cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7663010.v2
title: Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

description: This repository contains raw data and all scripts for the in situ sequencing processing pipeline (Mats Nilsson Lab, Stockholm University) and downstream analysis applied in the manuscript “<b>Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma”.</b> <b>Raw data in folders:</b> Lung csv files Bacteria csv files DAPI for plotting HE folder <b>Scripts folder:</b> Matlab scripts Cellprofiler pipelines <b>Identification and plotting of transcripts:</b> For all matlab scripts: Download the “Matlab scripts” folder, add lib to MATLAB path. Except MATLAB, no additional Mathworks product is required. Tested on R2017b. <b>InSituSequencing.m</b> is the top-level script processing sequencing images to positional visualization of decoded transcripts. Input images are available on request, those were tiled and then processed in the cell profiler pipeline “Blob identification” generating csv files containing position and intensity of each identified signal.csv files for all lung scans (3 per time point) are in “lung csv files” folder and can be plotted on DAPI images (10% of original size) found in “DAPI for plotting” folder using InSituSequencing.m. High resolution H&E scans of in situ-sequenced lungs for lung section per time point are in the “HE folder” at 50% of original size. For all images 1 pixel corresponds to 0.325 mm. <b>Identification and plotting of transcripts in given proximity to bacteria:</b> Use the cellprofiler pipeline “Bacteria identification” instead of “Blob identification” to identify signal in indicated distances from identified bacteria. The folder “bacteria csv files” contains identified signals in the indicated distances to identified bacteria. Input images are available on request. <b>Downstream analysis (Matlab Scripts folder)</b> <b>DensityEstimation.m</b> was used to display not absolute reads but a kernel density estimation of a certain gene in a 2log scale. <b>ROI_draw_onImage.m</b> was applied to extract reads from annotated regions. Pictures of annotations can be found in the manuscript supplementary figure S1. <b>HexbinClustering.m </b>performed an unsupervised clustering (kmeans) of spatial data with a given number of distinct clusters in a given radius. <br>
DOI: 10.6084/m9.figshare.7661384
title: Fast negative breakdown in thunderstorms

description: Data for observations obtained at Kennedy Space Center, Florida from a 2016 August 24 thunderstorm, which support the findings in "Fast negative breakdown in thunderstorms," currently under review at <i>Nature Communications</i>. The observations include three-dimensional lightning mapping array (LMA) data (.dat.gz) from the 10-station Kennedy Space Center LMA, VHF (20-80 MHz) waveforms (.chA, .chB, .chC) recorded by the New Mexico Tech Broadband Interferometer, and waveforms recorded by a flat-plate fast antenna (.chD) that measured the change in vertical electric field at the ground with a 100 microsecond decay constant.
DOI: 10.7284/106560
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB949 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661372
title: S2: Whole-rock geochemical modelling of granite genesis – the current state of play

description: The R code used to generate Figure 2.
DOI: 10.6084/m9.figshare.7661375
title: S4: Whole-rock geochemical modelling of granite genesis – the current state of play

description: The R code used to generate Figure 3.
DOI: 10.6084/m9.figshare.7663010.v3
title: Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

