cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13507190
title: A novel four-gene of iron metabolism-related and methylated for prognosis prediction of hepatocellular carcinoma

description: Hepatocellular carcinoma (HCC) is a liver disease with a complex underlying mechanism, and patients with HCC have low survival rates. Iron metabolism plays a crucial role in the pathogenesis of HCC; however, the prognostic value of iron metabolism-related and methylated genes for HCC needs to be further explored. In the present study, we identified differentially expressed genes (DEGs) that play a role in iron metabolism and DNA methylation in HCC from The Cancer Genome Atlas. Four of these DEGs, whose expression levels are correlated with HCC prognosis, namely, RRM2, FTCD, CYP2C9, and ATP6V1C1, were further used to construct a prognostic model for HCC, wherein the risk score was calculated using the gene expression of the four DEGs. This could be used to predict the overall survival of HCC patients for 1, 3, and 5 years. Results of a multivariate Cox regression analysis further indicated that the risk score was an independent variable correlated with the prognosis of HCC patients. The identified gene signature was further validated using an independent cohort of HCC patients from the International Cancer Genome Consortium. Weighted gene co-expression network analysis and gene set enrichment analysis were performed to identify potential regulatory mechanisms of the gene signature in HCC. Taken together, we identified key prognostic factors of iron metabolism-related and methylated genes for HCC, providing a potential treatment strategy for HCC.
DOI: 10.6084/m9.figshare.13507190.v1
title: A novel four-gene of iron metabolism-related and methylated for prognosis prediction of hepatocellular carcinoma

description: Hepatocellular carcinoma (HCC) is a liver disease with a complex underlying mechanism, and patients with HCC have low survival rates. Iron metabolism plays a crucial role in the pathogenesis of HCC; however, the prognostic value of iron metabolism-related and methylated genes for HCC needs to be further explored. In the present study, we identified differentially expressed genes (DEGs) that play a role in iron metabolism and DNA methylation in HCC from The Cancer Genome Atlas. Four of these DEGs, whose expression levels are correlated with HCC prognosis, namely, RRM2, FTCD, CYP2C9, and ATP6V1C1, were further used to construct a prognostic model for HCC, wherein the risk score was calculated using the gene expression of the four DEGs. This could be used to predict the overall survival of HCC patients for 1, 3, and 5 years. Results of a multivariate Cox regression analysis further indicated that the risk score was an independent variable correlated with the prognosis of HCC patients. The identified gene signature was further validated using an independent cohort of HCC patients from the International Cancer Genome Consortium. Weighted gene co-expression network analysis and gene set enrichment analysis were performed to identify potential regulatory mechanisms of the gene signature in HCC. Taken together, we identified key prognostic factors of iron metabolism-related and methylated genes for HCC, providing a potential treatment strategy for HCC.
DOI: 10.5281/zenodo.10667014
title: CellCanvas sample data for Winter 2024 UX Evaluation

description: This deposit contains 3 zarr datasets that contain cropped images and feature maps. Feature maps were computed with scikit-image and TomoTwin.

Cropped images taken from images from this paper: https://doi.org/10.1101/2022.04.12.488077









Convolutional networks for supervised mining of molecular patterns within cellular context


Irene de Teresa, Sara K. Goetz, Alexander Mattausch, Frosina Stojanovska, Christian E. Zimmerli, Mauricio Toro-Nahuelpan, Dorothy W.C. Cheng, Fergus Tollervey, Constantin Pape, Martin Beck, Anna Kreshuk, Julia Mahamid, Judith Zaugg

bioRxiv 2022.04.12.488077; doi: https://doi.org/10.1101/2022.04.12.488077 

Now published in Nature Methods doi: 10.1038/s41592-022-01746-2

 

Other links to the data:

- https://www.ebi.ac.uk/empiar/EMPIAR-10988/

- https://cryoetdataportal.czscience.com/datasets/10000?prev=%2Fbrowse-data%2Fdatasets%3Fportal_id%3D10000

- https://cryoetdataportal.czscience.com/datasets/10001?prev=%2Fbrowse-data%2Fdatasets%3Fportal_id%3D10001
DOI: 10.34740/kaggle/dsv/7670932
title: RAVDESSpeechEmotions:EmotionRecognition daatset
DOI: 10.5281/zenodo.10667013
title: CellCanvas sample data for Winter 2024 UX Evaluation (extended)

description: This deposit contains 5 zarr datasets that contain cropped images and feature maps. Feature maps were computed with scikit-image and TomoTwin.

