cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12408881.v1
title: Supplementary Material for: An International Survey of Mediastinal Staging Practices amongst Interventional Bronchoscopists

description: <b><i>Introduction:</i></b> In potentially curable non-small-cell lung cancer, different practice guidelines recommend invasive me­diastinal staging in tumors larger than 3 cm, central, or hy­permetabolic N1 lymph nodes. There is no consensus concerning the use of an endosonographic procedure or a mediastinoscopy in the first line in patients with a radiologically normal mediastinum, while in case of a mediastinal involvement, the latest European guidelines recommend the combination of endobronchial ultrasound (EBUS) and endoscopic ultrasound/endoscopic ultrasound with EBUS endoscope (EUS/EUS-B), using a systematic endosonographic procedure. This international survey was conducted to describe current medical practices in endoscopic mediastinal staging amongst interventional bronchoscopists. <b><i>Methods:</i></b> A survey was developed and sent to all members of different interventional pulmonology societies, with the purpose to describe who, when and how an endoscopic mediastinal staging was performed. <b><i>Results:</i></b> One hundred and fifty-three bronchoscopists responded to the survey. Most of them practiced in Europe (<i>n</i> = 84, 55%) and North America (<i>n</i> = 52, 34%). In the first line, EBUS alone was the most widely used endoscopic procedure for mediastinal staging. Half of the responders performed a systematic endoscopic staging procedure, including a systematic examination of all accessible nodal stations and a sampling of all lymph nodes &gt;5 mm in the short axis at each station. A higher proportion of bronchoscopists who have completed a dedicated fellowship program performed systematic endoscopic mediastinal staging. Few endoscopists routinely perform combined EBUS/EUS(-B) for mediastinal staging and use the combination only in selected cases. <b><i>Conclusion:</i></b> There are several areas of divergence between published guidelines and current practices reported by interventional bronchoscopists. EBUS alone is the most widely used endoscopic procedure for mediastinal staging in lung cancer, and a combined endoscopic approach is frequently omitted by the responders. A fellowship program appears to be associated with a higher rate of systematic endoscopic staging procedures.
DOI: 10.6084/m9.figshare.12408803
title: Multiple Low Dose manuscript_RAW data

description: Description of the experiments are present in the manuscript
DOI: 10.6084/m9.figshare.12408782
title: Online Material - Automatic Identification of Rollback Edit with Reasons in Stack Overflow Q&A Sites

description: Manually analyzed rollback edits of Stack Overflow (Questions & Answers) with reasons.
DOI: 10.6084/m9.figshare.12408707
title: data_2k_3seed

description: A dataset with learning curves of 2000 configurations evaluated on 35 datasets for 6, 12, 25 and 50 epochs.
DOI: 10.6084/m9.figshare.12408761
title: Supplementary Material for: Associations between Proton Pump Inhibitor and Histamine-2 Receptor Antagonist and Bone Mineral Density among Kidney Transplant Recipients

description: <b><i>Background:</i></b> In the general population, use of proton pump inhibitor (PPI) has been linked to higher risk of osteoporotic fractures. PPI is commonly prescribed in kidney transplant recipients (KTRs). However, the effect of PPI on osteoporosis in KTRs is largely unstudied. <b><i>Methods:</i></b> A total of 1,774 adult KTRs in the Wisconsin Allograft Recipient Database with at least one eligible bone mineral density (BMD) measurement at least 3 months after transplantation were included in the analyses. Associations between use of PPI and histamine-2 receptor antagonist (H2RA) at 3 months after transplantation and subsequent slope of T-score were assessed. <b><i>Results:</i></b> A total of 1,478 (83.3%) participants were using a PPI at 3 months after transplantation. Compared to the use of H2RA, use of PPI was not significantly associated with annualized slope of hip T-score (β = –0.0039, 95% CI –0.00497 to 0.0021) or annualized slope of spine T-score (β = –0.017, 95% CI –0.049 to 0.083) after adjustment for potential confounders. Similarly, no significant association between use of PPI and slope of T-score was observed when defining PPI/H2RA exposure as use within 6 months of the initial BMD measurement, or only including participants with at least 2 BMD measurements, or stratified by different age and sex. <b><i>Conclusions:</i></b> Use of PPI was not associated with an increased rate of BMD loss in KTRs. Our results support previous findings that PPI use does not have a significant effect on bone mineral loss.
DOI: 10.6084/m9.figshare.12408782.v2
title: Online Material - Automatic Identification of Rollback Edit with Reasons in Stack Overflow Q&A Sites