description: This repository contains raw data and all scripts for the in situ sequencing processing pipeline (Mats Nilsson Lab, Stockholm University) and downstream analysis applied in the manuscript “<b>Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma”. </b> <b><i></i><i></i>Raw data in folders:</b> Lung csv files Bacteria csv files DAPI for plotting HE folder <b>Scripts folder:</b> Matlab scripts Cellprofiler pipelines <b>Identification and plotting of transcripts:</b> For all matlab scripts: Download the “Matlab scripts” folder, add lib to MATLAB path. Except MATLAB, no additional Mathworks product is required. Tested on R2017b. <b>InSituSequencing.m</b> is the top-level script processing sequencing images to positional visualization of decoded transcripts. Input images are available on request, those were tiled and then processed in the cell profiler pipeline “Blob identification” generating csv files containing position and intensity of each identified signal.csv files for all lung scans (3 per time point) are in “lung csv files” folder and can be plotted on DAPI images (10% of original size) found in “DAPI for plotting” folder using InSituSequencing.m. High resolution H&E scans of in situ-sequenced lungs for lung section per time point are in the “HE folder” at 50% of original size. For all images 1 pixel corresponds to 0.325 mm. <b>Identification and plotting of transcripts in given proximity to bacteria:</b> Use the cellprofiler pipeline “Bacteria identification” instead of “Blob identification” to identify signal in indicated distances from identified bacteria. The folder “bacteria csv files” contains identified signals in the indicated distances to identified bacteria. Input images are available on request. <b>Downstream analysis (Matlab Scripts folder)</b> <b>DensityEstimation.m</b> was used to display not absolute reads but a kernel density estimation of a certain gene in a 2log scale. <b>ROI_draw_onImage.m</b> was applied to extract reads from annotated regions. Pictures of annotations can be found in the manuscript supplementary figure S1. <b>HexbinClustering.m </b>performed an unsupervised clustering (kmeans) of spatial data with a given number of distinct clusters in a given radius.<br><b>Table 1-3 </b>contain sequences of used specific primers, padlock probes and detection oligos. <br>
DOI: 10.7284/106561
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB953 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661369
title: S3: Whole-rock geochemical modelling of granite genesis – the current state of play

description: The R code used to generate Figure 3.
DOI: 10.6084/m9.figshare.7661372.v1
title: S2: Whole-rock geochemical modelling of granite genesis – the current state of play

description: The R code used to generate Figure 2.
DOI: 10.6084/m9.figshare.7661366
title: S1: Whole-rock geochemical modelling of granite genesis – the current state of play

description: The R code used to generate Figure 2.
DOI: 10.6084/m9.figshare.7661375.v1
title: S4: Whole-rock geochemical modelling of granite genesis – the current state of play

description: The R code used to generate Figure 3.
DOI: 10.7284/106562
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB954 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661369.v1
title: S3: Whole-rock geochemical modelling of granite genesis – the current state of play

description: The R code used to generate Figure 3.
DOI: 10.6084/m9.figshare.7661366.v1
title: S1: Whole-rock geochemical modelling of granite genesis – the current state of play

description: The R code used to generate Figure 2.
DOI: 10.7284/106563
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB955 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106564
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB956 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106565
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB958 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106566
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB959 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106567
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB960 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106568
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB961 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106569
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB962 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106570
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB963 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106571
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB964 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106572
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB965 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106573
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB966 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106574
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB967 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106575
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB968 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106576
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB969 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661210
title: Quantification of DNA damage in patients undergoing non-contrast and contrast enhanced whole body PET/CT investigations using comet assay and micronucleus assay

description: <b>Objective:</b> To quantify DNA damage in patients undergoing non-contrast and contrast-enhanced <sup>18</sup>F-FDG PET/CT whole body positron emission tomography/computed tomography (WB PET/CT) investigations using comet assay technique and micronucleus assay, and to study the effect of other baseline parameters of patients on DNA damage. <b>Methodology:</b> Eighty-four patients referred for <sup>18</sup>F-FDG PET/CT investigation were included in the study of which 44 patients underwent contrast-enhanced WB PET/CT and 40 patients underwent non-contrast WB PET/CT investigations. The investigations were performed on Discovery 690 PET/CT. For contrast-enhanced investigation, Omnipaque300 was injected intravenously based on the patient body weight. Absorbed dose resulting from the intravenous administration of <sup>18</sup>F-FDG was estimated using the ICRP 106 dose coefficients. Radiation dose from the acquisition of CT scans was estimated using CT dose index and dose-length product. Blood samples were collected from the patients for DNA damage analysis. Comet assay and MN assay was used to assess the DNA damage. The Differences in the comet TM (Tail Moment) and MNBC % in both groups were calculated. <b>Result:</b> The radiation dose received by the study population during <sup>18</sup>F-FDG WB PET/CT examination was 27.03 ± 2.33 mSv. Comet TM and percentage frequency of MNBC % was 65.22 ± 35.42 and 18.55 ± 10.14, respectively in the patients injected with contrast and 42.49 ± 28.52 and 13.76 ± 7.52 for non-contrast group. Significant increase in DNA damage was observed in the contrast group as compared to non-contrast group. Significant association was observed between patient weight, contrast volume and TM and MNBC%. Baseline parameters of the patients did not show significant correlation with TM and MNBC%. <b>Conclusion:</b> The patients undergoing contrast-enhanced WB PET/CT investigations have demonstrated higher DNA damage. The DNA damage was also observed to be more in heavier patients. The other baseline parameters of patients like age, sex, CBG, serum creatinine did not show any correlation with DNA damage.
DOI: 10.7284/106577
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB971 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661210.v2
title: Quantification of DNA damage in patients undergoing non-contrast and contrast enhanced whole body PET/CT investigations using comet assay and micronucleus assay

