cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20026136.v1
title: Figures code from Religious celibacy brings inclusive fitness benefits

description: R code used to generate the figures
DOI: 10.6084/m9.figshare.20026162
title: Improved model for the establishment and evaluation of detrusor overactivity in female Wistar rats

description: Objective To improve the model for establishment and evaluation of detrusor overactivity in female Wistar rats. Materials and Methods We ligated the perineal urethra of female Wistar rats and then performed filling cystometry. The probability of detrusor overactivity, bladder capacity, peak voiding pressure and histological changes were investigated. Results Detrusor overactivity ratio of the obstruction group was 32.4%. Bladder capacity increased from 0.273 ± 0.036mL in control group to 0.89 ± 0.19mL in detrusor overactivity group (P &lt; 0.001), and peak voiding pressure increased from 45.9 ± 4.1 cm.H2O to 63.5 ± 17.4cm.H2O (P = 0.007). For obstruction group, compared to no detrusor overactivity rats, detrusor overactivity rats had higher bladder capacity (0.89 ± 0.19mL versus 0.43 ± 0.09mL, P &lt; 0.001) and higher peak voiding pressure (63.5 ± 17.4cm.H2O versus 44.8 ± 6.2cm.H2O, P = 0.005). Detrusor overactivity rats were classified according to peak voiding pressure (49.2 ± 4.2cm.H2O versus 80.8 ± 7.1cm.H2O, P &lt; 0.001). Moreover, bladder weight increased significantly in detrusor overactivity rats (P = 0.003, P = 0.028) and detrusor histological hypertrophy was observed. Conclusions Ligating perineal urethra and filling cystometry with intra-urethral cannula approach is a simple and easily reproducible method to establish and evaluate the model of detrusor overactivity in rats.
DOI: 10.6084/m9.figshare.20026192.v1
title: Intraoperative breakage of Sachse’s knife blade: a rare complication of optical internal urethrotomy (one case managing experience)

description: ABSTRACT Optical internal urethrotomy (OIU) is the most common procedure performed for short segment bulbar urethral stricture worldwide. This procedure most commonly performed using Sachse’s cold knife. Various perioperative complications of internal urethrotomy have been described in literature including bleeding, urinary tract infection, extravasation of fluid, incontinence, impotence, and recurrence of stricture. Here we report a unique complication of breakage of Sachse knife blade intraoperatively and its endoscopic management.
DOI: 10.6084/m9.figshare.7967579
title: Additional file 2 of Relation path feature embedding based convolutional neural network method for drug discovery

description: The gold standard drug-disease cases extracted from TTD. There are 300 drug-disease case are selected from TTD as gold standard test data for drug rediscovery. (TXT 11 kb)
DOI: 10.6084/m9.figshare.20026192
title: Intraoperative breakage of Sachse’s knife blade: a rare complication of optical internal urethrotomy (one case managing experience)

description: ABSTRACT Optical internal urethrotomy (OIU) is the most common procedure performed for short segment bulbar urethral stricture worldwide. This procedure most commonly performed using Sachse’s cold knife. Various perioperative complications of internal urethrotomy have been described in literature including bleeding, urinary tract infection, extravasation of fluid, incontinence, impotence, and recurrence of stricture. Here we report a unique complication of breakage of Sachse knife blade intraoperatively and its endoscopic management.
DOI: 10.6084/m9.figshare.7967570
title: Additional file 1 of Relation path feature embedding based convolutional neural network method for drug discovery

description: The 1714 drug-target-disease cases which are extracted from Therapeutic Target Database(TTD) as true cases for constructing training data. (TXT 87 kb)
DOI: 10.6084/m9.figshare.7967579.v1
title: Additional file 2 of Relation path feature embedding based convolutional neural network method for drug discovery

description: The gold standard drug-disease cases extracted from TTD. There are 300 drug-disease case are selected from TTD as gold standard test data for drug rediscovery. (TXT 11 kb)
DOI: 10.6084/m9.figshare.12162072
title: Evaluating Supplemental Samples in Longitudinal Research: Replacement and Refreshment Approaches