description: Manually analyzed rollback edits of Stack Overflow (Questions & Answers) with reasons.
DOI: 10.6084/m9.figshare.12408761.v1
title: Supplementary Material for: Associations between Proton Pump Inhibitor and Histamine-2 Receptor Antagonist and Bone Mineral Density among Kidney Transplant Recipients

description: <b><i>Background:</i></b> In the general population, use of proton pump inhibitor (PPI) has been linked to higher risk of osteoporotic fractures. PPI is commonly prescribed in kidney transplant recipients (KTRs). However, the effect of PPI on osteoporosis in KTRs is largely unstudied. <b><i>Methods:</i></b> A total of 1,774 adult KTRs in the Wisconsin Allograft Recipient Database with at least one eligible bone mineral density (BMD) measurement at least 3 months after transplantation were included in the analyses. Associations between use of PPI and histamine-2 receptor antagonist (H2RA) at 3 months after transplantation and subsequent slope of T-score were assessed. <b><i>Results:</i></b> A total of 1,478 (83.3%) participants were using a PPI at 3 months after transplantation. Compared to the use of H2RA, use of PPI was not significantly associated with annualized slope of hip T-score (β = –0.0039, 95% CI –0.00497 to 0.0021) or annualized slope of spine T-score (β = –0.017, 95% CI –0.049 to 0.083) after adjustment for potential confounders. Similarly, no significant association between use of PPI and slope of T-score was observed when defining PPI/H2RA exposure as use within 6 months of the initial BMD measurement, or only including participants with at least 2 BMD measurements, or stratified by different age and sex. <b><i>Conclusions:</i></b> Use of PPI was not associated with an increased rate of BMD loss in KTRs. Our results support previous findings that PPI use does not have a significant effect on bone mineral loss.
DOI: 10.6084/m9.figshare.12408782.v1
title: Dataset

description: Manually analyzed rollback edits of Stack Overflow (Questions & Answers) with reasons.
DOI: 10.6084/m9.figshare.12408554
title: Data_ Origin of hydrous magma_Baishiquan and Tianyu

description: This table contains the Li-O isotopes and H2O contents data in olivine, Hf-O isotopes data in zircon, and model parameters as well as calculations for Hf-O-Li isotopes.
DOI: 10.6084/m9.figshare.12408653
title: Sequence Data

description: Over the years, several methods have been proposed for the computational PPI prediction with different performance evaluation strategies. While attempting to benchmark performance scores, most of these methods often suffer with ill-treated cross-validation strategies, adhoc selection of positive/negative samples etc. To address these issues, in our proposed multi-level feature based PPI prediction approach <i>JUPPI</i>, using sequence, domain and GO information as features, a refined evaluation strategy has been introduced. During the evaluation process, we first extract high quality negative data using three-stage filtering, and then introduce a pair-input based cross validation strategy with three difficulty levels for test-set predictions. Our proposed evaluation strategy reduces the component-level overlapping issue in test sets. Performance of <i>JUPPI</i> is compared with those of the <i>state-of-the-art</i> approaches in this domain and tested on six independent PPI datasets. In almost all the datasets, <i>JUPPI</i> outperforms the <i>state-of-the-art</i> not only at human proteome level for PPI prediction, but also for prediction of interactors for intrinsic disordered human proteins.
DOI: 10.26180/5ed5e6a23e4ad
title: Numerical Model dataset

description: Models presented in the publication
DOI: 10.6084/m9.figshare.12408653.v1
title: Sequence Data

description: Over the years, several methods have been proposed for the computational PPI prediction with different performance evaluation strategies. These methods have limitations over different issues such as ill-treated cross-validation design, positive and negative sample selection strategies etc. To address these issues, we propose a multi-level feature based approach (<i>JUPPI</i>) using sequence, domain and GO information for PPI prediction, and an evaluation strategy that, 1) filters high quality negative data, and 2) introduces a pair-input based cross validation strategy with three difficulty levels for prediction of test sets. Our proposed evaluation strategy reduces the component-level overlapping issue in test sets. The proposed method has shown a strong confidence for PPI prediction in both test and train sets in strict categories of test sets. Performance of <i>JUPPI </i>is compared with <i>state-of-the-art </i>approaches and tested on six independent PPI datasets. In almost all the datasets, <i>JUPPI </i>outperforms the <i>state-of-the-art </i>not only at human proteome level for PPI prediction, but also for prediction of interactors for intrinsic disordered human proteins.
DOI: 10.6084/m9.figshare.12408554.v1
title: Data_ Origin of hydrous magma_Baishiquan and Tianyu

description: This table contains the Li-O isotopes and H2O contents data in olivine, Hf-O isotopes data in zircon, and model parameters as well as calculations for Hf-O-Li isotopes.
DOI: 10.6084/m9.figshare.12408344
title: Additional file 5 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 5. The primer sequences used for qRT-PCR.
DOI: 10.6084/m9.figshare.12408338
title: Additional file 4 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 4 The FPKM value of FBP genes in tetraploid cotton species.
DOI: 10.6084/m9.figshare.12408344.v1
title: Additional file 5 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 5. The primer sequences used for qRT-PCR.
DOI: 10.6084/m9.figshare.12408335
title: Additional file 3 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 3 Ka/Ks ratio of FBP homologous genes.
DOI: 10.6084/m9.figshare.12408338.v1
title: Additional file 4 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 4 The FPKM value of FBP genes in tetraploid cotton species.
DOI: 10.6084/m9.figshare.12408329
title: Additional file 2 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 2. Amino acid compositions of FBP genes.
DOI: 10.15468/xf77rv
title: Terrestrial isopods from the Oued Laou basin, north-eastern Morocco (Crustacea: Oniscidea), with descriptions of two new genera and seven new species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Taiti, Stefano, Rossano, Claudia (2015): Terrestrial isopods from the Oued Laou basin, north-eastern Morocco (Crustacea: Oniscidea), with descriptions of two new genera and seven new species. Journal of Natural History 49 (33): 2067-2138, DOI: 10.1080/00222933.2015.100951
DOI: 10.6084/m9.figshare.12408335.v1
title: Additional file 3 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 3 Ka/Ks ratio of FBP homologous genes.
DOI: 10.6084/m9.figshare.12408314
title: Additional file 1 of Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

description: Additional file 1: Tables S1-S10 and FiguresS1-S14.
DOI: 10.6084/m9.figshare.12408320
title: Additional file 1 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 1 Multiple sequence alignment involving 114 sequences from the genomes of the following eight species: G. hirsutum, G. arboreum, G. barbadense, G. raimondii, A. thaliana, T. cacao, P. trichocarpa, G. max, Z. mays, V. vinifera, S. moellendorffii, P. patens, and O. sativa.
DOI: 10.6084/m9.figshare.12408329.v1
title: Additional file 2 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 2. Amino acid compositions of FBP genes.
DOI: 10.6084/m9.figshare.12408320.v1
title: Additional file 1 of Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

description: Additional file 1 Multiple sequence alignment involving 114 sequences from the genomes of the following eight species: G. hirsutum, G. arboreum, G. barbadense, G. raimondii, A. thaliana, T. cacao, P. trichocarpa, G. max, Z. mays, V. vinifera, S. moellendorffii, P. patens, and O. sativa.
DOI: 10.6084/m9.figshare.12408308
title: Additional file 1 of Adverse events in deceased hospitalised cancer patients as a measure of quality and safety in end-of-life cancer care

description: Additional file 1.
DOI: 10.6084/m9.figshare.12408314.v1
title: Additional file 1 of Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

description: Additional file 1: Tables S1-S10 and FiguresS1-S14.
DOI: 10.6084/m9.figshare.12408308.v1
title: Additional file 1 of Adverse events in deceased hospitalised cancer patients as a measure of quality and safety in end-of-life cancer care

description: Additional file 1.
DOI: 10.6084/m9.figshare.12408233
title: DICE microCT and MRI data for Mandibular musculature constrains brain-endocast disparity in sarcopterygians

description: The scan of the adult <i>Neoceratodus</i> specimen was obtained using the 3T GE Signa Exite HDx human MRI scanner (Signa Excite 750; GE Healthcare; Milwaukee, WI), equipped with an 8-Channel Cardiac Coil, as part of the Digital Fish Library project Berquist et al. (2012). The pulse sequence parameters used were: flip angle of 35 degrees, 12.4 ms repetition time, 3.9 ms echo time, and three averages. Images were collected with slice thickness of 0.7 mm and resulting image resolution of 703 microns. Data were converted to DICOM format for image processing and visualisation. The Magnetic Resonance Imaging (MRI) scan of the adult <i>Neoceratodus</i> specimen was obtained from the Digital Fish Library catalogue, University of California San Diego (http://www.digitalfishlibrary.org). Image segmentation of the brain and braincase was performed using MIMICS v.17 (Materialise MedicalCo Belgium). <br> <i>Protopterus aethiopicus and Protopterus dolloi.</i> Specimens <br> were stained in IKI using the method of Metscher (2009) for three months. Micro-CT (uCT) scans were obtained using a Feinfocus 10-160kV transmission X-ray source and a Perkin Elmer XRD0822 1 MP flat panel X-ray camera. The peak energy used was 120kV, and 2 second exposures were corrected with offset and gain images. The resulting exposures were reconstructed as a tif stack using OctopusV9 resulting in a voxel size of 87.3 and 86.9 microns for <i>P. aethiopicus </i>and <i>P. dolloi</i> respectively. <br> <br> <i>Salamanders. </i>DiceCT contrast staining was completed using a Lugol's Iodine (I2KI) solution. 11.75% Lugol's Iodine was prepared following the protocol of Gignac & Kley (2014) . <i>Ambystoma</i> was stained for 5 days prior to uCT scanning, whereas <i>Cynops</i> was scanned after only 72 hours. Both specimens were imaged using a Skyscan1173 (Bruker) desktop uCT scanner and were reconstructed as a stack of jpegs using NRecon 1.6.6. In both cases, the files were cropped in ImageJ (to reduce file size and sampled images from the stack at an interval of 2 in the Z-plane. The resultant voxel size for <i>Ambystoma</i> is 16.69 x 16.69 x 33.38 microns, and <i>Cynops</i> is 15.868 x 15.868 x 31.727 microns.<br>
DOI: 10.6084/m9.figshare.12408197
title: Protopterus aethiopicus DICE microCT data for Mandibular musculature constrains brain-endocast disparity in sarcopterygians

description: The specimen was stained in IKI using the method of Metscher (2009) for three months.<br> Micro-CT (uCT) scans were obtained using a Feinfocus 10-160kV transmission X-ray source and a Perkin Elmer XRD0822 1 MP flat panel X-ray camera. The peak energy used was 120kV, and 2 second exposures were corrected with offset and gain images. The resulting exposures were reconstructed as a tif stack using OctopusV9 resulting in a voxel size of 87.3.
DOI: 10.6084/m9.figshare.12408185
title: Example data for bit slimming and summarizing GO terms

description: Example data for bit slimming and summarizing GO terms
DOI: 10.6084/m9.figshare.12408233.v1
title: Protopterus dolloi DICE microCT data for Mandibular musculature constrains brain-endocast disparity in sarcopterygians

description: The specimen was stained in IKI using the method of Metscher (2009) for three months.<br> p { margin-bottom: 0.25cm; direction: ltr; color: #000000; line-height: 115%; text-align: left; orphans: 2; widows: 2; background: transparent } p.western { font-family: "Calibri", serif; font-size: 11pt; so-language: en-AU } p.cjk { font-family: "Calibri"; font-size: 11pt; so-language: en-US } p.ctl { font-family: "DejaVu Sans"; font-size: 11pt; so-language: ar-SA } a:link { color: #0000ff; text-decoration: underline } Micro-CT (uCT) scans were obtained using a Feinfocus 10-160kV transmission X-ray source and a Perkin Elmer XRD0822 1 MP flat panel X-ray camera. The peak energy used was 120kV, and 2 second exposures were corrected with offset and gain images. The resulting exposures were reconstructed as a tif stack using OctopusV9 resulting in a voxel size of 86.9 microns. p { margin-bottom: 0.25cm; direction: ltr; color: #000000; line-height: 115%; text-align: left; orphans: 2; widows: 2; background: transparent } p.western { font-family: "Calibri", serif; font-size: 11pt; so-language: en-AU } p.cjk { font-family: "Calibri"; font-size: 11pt; so-language: en-US } p.ctl { font-family: "DejaVu Sans"; font-size: 11pt; so-language: ar-SA } a:link { color: #0000ff; text-decoration: underline }
DOI: 10.6084/m9.figshare.12408185.v1
title: Example data for bit slimming and summarizing GO terms

description: Example data for bit slimming and summarizing GO terms
DOI: 10.6084/m9.figshare.12408182
title: Latimeria MRI data for Mandibular musculature constrains brain-endocast disparity in sarcopterygians

description: Specimen MNHN C24 (CCC 27 was immersed for 1 month in a solution of phosphomolybdic acid solution (5 % in 70 % ethanol) to increase the contrast of the soft tissues for scanning. The specimen was scanned at the AST-RX facility of the Muséum national d'Histoire naturelle, Paris, France, using the following scanning parameters: voltage, 200 kV; current, 200 μA; number of slices, 1,289; voxel size, 0.260 mm; field of view, 262.34 mm. <br><br>
DOI: 10.6084/m9.figshare.12408182.v1
title: Latimeria MRI data for Mandibular musculature constrains brain-endocast disparity in sarcopterygians

