cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9116087.v1
title: Melanoma in older patients: declining gap in survival between younger and older patients with melanoma

description: <b>Background:</b> Older people have the highest incidence of melanoma and the population in most Western countries is ageing. We evaluated how the gap in incidence and survival between younger and older patients has developed during the past decades. <b>Material and methods:</b> All patients diagnosed with cutaneous melanoma between 1989 and 2015 (<i>n</i> = 84,827) were identified from the Netherlands Cancer Registry. Elderly were defined as aged ≥70 years. Differences in patient and tumor characteristics were described, age-specific incidence rates were calculated, and relative survival (RS) and multivariable analyses estimating the Relative Excess Rate of dying (RER) were conducted <b>Results:</b> In older men, the melanoma age-standardized incidence increased from 18 to 103/100,000 person-years (py) between 1989 and 2015 and in older women from 23 to 70/100,000 py. In younger men and women, it increased from 8 to 21 and from 13 to 28/100,000 py, respectively. Median Breslow thickness declined from 1.8 to 1.1 mm and from 1.6 to 1.1 mm in older men and women (2003 versus 2015), and from 1.1 to 0.9 mm and 0.9 to 0.8 mm in younger men and women. In older men, 5-year RS increased from 67% (95% CI: 63%–72%) in 1989–1997 to 85% (95% CI: 83%–87%) in 2007–2015 and in older women from 81% (95% CI: 78%–85%) to 89% (95% CI: 87%–91%). In younger men and women, RS increased from 82% (95% CI: 81%–83%) to 90% (95% CI: 90%–91%) and from 92% (95% CI: 92%–93%) to 96% (95% CI: 95%–96%). After case-mix correction , older men and women no longer showed an improved survival over time (RER 2010–2015 <i>versus</i> 2003–2009: 0.97; 95% CI: 0.81–1.16 and 0.95; 95% CI: 0.79–1.16). Whereas in younger men and women survival remained improved (RER 0.75; 95% CI: 0.67–0.83 and 0.77; 95%CI: 0.67–0.89). <b>Conclusion:</b> The gap in melanoma incidence between younger and older people is increasing due to a strong increase in incidence in older adults. Disparities in survival are declining, related to a narrowing gap in Breslow thickness.
DOI: 10.25386/genetics.8949227.v1
title: Supplemental Material for Harel et al., 2019

description: Figure S1 contains an illustration of a standard decision tree model. <br>Figure S2 contains an illustration of the InPhenotype algorithm.<br>Figure S3 contains results of applying InPhenotype on real data in yeast and mouse.<br>Figure S4 contains an illustration of the haplotype probabilities discretization pipeline.<br>Figure S5 contains performance comparisons.<br>Figure S6 shows InPhenotype's robustness to different method parameters.<br>Figure S7 illustrates the contribution of genetics data and the performance of InPhenotype in the presence and absence of a weighting scheme. <br>Figure S8 shows performance on additional analyses of synthetic datasets.<br>Figure S9 shows performance on various number of causal SNPs.<br>Figure S10 shows the molecular pathways of large modules which were discovered by InPhenotype.<br>Table S1 contains the gene-SNP pairs associated with yeast cell growth in response to Rapamycin. <br>Table S2 contains the gene-SNP pairs associated with mice weight loss following Influenza infection.
DOI: 10.6084/m9.figshare.9114833
title: Performance Characteristics of a Modified HIV-1 Drug Resistance Genotyping Method for use in Resource Limited Settings

description: This data set includes data that was generated in experiments aimed to modify and validate a commercially available HIV drug resistance testing. Data contain the Stanford HIV drug resistance reports generated from the Stanford HIV drug resistance online program. <br>Assay modification was performed by reducing the reagent volume by up to half at nested PCR and Sequencing reactions. Upon modification of the assay, the performance of the newly modifies assay was validated according to the WHO assay validation guidelines. Validation included testing for the assay accuracy,precision, reproducibility, and amplification sensitivity<br><br>This data is therefore presented in four different categories; accuracy testing data, precision testing data, reproducibility testing data and amplification sensitivity testing data. The assays were performed using remnant samples from HIV viral load testing thus the consent statements were waived by the committee.
DOI: 10.6084/m9.figshare.9116741
title: JAE-2018-00960_data.csv