description: Despite the wide application of longitudinal studies, they are often plagued by missing data and attrition. The majority of methodological approaches focus on participant retention or modern missing data analysis procedures. This paper, however, takes a new approach by examining how researchers may <i>supplement</i> the sample with additional participants. First, <i>refreshment</i> samples use the same selection criteria as the initial study. Second, <i>replacement</i> samples identify auxiliary variables that may help explain patterns of missingness and select new participants based on those characteristics. A simulation study compares these two strategies for a linear growth model with five measurement occasions. Overall, the results suggest that <i>refreshment</i> samples lead to less relative bias, greater relative efficiency, and more acceptable coverage rates than <i>replacement</i> samples or not supplementing the missing participants in any way. Refreshment samples also have high statistical power. The comparative strengths of the refreshment approach are further illustrated through a real data example. These findings have implications for assessing change over time when researching at-risk samples with high levels of permanent attrition.
DOI: 10.6084/m9.figshare.19501202.v1
title: Additional file 2 of The global, regional, and national disease burden of breast cancer attributable to low physical activity from 1990 to 2019: an analysis of the Global Burden of Disease Study 2019

description: Additional file 2.
DOI: 10.6084/m9.figshare.7967906.v1
title: Additional file 1 of Subtype classification and functional annotation of L1Md retrotransposon promoters

description: Table S1: Subtypes of A monomers in the mm10 genome. Table S2: Subtypes of G monomers in the mm10 genome. Table S3: Subtypes of T monomers in the mm10 genome. Table S4: Position preference values of A subtypes. Table S5: Position preference values of G subtypes. Table S6: Position preference values of T subtypes. Table S7: Position preference modes for G and T monomer subtypes. Table S8: Statistics of reads related with L1Md in various species. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.7967975.v1
title: MOESM1 of Detecting drug communities and predicting comprehensive drugâ drug interactions via balance regularized semi-nonnegative matrix factorization

description: Additional file 1. Predicted results of version-independent test.
DOI: 10.6084/m9.figshare.7968044
title: Additional file 5: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S3. Single-cell library statistics computed from randomly downsampled 1 million paired-end sequencing reads for mESCs performed using SMARTer and Smart-seq2 protocols and sequenced across HiSeq2500 and BGISEQ-500 platforms. (CSV 48 kb)
DOI: 10.6084/m9.figshare.6395153
title: Additional file 4: of Comparative transcriptome analysis reveals the regulatory networks of cytokinin in promoting the floral feminization in the oil plant Sapium sebiferum

description: Tables S2-S4. Information of the assembled genes at 6Â h, 12Â h and 24Â h. (XLSX 48555 kb)
DOI: 10.6084/m9.figshare.12162072.v1
title: Evaluating Supplemental Samples in Longitudinal Research: Replacement and Refreshment Approaches

description: Despite the wide application of longitudinal studies, they are often plagued by missing data and attrition. The majority of methodological approaches focus on participant retention or modern missing data analysis procedures. This paper, however, takes a new approach by examining how researchers may <i>supplement</i> the sample with additional participants. First, <i>refreshment</i> samples use the same selection criteria as the initial study. Second, <i>replacement</i> samples identify auxiliary variables that may help explain patterns of missingness and select new participants based on those characteristics. A simulation study compares these two strategies for a linear growth model with five measurement occasions. Overall, the results suggest that <i>refreshment</i> samples lead to less relative bias, greater relative efficiency, and more acceptable coverage rates than <i>replacement</i> samples or not supplementing the missing participants in any way. Refreshment samples also have high statistical power. The comparative strengths of the refreshment approach are further illustrated through a real data example. These findings have implications for assessing change over time when researching at-risk samples with high levels of permanent attrition.
DOI: 10.6084/m9.figshare.7968050
title: Additional file 6: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S4. Single-cell library statistics computed from raw paired-end sequencing reads for mESCs and K562 using plate-based Smart-seq2 protocol and sequenced across HiSeq4000 and BGISEQ-500 platforms. (CSV 87 kb)
DOI: 10.6084/m9.figshare.19502382
title: Additional file 1 of Differential gene expression of 3D primary human airway cultures exposed to cigarette smoke and electronic nicotine delivery system (ENDS) preparations