description: Specimen MNHN C24 (CCC 27 was immersed for 1 month in a solution of phosphomolybdic acid solution (5 % in 70 % ethanol) to increase the contrast of the soft tissues for scanning. The specimen was scanned at the AST-RX facility of the Muséum national d'Histoire naturelle, Paris, France, using the following scanning parameters: voltage, 200 kV; current, 200 μA; number of slices, 1,289; voxel size, 0.260 mm; field of view, 262.34 mm. <br><br>
DOI: 10.6084/m9.figshare.12408164.v1
title: ctd_residual.mat

description: CTD & mooring residual data for GRL manuscript "A possible bifurcation of the Korean Coastal Water into the middle of the Southern Yellow Sea in January of 2017"
DOI: 10.25392/leicester.data.12408119
title: Appendix VI: Sequencing platform comparison

description: PhD thesis: PRDM9 Diversity, Recombination Landscapes and Childhood Leukaemia by Ihthisham Ali <br><br>Appendix VI contains the consensus sequences from reads from different sequencing platforms (Sanger, Ion Torrent 200bp and 400bp formats and Illumina HiSeq2000 mapped to reference ZnF arrays confirmed via Sanger.<br>Appendix VI: A. L4 and A allele fragments mapped across platformsAppendix VI: B. L47 mapping across platforms for the PRDM9 L47/C carrierAppendix VI: C. C allele mapping across platforms for the PRDM9 L47/C carrier
DOI: 10.25392/leicester.data.12408119.v1
title: Appendix VI: Sequencing platform comparison

description: PhD thesis: PRDM9 Diversity, Recombination Landscapes and Childhood Leukaemia by Ihthisham Ali <br><br>Appendix VI contains the consensus sequences from reads from different sequencing platforms (Sanger, Ion Torrent 200bp and 400bp formats and Illumina HiSeq2000 mapped to reference ZnF arrays confirmed via Sanger.<br>Appendix VI: A. L4 and A allele fragments mapped across platformsAppendix VI: B. L47 mapping across platforms for the PRDM9 L47/C carrierAppendix VI: C. C allele mapping across platforms for the PRDM9 L47/C carrier
DOI: 10.26180/5ed5ac8c0ae8a
title: Ovens catchment recharge study

description: Datasets used in Cartwright et al. (2020) Ovens recharge study<br>
DOI: 10.6084/m9.figshare.12408056
title: Film flow associated constant soil water diffusivity in the falling rate soil evaporation stage

description: cumulative evaporation observed for sandy loam and loam soil from Suleiman and Ritchie (2003)
DOI: 10.6084/m9.figshare.12408056.v1
title: Film flow associated constant soil water diffusivity in the falling rate soil evaporation stage

description: cumulative evaporation observed for sandy loam and loam soil from Suleiman and Ritchie (2003)
DOI: 10.6084/m9.figshare.12408005
title: antiscam_all_symbolic_planner.txt

description: Annotated AntiScam Dataset
DOI: 10.6084/m9.figshare.12408005.v1
title: antiscam_all_symbolic_planner.txt

description: Annotated AntiScam Dataset
DOI: 10.6084/m9.figshare.12407735
title: Antibiotic sensitivity data for the bacterial strain LMJ (Bacterium strain clone LIB091_C05_1243 variant 16S ribosomal RNA; GenBank Accession # MN633292.1).

description: The Excel data file, Data S1 LMJ.xlsx contain information about the means and standard deviations of the zones of inhibitions of the bacterial strain LMJ and <i>Chlamydomonas</i>, induced by 4 antibiotics. <br><br>The Excel data file, Data S2 LMJ.xlsx contain statistical analyses of the zones of inhibitions of the bacterial strain LMJ and <i>Chlamydomonas</i>, induced by 4 antibiotics. <br><br>Antibiotics used are: Penicillin, Chloramphenicol, Neomycin & Polymyxin B. Three biological replicates were used for the generation of the data. Two different doses of antibiotics were used: 50 and 100 micrograms of each antibiotic.
DOI: 10.6084/m9.figshare.12407732
title: Journaling Dataset For Upload June 2020.sav

description: These data were collected from multiple classes regarding which themes covered during instruction most influenced their position on evolution.