cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11346755
title: Supplementary table 3

description: Table S3. Accessions imputation accuracy
DOI: 10.6084/m9.figshare.11346854.v3
title: Database of confusion matrices (Microsoft Access)

description: <b>Summary: </b>Database of confusion matrices retrieved from scientific literature. Suitable for research on the creation and explotation of the confusion matrix that remain as interestint topics, such as new tools, sampling design, indices derived from the matrix, proposals in testing statistical hypotheses and so on.<b><br></b><b>Format:</b> Microsoft Access
DOI: 10.6084/m9.figshare.11346746
title: Supplementary table 4

description: Table 4. Average correlation between CV-accuracy and AR2 metrics and the observed SNP accuracy, major allele accuracy and minor allele accuracy on test sets, by minor allele frequency categories. Values are given for one of the 20 test sets (for the other test sets, almost identical
DOI: 10.6084/m9.figshare.11346761.v1
title: Supplementary table 5

description: Table S5. Likelihood-based haplotype-trait association using imputed and 250K variant.
DOI: 10.6084/m9.figshare.11346740
title: Supplementary table 1

description: Table S1. Overview of available SNPs for the 1001G and RegMap populations, with different minor allele frequencies thresholds.
DOI: 10.6084/m9.figshare.11346680
title: Supplementary Material for: Risk Factors for Acute Kidney Injury and Chronic Kidney Disease following Allogeneic Hematopoietic Stem Cell Transplantation for Hematopoietic Malignancies

description: <b><i>Background:</i></b> Acute kidney injury (AKI) and chronic kidney disease (CKD) are considered common complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT). <b><i>Objectives and Method:</i></b> In this study, 114 patients who had undergone allo-HSCT were retrospectively analyzed to investigate the risk factors for onset of posttransplant AKI and CKD as defined by the new Kidney Disease Improving Global Outcomes criteria. <b><i>Results:</i></b> Seventy-four patients (64.9%) developed AKI and 25 (21.9%) developed CKD. The multivariate analysis showed that the risk factors for developing stage 1 or higher AKI were age ≥46 years at the time of transplant (<i>p</i> = 0.001) and use of ≥3 nephrotoxic drugs (<i>p</i> = 0.036). For CKD, the associated risk factors were disease status other than complete remission at the time of transplantation (<i>p</i> = 0.018) and onset of AKI after transplant (<i>p</i> = 0.035). The 5-year overall survival (OS) was significantly reduced by development of AKI (<i>p</i> &lt; 0.001), but not CKD. Posttransplant AKI significantly increased the 5-year nonrelapse mortality (<i>p</i> &lt; 0.001), whereas posttransplant CKD showed an increasing tendency, but the difference was not significant. <b><i>Conclusions:</i></b> Posttransplant AKI impacts OS, significantly increases the risk of CKD, and is significantly associated with disseminated intravascular coagulation and use of ˃3 nephrotoxic drugs.
DOI: 10.6084/m9.figshare.11346728
title: Supplementary table 2

description: Table S2. Imputation accuracy by chromosome, for one of the 20 test sets (for the other test sets, identical results were found). Averages and standard deviations (SD) were computed over all imputed SNPs on the chromosome in question. Accurate SNPs are defined by a SNP accuracy (proportion of correctly imputed accessions) above 0.95. <br>
DOI: 10.6084/m9.figshare.11346668
title: Pleiotropic analysis of lung cancer

description: We performed a systematic cross-cancer pleiotropic analysis to detect the effects of GWAS-identified variants from non-lung cancers on lung cancer risk in 12,843 cases and 12,639 controls from four lung cancer GWASs. Here, 6 independent SNPs associated with non-lung cancer risk were identified related to the susceptibility to lung cancer.
DOI: 10.6084/m9.figshare.11346680.v1
title: Supplementary Material for: Risk Factors for Acute Kidney Injury and Chronic Kidney Disease following Allogeneic Hematopoietic Stem Cell Transplantation for Hematopoietic Malignancies

description: <b><i>Background:</i></b> Acute kidney injury (AKI) and chronic kidney disease (CKD) are considered common complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT). <b><i>Objectives and Method:</i></b> In this study, 114 patients who had undergone allo-HSCT were retrospectively analyzed to investigate the risk factors for onset of posttransplant AKI and CKD as defined by the new Kidney Disease Improving Global Outcomes criteria. <b><i>Results:</i></b> Seventy-four patients (64.9%) developed AKI and 25 (21.9%) developed CKD. The multivariate analysis showed that the risk factors for developing stage 1 or higher AKI were age ≥46 years at the time of transplant (<i>p</i> = 0.001) and use of ≥3 nephrotoxic drugs (<i>p</i> = 0.036). For CKD, the associated risk factors were disease status other than complete remission at the time of transplantation (<i>p</i> = 0.018) and onset of AKI after transplant (<i>p</i> = 0.035). The 5-year overall survival (OS) was significantly reduced by development of AKI (<i>p</i> &lt; 0.001), but not CKD. Posttransplant AKI significantly increased the 5-year nonrelapse mortality (<i>p</i> &lt; 0.001), whereas posttransplant CKD showed an increasing tendency, but the difference was not significant. <b><i>Conclusions:</i></b> Posttransplant AKI impacts OS, significantly increases the risk of CKD, and is significantly associated with disseminated intravascular coagulation and use of ˃3 nephrotoxic drugs.
DOI: 10.6084/m9.figshare.11346650
title: Supplementary Material for: Continuous Sound Collection Using Smartphones and Machine Learning to Measure Cough

description: <b><i>Background:</i></b> Despite the efforts of research groups to develop and implement at least partial automation, cough counting remains impractical. Analysis of 24-h cough frequency is an established regulatory endpoint which, if addressed in an automated manner, has the potential to ease cough symptom evaluation over multiple 24-h periods in a patient-centric way, supporting the development of novel treatments for chronic cough, an unmet clinical need. <b><i>Objectives:</i></b> In light of recent technological advancements, we propose a system based on the use of smartphones for objective continuous sound collection, suitable for automated cough detection and analysis. Two capabilities were identified as necessary for naturalistic cough assessment: (1) recording sound in a continuous manner (sound collection), and (2) detection of coughs from the recorded sound (cough detection). <b><i>Methods:</i></b> This work did not involve any human subject testing or trials. For sound collection, we designed, built, and verified technical parameters of a smartphone application for sound collection. Our cough detection work describes the development of a mathematical model for sound analysis and cough identification. Performance of the model was compared to previously published results of commercially available solutions and to human raters. The compared solutions use the following methods to automatically or semi-automatically assess cough: 24-h sound recording with an ambulatory device with multiple microphones, automatic silence removal, and manual recording review for cough count. <b><i>Results:</i></b> Sound collection: the application demonstrated the ability to continuously record sounds using the phone’s internal microphone; the technical verification informed the configuration of the technical and user experience parameters. Cough detection: our cough recognition sensitivity to cough as determined by human listeners was 90 at 99.5% specificity preset and 75 at 99.9% specificity preset for a dataset created from publicly available data. <b><i>Conclusions:</i></b> Sound collection: the application reliably collects sound data and uploads them securely to a remote server for subsequent analysis; the developed sound data collection application is a critical first step toward future incorporation in clinical trials. Cough detection: initial experiments with cough detection techniques yielded encouraging results for application to patient-collected data from future studies.
DOI: 10.6084/m9.figshare.11346668.v1
title: Pleiotropic analysis of lung cancer

description: We performed a systematic cross-cancer pleiotropic analysis to detect the effects of GWAS-identified variants from non-lung cancers on lung cancer risk in 12,843 cases and 12,639 controls from four lung cancer GWASs. Here, 6 independent SNPs associated with non-lung cancer risk were identified related to the susceptibility to lung cancer.
DOI: 10.6084/m9.figshare.11346635
title: Supplementary Material for: Nomograms of Fetal Right Ventricular Fractional Area Change by 2D Echocardiography

description: <b><i>Objectives:</i></b> Fetal right ventricular (RV) function assessment is challenging due to the RV geometry and limitations of in utero assessment. Postnatally, 2D echocardiographic RV fractional area change (FAC) is used to assess RV global systolic function by calculating the percentage of change in RV area from systole to diastole. Reports on FAC are scarce in prenatal life, and nomograms throughout pregnancy are not available. Our aims were (1) to study prenatal RV FAC feasibility and reproducibility and (2) to construct nomograms for RV FAC and end-diastolic (ED) and end-systolic (ES) RV areas from 18 to 41 weeks of gestation. <b><i>Methods:</i></b> Prospective cohort study including 602 low-risk singleton pregnancies undergoing a fetal echocardiography from 18 to 41 weeks of gestation. RV ED and ES areas were measured following standard recommendations for ventricular dimensions and establishing strict landmarks to identify the different phases of the cardiac cycle. RV FAC was calculated as: ([ED area – ES area]/ED area) × 100. RV FAC intra- and inter-observer reproducibility was evaluated in 45 fetuses by calculating the intraclass correlation coefficient (ICC). Parametric regressions were tested to model each parameter against gestational age (GA) and estimated fetal weight (EFW). <b><i>Results:</i></b> RV areas and FAC were successfully obtained in ∼99% of fetuses with acceptable reproducibility throughout gestation (RV ED area inter-observer ICC [95% CI] 0.96 [0.93–0.98], RV ES area 0.97 [0.94–0.98], and FAC 0.69 [0.44–0.83]). Nomograms were constructed for RV ED and ES areas and FAC. RV areas showed a quadratic and logarithmic increase with GA and EFW, respectively. In contrast, RV FAC showed a slight quadratic decrease throughout gestation (mean RV FAC ranged from 36% at 18 weeks of gestation [10–90th centiles: 25–47%, respectively] to 29% at 41 weeks [10–90th centiles: 18–40%, respectively]). The best models for RV areas and FAC were a second-degree polynomial. <b><i>Conclusions:</i></b> RV FAC is a feasible and reproducible parameter to assess RV global systolic function in fetal life. We provide reference ranges adjusted by GA and EFW that can be used as normal references for the assessment of RV function in prenatal conditions.
DOI: 10.6084/m9.figshare.11346641.v1
title: Integrating the Physical and Genetic Map of Bread Wheat Facilitates the Detection of Chromosomal Rearrangements

description: <b>High-density genetic map including FISH markers</b>
DOI: 10.6084/m9.figshare.11346536
title: WT and NitroTyr Calmodulin Mass Spectrometry Data

description: Purified CaM samples were diluted to a concentration of 10 μM, desalted on Millipore C4 zip tips, and analyzed using an FT LTQ mass spectrometer. Samples included WT-CaM and nitroTyr-containing CaM. Spectra were collected using Tune-Plus (Thermo, v. 2.2) page of Xcalibur (Thermo, v. 2.0.5) using parameters described in (Rhoads, T. W., Williams, J. R., Lopez, N. I., Morre, J. T., Bradford, C. S., and Beckman, J. S. (2013) Using theoretical protein isotopic distributions to parse small-mass-difference post-translational modifications via mass spectrometry. J Am Soc Mass Spectrom 24, 115-124). Spectra were averaged over the three minutes CaM eluted from the ZipTip using the Qual Browser (Thermo, v. 2.0) The data were exported as text files containing two columns of m/z versus intensity to be analyzed by custom programs written in MatLab (Rhoads et al., 2013). This data includes the raw m/z and deconvoluted data in tabs for the WT-, nitroTyr99-, and nitroTyr138-CaM.<br>
DOI: 10.6084/m9.figshare.11346536.v1
title: WT and NitroTyr Calmodulin Mass Spectrometry Data

description: Purified CaM samples were diluted to a concentration of 10 μM, desalted on Millipore C4 zip tips, and analyzed using an FT LTQ mass spectrometer. Samples included WT-CaM and nitroTyr-containing CaM. Spectra were collected using Tune-Plus (Thermo, v. 2.2) page of Xcalibur (Thermo, v. 2.0.5) using parameters described in (Rhoads, T. W., Williams, J. R., Lopez, N. I., Morre, J. T., Bradford, C. S., and Beckman, J. S. (2013) Using theoretical protein isotopic distributions to parse small-mass-difference post-translational modifications via mass spectrometry. J Am Soc Mass Spectrom 24, 115-124). Spectra were averaged over the three minutes CaM eluted from the ZipTip using the Qual Browser (Thermo, v. 2.0) The data were exported as text files containing two columns of m/z versus intensity to be analyzed by custom programs written in MatLab (Rhoads et al., 2013). This data includes the raw m/z and deconvoluted data in tabs for the WT-, nitroTyr99-, and nitroTyr138-CaM.<br>
DOI: 10.6084/m9.figshare.11346329
title: Code and simulated data from A quantitative account of mammalian rod phototransduction with PDE6 dimeric activation: responses to bright flashes

description: We develop an improved quantitative model of mammalian rod phototransduction, and we apply it to the prediction of responses to bright flashes of light. We take account of the recently characterized dimeric nature of PDE6 activation, where the configuration of primary importance has two transducin molecules bound. We simulate the stochastic nature of the activation and shut-off reactions, to generate the predicted kinetics of the active molecular species on the disc membrane surfaces, and then we integrate the differential equations for the downstream cytoplasmic reactions to obtain the predicted electrical responses. The simulated responses recover the qualitative form of bright-flash response families recorded from mammalian rod photoreceptors. Furthermore, they provide an accurate description of the relationship between the time spent in saturation and flash intensity, predicting the transition between first and second ‘dominant time constants’ to occur at an intensity around 5000 isomerizations per flash, when the rate of transducin activation is taken to be 1250 transducins s<sup>−1</sup> per activated rhodopsin. This rate is consistent with estimates from light-scattering experiments, but is around fourfold higher than has typically been assumed in other studies. We conclude that our model and parameters provide a compelling description of rod photoreceptor bright-flash responses.
DOI: 10.6084/m9.figshare.11346320
title: Random and block conjugated polymers: a comparative study of properties

description: The synthesis and comparative study of four conjugated terpolymers with different arrangements for application in polymer solar cells (PSC’s) as electron donor materials is reported. The synthesized polymers were characterized by NMR, GPC, UV–Vis, TGA, FTIR, Cyclic Voltammetry (CV) and AFM. The photovoltaic devices were characterized by comparison between J(V) curves in dark and standard illumination conditions (100 µW/cm<sup>2</sup>). All materials synthesized showed good solubility and thermal stability, indicating that they are suitable for PSC's. Terpolymers (random and block) were synthesized by the Suzuki–Miyaura route varying proportion of carbazole and fluorene monomers, showing high yields. The optical and electronic characterizations showed that increasing carbazole amount decreases the polymer energy band gap, a strategic issue in order to improve photovoltaic device efficiency. The block and the random terpolymer presented similar maximum absorbance λmax, HOMO, LUMO, and band gap. Therefore, the light absorption is more influenced by composition than by differences in microstructure between random and block arrangements. Additionally, the low roughness obtained from AFM indicated a good mixture between polymers and fullerene derivative PCBM, also a key factor in the PSCs efficiency. However, the device efficiency presented not only a strong dependence on the fluorene/carbazole ratio but also on polymer structure.
DOI: 10.6084/m9.figshare.11346329.v1
title: Code and simulated data from A quantitative account of mammalian rod phototransduction with PDE6 dimeric activation: responses to bright flashes

description: We develop an improved quantitative model of mammalian rod phototransduction, and we apply it to the prediction of responses to bright flashes of light. We take account of the recently characterized dimeric nature of PDE6 activation, where the configuration of primary importance has two transducin molecules bound. We simulate the stochastic nature of the activation and shut-off reactions, to generate the predicted kinetics of the active molecular species on the disc membrane surfaces, and then we integrate the differential equations for the downstream cytoplasmic reactions to obtain the predicted electrical responses. The simulated responses recover the qualitative form of bright-flash response families recorded from mammalian rod photoreceptors. Furthermore, they provide an accurate description of the relationship between the time spent in saturation and flash intensity, predicting the transition between first and second ‘dominant time constants’ to occur at an intensity around 5000 isomerizations per flash, when the rate of transducin activation is taken to be 1250 transducins s<sup>−1</sup> per activated rhodopsin. This rate is consistent with estimates from light-scattering experiments, but is around fourfold higher than has typically been assumed in other studies. We conclude that our model and parameters provide a compelling description of rod photoreceptor bright-flash responses.
DOI: 10.6084/m9.figshare.11346308
title: Data for Newly identified norite/A2-type granite belt from Bangong-Nujiang collision zone in Tibet Plateau: Evidences for the slab break-off beneath the Lhasa Terrance

description: Data for Newly identified norite/A2-type granite belt from Bangong-Nujiang collision zone in Tibet Plateau: Evidences for the slab break-off beneath the Lhasa Terrance submit to JGR solid earth.
DOI: 10.6084/m9.figshare.11346320.v1
title: Random and block conjugated polymers: a comparative study of properties