description: Additional file 1. showing the genes listed in Figure 1: “Significant DEGs were identified with low, medium and high dose of WS-CM at 4hrs (Tab 1) and 24hrs (Tab 2) exposure. Genes highlighted yellow were consistently observed in all three doses. Genes highlighted in orange were observed in both medium and high doses, but not low dose. Log2 fold change cut-off is set to ±2 and p-value ≤ 0.05. A list of genes identified across both exposure times (4hrs and 24hrs), and within each dose (low, medium and high) is provided in Tab 3.”
DOI: 10.6084/m9.figshare.19502390
title: Additional file 2 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 2: Supplementary Table 2. The transcriptome sequencing results of control and sunburned pomegranate fruits.
DOI: 10.6084/m9.figshare.12162075
title: A Diagnostic Procedure for Detecting Outliers in Linear State–Space Models

description: Outliers can be more problematic in longitudinal data than in independent observations due to the correlated nature of such data. It is common practice to discard outliers as they are typically regarded as a nuisance or an aberration in the data. However, outliers can also convey meaningful information concerning potential model misspecification, and ways to modify and improve the model. Moreover, outliers that occur among the latent variables (innovative outliers) have distinct characteristics compared to those impacting the observed variables (additive outliers), and are best evaluated with different test statistics and detection procedures. We demonstrate and evaluate the performance of an outlier detection approach for multi-subject state-space models in a Monte Carlo simulation study, with corresponding adaptations to improve power and reduce false detection rates. Furthermore, we demonstrate the empirical utility of the proposed approach using data from an ecological momentary assessment study of emotion regulation together with an open-source software implementation of the procedures.
DOI: 10.6084/m9.figshare.12162075.v1
title: A Diagnostic Procedure for Detecting Outliers in Linear State–Space Models

description: Outliers can be more problematic in longitudinal data than in independent observations due to the correlated nature of such data. It is common practice to discard outliers as they are typically regarded as a nuisance or an aberration in the data. However, outliers can also convey meaningful information concerning potential model misspecification, and ways to modify and improve the model. Moreover, outliers that occur among the latent variables (innovative outliers) have distinct characteristics compared to those impacting the observed variables (additive outliers), and are best evaluated with different test statistics and detection procedures. We demonstrate and evaluate the performance of an outlier detection approach for multi-subject state-space models in a Monte Carlo simulation study, with corresponding adaptations to improve power and reduce false detection rates. Furthermore, we demonstrate the empirical utility of the proposed approach using data from an ecological momentary assessment study of emotion regulation together with an open-source software implementation of the procedures.
DOI: 10.6084/m9.figshare.6395153.v1
title: Additional file 4: of Comparative transcriptome analysis reveals the regulatory networks of cytokinin in promoting the floral feminization in the oil plant Sapium sebiferum

description: Tables S2-S4. Information of the assembled genes at 6Â h, 12Â h and 24Â h. (XLSX 48555 kb)
DOI: 10.6084/m9.figshare.7968023
title: Additional file 3: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S1. The sequencing throughput and costs for single- and paired-end reads across both Illumina and BGISEQ-500 platform. (XLSX 9 kb)
DOI: 10.25549/usctheses-c3-546527
title: etd-WaltonTiff-3272
DOI: 10.6084/m9.figshare.7968035
title: Additional file 4: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S2. Single-cell library statistics computed from raw paired-end sequencing reads for mESCs using SMARTer and Smart-seq2 protocols and sequenced across HiSeq2500 and BGISEQ-500 platforms. (CSV 50 kb)
DOI: 10.6084/m9.figshare.19502396
title: Additional file 4 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 4: Supplementary Table 4. Quantity and function of differently expressed transcription factors between healthy and sunburned pomegranate pericarps.
DOI: 10.6084/m9.figshare.7967975
title: MOESM1 of Detecting drug communities and predicting comprehensive drugâ drug interactions via balance regularized semi-nonnegative matrix factorization

description: Additional file 1. Predicted results of version-independent test.
DOI: 10.6084/m9.figshare.6395276
title: Additional file 3: of Microarray analysis of long non-coding RNA expression profiles in monocytic myeloid-derived suppressor cells in Echinococcus granulosus-infected mice

