cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7772921
title: Mucosal and humoral response data gathered from specific-pathogen-free chickens inoculated with avian influenza subtype H9N2 and Bacillus cereus

description: These data present the results and data underlying the figures of the related study - <i>Contaminated feed-borne Bacillus cereus aggravates respiratory distress post avian influenza virus H9N2 infection by inducing pneumonia</i> - in which the humoral and mucosal responses of specific-pathogen-free (SPF) chickens to <i>Bacillus cereus</i> and avian influenza A subtype H9N2 coinfection were evaluated.<br>Data are presented in an XLSX file and are arranged based on their associated figure and specific panel therein from the accompany paper. Data are further grouped based on the 5 study groups observed:<br>* SPF chicks inoculated with <i>B. cereus</i> followed by H9N2 (n=21)* SPF chicks inoculated with H9N2 followed by <i>B. cereus </i>(n=21)* SPF chicks inoculated with <i>B. cereus </i>only (n=21)* SPF chicks inoculated with H9N2 only (n=21)* Control (n=21)<br>The contents of the data provided are listed below by their associated figure and containing sheet within the XLSX file:<br><b>Figure 1</b><b>A.</b> Mean body weights across each study group pre-inoculation. <b>B.</b> Mean body weights across each group and 7, 14 and 21 days post-inoculation.<b><br></b><b>Figure 4</b><b>A.</b> Scoring of air sac lesions present across each study group (as per Table 1 of the accompanying paper) at 14 and 21 days post-inoculation.<b>B. </b>Scoring of lung inflammation present across each study group (as per Table 1 of the accompanying paper) at 14 and 21 days post-inoculation. <b><br></b><b>Figure 5</b><b>A.</b> H9N2 viral load at days 14 and 21 post-inoculation compared to <i>B. cereus</i> / H9N2 and H9N2 / <i>B. cereus</i> groups.<b>B.</b> <i>B. cereus</i> load at days 14 and 21 post-inoculation compared to <i>B. cereus</i> / H9N2 and H9N2 / <i>B. cereus</i> groups<b><br></b><b>Figure 6</b><b>A.</b> Newcastle Disease Virus (NDV)-specific antibody levels for each study group at 7, 14 and 21 days post-inoculation.<b>B.</b> Non-specific IgA antibody levels for each study group at 7, 14 and 21 days post-inoculation.<b><br></b><b>Figure 7</b>Lymphocyte proliferation indices for each study study group at 7 and 14 days post-inoculation.<b><br></b><b>Figure 8</b><b>A. </b>IL-2 expression for each study study group at 7 and 14 days post-inoculation.<b>B. </b>IL-6 expression for each study study group at 7 and 14 days post-inoculation.<b>C. </b>IL-γ expression for each study study group at 7 and 14 days post-inoculation.<b>D. </b>IL-12 expression for each study study group at 7 and 14 days post-inoculation.
DOI: 10.6084/m9.figshare.7772921.v1
title: Mucosal and humoral response data gathered from specific-pathogen-free chickens inoculated with avian influenza subtype H9N2 and Bacillus cereus

description: These data present the results and data underlying the figures of the related study - <i>Contaminated feed-borne Bacillus cereus aggravates respiratory distress post avian influenza virus H9N2 infection by inducing pneumonia</i> - in which the humoral and mucosal responses of specific-pathogen-free (SPF) chickens to <i>Bacillus cereus</i> and avian influenza A subtype H9N2 coinfection were evaluated.<br>Data are presented in an XLSX file and are arranged based on their associated figure and specific panel therein from the accompany paper. Data are further grouped based on the 5 study groups observed:<br>* SPF chicks inoculated with <i>B. cereus</i> followed by H9N2 (n=21)* SPF chicks inoculated with H9N2 followed by <i>B. cereus </i>(n=21)* SPF chicks inoculated with <i>B. cereus </i>only (n=21)* SPF chicks inoculated with H9N2 only (n=21)* Control (n=21)<br>The contents of the data provided are listed below by their associated figure and containing sheet within the XLSX file:<br><b>Figure 1</b><b>A.</b> Mean body weights across each study group pre-inoculation. <b>B.</b> Mean body weights across each group and 7, 14 and 21 days post-inoculation.<b><br></b><b>Figure 4</b><b>A.</b> Scoring of air sac lesions present across each study group (as per Table 1 of the accompanying paper) at 14 and 21 days post-inoculation.<b>B. </b>Scoring of lung inflammation present across each study group (as per Table 1 of the accompanying paper) at 14 and 21 days post-inoculation. <b><br></b><b>Figure 5</b><b>A.</b> H9N2 viral load at days 14 and 21 post-inoculation compared to <i>B. cereus</i> / H9N2 and H9N2 / <i>B. cereus</i> groups.<b>B.</b> <i>B. cereus</i> load at days 14 and 21 post-inoculation compared to <i>B. cereus</i> / H9N2 and H9N2 / <i>B. cereus</i> groups<b><br></b><b>Figure 6</b><b>A.</b> Newcastle Disease Virus (NDV)-specific antibody levels for each study group at 7, 14 and 21 days post-inoculation.<b>B.</b> Non-specific IgA antibody levels for each study group at 7, 14 and 21 days post-inoculation.<b><br></b><b>Figure 7</b>Lymphocyte proliferation indices for each study study group at 7 and 14 days post-inoculation.<b><br></b><b>Figure 8</b><b>A. </b>IL-2 expression for each study study group at 7 and 14 days post-inoculation.<b>B. </b>IL-6 expression for each study study group at 7 and 14 days post-inoculation.<b>C. </b>IL-γ expression for each study study group at 7 and 14 days post-inoculation.<b>D. </b>IL-12 expression for each study study group at 7 and 14 days post-inoculation.
DOI: 10.6084/m9.figshare.7772903
title: Metabolic comparison of aerial and submerged mycelia formed in the liquid surface culture of Cordyceps militaris