description: <b>Objective:</b> To quantify DNA damage in patients undergoing non-contrast and contrast-enhanced <sup>18</sup>F-FDG PET/CT whole body positron emission tomography/computed tomography (WB PET/CT) investigations using comet assay technique and micronucleus assay, and to study the effect of other baseline parameters of patients on DNA damage. <b>Methodology:</b> Eighty-four patients referred for <sup>18</sup>F-FDG PET/CT investigation were included in the study of which 44 patients underwent contrast-enhanced WB PET/CT and 40 patients underwent non-contrast WB PET/CT investigations. The investigations were performed on Discovery 690 PET/CT. For contrast-enhanced investigation, Omnipaque300 was injected intravenously based on the patient body weight. Absorbed dose resulting from the intravenous administration of <sup>18</sup>F-FDG was estimated using the ICRP 106 dose coefficients. Radiation dose from the acquisition of CT scans was estimated using CT dose index and dose-length product. Blood samples were collected from the patients for DNA damage analysis. Comet assay and MN assay was used to assess the DNA damage. The Differences in the comet TM (Tail Moment) and MNBC % in both groups were calculated. <b>Result:</b> The radiation dose received by the study population during <sup>18</sup>F-FDG WB PET/CT examination was 27.03 ± 2.33 mSv. Comet TM and percentage frequency of MNBC % was 65.22 ± 35.42 and 18.55 ± 10.14, respectively in the patients injected with contrast and 42.49 ± 28.52 and 13.76 ± 7.52 for non-contrast group. Significant increase in DNA damage was observed in the contrast group as compared to non-contrast group. Significant association was observed between patient weight, contrast volume and TM and MNBC%. Baseline parameters of the patients did not show significant correlation with TM and MNBC%. <b>Conclusion:</b> The patients undergoing contrast-enhanced WB PET/CT investigations have demonstrated higher DNA damage. The DNA damage was also observed to be more in heavier patients. The other baseline parameters of patients like age, sex, CBG, serum creatinine did not show any correlation with DNA damage.
DOI: 10.6084/m9.figshare.7661210.v1
title: Quantification of DNA damage in patients undergoing non-contrast & contrast enhanced whole body PET/CT investigations using comet assay and micronucleus assay

