cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4732645
title: Supplementary datasets "The largest plagiogranite on Earth formed by re-melting of juvenile proto-continental crust"

description: Supplementary datasets for the recently accepted paper in <em>Communications Earth & Environment </em> <strong>"The largest plagiogranite on Earth formed by re-melting of juvenile proto-continental crust"</strong>
DOI: 10.6084/m9.figshare.14526201.v1
title: Additional file 1 of SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

description: Additional file 1. Figure S1: Expected vs. Actual ERCC concentration. SPEAQeasy produces plots for each sample, for easy visual comparison of expected ERCC transcript abundance with the kallisto-measured concentration.
DOI: 10.6084/m9.figshare.14526204.v1
title: Additional file 2 of SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

description: Additional file 2: Figure S2: SPEAQeasy logs tracing computational steps by sample. To aid transparency and greatly simplify the source of execution errors, SPEAQeasy automatically generates logs with several pieces of information for every sample. In order of submission, the name of each Nextflow process is printed, along with (1) the working directory: where all relevant files are present, (2) the exit code: a standard indication of whether the process succeeded or how it failed, (3) a list of the specific commands run during the given process. Above is a snapshot of the top of an example log
DOI: 10.6084/m9.figshare.14526207.v1
title: Additional file 3 of SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

description: Additional file 3: Table S1. Available configuration profiles. Configuration files exist under the SPEAQeasy/conf directory. Configuration profiles exist for SGE and SLURM clusters, as well as local execution on a Linux machine. These profiles can be customized for specific clusters, such as the JHPCE configuration file jhpce.config, which runs on an SGE cluster. The file a user chooses also depends on whether software dependencies are managed with docker, or are installed locally. Table S2. SPEAQeasy output files. Table of intermediary outputs generated by SPEAQeasy. These do not include the major output files of interest (Fig. 2), but other miscellaneous outputs from each processing step. In the Filename column, brackets denote one or more values dependent on a relevant variable; for example, the files [sample_name]_process_trace.log refer to a set of several files, each named distinctly according to the sample associated with the particular file. An asterisk represents a wildcard matching more than one file, when individual file names may depend on the experiment. For example, [sample_name]_trimmed*.fastq could refer to sample1_trimmed_1.fastq and sample1_trimmed_2.fastq. The next columns provide the directory containing each given file, relative to the output folder, and a description of the files’ content, respectively. Table S3. Quality metrics recorded in SPEAQeasy outputs. One of the major pipeline outputs is a comma-separated values (CSV) file where fields (columns) are different quality metrics, and each line (row) is associated with one sample. A list of the exact field names and their descriptions is given above. Table S4. SPEAQeasy-example differential expression and gene ontology results. (A) Differential expression results using the subset of BipSeq data analyzed in http://research.libd.org/SPEAQeasy-example/ . (B) Gene ontology enrichment results from the genes with a p-value
DOI: 10.6084/m9.figshare.14526207
title: Additional file 3 of SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

description: Additional file 3: Table S1. Available configuration profiles. Configuration files exist under the SPEAQeasy/conf directory. Configuration profiles exist for SGE and SLURM clusters, as well as local execution on a Linux machine. These profiles can be customized for specific clusters, such as the JHPCE configuration file jhpce.config, which runs on an SGE cluster. The file a user chooses also depends on whether software dependencies are managed with docker, or are installed locally. Table S2. SPEAQeasy output files. Table of intermediary outputs generated by SPEAQeasy. These do not include the major output files of interest (Fig. 2), but other miscellaneous outputs from each processing step. In the Filename column, brackets denote one or more values dependent on a relevant variable; for example, the files [sample_name]_process_trace.log refer to a set of several files, each named distinctly according to the sample associated with the particular file. An asterisk represents a wildcard matching more than one file, when individual file names may depend on the experiment. For example, [sample_name]_trimmed*.fastq could refer to sample1_trimmed_1.fastq and sample1_trimmed_2.fastq. The next columns provide the directory containing each given file, relative to the output folder, and a description of the files’ content, respectively. Table S3. Quality metrics recorded in SPEAQeasy outputs. One of the major pipeline outputs is a comma-separated values (CSV) file where fields (columns) are different quality metrics, and each line (row) is associated with one sample. A list of the exact field names and their descriptions is given above. Table S4. SPEAQeasy-example differential expression and gene ontology results. (A) Differential expression results using the subset of BipSeq data analyzed in http://research.libd.org/SPEAQeasy-example/ . (B) Gene ontology enrichment results from the genes with a p-value
DOI: 10.6084/m9.figshare.14526204
title: Additional file 2 of SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