description: Table S3. Significantly and differentially expressed mRNAs in M-MDSCs. (XLSX 83 kb)
DOI: 10.6084/m9.figshare.6395300.v1
title: Additional file 3: of Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers

description: Prediction performance of specific CpGs in distinguishing HCC from normal tissue and other tumors. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.7967906
title: Additional file 1 of Subtype classification and functional annotation of L1Md retrotransposon promoters

description: Table S1: Subtypes of A monomers in the mm10 genome. Table S2: Subtypes of G monomers in the mm10 genome. Table S3: Subtypes of T monomers in the mm10 genome. Table S4: Position preference values of A subtypes. Table S5: Position preference values of G subtypes. Table S6: Position preference values of T subtypes. Table S7: Position preference modes for G and T monomer subtypes. Table S8: Statistics of reads related with L1Md in various species. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.7968023.v1
title: Additional file 3: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S1. The sequencing throughput and costs for single- and paired-end reads across both Illumina and BGISEQ-500 platform. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.12686621
title: Micronuclear genome and macronuclear transcriptome with annotation, of marine tintinnid ciliate Schmidingerella arcuata (Spirotrichea).

description: The files above are associated with the following publication:<br><br><b>­Combined genome and transcriptome analyses of the ciliate </b><i>Schmidingerella arcuata</i><b> (Spirotrichea) reveal patterns of DNA elimination, scrambling, and inversion<br></b><br> in Genome Biology and Evolution<b> </b><b> </b>Susan A. Smith<sup>1</sup>*, Xyrus X. Maurer-Alcalá<sup>2</sup>, Ying Yan<sup>3</sup>, Laura A. Katz<sup>3</sup>, Luciana F. Santoferrara<sup>1</sup><sup>,4</sup><sub>,</sub> George B. McManus<sup>1</sup><sup>1</sup>Department of Marine Sciences, University of Connecticut, Groton, USA<sup>2</sup>Institute of Cell Biology, University of Bern, Bern, Switzerland<sup>3</sup>Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA<sup>4</sup>Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, USA<b>*</b>Author for Correspondence: Department of Marine Sciences, University of Connecticut, Groton, USA, susan.smith@uconn.edu<br><br><em>Genome Biology and Evolution</em>, evaa185, https://doi.org/10.1093/gbe/evaa185Published: 01 September 2020<br><br>_____________________________________These files are associated with the following Bioprojects and accession numbers on Genbank.<br><br><b>Bioproject PRJNA626068</b> : Genome and transcriptome of marine ciliate Schmidingerella arcuata (TaxID: 1229734) <b>Biosample SAMN14615214</b>: <i>Schmidingerella arcuata,</i> macronuclear transcriptome (TaxID: 1229734)<b>TSA (Transcriptome assembly) GISN00000000: </b><i>Schmidingerella arcuata,</i> macronuclear transcriptome<b></b><b>Biosample SAMN14615117:</b> <i>Schmidingerella arcuata</i>, micronuclear genome, partial <br>(TaxID: 1229734)<b>SRA (Sequence Read Archive) SRR11933493</b>: Genome and transcriptome of marine ciliate <i>Schmidingerella arcuata</i><i><br></i><i><br></i><br>
DOI: 10.6084/m9.figshare.6395174
title: Additional file 5: of Comparative transcriptome analysis reveals the regulatory networks of cytokinin in promoting the floral feminization in the oil plant Sapium sebiferum

description: Tables S5-S7. Differentially expressed genes at 6Â h, 12Â h and 24Â h after 6-BA treatment. (XLSX 363 kb)
DOI: 10.6084/m9.figshare.7968074
title: Additional file 9: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S7. Metadata for all single-cell libraries profiled in this manuscript. Each cell is labeled with a sample id (accession number), protocol, place of experiment, read type, and sequencing platform.
DOI: 10.6084/m9.figshare.6395174.v1
title: Additional file 5: of Comparative transcriptome analysis reveals the regulatory networks of cytokinin in promoting the floral feminization in the oil plant Sapium sebiferum