description: Data set of Eurasian beavers from Norway, containing information about age, sex, spatial location, and reaction towards a simulated intruder.<br>
DOI: 10.6084/m9.figshare.9116741.v1
title: JAE-2018-00960_data.csv

description: Data set of Eurasian beavers from Norway, containing information about age, sex, spatial location, and reaction towards a simulated intruder.<br>
DOI: 10.6084/m9.figshare.9116864.v1
title: Bivariate residual plots with simulation polygons

description: When using univariate models, goodness-of-fit can be assessed through many different methods, including graphical tools such as half-normal plots with a simulation envelope. This is straightforward due to the notion of ordering of a univariate sample, which can readily reveal possible outliers. In the bivariate case, however, it is often difficult to detect extreme points and verify whether a sample of residuals is a reasonable realisation from a fitted model. We propose a new framework, implemented as the bivrp R package, available on CRAN. Our framework uses the same principles of the simulation envelope in a half-normal plot, but as a simulation polygon for each point in a bivariate sample. By using algorithms of convex hull construction and polygon area reduction, we describe how our method works and illustrate its functionality with examples using simulated bivariate normal data and real bivariate count data. We show how different model diagnostics can produce different results and pinpoint potential drawbacks of our approach, such as the limitations in terms of computational burden.
DOI: 10.6084/m9.figshare.9117092.v1
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(yadd)

description: secondary structures of eukaryotic group II introns rfam set (yadd)
DOI: 10.6084/m9.figshare.9117095
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(no_yadd)

description: secondary structures of eukaryotic group II introns rfam set (no yadd)
DOI: 10.6084/m9.figshare.9117104
title: copy_of_putative_transposons

description: copy of putative transposons
DOI: 10.25386/genetics.8949227
title: Supplemental Material for Harel et al., 2019

description: Figure S1 contains an illustration of a standard decision tree model. <br>Figure S2 contains an illustration of the InPhenotype algorithm.<br>Figure S3 contains results of applying InPhenotype on real data in yeast and mouse.<br>Figure S4 contains an illustration of the haplotype probabilities discretization pipeline.<br>Figure S5 contains performance comparisons.<br>Figure S6 shows InPhenotype's robustness to different method parameters.<br>Figure S7 illustrates the contribution of genetics data and the performance of InPhenotype in the presence and absence of a weighting scheme. <br>Figure S8 shows performance on additional analyses of synthetic datasets.<br>Figure S9 shows performance on various number of causal SNPs.<br>Figure S10 shows the molecular pathways of large modules which were discovered by InPhenotype.<br>Table S1 contains the gene-SNP pairs associated with yeast cell growth in response to Rapamycin. <br>Table S2 contains the gene-SNP pairs associated with mice weight loss following Influenza infection.
DOI: 10.6084/m9.figshare.9117062
title: pat 7 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9117092
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(yadd)

description: secondary structures of eukaryotic group II introns rfam set (yadd)
DOI: 10.6084/m9.figshare.9117095.v2
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(no_yadd)

description: secondary structures of eukaryotic group II introns rfam set (no yadd)
DOI: 10.6084/m9.figshare.9117101
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(putative_transposon)

description: secondary structures of eukaryotic group II introns rfam set (putative transposon)
DOI: 10.6084/m9.figshare.9117101.v1
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(putative_transposon)

description: secondary structures of eukaryotic group II introns rfam set (putative transposon)
DOI: 10.6084/m9.figshare.9117101.v2
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(putative_transposon)