Cropped images taken from images from this paper: https://doi.org/10.1101/2022.04.12.488077









Convolutional networks for supervised mining of molecular patterns within cellular context


Irene de Teresa, Sara K. Goetz, Alexander Mattausch, Frosina Stojanovska, Christian E. Zimmerli, Mauricio Toro-Nahuelpan, Dorothy W.C. Cheng, Fergus Tollervey, Constantin Pape, Martin Beck, Anna Kreshuk, Julia Mahamid, Judith Zaugg

bioRxiv 2022.04.12.488077; doi: https://doi.org/10.1101/2022.04.12.488077

Now published in Nature Methods doi: 10.1038/s41592-022-01746-2

 

Other links to the data:

- https://www.ebi.ac.uk/empiar/EMPIAR-10988/

- https://cryoetdataportal.czscience.com/datasets/10000?prev=%2Fbrowse-data%2Fdatasets%3Fportal_id%3D10000

- https://cryoetdataportal.czscience.com/datasets/10001?prev=%2Fbrowse-data%2Fdatasets%3Fportal_id%3D10001
DOI: 10.5281/zenodo.10687662
title: CellCanvas sample data for Winter 2024 UX Evaluation (extended)

description: This deposit contains 5 zarr datasets that contain cropped images and feature maps. Feature maps were computed with scikit-image and TomoTwin.

Cropped images taken from images from this paper: https://doi.org/10.1101/2022.04.12.488077









Convolutional networks for supervised mining of molecular patterns within cellular context


Irene de Teresa, Sara K. Goetz, Alexander Mattausch, Frosina Stojanovska, Christian E. Zimmerli, Mauricio Toro-Nahuelpan, Dorothy W.C. Cheng, Fergus Tollervey, Constantin Pape, Martin Beck, Anna Kreshuk, Julia Mahamid, Judith Zaugg

bioRxiv 2022.04.12.488077; doi: https://doi.org/10.1101/2022.04.12.488077

Now published in Nature Methods doi: 10.1038/s41592-022-01746-2

 

Other links to the data:

- https://www.ebi.ac.uk/empiar/EMPIAR-10988/

- https://cryoetdataportal.czscience.com/datasets/10000?prev=%2Fbrowse-data%2Fdatasets%3Fportal_id%3D10000

- https://cryoetdataportal.czscience.com/datasets/10001?prev=%2Fbrowse-data%2Fdatasets%3Fportal_id%3D10001
DOI: 10.58142/swps-3b96
title: GEMTRA
DOI: 10.34740/kaggle/dsv/7671011
title: ⏳ endoflife.date database (duckdb)
DOI: 10.6084/m9.figshare.17701556
title: Additional file 5 of Urine proteomics identifies biomarkers for diabetic kidney disease at different stages

description: Additional file 5: Table S3. Differentially excreted proteins of diabetes and DKD. Sheet 1: differentially excreted proteins between diabetes and DKD in the discovery dataset (Batch 1). Sheet 2: differentially excreted proteins between diabetes and DKD in the validation dataset (Batch 2).
DOI: 10.6084/m9.figshare.17701556.v1
title: Additional file 5 of Urine proteomics identifies biomarkers for diabetic kidney disease at different stages

description: Additional file 5: Table S3. Differentially excreted proteins of diabetes and DKD. Sheet 1: differentially excreted proteins between diabetes and DKD in the discovery dataset (Batch 1). Sheet 2: differentially excreted proteins between diabetes and DKD in the validation dataset (Batch 2).
DOI: 10.6084/m9.figshare.17701565
title: Additional file 8 of Urine proteomics identifies biomarkers for diabetic kidney disease at different stages

description: Additional file 8: Table S6. Differentially excreted proteins of diabetes and pre-DKD3.
DOI: 10.6084/m9.figshare.17701565.v1
title: Additional file 8 of Urine proteomics identifies biomarkers for diabetic kidney disease at different stages

description: Additional file 8: Table S6. Differentially excreted proteins of diabetes and pre-DKD3.
DOI: 10.6084/m9.figshare.17701619
title: Additional file 3 of An Adenylate Kinase OsAK3 Involves Brassinosteroid Signaling and Grain Length in Rice (Oryza sativa L.)

