cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15131/shef.data.5568151
title: Automatic Assessment of Full LV Coverage in Cardiac Cine MRI Using Learned Intensity Attributes with Discriminative 3D CNNs

description: This dataset has been created to serve as complimentary material to a journal publication currently under review by IEEE Transactions on Medical Imaging. <br>The dataset contains two files, a comma-separated file (.csv) and a video (.avi). The first file contains the results of applying our Discriminative 3D CNN (D3D CNN) Image Quality Assessment (IQA) algorithm to a set of images from the UK Biobank dataset. The Image Quality Assessment file named "IQA spreadsheet.csv" contains 3 columns. The first column labeled "f.eid" lists 5000+ patient IDs, the next column labeled "MBS" (Missing Basal Slice) contains binary values indicating the presence or absence of the basal slice. Similarly the last column labeled "MAS" (Missing Apical Slice) indicates the presence or absence of the apical slice in the image volume. <br>The second file is a demo of the algorithm's functionality. The video shows a unique patient's cardiac image volume, and the result of the detection/non-detection of the basal and apical slices indicated with green and red labels on the images and on a side panel. <br>This dataset has been created to serve as complementary material to a journal publication currently under review by IEEE Transactions on Medical Imaging.<br>The dataset contains two files, a comma-separated file (.csv) and a video (.avi). The first file contains the results of applying our Discriminative 3D CNN (D3D CNN) Image Quality Assessment (IQA) algorithm to a set of images from the UK Biobank dataset. The Image Quality Assessment file named "IQA spreadsheet.csv" contains 3 columns. The first column labeled "f.eid" lists 5000+ patient IDs, the next column labeled "MBS" (Missing Basal Slice) contains binary values indicating the presence or absence of the basal slice. Similarly the last column labeled "MAS" (Missing Apical Slice) indicates the presence or absence of the apical slice in the image volume.<br>The second file is a demo of the algorithm's functionality. The video shows a unique patient's cardiac image volume, and the result of the detection/non-detection of the basal and apical slices indicated with green and red labels on the images and on a side panel.
DOI: 10.6084/m9.figshare.5568124
title: JHI_5088

description: JHI_5088 E. coli bovine slurry isolate
DOI: 10.15131/shef.data.5568151.v1
title: Automatic Assessment of Full LV Coverage in Cardiac Cine MRI Using Learned Intensity Attributes with Discriminative 3D CNNs

description: This dataset has been created to serve as complimentary material to a journal publication currently under review by IEEE Transactions on Medical Imaging. <br>The dataset contains two files, a comma-separated file (.csv) and a video (.avi). The first file contains the results of applying our Discriminative 3D CNN (D3D CNN) Image Quality Assessment (IQA) algorithm to a set of images from the UK Biobank dataset. The Image Quality Assessment file named "IQA spreadsheet.csv" contains 3 columns. The first column labeled "f.eid" lists 5000+ patient IDs, the next column labeled "MBS" (Missing Basal Slice) contains binary values indicating the presence or absence of the basal slice. Similarly the last column labeled "MAS" (Missing Apical Slice) indicates the presence or absence of the apical slice in the image volume. <br>The second file is a demo of the algorithm's functionality. The video shows a unique patient's cardiac image volume, and the result of the detection/non-detection of the basal and apical slices indicated with green and red labels on the images and on a side panel. <br>
DOI: 10.6084/m9.figshare.5568124.v1
title: JHI_5088

description: JHI_5088 E. coli bovine slurry isolate
DOI: 10.6084/m9.figshare.5568031
title: Supplementary Material for: Pre-End-Stage Renal Disease Hemoglobin Variability Predicts Post-End-Stage Renal Disease Mortality in Patients Transitioning to Dialysis

