cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc1nl1q0
title: CCDC 1536692: Experimental Crystal Structure Determination

description: Related Article: N. Manju, Balakrishna Kalluraya, Asma, Madan S. Kumar|2019|J.Mol.Struct.|1193|386|doi:10.1016/j.molstruc.2019.05.049
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.2877645
title: A comparison of automatic cell identification methods for single-cell RNA-sequencing data

description: Benchmark datasets used to evaluate the performance of 22 classifiers for cell type classification for scRNA-seq data
DOI: 10.5281/zenodo.2877646
title: A comparison of automatic cell identification methods for single-cell RNA-sequencing data

description: Benchmark datasets used to evaluate the performance of 20 classifiers for cell type classification for scRNA-seq data
DOI: 10.5281/zenodo.2871796
title: Dataset: An Open-hardware Platform for MPSoC Thermal Modeling

description: This repository contains the experimental data for the paper "An Open-hardware Platform for MPSoC Thermal Modeling" published at 2019 samos conference http://samos-conference.com The data is released under a CC-BY Creative Commons license.<br> If you use this dataset, cite the following paper:<br> Federico Terraneo, Alberto Leva, William Fornaciari, "An Open-hardware Platform for MPSoC Thermal Modeling", 2019 IEEE International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation (SAMOS)
DOI: 10.5281/zenodo.2871797
title: Dataset: An Open-hardware Platform for MPSoC Thermal Modeling

description: This repository contains the experimental data for the paper

"An Open-hardware Platform for MPSoC Thermal Modeling"

published at 2019 samos conference

http://samos-conference.com

The data is released under a CC-BY Creative Commons license.<br>
If you use this dataset, cite the following paper:<br>
Federico Terraneo, Alberto Leva, William Fornaciari, "An Open-hardware Platform for MPSoC Thermal Modeling", 2019 IEEE International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation (SAMOS)
DOI: 10.5281/zenodo.2878368
title: JTeC: A Large Collection of Java Test Classes forTest Code Analysis and Processing

description: The recent push towards test automation and test-driven development continues to scale up the dimensions of test code that needs to be maintained, analysed, and processed side-by-side with production code. As a consequence, on the one side regression testing techniques, e.g., for test suite prioritization or test case selection, capable to handle such large-scale test suites become indispensable; on the other side, as test code exposes own characteristics, specific techniques for its analysis and refactoring are actively sought. We present JTeC, a large-scale dataset of test cases that researchers can use for benchmarking the above techniques or any other type of tool expressly targeting test code. JTeC collects more than 2.5M+ test classes belonging to 31K+ GitHub projects and summing up to more than 430 Million LOCs of ready-to-use real-world test code.
description: Companion page for the JTeC dataset at https://github.com/JTeCDataset/JTeC
DOI: 10.25828/jrhx-yd59
title: Continuous Multi-Purpose Household Survey 2011
DOI: 10.6084/m9.figshare.14286602.v1
title: Preoperative hydronephrosis predicts adverse pathological features and postoperative survival in patients with high-grade upper tract urothelial carcinoma