description: secondary structures of eukaryotic group II introns rfam set (putative transposon)
DOI: 10.6084/m9.figshare.9117101.v3
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(putative_transposon)

description: secondary structures of eukaryotic group II introns rfam set (putative transposon)
DOI: 10.6084/m9.figshare.9117101.v4
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(putative_transposon)

description: secondary structures of eukaryotic group II introns rfam set (putative transposon)
DOI: 10.6084/m9.figshare.9117104.v1
title: copy_of_putative_transposons

description: copy of putative transposons
DOI: 10.6084/m9.figshare.9117140
title: pat 7 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9117155
title: pat 8 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118364.v1
title: MHcut analysis of dbSNP/ClinVar deletions

description: dnSNP and ClinVar deletions annotated with micro-homology at the breakpoints and with available Cas9 cut that could efficiently recreate the deletion.<br>This dataset can be explored online with the MHcut browser: https://mhcut-browser.genap.ca/<br><br>It was produced with MHcut: https://github.com/WoltjenLab/MHcut<br><br>
DOI: 10.6084/m9.figshare.9118391
title: Radiation-inducible radioprotective exopolysaccharides of <i>Bacillus siamensis</i> CV5 from irradiated roots of <i>Cistanche violacea</i> to decrease free radical damage produced by ionizing radiation

description: <b>Purpose:</b> To assess exopolysaccharides (EPS) of <i>Bacillus siamensis</i> CV5, isolated from irradiated roots of <i>Cistanche violacea</i>, for their induction by ionizing radiation (IR) and their antioxidant and radioprotective power. <b>Materials and methods:</b> Isolated bacteria from the roots of <i>C. violacea</i> were screened for EPS production. The most EPS-producing bacterium was selected and the response surface methodology (RSM) was applied to elucidate the IR dose effects on EPS production. Gamma irradiation effects on the morphology and functional groups of EPS were studied using microscopy and Fourier transform infra-red (FT-IR). The radioprotective potential of EPS on the survival of <i>B. siamensis</i> CV5 following IR was evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Free radicals scavenging potentialities (FRSP) of non-irradiated and irradiated EPS were evaluated through 2, 2<sup>−</sup>-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS) and ferric reducing ability of plasma (FRAP) assays. <b>Results:</b> Twenty strains, isolated from irradiated roots of <i>C. violacea</i>, were screened for their EPS production. IR-resistant <i>B. siamensis</i> CV5 was the most EPS-producing strain. Its purified EPS contained rhamnose, fructose, mannose and glucose. RSM indicated that EPS of CV5 (CV5-EPS) are radiation inducible. Micrographs of CV5-EPS suggested an increase in the total area and a decrease in the Feret’s statistical diameter following exposure to IR. FT-IR spectra of these EPS revealed an increase of various functional groups. The MTT survival assay demonstrated a positive correlation between the added quantity of CV5-EPS and the viability of irradiated CV5 (<i>p</i> p <b>Conclusions:</b> CV5-EPS were demonstrated as radiation-inducible and radioprotective biomolecules. This radioprotective potential of CV5-EPS could be associated with their antioxidant activities. In the future, irradiated EPS could be tested as a gel in cancer radiotherapy for minimizing the damage caused by rays to surrounding healthy tissues.
DOI: 10.6084/m9.figshare.9118406
title: Improving balance with wobble board exercises in stroke patients: single-blind, randomized clinical trial

description: <b>Background</b>: A primary objective in stroke rehabilitation is to restore functional balance, in order to reduce falls. <b>Objectives</b>: To identify the efficacy and safety of wobble board exercises when combined with conventional physiotherapy, in improving balance in hemiplegic patients following ischemic strokes. <b>Methods</b>: A block-randomized, controlled, observer blinded, superiority trial was conducted on ambulatory hemiplegic patients following ischemic strokes of middle cerebral artery territory. Subjects in the control group received a conventional physiotherapy regime. Subjects in the intervention group received training on a wobble board combined with conventional physiotherapy. Main Outcome measures were the improvement of Four-Square Step Test (FSST) and the Berg Balance Scale (BBS), both of which assess functional balance at the end of 6 weeks. <b>Results</b>: Thirty patients were randomly assigned for intervention (n = 15) and control (n = 15) groups. One patient dropped out from the study, leaving 29 eligible for the analysis. Intervention and control groups were comparable in sociodemographic characteristics and pre-test scores of balance. A repeated-measures MANOVA showed a significant difference in improvement of balance between the two study groups after 6 weeks [F(1,28) = 32.6,<i>p</i> = .000; Wilk’s lambda = .46]. The improvement of mean score of balance in interventional group was greater than in the control group [BBS:9.5 (intervention group),5.5 (control group); FSST:3.9 (intervention group),1.7 (control group)]. There were no injuries in both groups. <b>Conclusions</b>: Wobble board exercises, when combined with the conventional physiotherapy, are safe and effective in restoring functional balance in patients with hemiplegia following ischemic strokes.
DOI: 10.6084/m9.figshare.9118406.v1
title: Improving balance with wobble board exercises in stroke patients: single-blind, randomized clinical trial

description: <b>Background</b>: A primary objective in stroke rehabilitation is to restore functional balance, in order to reduce falls. <b>Objectives</b>: To identify the efficacy and safety of wobble board exercises when combined with conventional physiotherapy, in improving balance in hemiplegic patients following ischemic strokes. <b>Methods</b>: A block-randomized, controlled, observer blinded, superiority trial was conducted on ambulatory hemiplegic patients following ischemic strokes of middle cerebral artery territory. Subjects in the control group received a conventional physiotherapy regime. Subjects in the intervention group received training on a wobble board combined with conventional physiotherapy. Main Outcome measures were the improvement of Four-Square Step Test (FSST) and the Berg Balance Scale (BBS), both of which assess functional balance at the end of 6 weeks. <b>Results</b>: Thirty patients were randomly assigned for intervention (n = 15) and control (n = 15) groups. One patient dropped out from the study, leaving 29 eligible for the analysis. Intervention and control groups were comparable in sociodemographic characteristics and pre-test scores of balance. A repeated-measures MANOVA showed a significant difference in improvement of balance between the two study groups after 6 weeks [F(1,28) = 32.6,<i>p</i> = .000; Wilk’s lambda = .46]. The improvement of mean score of balance in interventional group was greater than in the control group [BBS:9.5 (intervention group),5.5 (control group); FSST:3.9 (intervention group),1.7 (control group)]. There were no injuries in both groups. <b>Conclusions</b>: Wobble board exercises, when combined with the conventional physiotherapy, are safe and effective in restoring functional balance in patients with hemiplegia following ischemic strokes.
DOI: 10.6084/m9.figshare.9118592
title: pat 8 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.3761562.v1173
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.9118364
title: MHcut analysis of dbSNP/ClinVar deletions

description: dnSNP and ClinVar deletions annotated with micro-homology at the breakpoints and with available Cas9 cut that could efficiently recreate the deletion.<br>This dataset can be explored online with the MHcut browser: https://mhcut-browser.genap.ca/<br><br>It was produced with MHcut: https://github.com/WoltjenLab/MHcut<br><br>
DOI: 10.6084/m9.figshare.9118391.v1
title: Radiation-inducible radioprotective exopolysaccharides of <i>Bacillus siamensis</i> CV5 from irradiated roots of <i>Cistanche violacea</i> to decrease free radical damage produced by ionizing radiation