description: <b>Objective:</b> To quantify DNA damage in patients undergoing non-contrast and contrast-enhanced <sup>18</sup>F-FDG PET/CT whole body positron emission tomography/computed tomography (WB PET/CT) investigations using comet assay technique & micronucleus assay. To study the effect of other baseline parameters of patients on DNA damage. <b>Methodology:</b> 84 patients referred for <sup>18</sup>F-FDG PET/CT investigation were included in the study of which 44 patients underwent contrast-enhanced WB PET/CT and 40 patients underwent non-contrast WB PET/CT investigations. The investigations were performed on Discovery 690 PET/CT. For contrast-enhanced investigation, Omnipaque300 was injected intravenously based on the patient body weight. Absorbed dose resulting from the intravenous administration of <sup>18</sup>F-FDG was estimated using the ICRP 106 dose coefficients. Radiation dose from the acquisition of CT scans was estimated using CTDI and DLP. Blood samples were collected from the patients for DNA damage analysis. Comet assay and MN assay was used to assess the DNA damage. The Differences in the comet TM (Tail Moment) and MNBC % in both groups were calculated. <b>Result:</b> The radiation dose received by the study population during <sup>18</sup>F-FDG WB PET/CT examination was 27.03 ± 2.33 mSv. Comet TM and percentage frequency of MNBC % was 65.22 ± 35.42 and 18.55 ± 10.14 respectively in the patients injected with contrast and 42.49 ± 28.52 and 13.76 ± 7.52 for non-contrast group. Significant increase in DNA damage was observed in the contrast group as compared to non-contrast group. Significant association was observed between patient weight, contrast volume and TM and MNBC%. Baseline parameters of the patients did not show significant correlation with TM and MNBC%. <b>Conclusion:</b> The patients undergoing contrast-enhanced WB PET/CT investigations have demonstrated higher DNA damage. The DNA damage was also observed to be more in heavier patients. The other baseline parameters of patients like age, sex, CBG, serum creatinine did not show any correlation with DNA damage.
DOI: 10.7284/106578
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB972 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106579
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB973 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111114
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB977 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111115
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB978 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111116
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB982 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661093.v1
title: RIL_v1.5_mapping_UN.csv.gz

description: Gene expression values for Brassica rapa<br>
DOI: 10.7284/111117
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB983 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661093
title: RIL_v1.5_mapping_UN.csv.gz

description: Gene expression values for Brassica rapa<br>
DOI: 10.6084/m9.figshare.7661015
title: Po_FL.lnc.classify

description: This dataset contains all of the predicted lncRNAs of <i>P. olivaceus</i>
DOI: 10.7284/111118
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB984 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661015.v1
title: Po_FL.lnc.classify

description: This dataset contains all of the predicted lncRNAs of <i>P. olivaceus</i>
DOI: 10.23645/epacomptox.7660979
title: Chemical Structures that failed during mass spectral prediction

description: Predicted spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4 and https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive and negative modes and EI-MS. Due to structural errors and model constraints, the prediction of all MS modes failed for 56 structures.
DOI: 10.6084/m9.figshare.7660997
title: Patients characteristics and surgical outcome data for 208 patients who underwent either integrated robotic distal gastrectomy or conventional laparoscopic distal gastrectomy

description: This dataset comprises a single <b>.xlsx </b>spreadsheet. The data are patient characteristics and surgical outcomes for patients who underwent gastrectomies. Two types of gastrectomy are covered: integrated robotic distal gastrectomy (IRDG), which combines fluorescence imaging with a Single-Site robotic platform (Intuitive Surgical), and conventional laparoscopic distal gastrectomy (CLDG).<br><br>Data are provided for 208 patients, with key variables including:- <b>Approach </b>(IRDG = 1, CLDG = 0)- <b>Age</b>- <b>Sex</b>- <b>BMI</b>- <b>ASA </b>(American Society of Anesthesiologists score)- <b>conversion </b>(to open surgery)- <b>Time </b>(operation time, in minutes)- <b>readmission </b>(1 = readmitted)<br>The related study compares the surgical success of IRDG versus CLDG. To do this, the authors performed retrospective analysis of patient characteristics and surgical outcomes for 208 patients: 56 who underwent IRDG and 152 who underwent CLDG. Surgical outcomes were measured by assessing: the frequency of perioperative morbidity, conversion to open surgery, readmission after discharge, positive resection margin, and retrieval of &lt;16 lymph nodes. The study reports that more favourable surgical outcomes are associated with IRDG.<br>
DOI: 10.7284/111119
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB986 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition