cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6949694
title: Supplementary Material for: Identification of Potential Prognostic Long Non-Coding RNA Biomarkers for Predicting Survival in Patients with Hepatocellular Carcinoma

description: <b><i>Background/Aims:</i></b> The aim of the current study was to identify potential prognostic long non-coding RNA (lncRNA) biomarkers for predicting survival in patients with hepatocellular carcinoma (HCC) using The Cancer Genome Atlas (TCGA) dataset and bioinformatics analysis. <b><i>Methods:</i></b> RNA sequencing and clinical data of HCC patients from TCGA were used for prognostic association assessment by univariate Cox analysis. A prognostic signature was built using stepwise multivariable Cox analysis, and a comprehensive analysis was performed to evaluate its prognostic value. The prognostic signature was further evaluated by functional assessment and bioinformatics analysis. <b><i>Results:</i></b> Thirteen differentially expressed lncRNAs (DELs) were identified and used to construct a single prognostic signature. Patients with high risk scores showed a significantly increased risk of death (adjusted <i>P</i> &lt; 0.0001, adjusted hazard ratio = 3.522, 95% confidence interval = 2.307–5.376). In the time-dependent receiver operating characteristic analysis, the prognostic signature performed well for HCC survival prediction with an area under curve of 0.809, 0.782 and 0.79 for 1-, 3- and 5-year survival, respectively. Comprehensive survival analysis of the 13-DEL prognostic signature suggested that it serves as an independent factor in HCC, showing a better performance for prognosis prediction than traditional clinical indicators. Functional assessment and bioinformatics analysis suggested that the prognostic signature was associated with the cell cycle and peroxisome proliferator-activated receptor signaling pathway. <b><i>Conclusions:</i></b> The novel lncRNA expression signature identified in the present study may be a potential biomarker for predicting the prognosis of HCC patients.
DOI: 10.6084/m9.figshare.6949634.v1
title: NPI-012-Radiograms

description: This is a series of 2D radiograms which was collected during the injection of a nanoparticle suspension (0.12 wt%). Image Dimensions: 1024×1024×5972 Image Type: 16 bit - unsigned
DOI: 10.6084/m9.figshare.6949694.v1
title: Supplementary Material for: Identification of Potential Prognostic Long Non-Coding RNA Biomarkers for Predicting Survival in Patients with Hepatocellular Carcinoma

description: <b><i>Background/Aims:</i></b> The aim of the current study was to identify potential prognostic long non-coding RNA (lncRNA) biomarkers for predicting survival in patients with hepatocellular carcinoma (HCC) using The Cancer Genome Atlas (TCGA) dataset and bioinformatics analysis. <b><i>Methods:</i></b> RNA sequencing and clinical data of HCC patients from TCGA were used for prognostic association assessment by univariate Cox analysis. A prognostic signature was built using stepwise multivariable Cox analysis, and a comprehensive analysis was performed to evaluate its prognostic value. The prognostic signature was further evaluated by functional assessment and bioinformatics analysis. <b><i>Results:</i></b> Thirteen differentially expressed lncRNAs (DELs) were identified and used to construct a single prognostic signature. Patients with high risk scores showed a significantly increased risk of death (adjusted <i>P</i> &lt; 0.0001, adjusted hazard ratio = 3.522, 95% confidence interval = 2.307–5.376). In the time-dependent receiver operating characteristic analysis, the prognostic signature performed well for HCC survival prediction with an area under curve of 0.809, 0.782 and 0.79 for 1-, 3- and 5-year survival, respectively. Comprehensive survival analysis of the 13-DEL prognostic signature suggested that it serves as an independent factor in HCC, showing a better performance for prognosis prediction than traditional clinical indicators. Functional assessment and bioinformatics analysis suggested that the prognostic signature was associated with the cell cycle and peroxisome proliferator-activated receptor signaling pathway. <b><i>Conclusions:</i></b> The novel lncRNA expression signature identified in the present study may be a potential biomarker for predicting the prognosis of HCC patients.
DOI: 10.6084/m9.figshare.6949628
title: WI-Radiograms