description: ABSTRACT Purpose: Epidemiological studies reported conflicting results about preoperative hydronephrosis in upper tract urothelial carcinoma (UTUC). This study aimed to investigate the association between preoperative hydronephrosis and pathologic features and oncologic outcomes in patients with UTUC treated by radical nephroureterectomy (RNU). Materials and Methods: This was a retrospective, single-center cohort study of 377 patients treated by RNU without perioperative chemotherapy between January 2001 and December 2014. Logistic regression, Cox regression, and survival analyses were performed. Results: Among the 226 patients with high-grade UTUC, 132 (58%) had preoperative hydronephrosis. Multivariable logistic regression revealed that hydronephrosis was independently associated with advanced pT stage (P=0.017) and lymph node or lymphovascular invasion (P=0.002). Median follow-up was 36 months (interquartile range: 20-48 months). The 3- and 5-year overall survival (OS) rates in patients with hydronephrosis were significantly lower than in those without hydronephrosis (both P &lt;0.001). The 3- and 5-year cancer-specific survival (CSS) rates in patients with hydronephrosis were significantly lower than in those without hydronephrosis (both P=0.001). Hydronephrosis was independently associated with OS and CSS (P=0.001 and P=0.004, respectively). Among the 151 patients with low-grade UTUC, hydronephrosis was not associated with pathologic features and postoperative survival. Conclusions: Preoperative hydronephrosis was significantly associated with adverse pathologic features and postoperative survival in patients with high-grade UTUC.
DOI: 10.6084/m9.figshare.21102304
title: Additional file 8 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 8: Supplementary Table 4. Blood biomedical measurements data for all study subjects.
DOI: 10.6084/m9.figshare.14286584
title: Partial nephrectomy provides equivalent oncologic outcomes and better renal function preservation than radical nephrectomy for pathological T3a renal cell carcinoma: A meta-analysis

description: ABSTRACT Purpose: Radical nephrectomy (RN) is the standard surgical type for pathological stage T3a (pT3a) renal cell carcinoma (RCC). Recently, some studies have suggested equivalence between partial nephrectomy (PN) and RN for oncologic control and have shown the benefits of PN for better renal function. We conducted this meta-analysis to assess oncologic outcomes, perioperative outcomes and renal function between two groups among patients with pT3a RCC. Materials and methods: PubMed, Scopus, Web of Science, Science Direct, Ovid MEDLINE, The Cochrane Library, Embase and Google Scholar were searched for eligible articles. The endpoints of the final analysis included overall survival (OS), cancer-specific survival (CSS), recurrence-free survival (RFS), surgical complications, operative time, estimated blood loss (EBL), serum creatinine and estimated glomerular filtration rate (eGFR). Results: Twelve studies of moderate to high quality, including 14.152 patients, were examined. PN showed superiority for renal functional preservation, providing higher eGFR (WMD=12.48mL/min; 95%CI: 10.28 to 14.67; P &lt;0.00001) and lower serum creatinine (WMD=-0.31mg/dL; 95%CI: −0.40 to −0.21; P &lt;0.00001). There were no significant differences between PN and RN regarding operative time, EBL, surgical complications, OS, RFS and CSS. Despite inherent selection bias, most pooled estimates were consistent in sensitivity analysis and subgroup analysis. More positive margins were found in the PN group (RR=2.42; 95%CI: 1.25-4.68; P=0.009). Conclusions: PN may be more suitable for treating pT3a RCC than RN because it provides a similar survival time (OS or RFS) and superior renal function. Nevertheless, this result is still disputed, and more high-quality studies are required.
DOI: 10.6084/m9.figshare.14286602
title: Preoperative hydronephrosis predicts adverse pathological features and postoperative survival in patients with high-grade upper tract urothelial carcinoma

description: ABSTRACT Purpose: Epidemiological studies reported conflicting results about preoperative hydronephrosis in upper tract urothelial carcinoma (UTUC). This study aimed to investigate the association between preoperative hydronephrosis and pathologic features and oncologic outcomes in patients with UTUC treated by radical nephroureterectomy (RNU). Materials and Methods: This was a retrospective, single-center cohort study of 377 patients treated by RNU without perioperative chemotherapy between January 2001 and December 2014. Logistic regression, Cox regression, and survival analyses were performed. Results: Among the 226 patients with high-grade UTUC, 132 (58%) had preoperative hydronephrosis. Multivariable logistic regression revealed that hydronephrosis was independently associated with advanced pT stage (P=0.017) and lymph node or lymphovascular invasion (P=0.002). Median follow-up was 36 months (interquartile range: 20-48 months). The 3- and 5-year overall survival (OS) rates in patients with hydronephrosis were significantly lower than in those without hydronephrosis (both P &lt;0.001). The 3- and 5-year cancer-specific survival (CSS) rates in patients with hydronephrosis were significantly lower than in those without hydronephrosis (both P=0.001). Hydronephrosis was independently associated with OS and CSS (P=0.001 and P=0.004, respectively). Among the 151 patients with low-grade UTUC, hydronephrosis was not associated with pathologic features and postoperative survival. Conclusions: Preoperative hydronephrosis was significantly associated with adverse pathologic features and postoperative survival in patients with high-grade UTUC.
DOI: 10.6084/m9.figshare.7996889.v1
title: Additional file 4: of Selective translational usage of TSS and core promoters revealed by translatome sequencing