description: <b><i>Background:</i></b> Hemoglobin variability (Hb-var) has been associated with increased mortality both in non-dialysis dependent chronic kidney disease (NDD-CKD) and end-stage renal disease (ESRD) patients. However, the impact of Hb-var in advanced NDD-CKD on outcomes after dialysis initiation remains unknown. <b><i>Methods:</i></b> Among 11,872 US veterans with advanced NDD-CKD transitioning to dialysis between October 2007 through September 2011, we assessed Hb-var calculated from the residual SD of at least 3 Hb values during the last 6 months before dialysis initiation (prelude period) using within-subject linear regression models, and stratified into quartiles. Outcomes included post-transition all-cause, cardiovascular, and infection-related mortality, assessed in Cox proportional hazards models and adjusted for demographics, comorbidities, length of hospitalization, medications, estimated glomerular filtration rate (eGFR), type of vascular access, Hb parameters (baseline Hb [i.e., intercept] and change in Hb [i.e., slope]), and number of Hb measurements. <b><i>Results:</i></b> Higher prelude Hb-var was associated with use of iron and antiplatelet agents, tunneled dialysis catheter use, higher levels of baseline Hb, change in Hb, eGFR, and serum ferritin. After multivariable adjustment, higher prelude Hb-var was associated with higher post-ESRD all-cause and infection-related mortality, but not cardiovascular mortality (adjusted hazard ratios [95% CI] for the highest [vs. lowest] quartile of Hb-var, 1.10 [1.02–1.19], 1.28 [0.93–1.75], and 0.93 [0.79–1.10], respectively). <b><i>Conclusions:</i></b> High pre-ESRD Hb-var is associated with higher mortality, particularly from infectious causes rather than cardiovascular causes. Further research is required to clarify the underlying mechanisms and true causal nature of the observed association.
DOI: 10.17028/rd.lboro.5568028
title: Supplementary information files for The Pseudocapacitive Nature of CoFe2O4 Thin Films

description: Supplementary information files for The Pseudocapacitive Nature of CoFe2O4 Thin Films.Nanostructured Cobalt ferrite (CoFe<sub>2</sub>O<sub>4</sub>) thin films are fabricated by aerosol-assisted chemical vapour deposition (AACVD) and studied for application in supercapacitors. XRD and Raman spectroscopic analysis confirms the formation of single phase CoFe<sub>2</sub>O<sub>4</sub>. SEM analysis shows that the thin film morphology consists of nanoparticles less than 100 nm in size that are sintered together to form larger dendrites raised from the substrate. The larger dendrites range from 0.5–1 μm in diameter and are uniformly distributed over the FTO substrate, providing a highly porous structure which is desired for supercapacitor electrodes. Three-electrode electrochemical measurements reveal that CoFe<sub>2</sub>O<sub>4</sub> is pseudocapacitive and is highly conducting. Studies of CoFe<sub>2</sub>O<sub>4</sub> thin films in two-electrode symmetric supercapacitor configuration show a capacitance of 540 μF cm<sup>−2</sup> and a relaxation time constant of 174 ms. Around 80% of the capacitance is retained after 7000 charge-discharge cycles when a maximum charging voltage of 1 V was used, indicating that the pseudocapacitive processes in CoFe<sub>2</sub>O<sub>4</sub> are highly reversible and that it exhibits excellent chemical stability in 1 M NaOH alkaline electrolyte solution. The results show that CoFe<sub>2</sub>O<sub>4</sub> is a cheap and promising alternative pseudocapacitive material to replace the expensive pseudocapacitive materials.<br>
DOI: 10.6084/m9.figshare.5568031.v1
title: Supplementary Material for: Pre-End-Stage Renal Disease Hemoglobin Variability Predicts Post-End-Stage Renal Disease Mortality in Patients Transitioning to Dialysis

description: <b><i>Background:</i></b> Hemoglobin variability (Hb-var) has been associated with increased mortality both in non-dialysis dependent chronic kidney disease (NDD-CKD) and end-stage renal disease (ESRD) patients. However, the impact of Hb-var in advanced NDD-CKD on outcomes after dialysis initiation remains unknown. <b><i>Methods:</i></b> Among 11,872 US veterans with advanced NDD-CKD transitioning to dialysis between October 2007 through September 2011, we assessed Hb-var calculated from the residual SD of at least 3 Hb values during the last 6 months before dialysis initiation (prelude period) using within-subject linear regression models, and stratified into quartiles. Outcomes included post-transition all-cause, cardiovascular, and infection-related mortality, assessed in Cox proportional hazards models and adjusted for demographics, comorbidities, length of hospitalization, medications, estimated glomerular filtration rate (eGFR), type of vascular access, Hb parameters (baseline Hb [i.e., intercept] and change in Hb [i.e., slope]), and number of Hb measurements. <b><i>Results:</i></b> Higher prelude Hb-var was associated with use of iron and antiplatelet agents, tunneled dialysis catheter use, higher levels of baseline Hb, change in Hb, eGFR, and serum ferritin. After multivariable adjustment, higher prelude Hb-var was associated with higher post-ESRD all-cause and infection-related mortality, but not cardiovascular mortality (adjusted hazard ratios [95% CI] for the highest [vs. lowest] quartile of Hb-var, 1.10 [1.02–1.19], 1.28 [0.93–1.75], and 0.93 [0.79–1.10], respectively). <b><i>Conclusions:</i></b> High pre-ESRD Hb-var is associated with higher mortality, particularly from infectious causes rather than cardiovascular causes. Further research is required to clarify the underlying mechanisms and true causal nature of the observed association.
DOI: 10.6084/m9.figshare.5568043.v1
title: Nasogastric aspiration/lavage in patients with gastrointestinal bleeding: a review of the evidence

description: <b>Introduction</b>: The usefulness of nasogastric aspiration and nasogastric lavage in patients with gastrointestinal bleeding is controversial, as evidenced by conflicting recommendations, both among and within society guidelines. <b>Areas covered</b>: Considering these controversies, we reviewed the evidence regarding the following questions: 1) Can nasogastric lavage stop or slow down the bleeding and improve subsequent endoscopic visualization? 2) Is nasogastric aspiration helpful for the localization of bleeding? 3) Can nasogastric aspiration identify high risk patients that might benefit from earlier endoscopy? 4) Is there evidence for benefit in terms of outcomes from using nasogastric aspiration? 5) Is nasogastric intubation safe in patients with possible esophageal varices? Our review was conducted according to PRISMA guidelines. <b>Expert commentary</b>: Based on the available literature, nasogastric lavage or aspiration cannot be routinely recommended unless a large properly designed randomized trial (which is currently lacking) proves otherwise. It is a painful and time-consuming procedure with no demonstrated benefit for the patient in terms of outcomes. Other clinical and laboratory parameters, and risk scores, are less invasive and are effective for guiding the stratification and management of patients, while pre-endoscopic erythromycin infusion is a good if not better alternative for improving visualization of the stomach.
DOI: 10.17028/rd.lboro.5568028.v1
title: Supplementary information files for The Pseudocapacitive Nature of CoFe2O4 Thin Films

description: Supplementary information files for The Pseudocapacitive Nature of CoFe2O4 Thin Films.Nanostructured Cobalt ferrite (CoFe<sub>2</sub>O<sub>4</sub>) thin films are fabricated by aerosol-assisted chemical vapour deposition (AACVD) and studied for application in supercapacitors. XRD and Raman spectroscopic analysis confirms the formation of single phase CoFe<sub>2</sub>O<sub>4</sub>. SEM analysis shows that the thin film morphology consists of nanoparticles less than 100 nm in size that are sintered together to form larger dendrites raised from the substrate. The larger dendrites range from 0.5–1 μm in diameter and are uniformly distributed over the FTO substrate, providing a highly porous structure which is desired for supercapacitor electrodes. Three-electrode electrochemical measurements reveal that CoFe<sub>2</sub>O<sub>4</sub> is pseudocapacitive and is highly conducting. Studies of CoFe<sub>2</sub>O<sub>4</sub> thin films in two-electrode symmetric supercapacitor configuration show a capacitance of 540 μF cm<sup>−2</sup> and a relaxation time constant of 174 ms. Around 80% of the capacitance is retained after 7000 charge-discharge cycles when a maximum charging voltage of 1 V was used, indicating that the pseudocapacitive processes in CoFe<sub>2</sub>O<sub>4</sub> are highly reversible and that it exhibits excellent chemical stability in 1 M NaOH alkaline electrolyte solution. The results show that CoFe<sub>2</sub>O<sub>4</sub> is a cheap and promising alternative pseudocapacitive material to replace the expensive pseudocapacitive materials.<br>
DOI: 10.6084/m9.figshare.5567998
title: Raw transcriptome - Capsaspora owczarzaki

description: Raw counts of ​RNA-seq mapping experiments of adherent, cystic and aggregative <i>Capsaspora owczarzaki</i> cells. For each sample, the table contains the raw read counts (appendix: -#) and ​cRPKM values (appendix: -R). Methodological details in Sebé-Pedrós <i>et al. </i>eLIFE<i> </i>2013 (doi: 10.7554/eLife.01287). ​Raw reads can be found in NCBI under BioProject accession number​PRJNA20341​.​Sample description (see details in SRA):​<br>SRR343047 Adherent cells (Stage 1)<br>SRR343054 Floating cells (Stage 2)<br>SRR515464 Capsaspora_owczarzaki_ATCC 30868_Line_2_Floating<br>SRR515465 Capsaspora_owczarzaki_ATCC 30872_Line_3_Aggregative<br>SRR515466 Capsaspora_owczarzaki_ATCC 30870_Line_1_Aggregative<br>SRR515467 Capsaspora_owczarzaki_ATCC 30871_Line_2_Aggregative<br>SRR515468 Capsaspora_owczarzaki_ATCC 30872_Line_3_Aggregative<br>SRR515469 Capsaspora_owczarzaki_ATCC 30870_Line_1_Aggregative<br>SRR515470 Capsaspora_owczarzaki_ATCC 30868_Line_2_Floating<br>SRR515471 Capsaspora_owczarzaki_ATCC 30871_Line_2_Aggregative<br>SRR515472 Capsaspora_owczarzaki_ATCC 30865_Line_2_Adherent<br>SRR515473 Capsaspora_owczarzaki_ATCC 30867_Line_1_Floating<br>SRR515474 Capsaspora_owczarzaki_ATCC 30866_Line_3_Adherent<br>SRR515475 Capsaspora_owczarzaki_ATCC 30864_Line_1_Adherent<br>SRR515476 Capsaspora_owczarzaki_ATCC 30869_Line_3_Floating<br>SRR515477 Capsaspora_owczarzaki_ATCC 30867_Line_1_Floating<br>SRR515478 Capsaspora_owczarzaki_ATCC 30865_Line_2_Adherent<br>SRR515479 Capsaspora_owczarzaki_ATCC 30869_Line_3_Floating<br>SRR515480 Capsaspora_owczarzaki_ATCC 30866_Line_3_Adherent<br>SRR515481 Capsaspora_owczarzaki_ATCC 30864_Line_1_Adherent<br>www.multicellgenome.comInstitute of Evolutionary Biology (CSIC-UPF)
DOI: 10.6084/m9.figshare.5567989
title: Supplementary Material for: Detection of a Splice Site Variant in a Patient with Glomerulopathy and Fibronectin Deposits

description: <b><i>Background/Aims:</i></b> Glomerulopathy with fibronectin deposits (GFND; OMIM: 601894) is a very rare inherited kidney disease caused by pathogenic variants in the <i>FN1</i> gene. Only 9 exonic pathogenic variants in <i>FN1</i>, 9 at the heparin-binding site, and 1 at the integrin-binding site have been reported. No intronic variants in <i>FN1</i> have been detected. <b><i>Methods:</i></b> We found a pathogenic intronic variant in intron 36 (c.5888–2A&gt;G) located at the heparin-binding site. To determine whether this mutation influences splicing processes, we conducted RT-PCR analysis and an in vitro splicing assay using minigene construction. <b><i>Results:</i></b> RT-PCR using RNA extracted from leukocytes of the proband failed because of the low expression of <i>FN1</i> mRNA in leukocytes. We conducted in vitro functional splicing analysis using minigenes and found that c.5888–2A&gt;G caused a 12 bp deletion at exon 37 by the activation of a novel splicing acceptor site within exon 37. We were able to detect the same abnormal transcript in mRNA extracted from the patient’s urinary sediment and confirmed the pathogenicity of c.5888–2A&gt;G by both RT-PCR using the patient sample and an in vitro splicing assay. <b><i>Conclusion:</i></b> Intronic variants can cause GFND. Minigene analysis is useful for determining the pathogenicity of the intronic variants and could be used for all inherited kidney diseases.
DOI: 10.6084/m9.figshare.5567998.v1
title: Raw transcriptome - Capsaspora owczarzaki