description: Additional file 2: Figure S2: SPEAQeasy logs tracing computational steps by sample. To aid transparency and greatly simplify the source of execution errors, SPEAQeasy automatically generates logs with several pieces of information for every sample. In order of submission, the name of each Nextflow process is printed, along with (1) the working directory: where all relevant files are present, (2) the exit code: a standard indication of whether the process succeeded or how it failed, (3) a list of the specific commands run during the given process. Above is a snapshot of the top of an example log
DOI: 10.6084/m9.figshare.14526201
title: Additional file 1 of SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

description: Additional file 1. Figure S1: Expected vs. Actual ERCC concentration. SPEAQeasy produces plots for each sample, for easy visual comparison of expected ERCC transcript abundance with the kallisto-measured concentration.
DOI: 10.5281/zenodo.4732665
title: Dataset of the Paper "System and Software Processes in Practice: Insights from Chinese Industry"

description: This is the dataset of the paper: "System and Software Processes in Practice: Insights from Chinese Industry".
DOI: 10.5281/zenodo.4726379
title: Dataset of the Paper "System and Software Processes in Practice: Insights from Chinese Industry"

description: This is the dataset of the paper: "System and Software Processes in Practice: Insights from Chinese Industry".
DOI: 10.5281/zenodo.4732670
title: Dataset of the Paper "System and Software Processes in Practice: Insights from Chinese Industry"

description: This is the dataset of the paper: "System and Software Processes in Practice: Insights from Chinese Industry".
DOI: 10.5281/zenodo.4732669
title: Dataset of the Paper "System and Software Processes in Practice: Insights from Chinese Industry"

description: This is the dataset of the paper: "System and Software Processes in Practice: Insights from Chinese Industry".
DOI: 10.5286/isis.e.rb1920024-1
title: Neutron Diffraction Studies of Metal-Organic Frameworks for Hydrocarbon Separations

description: The research of porous metal-organic frameworks (MOFs) is receiving considerable attention owing to their potential for gas adsorption and separation. In particular, separation of light hydrocarbons is a highly challenging and energy-intensive industrial process. We seek to develop highly robust MOF materials as efficient hydrocarbon separation systems and request 3 days on WISH to study the preferred binding sites of adsorbed hydrocarbon molecules (C2D2/C2D4/C2D6/C3D6/C3D8) within a recently developed MOF, MFM-520. This proposed study will investigate the precise locations of light hydrocarbon molecules, defining the preferred orientation of molecules with respect to the binding sites in MFM-520. MFM-520 exhibits exceptionally high separation capacity for C2H2/C2H4/C2H6 and C3H6/C3H8 at ambient conditions with fully repeatable cycles.
DOI: 10.6084/m9.figshare.14526622
title: Development and validation of liquid chromatography-tandem mass spectrometry method for screening six selective androgen receptor modulators in dietary supplements