description: Table S2. Length difference of the 5’ UTR between translatome and transcriptome. “Length Difference” shows the difference in length of the 5’ UTR. “Length Status” shows whether the length of the 5’UTR in translatome is the same as, or shorter than, or longer than that in transcriptome. The definitions of the other column names are the same as in Additional file 3: Table S1. (XLSX 1009 kb)
DOI: 10.6084/m9.figshare.21102277.v1
title: Additional file 11 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 11: Supplementary Table 7. Ethnicity-specific EGGNOG and MetaCyc functions in the gut archaeome.
DOI: 10.6084/m9.figshare.21102295
title: Additional file 5 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 5: Supplementary Table 1. Demographic summary of studied healthy Chinese populations.
DOI: 10.6084/m9.figshare.21102301
title: Additional file 7 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 7: Supplementary Table 3. Diet record data for all study subjects.
DOI: 10.6084/m9.figshare.21102307.v1
title: Additional file 9 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 9: Supplementary Table 5. Significant correlations between consumption of food items and archaeal species, identified by MaAsLin2.
DOI: 10.6084/m9.figshare.21102307
title: Additional file 9 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 9: Supplementary Table 5. Significant correlations between consumption of food items and archaeal species, identified by MaAsLin2.
DOI: 10.6084/m9.figshare.21102280
title: Additional file 12 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 12: Supplementary Table 8. EGGNOG and MetaCyc functions enriched in the gut archaeome of rural versus urban Chinese.
DOI: 10.6084/m9.figshare.21102298
title: Additional file 6 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 6: Supplementary Table 2. Metadata for all study subjects.
DOI: 10.6084/m9.figshare.14286587.v1
title: Long term outcomes of one-stage augmentation anterior urethroplasty: a systematic review and meta-analysis

description: ABSTRACT Objective: The objective is to summarize and characterize the long-term success of anterior augmentation urethroplasty (AU) in published series. The current literature on AU consists largely of retrospective series reporting intermediate follow-up and incompletely characterize the long term outcomes of AU. Materials and Methods: A systematic literature review was performed consistent with PRISMA guidelines to characterize long-term outcomes of AU with a minimum upper limit follow-up of 100 months. Penile/preputial skin flaps and graft and oral mucosal graft urethroplasties were included. The primary outcome was stricture-free survival for one-stage AU. Secondary analysis evaluated differences in outcomes based on two failure definitions: the need for intervention versus presence of recurrent stricture on cystoscopy or urethrography. Hazard rates were induced from the reported failure rates of one-stage AU and fixed and random effect models were fitted to the data. Additional subset analysis, removing potential confounders (lichen sclerosus, hypospadias and penile skin graft), was performed. Results: Ten studies met inclusion criteria, and two studies reported separate outcomes for grafts and flaps, and thus were included separately in the analysis. The mean hazard rate across all studies was 0.0044, the corresponding survival rates at 1 year 0.948, 5 years 0.766, 10 years 0.587, and 15 years 0.45. Subset analysis of the 4 select and homogeneous studies noted 1, 5, 10, and 15 years survival rates of 0.97, 0.96, 0.74, and 0.63, respectively. Conclusions: The long-term success rates of augmentation urethroplasty are appear to be worse than previously appreciated and patients should be counseled accordingly.
DOI: 10.6084/m9.figshare.21102295.v1
title: Additional file 5 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 5: Supplementary Table 1. Demographic summary of studied healthy Chinese populations.
DOI: 10.6084/m9.figshare.21102301.v1
title: Additional file 7 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 7: Supplementary Table 3. Diet record data for all study subjects.
DOI: 10.6084/m9.figshare.21102304.v1
title: Additional file 8 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 8: Supplementary Table 4. Blood biomedical measurements data for all study subjects.
DOI: 10.6084/m9.figshare.7470869.v1
title: Additional file 10: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S9. qRT-PCR validation of the RNA-Seq results. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.14286621.v1
title: Survival nomogram for patients with bone metastatic renal cell carcinoma: A population-based study