description: This is a series of 2D radiograms which was collected during the injection of water in the core (also referred to as waterflooding). This step is after oil injection. Image Dimensions: 1024×1024×2558 Image Type: 16 bit - unsigned
DOI: 10.6084/m9.figshare.6949631
title: NPI-006-Radiograms

description: This is a series of 2D radiograms which was collected during the injection of a nanoparticle suspension (0.06 wt%). Image Dimensions: 1024×1024×5850 Image Type: 16 bit - unsigned
DOI: 10.6084/m9.figshare.6949628.v1
title: WI-Radiograms

description: This is a series of 2D radiograms which was collected during the injection of water in the core (also referred to as waterflooding). This step is after oil injection. Image Dimensions: 1024×1024×2558 Image Type: 16 bit - unsigned
DOI: 10.6084/m9.figshare.6949631.v1
title: NPI-006-Radiograms

description: This is a series of 2D radiograms which was collected during the injection of a nanoparticle suspension (0.06 wt%). Image Dimensions: 1024×1024×5850 Image Type: 16 bit - unsigned
DOI: 10.6084/m9.figshare.6949604
title: Supplementary Material for: Order of Treatment Matters in Ischemic Stroke: Mechanical Thrombectomy First, Then Carotid Artery Stenting for Tandem Lesions of the Anterior Circulation

description: <b><i>Background:</i></b> One endovascular treatment option of acute ischemic stroke due to tandem occlusion (TO) comprises intracranial thrombectomy and acute extracranial carotid artery stenting (CAS). In this setting, the order of treatment may impact the clinical outcome in this stroke subtype. <b><i>Methods:</i></b> Retrospective analysis was performed on data prospectively collected in 4 international stroke centers between 2013 and 2017. One hundred sixty-five patients with anterior TO were treated by endovascular therapy. Clinical and procedural data were evaluated. Favorable clinical outcome was defined as modified Rankin Scale (mRS) ≤2 at 90 days. Propensity score matching was performed for different treatment strategies. <b><i>Results:</i></b> Patients’ mean age was 65 ± 11 years and 118 were male (69%). The median admission National Institutes of Health Stroke Scale was 15 (interquartile range 8). In 59% of the patients (<i>n</i> = 101), the antegrade strategy (first stenting, then thrombectomy) was ­performed, in 41% (<i>n</i> = 70) retrograde treatment (first thrombectomy, then stenting). Successful reperfusion (mTICI ≥2b) was achieved in 128 patients (75%). Fifty-nine patients (39%) showed a favorable clinical outcome after 90 days. After propensity score matching, data of 100 patients could be analyzed. Analysis revealed that the retrograde strategy yielded a significantly higher rate of successful reperfusion compared to the antegrade strategy (92 vs. 56%; <i>p</i> &lt; 0.001). The rate of favorable clinical outcome after 90 days (mRS ≤2) was consistently higher (44 vs. 30%; <i>p</i> &lt; 0.05) in the retrograde strategy group. <b><i>Conclusion:</i></b> Mechanical thrombectomy prior to acute CAS in TO is a predictive factor for favorable clinical outcome at 90 days.
DOI: 10.6084/m9.figshare.6949511
title: Potier et al. supporting figures and table from High resolution of colour vision, but low contrast sensitivity in a diurnal raptor

description: Animals are thought to use achromatic signals to detect small (or distant) objects and chromatic signals for large (or nearby) objects. While the spatial resolution of the achromatic channel has been widely studied, the spatial resolution of the chromatic channel has rarely been estimated. Using an operant conditioning method, we determined (i) the achromatic contrast sensitivity function and (ii) the spatial resolution of the chromatic channel of a diurnal raptor, the Harris's hawk <i>Parabuteo unicinctus</i>. The maximal spatial resolution for achromatic gratings was 62.3 c deg<sup>−1</sup>, but the contrast sensitivity was relatively low (10.8–12.7). The spatial resolution for isoluminant red-green gratings was 21.6 c deg<sup>−1</sup>—lower than that of the achromatic channel, but the highest found in the animal kingdom to date. Our study reveals that Harris's hawks have high spatial resolving power for both achromatic and chromatic vision, suggesting the importance of colour vision for foraging. By contrast, similar to other bird species, Harris's hawks have low contrast sensitivity possibly suggesting a trade-off with chromatic sensitivity. The result is interesting in the light of the recent finding that double cones—thought to mediate high-resolution vision in birds—are absent in the central fovea of raptors.
DOI: 10.6084/m9.figshare.6949511.v1
title: Potier et al. supporting figures and table from High resolution of colour vision, but low contrast sensitivity in a diurnal raptor

description: Animals are thought to use achromatic signals to detect small (or distant) objects and chromatic signals for large (or nearby) objects. While the spatial resolution of the achromatic channel has been widely studied, the spatial resolution of the chromatic channel has rarely been estimated. Using an operant conditioning method, we determined (i) the achromatic contrast sensitivity function and (ii) the spatial resolution of the chromatic channel of a diurnal raptor, the Harris's hawk <i>Parabuteo unicinctus</i>. The maximal spatial resolution for achromatic gratings was 62.3 c deg<sup>−1</sup>, but the contrast sensitivity was relatively low (10.8–12.7). The spatial resolution for isoluminant red-green gratings was 21.6 c deg<sup>−1</sup>—lower than that of the achromatic channel, but the highest found in the animal kingdom to date. Our study reveals that Harris's hawks have high spatial resolving power for both achromatic and chromatic vision, suggesting the importance of colour vision for foraging. By contrast, similar to other bird species, Harris's hawks have low contrast sensitivity possibly suggesting a trade-off with chromatic sensitivity. The result is interesting in the light of the recent finding that double cones—thought to mediate high-resolution vision in birds—are absent in the central fovea of raptors.
DOI: 10.34740/kaggle/dsv/1447802
title: Turkey Covid-19 Dataset
DOI: 10.6084/m9.figshare.6949499.v1
title: Fully Bayesian analysis of RNA-seq counts for the detection of gene expression heterosis

description: Heterosis, or hybrid vigor, is the enhancement of the phenotype of hybrid progeny relative to their inbred parents. Heterosis is extensively used in agriculture, and the underlying mechanisms are unclear. To investigate the molecular basis of phenotypic heterosis, researchers search tens of thousands of genes for heterosis with respect to expression in the transcriptome. Difficulty arises in the assessment of heterosis due to composite null hypotheses and non-uniform distributions for p-values under these null hypotheses. Thus, we develop a general hierarchical model for count data and a fully Bayesian analysis in which an efficient parallelized Markov chain Monte Carlo algorithm ameliorates the computational burden. We use our method to detect gene expression heterosis in a two-hybrid plant-breeding scenario, both in a real RNA-seq maize dataset and in simulation studies. In the simulation studies, we show our method has well-calibrated posterior probabilities and credible intervals when the model assumed in analysis matches the model used to simulate the data. Although model misspecification can adversely affect calibration, the methodology is still able to accurately rank genes. Finally, we show that hyperparameter posteriors are extremely narrow and an empirical Bayes (eBayes) approach based on posterior means from the fully Bayesian analysis provides virtually equivalent posterior probabilities, credible intervals, and gene rankings relative to the fully Bayesian solution. This evidence of equivalence provides support for the use of eBayes procedures in RNA-seq data analysis if accurate hyperparameter estimates can be obtained.
DOI: 10.6084/m9.figshare.6949448
title: Fig S5. Humpback whale songs delineated

description: <b>Fig S5. A spectrographic view of a 10 minute song recording.</b> A spectrographic view of a 10 minute recording where phrase sequences from at least 3 different singers have been recorded. Each singer has an assigned color, with a single phrase identified using both a colored box and a corresponding colored phrase label (singer A = red, singer B = green, singer C = blue, singer D = black). Arrows between phrase labels indicate a transitional phrase. Singer B’s signal attenuates at the beginning of the recording and because it is not certain if singer D is the same singer, a new label is assigned. At least 3 songs overlapped at time periods within the recording, indicating that a minimum of 3 singers were singing within the detection range of the EARs during this recording. A full song sequence captured from singer A, measured from phrase-14a to phrase-14a, lasted approximately 8 minutes and 50 seconds.
DOI: 10.6084/m9.figshare.6949445
title: Fig S2 The effect of number of singers, SNR and the percentage of song units within a sound file on automatic song unit detections

description: <b>Fig S2. </b>All tested variables showed significant positive correlation with the detection rate by the automatic detector using the non-parametric Spearman’s rank correlation (r =roh) indicating a significant effect on the resulting detection rate (per minute of effort) in each sound file. A) correlation between the minimum number of singers per sound file and the detection rate, B) correlation between the signal to noise ratio (SNR) per sound file and the detection rate, C) correlation between the % of each sound file which included song units and the detection rate.
DOI: 10.6084/m9.figshare.6949448.v3
title: Fig S5. Humpback whale songs delineated

description: <b>Fig S5. A spectrographic view of a 10 minute song recording.</b> A spectrographic view of a 10 minute recording where phrase sequences from at least 3 different singers have been recorded. Each singer has an assigned color, with a single phrase identified using both a colored box and a corresponding colored phrase label (singer A = red, singer B = green, singer C = blue, singer D = black). Arrows between phrase labels indicate a transitional phrase. Singer B’s signal attenuates at the beginning of the recording and because it is not certain if singer D is the same singer, a new label is assigned. At least 3 songs overlapped at time periods within the recording, indicating that a minimum of 3 singers were singing within the detection range of the EARs during this recording. A full song sequence captured from singer A, measured from phrase-14a to phrase-14a, lasted approximately 8 minutes and 50 seconds.
DOI: 10.6084/m9.figshare.6949445.v1
title: Fig_S1.tiff

description: <b>Fig S1. </b>All tested variables showed significant positive correlation with the detection rate by the automatic detector using the non-parametric Spearman’s rank correlation (r =roh) indicating a significant effect on the resulting detection rate (per minute of effort) in each sound file. A) correlation between the minimum number of singers per sound file and the detection rate, B) correlation between the signal to noise ratio (SNR) per sound file and the detection rate, C) correlation between the % of each sound file which included song units and the detection rate.
DOI: 10.6084/m9.figshare.6949448.v2
title: Fig_S3.tif

description: <b>Fig S3. A spectrographic view of a 10 minute song recording.</b> A spectrographic view of a 10 minute recording where phrase sequences from at least 3 different singers have been recorded. Each singer has an assigned color, with a single phrase identified using both a colored box and a corresponding colored phrase label (singer A = red, singer B = green, singer C = blue, singer D = black). Arrows between phrase labels indicate a transitional phrase. Singer B’s signal attenuates at the beginning of the recording and because it is not certain if singer D is the same singer, a new label is assigned. At least 3 songs overlapped at time periods within the recording, indicating that a minimum of 3 singers were singing within the detection range of the EARs during this recording. A full song sequence captured from singer A, measured from phrase-14a to phrase-14a, lasted approximately 8 minutes and 50 seconds.
DOI: 10.6084/m9.figshare.6949445.v2
title: Fig_S2.tiffSupplementari material for "Subarctic singers: Humpback whale (Megaptera novaeangliae) song structure and progression from an Icelandic feeding ground during winter"

description: <b>Fig S1. </b>All tested variables showed significant positive correlation with the detection rate by the automatic detector using the non-parametric Spearman’s rank correlation (r =roh) indicating a significant effect on the resulting detection rate (per minute of effort) in each sound file. A) correlation between the minimum number of singers per sound file and the detection rate, B) correlation between the signal to noise ratio (SNR) per sound file and the detection rate, C) correlation between the % of each sound file which included song units and the detection rate.
DOI: 10.6084/m9.figshare.6949445.v3
title: Fig S2 The effect of number of singers, SNR and the percentage of song units within a sound file on automatic song unit detections

description: <b>Fig S2. </b>All tested variables showed significant positive correlation with the detection rate by the automatic detector using the non-parametric Spearman’s rank correlation (r =roh) indicating a significant effect on the resulting detection rate (per minute of effort) in each sound file. A) correlation between the minimum number of singers per sound file and the detection rate, B) correlation between the signal to noise ratio (SNR) per sound file and the detection rate, C) correlation between the % of each sound file which included song units and the detection rate.
DOI: 10.6084/m9.figshare.6949442
title: Fig S3 Increased automatic song unit detections indicate increased number of singers