description: Supplemeatary Table S1: Predictive metabolites<b>GC/MS analysis</b> Fifty milliliters of <i>C. militaris </i>liquid surface culture broth at 5, 12, and 19 d was separately collected and stored at -80ºCbefore further analysis. Each sample of 15 mL was diluted in 35 mL of water, centrifuged at 16,000 × g for 10 min at 4°C, and the pellets were collected for freeze-drying. Twenty-five microliters of methoxyamine hydrochloride in pyridine (20 mg/mL) was added, and the mixture was vortexed for 30 s and incubated at 90°C for 90 min. Finally, 75 μL of N-methyl-N-trimethyl-silyltrifluoroacetamide (MSTFA)<i></i>was added, and the mixture was incubated at 37°C for 30 min. The mixture was centrifuged at 13,000 × g for 10 min at 4°C, and the supernatant (n=7 for each sample) was subjected to gas chromatography/mass spectrometry (GC/MS)(Agilent Technologies 7890A GC system, Agilent Technologies, Inc., Wilmington, DE, USA) equipped with an inertcap 5MS capillary column (5% phenylmethylsiloxane: 30 m × 0.25 mm internal diameter, 0.25 μm film thickness; GL-science Co. Ltd., Tokyo, Japan)and JEOL JMS-T100GCv Time-of-flight Mass Spectrometer (JEOL, Tokyo, Japan). The GC was operated at a constant flow of helium (1 mL/min), an injector temperature of 250°C, and an ion source and transfer line temperature of 280°C. The oven temperature program was as follows: 40°C for 4 min, increased at 15°C/min to 300°C, and held for 10 min. The samples were injected with a split ratio of 100:1. The ionization was conducted in the EI positive mode. The detection mass range was m/z 50–600. To tentatively identify a compound, the mass spectra and measured exact mass were compared against a spectral library (NIST) and the exact mass simulated. The spectra, exact mass, and retention times were compared with authentic standards when they were available. <b>Data statistics</b> The GC-MS raw results were converted to .<i>cdf</i>format and analyzed using an XCMS online program (https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage) (Tautenhahn et al., 2012) based on default parameters. Finally, the metabolite annotation of GC-MS was performed using the automatic processing and identification system (AMDIS) databases of the National Institute of Standards and Technology (NIST).
DOI: 10.6084/m9.figshare.7772903.v1
title: Metabolic comparison of aerial and submerged mycelia formed in the liquid surface culture of Cordyceps militaris