description: Raw counts of ​RNA-seq mapping experiments of adherent, cystic and aggregative <i>Capsaspora owczarzaki</i> cells. For each sample, the table contains the raw read counts (appendix: -#) and ​cRPKM values (appendix: -R). Methodological details in Sebé-Pedrós <i>et al. </i>eLIFE<i> </i>2013 (doi: 10.7554/eLife.01287). ​Raw reads can be found in NCBI under BioProject accession number​PRJNA20341​.​Sample description (see details in SRA):​<br>SRR343047 Adherent cells (Stage 1)<br>SRR343054 Floating cells (Stage 2)<br>SRR515464 Capsaspora_owczarzaki_ATCC 30868_Line_2_Floating<br>SRR515465 Capsaspora_owczarzaki_ATCC 30872_Line_3_Aggregative<br>SRR515466 Capsaspora_owczarzaki_ATCC 30870_Line_1_Aggregative<br>SRR515467 Capsaspora_owczarzaki_ATCC 30871_Line_2_Aggregative<br>SRR515468 Capsaspora_owczarzaki_ATCC 30872_Line_3_Aggregative<br>SRR515469 Capsaspora_owczarzaki_ATCC 30870_Line_1_Aggregative<br>SRR515470 Capsaspora_owczarzaki_ATCC 30868_Line_2_Floating<br>SRR515471 Capsaspora_owczarzaki_ATCC 30871_Line_2_Aggregative<br>SRR515472 Capsaspora_owczarzaki_ATCC 30865_Line_2_Adherent<br>SRR515473 Capsaspora_owczarzaki_ATCC 30867_Line_1_Floating<br>SRR515474 Capsaspora_owczarzaki_ATCC 30866_Line_3_Adherent<br>SRR515475 Capsaspora_owczarzaki_ATCC 30864_Line_1_Adherent<br>SRR515476 Capsaspora_owczarzaki_ATCC 30869_Line_3_Floating<br>SRR515477 Capsaspora_owczarzaki_ATCC 30867_Line_1_Floating<br>SRR515478 Capsaspora_owczarzaki_ATCC 30865_Line_2_Adherent<br>SRR515479 Capsaspora_owczarzaki_ATCC 30869_Line_3_Floating<br>SRR515480 Capsaspora_owczarzaki_ATCC 30866_Line_3_Adherent<br>SRR515481 Capsaspora_owczarzaki_ATCC 30864_Line_1_Adherent<br>www.multicellgenome.comInstitute of Evolutionary Biology (CSIC-UPF)
DOI: 10.6084/m9.figshare.5567989.v1
title: Supplementary Material for: Detection of a Splice Site Variant in a Patient with Glomerulopathy and Fibronectin Deposits

description: <b><i>Background/Aims:</i></b> Glomerulopathy with fibronectin deposits (GFND; OMIM: 601894) is a very rare inherited kidney disease caused by pathogenic variants in the <i>FN1</i> gene. Only 9 exonic pathogenic variants in <i>FN1</i>, 9 at the heparin-binding site, and 1 at the integrin-binding site have been reported. No intronic variants in <i>FN1</i> have been detected. <b><i>Methods:</i></b> We found a pathogenic intronic variant in intron 36 (c.5888–2A&gt;G) located at the heparin-binding site. To determine whether this mutation influences splicing processes, we conducted RT-PCR analysis and an in vitro splicing assay using minigene construction. <b><i>Results:</i></b> RT-PCR using RNA extracted from leukocytes of the proband failed because of the low expression of <i>FN1</i> mRNA in leukocytes. We conducted in vitro functional splicing analysis using minigenes and found that c.5888–2A&gt;G caused a 12 bp deletion at exon 37 by the activation of a novel splicing acceptor site within exon 37. We were able to detect the same abnormal transcript in mRNA extracted from the patient’s urinary sediment and confirmed the pathogenicity of c.5888–2A&gt;G by both RT-PCR using the patient sample and an in vitro splicing assay. <b><i>Conclusion:</i></b> Intronic variants can cause GFND. Minigene analysis is useful for determining the pathogenicity of the intronic variants and could be used for all inherited kidney diseases.
DOI: 10.6084/m9.figshare.5567806
title: Cleavage and polyadenylation sites