description: The synthesis and comparative study of four conjugated terpolymers with different arrangements for application in polymer solar cells (PSC’s) as electron donor materials is reported. The synthesized polymers were characterized by NMR, GPC, UV–Vis, TGA, FTIR, Cyclic Voltammetry (CV) and AFM. The photovoltaic devices were characterized by comparison between J(V) curves in dark and standard illumination conditions (100 µW/cm<sup>2</sup>). All materials synthesized showed good solubility and thermal stability, indicating that they are suitable for PSC's. Terpolymers (random and block) were synthesized by the Suzuki–Miyaura route varying proportion of carbazole and fluorene monomers, showing high yields. The optical and electronic characterizations showed that increasing carbazole amount decreases the polymer energy band gap, a strategic issue in order to improve photovoltaic device efficiency. The block and the random terpolymer presented similar maximum absorbance λmax, HOMO, LUMO, and band gap. Therefore, the light absorption is more influenced by composition than by differences in microstructure between random and block arrangements. Additionally, the low roughness obtained from AFM indicated a good mixture between polymers and fullerene derivative PCBM, also a key factor in the PSCs efficiency. However, the device efficiency presented not only a strong dependence on the fluorene/carbazole ratio but also on polymer structure.
DOI: 10.6084/m9.figshare.11346308.v1
title: Data for Newly identified norite/A2-type granite belt from Bangong-Nujiang collision zone in Tibet Plateau: Evidences for the slab break-off beneath the Lhasa Terrance

description: Data for Newly identified norite/A2-type granite belt from Bangong-Nujiang collision zone in Tibet Plateau: Evidences for the slab break-off beneath the Lhasa Terrance submit to JGR solid earth.
DOI: 10.6084/m9.figshare.11346005
title: MOESM7 of The majority of A-to-I RNA editing is not required for mammalian homeostasis

description: Additional file 7: Dataset S5. ADAR1 and ADAR2 specific editing events â€“ frequency of editing. Related to Fig. 4c.
DOI: 10.6084/m9.figshare.11345996
title: MOESM9 of Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. ‘Moscatel Galego’)

description: Additional file 9. List of primers used for molecular analyses.
DOI: 10.6084/m9.figshare.11345996.v1
title: MOESM9 of Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. ‘Moscatel Galego’)

description: Additional file 9. List of primers used for molecular analyses.
DOI: 10.6084/m9.figshare.11346005.v1
title: MOESM7 of The majority of A-to-I RNA editing is not required for mammalian homeostasis

description: Additional file 7: Dataset S5. ADAR1 and ADAR2 specific editing events â€“ frequency of editing. Related to Fig. 4c.
DOI: 10.6084/m9.figshare.11345984
title: MOESM6 of Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. ‘Moscatel Galego’)

description: Additional file 6. Phenylpropanoid pathway genes with normalized and averaged expression values (FPKM) obtained from this study. R: red-skinned variant (cv. ‘Moscatel Galego Roxo’), W: white-skinned variant (cv. ‘Moscatel Galego Branco’), V: veraison, R: ripening (2WAV).
DOI: 10.6084/m9.figshare.11345990
title: MOESM6 of The majority of A-to-I RNA editing is not required for mammalian homeostasis

description: Additional file 6: Dataset S4B. De novo discovery of RNA editing sites in each genotype using JACUSA2.0.0 (transcriptome comparison to C57Bl/6 reference genome). Related to Fig 3 and Fig 4.
DOI: 10.6084/m9.figshare.11345981
title: MOESM5 of The majority of A-to-I RNA editing is not required for mammalian homeostasis

description: Additional file 5: Dataset S4A. Editing analysis of the known sites. Related to Fig. 3 and Fig. 4.
DOI: 10.6084/m9.figshare.11345984.v1
title: MOESM6 of Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. ‘Moscatel Galego’)

description: Additional file 6. Phenylpropanoid pathway genes with normalized and averaged expression values (FPKM) obtained from this study. R: red-skinned variant (cv. ‘Moscatel Galego Roxo’), W: white-skinned variant (cv. ‘Moscatel Galego Branco’), V: veraison, R: ripening (2WAV).
DOI: 10.6084/m9.figshare.11345978
title: MOESM5 of Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. ‘Moscatel Galego’)

description: Additional file 5. Common and unique gene ontology terms in up- and down-regulated genes at both veraison and ripening stages.
DOI: 10.6084/m9.figshare.11345990.v1
title: MOESM6 of The majority of A-to-I RNA editing is not required for mammalian homeostasis

description: Additional file 6: Dataset S4B. De novo discovery of RNA editing sites in each genotype using JACUSA2.0.0 (transcriptome comparison to C57Bl/6 reference genome). Related to Fig 3 and Fig 4.