description: Additional file 3: Table S1. Primers used in this study. Table S2. List of DEGs used for RT-qPCR validation. Table S3. List of DEGs associated with floral organ development detected in DJ and osak3. Table S4. List of DEGs associated with stress response detected in DJ and osak3.
DOI: 10.6084/m9.figshare.17701631
title: Additional file 3 of The optimal vaccination strategy to control COVID-19: a modeling study in Wuhan City, China

description: Additional file 3: Table S2. Description and source of parameters in the age-specific model.
DOI: 10.6084/m9.figshare.17701631.v1
title: Additional file 3 of The optimal vaccination strategy to control COVID-19: a modeling study in Wuhan City, China

description: Additional file 3: Table S2. Description and source of parameters in the age-specific model.
DOI: 10.57932/4c264750-4eb4-4cf8-9432-1c79048116d3
title: CO2 total columns in Mexico-City

description: Seven solar-viewing Fourier transform infrared (FTIR) spectrometers were deployed during an intensive 7-month field campaign (part of the French-Mexican project MERCI-CO2) in the MCMA area during October 2020 to May 2021. One FTIR has been continuously operated since 2012 from an NDACC station (Altzomoni Atmospheric Observatory) located on a mountain top (3,985 m a.s.l), which is 60 km from Mexico City. This high-resolution IFS 120/5HR (spectral resolution &lt; 0.02 cm-1) spectrometer performs regular NDACC and XCO2 TCCON-like measurements using alternate optical components and retrieval strategies but producing similar results. Two low-resolution portable EM27/SUN (spectral resolution &lt; 0.5 cm-1) FTIR instruments are permanently operated at the university campus (UNAM) South of the city, and at a northern site (Vallejo) since 2016 and 2019, respectively. The other 4 EM27/SUN instruments were deployed as part of the MERCI-CO2 project.
The measurement campaign was funded by the CONACyT-ANR project 290589 ‘Mexico City’s Regional Carbon Impacts’ (ANR-17-CE04-0013-01).
DOI: 10.14473/csda/icjgda/clf3hl
title: kf_data_bez_diakritiky_w4_chps_cz_v1.0_ENG.tab

description: Data_Contact forms
DOI: 10.6084/m9.figshare.16653127
title: Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

description: Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with the mixture model parameters can represent the original data effectively and much more compactly. We thus cluster the data using the latent states and select variables according to the relationship between the states and the clusters. As true class labels are unknown in the unsupervised setting, we first generate more refined clusters, namely, semi-clusters, for variable selection and then determine the final clusters based on the dimension reduced data. Experiments on simulated and real data show that the new method is highly competitive in terms of clustering accuracy compared with several widely used methods. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.16653127.v2
title: Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

description: Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with the mixture model parameters can represent the original data effectively and much more compactly. We thus cluster the data using the latent states and select variables according to the relationship between the states and the clusters. As true class labels are unknown in the unsupervised setting, we first generate more refined clusters, namely, semi-clusters, for variable selection and then determine the final clusters based on the dimension reduced data. Experiments on simulated and real data show that the new method is highly competitive in terms of clustering accuracy compared with several widely used methods. Supplementary materials for this article are available online.
DOI: 10.14473/csda/icjgda/p0amo9
title: TI_CHPS104, 105, 204, 205, 304, 305.pdf

description: Technical information
DOI: 10.6084/m9.figshare.25257136.v1
title: Table S10.csv

description: Genes set of mitochondrial factors and biogenesis.
DOI: 10.6084/m9.figshare.7216028.v1
title: Damping of Fe-Al Alloy Electrodeposited in an Ionic Liquid

description: Iron-Aluminium alloys were produced by the electro-deposition of iron-aluminium on a copper substrate. The electro-deposition process was done in the ionic liquid 1-butyl-1-methylpyrrolidinium trifluoromethylsulfonate, [Py1,4]TfO. A solution of (0.2 M FeCl2 + 2.75 M AlCl3)/ [Py1,4] TfO was used at a temperature of T=363 K because this mixture is solid at room temperature. Electrodeposited samples were studied by means of mechanical spectroscopy, differential thermal analysis and laser light microscopy. Mechanical spectroscopy studies were performed as a function of temperature, frequency and strain. The usual damping peaks for copper, low temperature grain boundary peak, recovery peak and intermediate temperature grain boundary peak were observed. In addition, a new damping peak at around 800 K which is not thermally activated was discovered. The physical mechanism controlling the appearance of this new peak is the dissolution of small precipitates or agglomerates of defects which take place at around 800 K during the warming and the subsequent re-precipitation/re-agglomeration during the cooling. This process could occur either in the copper substrate or at the Fe-Al electrodeposit.
DOI: 10.6084/m9.figshare.7216028
title: Damping of Fe-Al Alloy Electrodeposited in an Ionic Liquid