description: ABSTRACT Purpose: Increased attention has been focused on the survival of renal cell carcinoma (RCC) patients with bone metastasis. This study proposed to establish and evaluate a nomogram for predicting the overall survival (OS) and cancer-specific survival (CSS) of RCC patients with bone metastasis. Materials and Methods: RCC patients with bone metastasis between 2010 and 2015 were captured from the surveillance, epidemiology and end results (SEER) database. Univariate and multivariate cox regressions were performed to assess the effects of clinical variables on OS and CSS. The nomogram based on the Cox hazards regression model was developed. Concordance index (C-index) and calibration curve were performed to evaluate the accuracy of nomogram models, receiver operating characteristic (ROC) curves and decision curve analysis (DCA) were conducted to assess the predict performance. Results: A total of 2.471 eligible patients were enrolled in this study. The patients were assigned to primary (n=1.672) and validation (n=799) cohorts randomly. The 1-, 2-, and 3-year OS and CSS nomogram models were constructed based on age at diagnosis, sex, marital status, pathological grade, T-stage, N-stage, brain/liver/lung metastasis, surgery, radiotherapy and chemotherapy. The c for OS and CSS prediction was 0.730 (95% confidence interval [CI]: 0.719-0.741) and 0.714 (95%CI:0.702-0.726). The calibration curves showed significant agreement between nomogram models and actual observations. ROC and DCA indicated nomograms had better predict performance. Conclusions: The nomograms for predicting prognosis provided an accurate prediction of OS and CSS in RCC patients with bone metastasis, and contributed clinicians to optimize individualized treatment plans.
DOI: 10.6084/m9.figshare.7470893.v1
title: Additional file 3: of Comparative toxicogenomics of three insensitive munitions constituents 2,4-dinitroanisole, nitroguanidine and nitrotriazolone in the soil nematode Caenorhabditis elegans

description: UniProt genes mapping to computationally inferred C. elegans pathways in the Reactome database. (XLSX 508 kb)
DOI: 10.6084/m9.figshare.7470890
title: Additional file 2: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S1. The conserved milRNA identified in T. rubrum. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7470899.v1
title: Additional file 4: of Comparative toxicogenomics of three insensitive munitions constituents 2,4-dinitroanisole, nitroguanidine and nitrotriazolone in the soil nematode Caenorhabditis elegans

description: Gene set file (i.e., gene mapping to KEGG-curated C. elegans pathways) used for gene set enrichment analysis (GSEA). (XLSX 31694 kb)
DOI: 10.6084/m9.figshare.7470902.v1
title: Additional file 4: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S3. GO classification and KEGG enrichment of the target genes. (XLSX 97 kb)
DOI: 10.6084/m9.figshare.7470905
title: Additional file 5: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S4. The secreted proteases targeted by milRNAs in T. rubrum. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.14286587
title: Long term outcomes of one-stage augmentation anterior urethroplasty: a systematic review and meta-analysis