description: <b>Purpose:</b> To assess exopolysaccharides (EPS) of <i>Bacillus siamensis</i> CV5, isolated from irradiated roots of <i>Cistanche violacea</i>, for their induction by ionizing radiation (IR) and their antioxidant and radioprotective power. <b>Materials and methods:</b> Isolated bacteria from the roots of <i>C. violacea</i> were screened for EPS production. The most EPS-producing bacterium was selected and the response surface methodology (RSM) was applied to elucidate the IR dose effects on EPS production. Gamma irradiation effects on the morphology and functional groups of EPS were studied using microscopy and Fourier transform infra-red (FT-IR). The radioprotective potential of EPS on the survival of <i>B. siamensis</i> CV5 following IR was evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Free radicals scavenging potentialities (FRSP) of non-irradiated and irradiated EPS were evaluated through 2, 2<sup>−</sup>-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS) and ferric reducing ability of plasma (FRAP) assays. <b>Results:</b> Twenty strains, isolated from irradiated roots of <i>C. violacea</i>, were screened for their EPS production. IR-resistant <i>B. siamensis</i> CV5 was the most EPS-producing strain. Its purified EPS contained rhamnose, fructose, mannose and glucose. RSM indicated that EPS of CV5 (CV5-EPS) are radiation inducible. Micrographs of CV5-EPS suggested an increase in the total area and a decrease in the Feret’s statistical diameter following exposure to IR. FT-IR spectra of these EPS revealed an increase of various functional groups. The MTT survival assay demonstrated a positive correlation between the added quantity of CV5-EPS and the viability of irradiated CV5 (<i>p</i> p <b>Conclusions:</b> CV5-EPS were demonstrated as radiation-inducible and radioprotective biomolecules. This radioprotective potential of CV5-EPS could be associated with their antioxidant activities. In the future, irradiated EPS could be tested as a gel in cancer radiotherapy for minimizing the damage caused by rays to surrounding healthy tissues.
DOI: 10.6084/m9.figshare.9118490
title: Data from: Aerial Seismology using Balloon-Based Barometers

description: These data are related to the seismic hammer experiment discussed in "Aerial Seismology using Balloon-Based Barometers" by Krishnamoorthy et al. (IEEE Transactions on Geoscience and Remote Sensing, 2019).<br><br>The zip file contains the location, time and vertical motion velocity data in m/s from geophones placed near the seismic hammer. The first line in each .dat file contains the lat-long of the geophone. The time is shot relative: t=0 is the shot time. The shots are also highly repeatable, each trace is representative of all shots in the 39 shot sequence used in the main paper.<br>The location of the hammer, shot times, and barometer data may be obtain from the Figshare data repository at <br><br>https://figshare.com/articles/Data_from_Detection_of_Artificially_Generated_Seismic_Signals_using_Balloon-borne_Infrasound_Sensor/6137507<br>
DOI: 10.6084/m9.figshare.9118718
title: pat 9 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118718.v1
title: pat 9 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118781
title: pat 9 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118781.v1
title: pat 9 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118790
title: pat 10 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118790.v1
title: pat 10 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118820.v1
title: Questionnaire

description: Test
DOI: 10.6084/m9.figshare.9118868
title: pat 11 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118904
title: pat 11 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9118949
title: Analyzing the Students’ Perception of UML Diagrams: Instruments Used in Evaluation

description: Unified Modeling Language (UML) has been adopted as a standard modeling language in the software industry for the graphical representation of analysis and design models. Due to its importance, UML is taught in most undergraduate majors in Software Engineering and Computing. However, little is known about the students’ perception regarding the UML diagrams. We conducted an exploratory study to investigate the students’ perception regarding UML diagrams acceptance. In this study, we investigated five UML diagrams taught for the undergraduate students from Federal University of Amazonas. These UML diagrams are: class diagrams, use case diagrams (and specifications), sequence diagrams, state machine diagrams, and activity diagrams. In order to evaluate the perceptions of senior undergraduate students on UML diagrams and thus help instructors improving the teaching of its importance, we applied Technology Acceptance Model (TAM) questionnaires. This technical report presents the TAM questionnaires for each UML diagram. Thus, other researchers may replicate it, providing outcomes in different contexts.