description: Tables S5-S7. Differentially expressed genes at 6Â h, 12Â h and 24Â h after 6-BA treatment. (XLSX 363 kb)
DOI: 10.6084/m9.figshare.7968221
title: Additional file 11: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S11. KASP assay primers used in the study. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.19502387
title: Additional file 1 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 1: Supplementary Table 1. Differentially accumulated metabolites in sunburned compared with healthy pomegranate pericarps.
DOI: 10.6084/m9.figshare.7968224.v1
title: Additional file 2: of GTSE1 is involved in breast cancer progression in p53 mutation-dependent manner

description: The GTSE1 protein expression level with clinical and pathological characteristics in 90 TNBC patients. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7968230
title: Additional file 1: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S1. Primers for sequencing and genotyping. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7968236.v1
title: Additional file 2: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S2. List of the rice germplasm used in this study. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.19502393.v1
title: Additional file 3 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 3: Supplementary Table 3. Differentially expressed genes in the control and sunburned pomegranate pericarps.
DOI: 10.6084/m9.figshare.25195343
title: Dataset - Effect of forgiveness therapy on negative affect among patients with Alcohol Dependence Syndrome.xlsx

description: Study done aimed to see the effect of forgiveness therapy on negative affect among patients with alcohol dependent syndrome (ADS) using ERP as compared to those receiving treatment as usual (TAU).<br>
DOI: 10.6084/m9.figshare.25195343.v1
title: Dataset - Effect of forgiveness therapy on negative affect among patients with Alcohol Dependence Syndrome.xlsx

description: Study done aimed to see the effect of forgiveness therapy on negative affect among patients with alcohol dependent syndrome (ADS) using ERP as compared to those receiving treatment as usual (TAU).<br>
DOI: 10.6084/m9.figshare.19502382.v1
title: Additional file 1 of Differential gene expression of 3D primary human airway cultures exposed to cigarette smoke and electronic nicotine delivery system (ENDS) preparations

description: Additional file 1. showing the genes listed in Figure 1: “Significant DEGs were identified with low, medium and high dose of WS-CM at 4hrs (Tab 1) and 24hrs (Tab 2) exposure. Genes highlighted yellow were consistently observed in all three doses. Genes highlighted in orange were observed in both medium and high doses, but not low dose. Log2 fold change cut-off is set to ±2 and p-value ≤ 0.05. A list of genes identified across both exposure times (4hrs and 24hrs), and within each dose (low, medium and high) is provided in Tab 3.”
DOI: 10.25549/usctheses-c3-599901
title: etd-RuizSusana-3651~058
DOI: 10.25549/usctheses-c3-577171
title: etd-CardenasMi-3510_063
DOI: 10.6084/m9.figshare.19502399.v1
title: Additional file 5 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 5: Supplementary Table 5. Primers designed for the qRT-PCR expression analysis.
DOI: 10.6084/m9.figshare.7968035.v1
title: Additional file 4: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S2. Single-cell library statistics computed from raw paired-end sequencing reads for mESCs using SMARTer and Smart-seq2 protocols and sequenced across HiSeq2500 and BGISEQ-500 platforms. (CSV 50 kb)
DOI: 10.6084/m9.figshare.7968044.v1
title: Additional file 5: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S3. Single-cell library statistics computed from randomly downsampled 1 million paired-end sequencing reads for mESCs performed using SMARTer and Smart-seq2 protocols and sequenced across HiSeq2500 and BGISEQ-500 platforms. (CSV 48 kb)
DOI: 10.6084/m9.figshare.7968065
title: Additional file 8: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S6. Single-cell library statistics computed from raw single-end sequencing reads for mESCs and K562 using plate-based Smart-seq2 protocol and sequenced across HiSeq4000 and BGISEQ-500 platforms. (CSV 75 kb)
DOI: 10.6084/m9.figshare.6395237
title: Additional file 1: of Microarray analysis of long non-coding RNA expression profiles in monocytic myeloid-derived suppressor cells in Echinococcus granulosus-infected mice

description: Table S1. Primers used in qPCR detection of selected lncRNAs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7968065.v1
title: Additional file 8: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S6. Single-cell library statistics computed from raw single-end sequencing reads for mESCs and K562 using plate-based Smart-seq2 protocol and sequenced across HiSeq4000 and BGISEQ-500 platforms. (CSV 75 kb)