationship between cfDNA and apoptosis can potentially be used non-invasively to predict local alterations. In addition, direct detection of altered DNA methylation patterns performs well as a biomarker. In a previous study, we demonstrated marked DNA methylation alterations in brain tissue from patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE–HS). Results We performed DNA methylation profiling in cfDNA isolated from the serum of MTLE patients and healthy controls using BeadChip arrays followed by systematic bioinformatic analysis including deconvolution analysis and integration with DNase accessibility data sets. Differential cfDNA methylation analysis showed an overrepresentation of gene ontology terms and transcription factors related to central nervous system function and regulation. Deconvolution analysis of the DNA methylation data sets ruled out the possibility that the observed differences were due to changes in the proportional contribution of cortical neurons in cfDNA. Moreover, we found no overrepresentation of neuron- or glia-specific patterns in the described cfDNA methylation patterns. However, the MTLE–HS cfDNA methylation patterns featured a significant overrepresentation of the epileptic DNA methylation alterations previously observed in the hippocampus. Conclusions Our results support the use of cfDNA methylation profiling as a rational approach to seeking non-invasive and reproducible epilepsy biomarkers.

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    Authors: Yang, Xun; Becker, Fabian; Nykamp, Moritz; Schütt, Brigitta;

    The data contains 34 files, including 1 excel file of meta information, 1 R code for data calculation and illustration, 1 excel file of calculated/summarized data, 1 excel file of field description guide, 7 csv files of sediment profile raw data, 7 csv files of simplified data, 7 csv files of sediment unit boundary, 4 csv files of raw elemental components data from pXRF device, and 5 field photos.1. includes the information of event level, study area coverage, parameters.2. is the code used in R studio for calculation and illustration of the sediment parameters. Some values in the code may need to change manually according to the profile characters.3. is the results calculated and summarized from the above-mentioned R code. Simplified sediment parameter data and sediment unit boundary data are used in the code.4. summarizes the classes and details that are used during the field work, including the unit contact, fabric, clast feature, sorting, grain size, textural classification, mottling, concertation, carbonate/gypsum content, beds, erosional/post-depositional structures, soil features, biological modifications and archaeological findings and pH terms.5. includes the raw data of 14 samples from Tek-1 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, and 3 times of low frequency of magnetic susceptibility.6. includes the raw data of 11 samples from Tek-2 with the sampling range (upper and lower boundary), 2 times of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, and 3 times of low frequency of magnetic susceptibility.7. includes the raw data of 19 samples from Tek-3 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, and 3 times of low frequency of magnetic susceptibility.8. includes the raw data of 32 samples from Tek-4-2 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition.9. includes the raw data of 48 samples from Tek-5 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, 7 times of low frequency of magnetic susceptibility measured by MS2B sensor, and the element ratios of Ca/Ti and Zr/Rb.10. includes the raw data of 17 samples from Tek-5-2 with the sampling range (upper and lower boundary), 1 time of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, and the element ratios of Ca/Ti and Zr/Rb.11. includes the raw data of 50 samples from Tek-6 with the sampling range (upper and lower boundary), 2 times of pH, 2 times of electrical conductivity (EC, us cm-1), the measurement weight of loss on ignition, 3 times of low frequency of magnetic susceptibility (only 41 samples), and the element ratios of Ca/Ti and Zr/Rb.12-18 files are the simplified data which are calculated from the raw data according to the corresponding equations.19-25 files are the sediment unit boundary based on the sediment features.26. is the raw data of sediment profile of Tek-5 exported from a portable energy-dispersive X-ray fluorescence spectrometer (p-ED-XRF; Thermo Fisher Scientific NITON XL3t) in the manufacture's "Mining Cu/Zn" mode with main, high, low, and light filters (50, 50, 15/20, and 8 kV, respectively) in a total of 120 seconds. A certified reference material (LKSD‐4) {Lynch, 1990 #1283} and an acid-purified silica sand were measured regularly to ensure the measurement quality.27. is the raw data of sediment profile of Tek-5-2 exported from the same p-ED-XRF device (Thermo Fisher Scientific NITON XL3t).28. is the raw data of sediment profile of Tek-6 exported from the same p-ED-XRF device (Thermo Fisher Scientific NITON XL3t).29. is the raw data of reference samples (a certified reference material (LKSD‐4, rf-2) {Lynch, 1990 #1283} and an acid-purified silica sand, si) exported from the same p-ED-XRF device (Thermo Fisher Scientific NITON XL3t).30-34 files are the 5 field photos from Tek-4, Tek-4-2, Tek-5, Tek-5-2 and Tek-6. The data support the interpretation of varying sediment facies and the reconstruction of the Mid-Late Holocene alluvial dynamics on the Tekkedere valley and the alluvial fan in the micro-region of an ancient city Pergamon, west Turkey (Yang et al. 2023). This dataset of sediment analyses was collected through the field work and laboratory measurements in the Bergama excavation house in 2019–2020. It comprises the geochemical and element composition of the sediment samples from seven sediment sequences (Tek-1, Tek-2, Tek-3, Tek-4-2, Tek-5, Tek-5-2 and Tek-6). Bulk geochemical sediment analyses include pH and electrical conductivity (EC) by a TDS/EC/pH/TEMP meter, mass magnetic susceptibility of low frequency (XLF) by Bartington magnetic susceptibility system (MS2B or MS3 sensor), and loss on ignition on 550 °C (LOI550) by temperature-controlled furnace. The element composition was analyzed using the p-XRF device. The data of sediment samples were recorded in Excel, calculated and illustrated in R software (version 3.6) (R Core Team, 2020) and imported into Inkscape software. The sample's depth is simplified by its middle depth. For the XLF measurement, the confidence intervals of the median are estimated by simple quantile bootstrapping (B = 1,000) in R. The sediment parameters of each sediment unit in this study are summarized in median and median absolute deviation (MAD, in brackets) which was calculated in R and they are descripted into 5 classes using the equal interval classification of the sediment parameters. Besides, we also summarize the sediment description guide during the field work and include the field photos of the sediment profiles from the alluvial fan.