description: ABSTRACT Objective: The objective is to summarize and characterize the long-term success of anterior augmentation urethroplasty (AU) in published series. The current literature on AU consists largely of retrospective series reporting intermediate follow-up and incompletely characterize the long term outcomes of AU. Materials and Methods: A systematic literature review was performed consistent with PRISMA guidelines to characterize long-term outcomes of AU with a minimum upper limit follow-up of 100 months. Penile/preputial skin flaps and graft and oral mucosal graft urethroplasties were included. The primary outcome was stricture-free survival for one-stage AU. Secondary analysis evaluated differences in outcomes based on two failure definitions: the need for intervention versus presence of recurrent stricture on cystoscopy or urethrography. Hazard rates were induced from the reported failure rates of one-stage AU and fixed and random effect models were fitted to the data. Additional subset analysis, removing potential confounders (lichen sclerosus, hypospadias and penile skin graft), was performed. Results: Ten studies met inclusion criteria, and two studies reported separate outcomes for grafts and flaps, and thus were included separately in the analysis. The mean hazard rate across all studies was 0.0044, the corresponding survival rates at 1 year 0.948, 5 years 0.766, 10 years 0.587, and 15 years 0.45. Subset analysis of the 4 select and homogeneous studies noted 1, 5, 10, and 15 years survival rates of 0.97, 0.96, 0.74, and 0.63, respectively. Conclusions: The long-term success rates of augmentation urethroplasty are appear to be worse than previously appreciated and patients should be counseled accordingly.
DOI: 10.6084/m9.figshare.14286621
title: Survival nomogram for patients with bone metastatic renal cell carcinoma: A population-based study

description: ABSTRACT Purpose: Increased attention has been focused on the survival of renal cell carcinoma (RCC) patients with bone metastasis. This study proposed to establish and evaluate a nomogram for predicting the overall survival (OS) and cancer-specific survival (CSS) of RCC patients with bone metastasis. Materials and Methods: RCC patients with bone metastasis between 2010 and 2015 were captured from the surveillance, epidemiology and end results (SEER) database. Univariate and multivariate cox regressions were performed to assess the effects of clinical variables on OS and CSS. The nomogram based on the Cox hazards regression model was developed. Concordance index (C-index) and calibration curve were performed to evaluate the accuracy of nomogram models, receiver operating characteristic (ROC) curves and decision curve analysis (DCA) were conducted to assess the predict performance. Results: A total of 2.471 eligible patients were enrolled in this study. The patients were assigned to primary (n=1.672) and validation (n=799) cohorts randomly. The 1-, 2-, and 3-year OS and CSS nomogram models were constructed based on age at diagnosis, sex, marital status, pathological grade, T-stage, N-stage, brain/liver/lung metastasis, surgery, radiotherapy and chemotherapy. The c for OS and CSS prediction was 0.730 (95% confidence interval [CI]: 0.719-0.741) and 0.714 (95%CI:0.702-0.726). The calibration curves showed significant agreement between nomogram models and actual observations. ROC and DCA indicated nomograms had better predict performance. Conclusions: The nomograms for predicting prognosis provided an accurate prediction of OS and CSS in RCC patients with bone metastasis, and contributed clinicians to optimize individualized treatment plans.
DOI: 10.6084/m9.figshare.7470881.v1
title: Additional file 1: of Comparative toxicogenomics of three insensitive munitions constituents 2,4-dinitroanisole, nitroguanidine and nitrotriazolone in the soil nematode Caenorhabditis elegans

description: Differentially expressed genes derived for sublethal DNAN, NTO and NQ exposures in C. elegans. (XLSX 345 kb)
DOI: 10.6084/m9.figshare.7470890.v1
title: Additional file 2: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S1. The conserved milRNA identified in T. rubrum. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7470908.v1
title: Additional file 6: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S5. Conservation of milRNAs and corresponding target genes in dermatophytes. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7470869
title: Additional file 10: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S9. qRT-PCR validation of the RNA-Seq results. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7470896.v1
title: Additional file 3: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S2. The predicted target genes of milRNAs. (XLSX 824 kb)
DOI: 10.6084/m9.figshare.7470902
title: Additional file 4: of Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

description: Table S3. GO classification and KEGG enrichment of the target genes. (XLSX 97 kb)