description: Supplemeatary Table S1: Predictive metabolites<b>GC/MS analysis</b> Fifty milliliters of <i>C. militaris </i>liquid surface culture broth at 5, 12, and 19 d was separately collected and stored at -80ºCbefore further analysis. Each sample of 15 mL was diluted in 35 mL of water, centrifuged at 16,000 × g for 10 min at 4°C, and the pellets were collected for freeze-drying. Twenty-five microliters of methoxyamine hydrochloride in pyridine (20 mg/mL) was added, and the mixture was vortexed for 30 s and incubated at 90°C for 90 min. Finally, 75 μL of N-methyl-N-trimethyl-silyltrifluoroacetamide (MSTFA)<i></i>was added, and the mixture was incubated at 37°C for 30 min. The mixture was centrifuged at 13,000 × g for 10 min at 4°C, and the supernatant (n=7 for each sample) was subjected to gas chromatography/mass spectrometry (GC/MS)(Agilent Technologies 7890A GC system, Agilent Technologies, Inc., Wilmington, DE, USA) equipped with an inertcap 5MS capillary column (5% phenylmethylsiloxane: 30 m × 0.25 mm internal diameter, 0.25 μm film thickness; GL-science Co. Ltd., Tokyo, Japan)and JEOL JMS-T100GCv Time-of-flight Mass Spectrometer (JEOL, Tokyo, Japan). The GC was operated at a constant flow of helium (1 mL/min), an injector temperature of 250°C, and an ion source and transfer line temperature of 280°C. The oven temperature program was as follows: 40°C for 4 min, increased at 15°C/min to 300°C, and held for 10 min. The samples were injected with a split ratio of 100:1. The ionization was conducted in the EI positive mode. The detection mass range was m/z 50–600. To tentatively identify a compound, the mass spectra and measured exact mass were compared against a spectral library (NIST) and the exact mass simulated. The spectra, exact mass, and retention times were compared with authentic standards when they were available. <b>Data statistics</b> The GC-MS raw results were converted to .<i>cdf</i>format and analyzed using an XCMS online program (https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage) (Tautenhahn et al., 2012) based on default parameters. Finally, the metabolite annotation of GC-MS was performed using the automatic processing and identification system (AMDIS) databases of the National Institute of Standards and Technology (NIST).
DOI: 10.6084/m9.figshare.7772864
title: Customized silva sequences file

description: Customized silva sequences file for DADA2 taxonomy assignment. Sequences from glacier samples were added.
DOI: 10.6084/m9.figshare.7772852
title: sequencing summary, WIMP analysis output and BLAST analysis output plus a final_df summarized all the information.

description: This depository is for the related files used in the analysising and visualizing data within the project.The file final_df.all.zip combined all the information required for this project from the sequencing and analysis, and was used for plotting all figures generating all tables.<br>
DOI: 10.6084/m9.figshare.7772855
title: SIAM-CSE19-MS2-Coutinho.pdf

description: CSE simulations in high-performance computers are still costly. They often involve the selection of many computational parameters and options. The set-up of such parameters is usually a trial-and-error process even for experienced users. In this talk, we will show how to extend in-situ visualization techniques with in-transit data analysis to provide information to help control the simulations at runtime. Often, by only observing a region of interest, an experienced analyst can infer that something is not going well, deciding to stop it or change parameters. However, to do that, visual information should be complemented with information regarding the evolution of quantities of interest. We use for the simulations the libMesh library, which provides a platform for parallel, adaptive, multiphysics finite element computations. We discuss the integration of libMesh with in-situ visualization and in-transit data analysis tools. We present a parallel performance analysis showing that the overhead for both in-situ visualization and in-transit data analysis is negligible. Our tools enable monitoring the quantities of interest at runtime and steer the simulation based on the solver convergence or other data and visual information. The data analysis tool registers the provenance of the simulation data for reproducibility, including registering the runtime changes on simulation parameters.
DOI: 10.6084/m9.figshare.7772831
title: fastq_files

description: Original fastq files for Tokyo Skytree air, reference samples and controls.<br>Partial 16S rRNA gene sequences, spanning the V3 and V4 regions, were amplified using the primers Bakt_341F (5´ CCTACGGGNGGCWGCAG 3´) and Bakt_805R (5´ GACTACHVGGGTATCTAATCC 3´), with Illumina overhang adaptor sequences attached to their 5′ ends, by KAPA HiFi HotStart ReadyMix (KAPA Biosystems, MA, USA). <br>
DOI: 10.6084/m9.figshare.7772852.v1
title: sequencing summary, WIMP analysis output and BLAST analysis output plus a final_df summarized all the information.