description: Selective androgen receptor modulators (SARMs) are compounds with specific androgenic properties that have been investigated for the treatment of conditions such as muscle wasting disease. The reported androgenic properties have resulted in their use by athletes, and consequently they have been on the World Anti–Doping Agency prohibited list for more than a decade. To minimise the chance of an unattended positive doping test and to avoid potential serious health problems, adequate screening methods for the detection of a wide range of SARMs in these supplements is necessary. In this study, a rapid and accurate liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated simultaneously to screen and quantify six SARMs in dietary supplements, with confirmation by liquid chromatography-quadrupole-time of flight mass spectrometry (LC-Q-TOF/MS). The validated method was applied to 60 dietary supplements obtained by on-line and direct purchase from international vendors in 2020. Various SARMs were detected at high concentrations in 20 products which were advertised as having androgenic properties. For example, andarine was present at 7.2% in one product, and GW501516 was found at 3.49% in the another product. Furthermore, MK-677 and YK-11, not disclosed on the label, were detected in some products. YK-11 is easily hydrolysed in just a few hours. Although YK-11 is particularly unstable, such that the protonated ion [M + H]<sup>+</sup> at m/z 431 for YK-11 was not detected, mass fragmentation, and a [M+ Na]<sup>+</sup> ion at m/z 453.3 confirmed the presence of YK-11. Additionally, hydrolysed YK-11 under acidic conditions was confirmed by NMR spectral data, and <sup>1</sup>H NMR and <sup>13</sup>C NMR spectral data for YK-11 were in good agreement with literature data. This rapid and accurate LC-MS/MS method can therefore be successfully applied to screen and identify SARMs for the continuous control and supervision of dietary supplements.
DOI: 10.6084/m9.figshare.14526622.v1
title: Development and validation of liquid chromatography-tandem mass spectrometry method for screening six selective androgen receptor modulators in dietary supplements

description: Selective androgen receptor modulators (SARMs) are compounds with specific androgenic properties that have been investigated for the treatment of conditions such as muscle wasting disease. The reported androgenic properties have resulted in their use by athletes, and consequently they have been on the World Anti–Doping Agency prohibited list for more than a decade. To minimise the chance of an unattended positive doping test and to avoid potential serious health problems, adequate screening methods for the detection of a wide range of SARMs in these supplements is necessary. In this study, a rapid and accurate liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated simultaneously to screen and quantify six SARMs in dietary supplements, with confirmation by liquid chromatography-quadrupole-time of flight mass spectrometry (LC-Q-TOF/MS). The validated method was applied to 60 dietary supplements obtained by on-line and direct purchase from international vendors in 2020. Various SARMs were detected at high concentrations in 20 products which were advertised as having androgenic properties. For example, andarine was present at 7.2% in one product, and GW501516 was found at 3.49% in the another product. Furthermore, MK-677 and YK-11, not disclosed on the label, were detected in some products. YK-11 is easily hydrolysed in just a few hours. Although YK-11 is particularly unstable, such that the protonated ion [M + H]<sup>+</sup> at m/z 431 for YK-11 was not detected, mass fragmentation, and a [M+ Na]<sup>+</sup> ion at m/z 453.3 confirmed the presence of YK-11. Additionally, hydrolysed YK-11 under acidic conditions was confirmed by NMR spectral data, and <sup>1</sup>H NMR and <sup>13</sup>C NMR spectral data for YK-11 were in good agreement with literature data. This rapid and accurate LC-MS/MS method can therefore be successfully applied to screen and identify SARMs for the continuous control and supervision of dietary supplements.
DOI: 10.6084/m9.figshare.14526609
title: finite element mesh

description: The finite element mesh in ascii format for the Cascadia model and a sample Fortran code to read the mesh<br>
DOI: 10.6084/m9.figshare.14526609.v1
title: finite element mesh

description: The finite element mesh in ascii format for the Cascadia model<br>
DOI: 10.6084/m9.figshare.14526630.v1
title: Development of analytical protocol for the investigation of transformation products of pre-harvest fungicides in fruits using LC-MS/MS methods