description: GFF files containing 48,092 cleavage and polyadenylation and 25,450 3UTR sites from all published samples from West et al., Genome Biology 2017. Mapped against Wormbase WS250.<br>
DOI: 10.6084/m9.figshare.5567806.v1
title: Cleavage and polyadenylation sites

description: GFF files containing 48,092 cleavage and polyadenylation and 25,450 3UTR sites from all published samples from West et al., Genome Biology 2017. Mapped against Wormbase WS250.<br>
DOI: 10.6084/m9.figshare.5567041
title: Ratings

description: Participant comments on why the selected the statements they did
DOI: 10.6084/m9.figshare.5567041.v1
title: Ratings

description: Participant comments on why the selected the statements they did
DOI: 10.6084/m9.figshare.5567038
title: Dynamic time sweep and creep test measurement for 4.2 wt% waste activated sludge at various gas flow rates (0.5 – 1.5 LPM).

description: This submission contains the raw rheometer files from time sweep and creep test measurements of waste activated sludge (total solids content = 4.2 wt %). The sludge samples were measured at various gas flow rates (0.54 LPM and 1.5 LPM). The dynamic time sweep measurements were generated from the sludge sample first without gas at 0.08% strain across 25 minutes. Then the sample was conditioned and the gas was injected for 20 minutes before the measurement at similar conditions. Similarly, the dynamic creep test measurements were generated from the sludge sample first without gas at 0.89pa stress across 10 minutes. The measurements were carried out on a DHR-3 rheometer (TA-Instruments), equipped custom made cup. For detail procedure refer: Bobade, V, et al. 2017, 'Impact of gas injection on the apparent viscosity and viscoelastic property of waste activated sewage sludge', <i>Water Research</i>, vol. 114, pp. 296-307. Detailed experimental protocol is recorded in the .tri (TRIOS) file attached with each data set. This file can be read using the TRIOS software made available on TA-Instruments website (http://www.tainstruments.com/support/software-downloads-support/downloads/). Rheometer geometry dimensions and other details are also obtainable from these files.<br>Please contact authors for access to files. Contact: nicky.eshtiaghi@rmit.edu.au RMITRheologyGroup@gmail.com
DOI: 10.6084/m9.figshare.5566948
title: QCSE measurementsof type-I spherical quantum dots

description: The data are .tif files of QCSE measurements of single type-II ZnSe/CdS nanorods' spectra under electric field modulation. Each measurement contains two files, one regular wide-field image (100 frames in .tif format) and one prism-dispersed image (600 frames in .tif format). The prism-dispersed images were acquired in synchrony to a square voltage applied to a device, in which homogeneous electric field would be generated across the film where nanoparticles were located.<br>this doi contains all the measurement files of type-I spherical quantum dots. The measurement files of type-II ZnSe/CdS nanorods can be found here: 10.6084/m9.figshare.7439189<br>
DOI: 10.6084/m9.figshare.5566948.v1
title: QCSE measurements

description: The data are .tif files of QCSE measurements of single type-II ZnSe/CdS nanorods' spectra under electric field modulation. Each measurement contains two files, one regular wide-field image (100 frames in .tif format) and one prism-dispersed image (600 frames in .tif format). The prism-dispersed images were acquired in synchrony to a square voltage applied to a device, in which homogeneous electric field would be generated across the film where nanoparticles were located.<br>
DOI: 10.7910/dvn/ni6sbj/kvj0ea
title: sample1.Rdata

description: :unav
DOI: 10.7910/dvn/ni6sbj/5hljfb
title: sample2.Rdata

description: :unav
DOI: 10.7910/dvn/ni6sbj/aco77d
title: readme.txt

description: :unav