description: This depository is for the related files used in the analysising and visualizing data within the project.The file final_df.all.zip combined all the information required for this project from the sequencing and analysis, and was used for plotting all figures generating all tables.<br>
DOI: 10.6084/m9.figshare.7772828
title: testkl.xlsx

description: y6drfgiujotrstrvfyuhmij,
DOI: 10.6084/m9.figshare.7772855.v1
title: SIAM-CSE19-MS2-Coutinho.pdf

description: CSE simulations in high-performance computers are still costly. They often involve the selection of many computational parameters and options. The set-up of such parameters is usually a trial-and-error process even for experienced users. In this talk, we will show how to extend in-situ visualization techniques with in-transit data analysis to provide information to help control the simulations at runtime. Often, by only observing a region of interest, an experienced analyst can infer that something is not going well, deciding to stop it or change parameters. However, to do that, visual information should be complemented with information regarding the evolution of quantities of interest. We use for the simulations the libMesh library, which provides a platform for parallel, adaptive, multiphysics finite element computations. We discuss the integration of libMesh with in-situ visualization and in-transit data analysis tools. We present a parallel performance analysis showing that the overhead for both in-situ visualization and in-transit data analysis is negligible. Our tools enable monitoring the quantities of interest at runtime and steer the simulation based on the solver convergence or other data and visual information. The data analysis tool registers the provenance of the simulation data for reproducibility, including registering the runtime changes on simulation parameters.
DOI: 10.6084/m9.figshare.7772780
title: SuppTable1_IJNM.xlsx

description: Table S1. Proteomic profile of the protein corona (PC) recovered after incubation of human plasma with three different iron oxide nanoparticles. Proteins were identified using LC-MS/MS.
DOI: 10.6084/m9.figshare.7772828.v1
title: testkl.xlsx

description: y6drfgiujotrstrvfyuhmij,
DOI: 10.6084/m9.figshare.7772831.v2
title: fastq_files

description: Original fastq files for Tokyo Skytree air, reference samples and controls.<br>Partial 16S rRNA gene sequences, spanning the V3 and V4 regions, were amplified using the primers Bakt_341F (5´ CCTACGGGNGGCWGCAG 3´) and Bakt_805R (5´ GACTACHVGGGTATCTAATCC 3´), with Illumina overhang adaptor sequences attached to their 5′ ends, by KAPA HiFi HotStart ReadyMix (KAPA Biosystems, MA, USA). <br>
DOI: 10.6084/m9.figshare.7772864.v1
title: Costumed silva sequences file for DADA2 taxonomy assignment

description: Costumed silva sequences file for DADA2 taxonomy assignment. Sequences from glacier samples were added.
DOI: 10.6084/m9.figshare.7772780.v1
title: SuppTable1_IJNM.xlsx

description: Table S1. Proteomic profile of the protein corona (PC) recovered after incubation of human plasma with three different iron oxide nanoparticles. Proteins were identified using LC-MS/MS.
DOI: 10.6084/m9.figshare.7772831.v1
title: Original_fastq_files

description: Original fastq files for Tokyo Skytree air, reference samples and PCR control.
DOI: 10.6084/m9.figshare.7772864.v3
title: Customized silva sequences file

description: Customized silva sequences file for DADA2 taxonomy assignment. Sequences from glacier samples were added.
DOI: 10.6084/m9.figshare.7772753
title: Personal Data Management Bingo: a drop-in activity

description: This game was adapted from Data Management Plan Bingo into an activity that could be done on a drop-in basis. No Data Management Plans are used. The practices on the Bingo cards are either good or bad personal data management practices. <br><br>This Bingo game was derived from Data Management Plan Bingo by Megan O'Donnell.<br>Attached files include:<br>- Instructions for making Bingo cards and playing- Numbered list of personal data management practices for calling out- 1 set of 10 different Personal Data Management Bingo cards<br>
DOI: 10.6084/m9.figshare.7772864.v2
title: Customized silva sequences file for DADA2 taxonomy assignment

description: Customized silva sequences file for DADA2 taxonomy assignment. Sequences from glacier samples were added.
DOI: 10.6084/m9.figshare.7772723
title: ASV_table

description: Table for all ASVs from Tokyo Skytree air samples and control samples. ASV_table.csv include all samples, and ASV_table_no_negative_control include only air samples and reference samples.<br>
DOI: 10.6084/m9.figshare.7772747
title: All ASVs fasta

description: Sequence of all ASVs used in the study.<br><br>
DOI: 10.6084/m9.figshare.7772747.v1
title: Sequence of each ASV

description: All sequence used in the study.
DOI: 10.6084/m9.figshare.7772540
title: Meta_thinking:wind turbine meta studies 2005

description: Data for teaching metas and exploring reproducibility extracted from pdfs in this report: http://www.environmentalevidence.org/completed-reviews/effects-of-wind-turbines-on-bird-abundance<br>
DOI: 10.6084/m9.figshare.7772540.v2
title: Meta_thinking:wind turbine meta studies 2005