description: Chemical protection of plants is critical to permit all-year-long availability of plant products. These chemical agents are transformed both biotically and abiotically after spraying. Our purpose was to develop a workflow which is suitable to investigate those transformation products from plant matrices. Two field trials were set up in two years in two different plant matrices (apples, cherries) to develop a workflow to map the transformation products (TP) of three selected pre-harvest fungicides (boscalid, fluopyram, pyraclostrobin) in the fruits. Modified QuEChERS extraction method was applied for the extraction of TPs from the fruit matrices. We used liquid chromatograph-mass spectrometers to identify and confirm the transformation products of fungicides. LC-QTOF-MS method was suitable to map the key fragmentation routes of parent fungicides. Based on fragmentation pathways, MRM (multiple-reaction monitoring) transitions of fungicide-metabolites mentioned in the literature were predicted. HPLC-QTRAP-MS in target mode was successfully applied to monitor trace level of metabolites and in some cases their isomers. For confirmation of the identified metabolites, LC-QTOF-MS was used. Five earlier-documented as well as one novel transformation product (deschloro-FLP) were found in the investigated fruit samples, the latter has not been reported in plant matrices so far. Area-normalisation method was used to follow the relative concentration of the transformation products in the fruits as a function of time.
DOI: 10.6084/m9.figshare.14526630
title: Development of analytical protocol for the investigation of transformation products of pre-harvest fungicides in fruits using LC-MS/MS methods

description: Chemical protection of plants is critical to permit all-year-long availability of plant products. These chemical agents are transformed both biotically and abiotically after spraying. Our purpose was to develop a workflow which is suitable to investigate those transformation products from plant matrices. Two field trials were set up in two years in two different plant matrices (apples, cherries) to develop a workflow to map the transformation products (TP) of three selected pre-harvest fungicides (boscalid, fluopyram, pyraclostrobin) in the fruits. Modified QuEChERS extraction method was applied for the extraction of TPs from the fruit matrices. We used liquid chromatograph-mass spectrometers to identify and confirm the transformation products of fungicides. LC-QTOF-MS method was suitable to map the key fragmentation routes of parent fungicides. Based on fragmentation pathways, MRM (multiple-reaction monitoring) transitions of fungicide-metabolites mentioned in the literature were predicted. HPLC-QTRAP-MS in target mode was successfully applied to monitor trace level of metabolites and in some cases their isomers. For confirmation of the identified metabolites, LC-QTOF-MS was used. Five earlier-documented as well as one novel transformation product (deschloro-FLP) were found in the investigated fruit samples, the latter has not been reported in plant matrices so far. Area-normalisation method was used to follow the relative concentration of the transformation products in the fruits as a function of time.
DOI: 10.26302/sshade/experiment_lb_20170731_002
title: MIR absorbance spectra of pressed QUE99177 matrix grains (CR Chondrite) under vacuum at different temperatures

description: Raw and normalized (baseline-corrected) MIR absorbance spectra of several matrix grains of QUE99177 (CR Chondrite) pressed on a diamond window and measured under vacuum at ambient temperature (22°C) and after heating at 300°C
DOI: 10.26302/sshade/experiment_lb_20170731_003
title: Raw, normalized and baseline-corrected of MIR transmission spectra of GRA95229 matrix grains pressed on diamonds under vacuum at ambiant temperature and 300C

description: MIR spectra of several matrix grains of GRA95229 at different temperature, under vacuum
DOI: 10.26302/sshade/experiment_lb_20180326_001
title: Vis-NIR reflectance spectra (i=0°, e=30°) of powdered lunar meteorite MAC88105 at 80°C under vacuum
DOI: 10.26302/sshade/experiment_lb_20180718_001
title: MIR spectra of IOM from CM and C2-ungrouped chondrites under vacuum and at T=80C

description: MIR spectra of IOM extracted from a series of 20 CM and C2-ungrouped chondrites with the CF/HCl technique at IPAG and DTM, under vacuum and at low temperature
DOI: 10.26302/sshade/experiment_bs_20130103_003
title: NIR optical constant spectra of CH4 in solid solution in alpha and beta-N2 phases at 5 different temperatures (35K - 43K)

description: NIR optical constant spectra of CH4 in solid solution in two N2 ice phases: Beta-N2 phases at 43, 41, 38 and 36.5K. Changed to alpha-N2 phase at 35K
DOI: 10.15151/esrf-es-404835480
title: Biomimetic approach to develop a novel environmental-friendly cement inspired by mason bee nests