description: <b>Fig S3. </b>A boxplot showing the distribution of automatic detections with increased number of singers per sound file. All examined sound files with more than 15 detections per minute of effort, apart from one, included two or more singers. If the detection rate exceeded 25 detections per minute of effort the sound files included at least three singers while sound files with more than 30 detections per minute of effort included 4 or more singers.
DOI: 10.6084/m9.figshare.6949334
title: Population Enumerations Database

description: The Population Enumerations Database lists all modern population censuses since 1703 for all territories of the world (independent or not) in a standardized and readily-reusable format, indicating the population count, census type, date, territorial coverage and other relevant information on the enumeration procedure or accuracy. It is supplemented by additional datasets with lists of polities and population estimates, and Matlab code, to support the analysis of the data. See README file for more information.
DOI: 10.6084/m9.figshare.6949334.v2
title: Population Enumerations Database

description: The Population Enumerations Database lists all modern population censuses since 1703 for all territories of the world (independent or not) in a standardized and readily-reusable format, indicating the population count, census type, date, territorial coverage and other relevant information on the enumeration procedure or accuracy. It is supplemented by additional datasets with lists of polities and population estimates, and Matlab code, to support the analysis of the data. See README file for more information.
DOI: 10.6084/m9.figshare.6949334.v1
title: Population Enumerations Database

description: The Population Enumerations Database lists all modern population censuses since 1703 for all territories of the world (independent or not) in a standardized and readily-reusable format, indicating the population count, census type, date, territorial coverage and other relevant information on the enumeration procedure or accuracy. It is supplemented by additional datasets with lists of polities and population estimates, and Matlab code, to support the analysis of the data. See README file for more information.
DOI: 10.6084/m9.figshare.6949442.v4
title: Fig S3 Increased automatic song unit detections indicate increased number of singers

description: <b>Fig S3. </b>A boxplot showing the distribution of automatic detections with increased number of singers per sound file. All examined sound files with more than 15 detections per minute of effort, apart from one, included two or more singers. If the detection rate exceeded 25 detections per minute of effort the sound files included at least three singers while sound files with more than 30 detections per minute of effort included 4 or more singers.
DOI: 10.6084/m9.figshare.6949331
title: Data for publication: A rapid rate of sex-chromosome turnover and non-random transitions in true frogs

description: This data herein includes intermediate Stacks analyses files for RADsequencing of &gt;700 individuals from 20 species of frogs. Sample and methodological details can be found in the publication.<br>Also included are the intermediate files used in creation of the phylogeny used in the paper.
DOI: 10.6084/m9.figshare.6949316
title: Supplementary Material for: Estimation of the Prevalence of Amyotrophic Lateral Sclerosis in the United States Using National Administrative Healthcare Data from 2002 to 2004 and Capture-Recapture Methodology

description: <b><i>Background:</i></b> National administrative healthcare data may be used as a case-finding method for prevalence studies of chronic disease in the United States, but the completeness of ascertainment likely varies depending on the disease under study. <b><i>Methods:</i></b> We used 3 case-finding sources (Medicare, Medicaid, and Veterans Administration data) to estimate the prevalence of amyotrophic lateral sclerosis (ALS) in the United States for 2002–2004, and applied the capture-recapture methodology to estimate the degree of under-ascertainment when relying solely on these sources for case identification. <b><i>Results:</i></b> Case-finding completeness was 76% overall and did not vary by race, but was lower for males (77%) than for females (88%), and lower for patients under age 65 (66%) than patients over age 65 (79%). The uncorrected ALS prevalence ratio was 2.8/100,000 in 2002, 3.3/100,000 in 2003, and 3.7/100,000 in 2004. After correcting for under-ascertainment, the annual prevalence increased by approximately 1 per 100,000 to 3.7/100,000 in 2002 (95% CI 3.66–3.80), 4.4/100,000 in 2003 (95% CI 4.34–4.50), and 4.8/100,000 in 2004 (95% CI 4.76–4.91). <b><i>Conclusions:</i></b> Federal healthcare claims databases ascertained are a very efficient method for identifying the majority of ALS-prevalent cases in the National ALS Registry, and may be enhanced by having patients self-register through the registry web portal.