description: Data for teaching metas and exploring reproducibility extracted from pdfs in this report: http://www.environmentalevidence.org/completed-reviews/effects-of-wind-turbines-on-bird-abundance<br>
DOI: 10.6084/m9.figshare.7772540.v1
title: Meta_thinking:wind turbine meta studies 2005

description: Data for teaching metas and exploring reproducibility extracted from pdfs in this report: http://www.environmentalevidence.org/completed-reviews/effects-of-wind-turbines-on-bird-abundance<br>
DOI: 10.6084/m9.figshare.7771193
title: Supplement to "Inexpensive high-resolution genotyping of multiparent crosses by pooling and deconvolution using private haplotypes"

description: Supplementary files for the manuscript:Skelly DA, McCusker JH, Stone EA, Magwene PM. Inexpensive high-resolution genotyping of multiparent crosses by pooling and deconvolution using private haplotypes
DOI: 10.6084/m9.figshare.7771193.v1
title: Supplement to "Inexpensive high-resolution genotyping of multiparent crosses by pooling and deconvolution using private haplotypes"

description: Supplementary files for the manuscript:Skelly DA, McCusker JH, Stone EA, Magwene PM. Inexpensive high-resolution genotyping of multiparent crosses by pooling and deconvolution using private haplotypes
DOI: 10.6084/m9.figshare.7771184
title: Real-time deformability cytometry reference data

description: This dataset consists of four exemplary real-time fluorescence and deformability cytometry measurements. The HDF5-files can be opened with dclab [1] or Shape-Out [2].<br><br><b>calibration_beads.rtdc</b><br>The calibartion beads (8 Peaks, PolyAN) consist of eight bead populations with different mixtures of fluorophores.<br><br><br><b>CD34_HSPC.rtdc</b><br>Hematopoietic stem and progenitor cells (HSPCs) were obtained using apheresis. The cells were tagged with a fluorescently labeled antibody that binds to the CD34 transmembrane protein. CD34-positive HSPCs are gated with `fl3_max &gt; 90`. Set `area_ratio &lt; 1.05` to remove aggregates. Data were used in [3].<br><br><br><b>leukocytes.rtdc</b><br>The leukocyte population (white blood cells) of this blood sample can be visualized by setting `aspect &lt; 2` and `area_ratio &lt; 1.05`. For more information, see e.g. [4].<br><br><br><b>reticulocytes.rtdc</b><br>Blood contains mostly red blood cells (RBCs) and about 1% reticulocytes (which develop into mature RBCs). Reticulocytes contain ribosomal RNA which was stained with Syto13 for this measurement. Set `area_ratio &lt; 1.05` to remove aggregates. Data were used in [3].<br><br><br>[1] https://github.com/ZellMechanik-Dresden/dclab<br><br>[2] https://github.com/ZellMechanik-Dresden/ShapeOut<br><br>[3] Rosendahl et al., "Real-time fluorescence and deformability cytometry". Nature Methods, 15(5):355–358, 2018. doi:10.1038/nmeth.4639.<br><br>[4] Toepfner et al., "Detection of human disease conditions by single-cell morpho-rheological phenotyping of whole blood". eLife, 7:e29213, 2017. doi:10.1101/145078.<br><br><br>SHA256 sums:<br>08c2ef13eed903ef0f9e451727ab8484df09b5d3b39227dab726e0164dcbe244 calibration_beads.rtdc<br>663b44a9db88d85996500045489e37a317cf115719223a531d617f8e3d450e79 CD34_HSPC.rtdc<br>68bd538b42ffb990f1db52d5f3b21f37c9aff31208ab284f3910fd6872c40fdb leukocytes.rtdc<br>5c323ea75bf7eeb2a28d922730772d50270dd872d6957e60d6062663f3628fb3 reticulocytes.rtdc
DOI: 10.6084/m9.figshare.7771172
title: R code for AUC performance

description: Stability analysis and AUC values
DOI: 10.6084/m9.figshare.7771178
title: Coordinates for "Aromaticity and Antiaromaticity in the Excited States of Porphyrin Nanorings"

description: These are Cartesian coordinates supporting the results published in "Aromaticity and Antiaromaticity in the Excited States of Porphyrin Nanorings".
DOI: 10.6084/m9.figshare.7771178.v1
title: Coordinates for "Aromaticity and Antiaromaticity in the Excited States of Porphyrin Nanorings"

description: These are Cartesian coordinates supporting the results published in "Aromaticity and Antiaromaticity in the Excited States of Porphyrin Nanorings".
DOI: 10.6084/m9.figshare.7771172.v1
title: R code for AUC performance

description: Stability analysis and AUC values