description: To decrease the CO2 imprint of the cement and concrete industry, eco-friendly materials are necessary to replace the polluting building materials. Here, we propose a study based on biomimicry to develop a novel material bioinspired by mason bees’ nests. The nests are hard as a rock, “a safe house” of the future generation of bees, and remain in place for years until it is naturally destroyed. We propose to perform a quantitative characterization of the 3D microstructure of the nests with high-resolution by near-field X-ray ptychographic tomography. This will allow us to quantify the composition of the nests based on electron density values, and to analyze the wall structures and pore network with sufficiently high resolution to resolve small pores. The results will help us to understand the impact of the nest architecture design on CO2 exchange, ventilation, and thermoregulation. Additionally, this study may contribute to saving this endangered bee species (Megachile pyrenaica).
DOI: 10.15151/esrf-es-421464602
title: Next-generation DFXM
DOI: 10.15151/esrf-es-435441170
title: IHR

description: IHR
DOI: 10.15151/esrf-es-430265445
title: Fe- and Mn-based electrocatalysts investigation using XAS and XES

description: Two types of the electrocatalysts will be investigated ex situ using XAS and XES: (i) Fe-N-C catalysts and (ii) Birnessites. Fe-based materials will be analyzed before and after the accelerated stress tests in the electrochemical cell in order to shed light on the possible formation of iron oxides. In case of Mn-based materials (birnessite), several materials prepared via different synthetic routes will be analyzed ex situ in order to verify the possibility of their further in situ studies in the spectroelectrochemical cell.
DOI: 10.15151/esrf-es-432437293
title: RIXS exploration of the electronic and magnetic excitations in FePS3

description: In 2D antiferromagnetic MPS3 compounds – M is a 3d transition metal – the correlation between spin and orbital excitations often leads to strong coupling between the electronic transitions and the lattice magnetic order. This quantum behavior looks particularly appealing in view of the development of opto-spintronic devices. Unlike other members of the family, no evidences have been reported up to now for FePS3, despite the higher magnetic moment of iron. Our preliminary Resonant Inelastic X-ray Scattering (RIXS) measurements at the Fe L3 edge show indications of a possible correlation between dd electronic transitions and magnetic excitations, also supported by simulations. Our hypothesis deserves RIXS investigations with varying temperature, photon energy and exchange momentum in order to clarify the coupling mechanism.
DOI: 10.15151/esrf-es-406686297
title: Evidencing depth-resolved Li heterogeneties and Li plating across graphite electrodes during fast charging with microXRD

description: We propose to use operando micro X-ray diffraction (μXRD) to follow the depth-resolved lithiation state of graphite electrodes and possible lithium plating occurring during fast charging. Since heterogeneous lithiation and Li plating result in premature electrode ageing, there is a crucial need to experimentally probe these phenomena and to numerically predict their occurrence and magnitude. We have addressed the latter by developing a physics-based Newman-type performance model [2], the accuracy of which has been experimentally verified at the macro and micro scale for moderate C-rate using the feedback from our previous synchrotron experiment on ID13 (MA4110). To go further, we now require new experimental data (i) to adjust the performance model for the fast charge regimes, and (ii) to quantify lithium plating through the electrode thickness as function of the local state of graphite lithiation. This will provide a sound basis for accurate prediction of electrode ageing.
DOI: 10.15151/esrf-es-404929788
title: Mobilization of rhenium in magmatic fluids with implications for its exploration

description: Rhenium (Re) is one of the rarest elements on Earth (average abundance &lt; 1 ppb) and is of fundamental importance for our modern high-tech industry due to its high thermal stability (melting temperature beyond 3100 °C). Yet the enrichment process of Re in ore deposits is little understood mainly due to the difficulties to perform experiments at extremely high dilution levels and simultaneously at high P/T conditions. The new ESRF-extremely brilliant source capabilities and several recent technical developments at the ESRF beamlines FAME and BM23 allow overcoming these limitations. We therefore propose to study systematically the solubility and speciation of Re in fluids as a function of P/T and fluid composition using X-ray fluorescence spectroscopy and High-Energy Resolution Fluorescence Detection (HERFD) X-ray spectroscopy. The new data will improve our understanding of Re mobilization in magmatic systems and its enrichment process with implications for the exploration of Re.