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    PANGAEA
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      PANGAEA
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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file. 4. Meth_atlas output. Estimated cell and tissue proportions of contribution for all samples.

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    Authors: Machado, Carla; Oujja, Mohamed; Cerqueira Alves, Luís; Martínez-Weinbaum, Marina; +5 Authors

    Abstract Grisaille was the first paint applied on stained-glass panels, used in Europe since the twelfth century. Historical written sources described the use of iron and copper together with a high lead-silica base glass in the grisailles production. This project aims to study the evolution of the grisaille paint composition throughout time and the changes in the raw materials used in their production using non-destructive and non-invasive techniques. To achieve this objective, 23 grisaille samples dated from the 13th to the twentieth centuries from nine different countries (Portugal, Poland, United Kingdom, Sweden, Norway, Belgium, Low Countries, Germany, and France) were studied by means of micro particle-induced X-ray emission (μ-PIXE), micro energy dispersive X-ray fluorescence (μ-EDXRF), laser-induced breakdown spectroscopy (LIBS), laser-induced fluorescence (LIF), non-linear optical microscopy (NLOM) in the modality of multiphoton excitation fluorescence (MPEF) and optical microscopy (OM). The results showed that it was possible to identify compositional differences and patterns throughout the samples when compared with literature results. The preference for using copper in central and south-central European countries and the addition of new compounds (CoO, Cr2O3, MnO) as colouring agents since the nineteenth century was verified. The LIBS analyses allow the identification of boron on two samples, confirming the change of base glass components since the seventeenth century. The NLOM-MPEF showed the capability of this technique to measure the grisaille paint layers’ thickness. This non-invasive multi-analytical and complementary approach proves itself efficient in identifying changes in the grisaille’s composition throughout time, which can be interpreted as changes in the raw materials and manufacture used in the production of these paint materials.

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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file 6. Differentially methylated regions (DMRs) in cfDNA of MTLE patients in comparison with controls.

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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file 2. A Heatmap representation of gene-expression values (nTPM) of the protein-coding genes associated with enriched TF motifs in cfDNA DMRs across CNS tissues, extracted from the HPA. B Heatmap representation of the level of confidence of the protein-coding genes associated with enriched TF motifs in cfDNA DMRs across the brain-related tissue clusters, extracted from the HPA. C Heatmap representation of the level of confidence of the protein-coding genes associated with enriched TF motifs in cfDNA DMRs across the brain-related single-cell clusters, extracted from the HPA.

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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file 1. Individual estimated percentages of contribution of each cell and tissue type from the meth_atlas deconvolution tool for the serum samples analysed (11 CTR and 12 MTLE–HS). A Distribution of all percentages of contributions of individual samples. B Boxplot comparison of the individual estimated proportion of cfDNA for the tissue and cell types within each study group. Vascular endothelial cell percentage contribution was significantly lower in MTLE–HS patients (n=12) than in CTR (n=11) (Wilcoxon test).*p < 0.05; **p < 0.01; ***p < 0.001.

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    Authors: Martins-Ferreira, Ricardo; Leal, Bárbara; Chaves, João; Ciudad, Laura; +4 Authors

    Additional file 3 A Heatmap representation of DNA methylation of promoter, gene and CGI-DMRs in hippocampus of MTLE–HS patients compared with the hippocampus of controls. The DNA methylation value of each DMR corresponds to the mean beta value across the single-nucleotide positions encompassed by the DMR. Each individual is annotated with respect to age and sex. B Heatmap representation of DNA methylation of promoter, gene and CGI-DMRs in neocortex of MTLE–HS patients compared with the neocortex of controls. C Heatmap representation of DNA methylation of promoter, gene and CGI-DMRs in NeuN+ fractions from the prefrontal cortex of healthy individuals (GSE112179) compared with blood cells (GSE110555) D Heatmap representation of DNA methylation of promoter, gene, and CGI-DMRs in glial fractions from white matter of healthy individuals (GSE166207) compared with blood cells (GSE110555). E Representation of the overlap between cfDNA DMRs in MTLE–HS and neuron-specific DMRs. The sets of DMRs overlapped separately in relation to the type of DMR (promoter, gene, CGI) and to methylation behaviour (hypermethylated and hypomethylated). Red bars and lines correspond to the overlap of DMRs with coincidence in the direction of change. F. Heatmap matrix representation of the p values associated with the Fisher’s exact test of the overlaps between DMRs in cfDNA and neuron-specific DMRs. G Representation of the overlap between cfDNA DMRs in MTLE–HS glia-specific DMRs. The sets of DMRs overlapped separately in relation to the type of DMR (promoter, gene, CGI) and the methylation behaviour (hypermethylated and hypomethylated). Red bars and lines correspond to the overlap of DMRs with coincidence in the direction of change. H Heatmap matrix representation of the p values associated with the Fisher’s exact test of the overlaps between DMRs in cfDNA and glia-specific DMRs.

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