description: Iron-Aluminium alloys were produced by the electro-deposition of iron-aluminium on a copper substrate. The electro-deposition process was done in the ionic liquid 1-butyl-1-methylpyrrolidinium trifluoromethylsulfonate, [Py1,4]TfO. A solution of (0.2 M FeCl2 + 2.75 M AlCl3)/ [Py1,4] TfO was used at a temperature of T=363 K because this mixture is solid at room temperature. Electrodeposited samples were studied by means of mechanical spectroscopy, differential thermal analysis and laser light microscopy. Mechanical spectroscopy studies were performed as a function of temperature, frequency and strain. The usual damping peaks for copper, low temperature grain boundary peak, recovery peak and intermediate temperature grain boundary peak were observed. In addition, a new damping peak at around 800 K which is not thermally activated was discovered. The physical mechanism controlling the appearance of this new peak is the dissolution of small precipitates or agglomerates of defects which take place at around 800 K during the warming and the subsequent re-precipitation/re-agglomeration during the cooling. This process could occur either in the copper substrate or at the Fe-Al electrodeposit.
DOI: 10.6084/m9.figshare.25257466
title: Supplementary Material for: Tislelizumab vs sorafenib in first-line treatment of unresectable hepatocellular carcinoma: impact on health-related quality of life in RATIONALE-301 study

description: Introduction: RATIONALE-301 (NCT03412773) was a global, phase 3 study comparing the efficacy and safety of tislelizumab with sorafenib as first-line (1L) treatment in adult patients with unresectable hepatocellular carcinoma (HCC) that met its primary endpoint of noninferiority in overall survival (OS). This analysis compared health-related quality-of-life (HRQOL) outcomes between the arms.
Methods: Systemic therapy–naive adults with HCC were randomized 1:1 to receive tislelizumab n = 342) or sorafenib (n = 332). HRQOL was assessed using EORTC QLQ-C30, QLQ-HCC18, and EQ-5D-5L. At cycles 4 and 6, a mixed model for repeated measures was performed using key prespecified patient-reported outcome (PRO) endpoints of the QLQ-C30 and the QLQ-HCC18. Time to deterioration was analyzed with the Kaplan-Meier method using the PRO endpoints.
Results: At cycles 4 and 6, patients in the tislelizumab arm had better HRQOL outcomes than the patients in the sorafenib arm per mean-change differences in GHS/QOL, QLQ-C30 physical functioning and fatigue, and QLQ-HCC18 symptom index; however, no differences for pain were observed. Patients in the tislelizumab arm had lower risk of deterioration in GHS/QOL (HR, 0.68; 95% CI, 0.49-0.94), QLQ-C30 physical functioning (HR, 0.46; 95% CI, 0.33-0.64) and fatigue (HR, 0.48; 95% CI, 0.37-0.63), QLQ-HCC18 symptom index (HR, 0.53; 95% CI, 0.34-0.81), and HCC-specific fatigue (HR, 0.60; 95% CI, 0.46-0.80). For pain, both arms had similar risk of deterioration (HR, 0.78; 95% CI, 0.56-1.09). At cycle 4 and 6, patients in the tislelizumab arm maintained in EQ-5D-5L visual analog scale, whereas scores decreased for the patients in the sorafenib arm. 

Conclusion: Patients with 1L HCC treated with tislelizumab had better HRQOL outcomes compared with patients treated with sorafenib, particularly in fatigue and physical functioning. These results, along with favorable safety profile, better response rate, and OS noninferiority, support tislelizumab as a potential 1L treatment option for unresectable HCC.
DOI: 10.6084/m9.figshare.25257466.v1
title: Supplementary Material for: Tislelizumab vs sorafenib in first-line treatment of unresectable hepatocellular carcinoma: impact on health-related quality of life in RATIONALE-301 study

description: Introduction: RATIONALE-301 (NCT03412773) was a global, phase 3 study comparing the efficacy and safety of tislelizumab with sorafenib as first-line (1L) treatment in adult patients with unresectable hepatocellular carcinoma (HCC) that met its primary endpoint of noninferiority in overall survival (OS). This analysis compared health-related quality-of-life (HRQOL) outcomes between the arms.
Methods: Systemic therapy–naive adults with HCC were randomized 1:1 to receive tislelizumab n = 342) or sorafenib (n = 332). HRQOL was assessed using EORTC QLQ-C30, QLQ-HCC18, and EQ-5D-5L. At cycles 4 and 6, a mixed model for repeated measures was performed using key prespecified patient-reported outcome (PRO) endpoints of the QLQ-C30 and the QLQ-HCC18. Time to deterioration was analyzed with the Kaplan-Meier method using the PRO endpoints.
Results: At cycles 4 and 6, patients in the tislelizumab arm had better HRQOL outcomes than the patients in the sorafenib arm per mean-change differences in GHS/QOL, QLQ-C30 physical functioning and fatigue, and QLQ-HCC18 symptom index; however, no differences for pain were observed. Patients in the tislelizumab arm had lower risk of deterioration in GHS/QOL (HR, 0.68; 95% CI, 0.49-0.94), QLQ-C30 physical functioning (HR, 0.46; 95% CI, 0.33-0.64) and fatigue (HR, 0.48; 95% CI, 0.37-0.63), QLQ-HCC18 symptom index (HR, 0.53; 95% CI, 0.34-0.81), and HCC-specific fatigue (HR, 0.60; 95% CI, 0.46-0.80). For pain, both arms had similar risk of deterioration (HR, 0.78; 95% CI, 0.56-1.09). At cycle 4 and 6, patients in the tislelizumab arm maintained in EQ-5D-5L visual analog scale, whereas scores decreased for the patients in the sorafenib arm. 

Conclusion: Patients with 1L HCC treated with tislelizumab had better HRQOL outcomes compared with patients treated with sorafenib, particularly in fatigue and physical functioning. These results, along with favorable safety profile, better response rate, and OS noninferiority, support tislelizumab as a potential 1L treatment option for unresectable HCC.
DOI: 10.6084/m9.figshare.15080409
title: Additional file 1 of Mining a stroke knowledge graph from literature

description: Additional file 1. The list of stroke-related diseases.
DOI: 10.6084/m9.figshare.15080409.v1
title: Additional file 1 of Mining a stroke knowledge graph from literature

description: Additional file 1. The list of stroke-related diseases.
DOI: 10.5281/zenodo.10687779
title: Prognostic factors for death in patients hospitalised with malaria in pediatric units at the Regional Hospital Centre of Dori

description: Pronostic study
DOI: 10.5281/zenodo.10687780
title: Prognostic factors for death in patients hospitalised with malaria in pediatric units at the Regional Hospital Centre of Dori

description: Pronostic study
DOI: 10.5281/zenodo.10687297
title: Modelo Digital del Terreno - MDT25 - España Peninsular - EasyBasin plugin

description: El archivo raster adjunto (MDT25_SPAIN.tif) ha sido obtenido mediante el geoprocesamiento de todos los archivos PNOA-MDT25-ETRS89-(HUSO).tif del Centro de Descargas del Organismo Autónomo Centro Nacional de Información Geográfica (CNIG). Para ello se ha realizado una fusion (merge) de todos los MDTs de 25 m de resolución y recortado para la España peninsular. El objetivo final de este archivo es su descarga e implementación en la nueva versión del plugin de QGIS "EasyBasin". Para ello, es necesario descargarlo y extraerlo en la carpeta:  C:/EasyBasin/Rasters/MDT/
DOI: 10.5281/zenodo.10687298
title: Modelo Digital del Terreno - MDT25 - España Peninsular - EasyBasin plugin

description: El archivo raster adjunto (MDT25_SPAIN.tif) ha sido obtenido mediante el geoprocesamiento de todos los archivos PNOA-MDT25-ETRS89-(HUSO).tif del Centro de Descargas del Organismo Autónomo Centro Nacional de Información Geográfica (CNIG). Para ello se ha realizado una fusion (merge) de todos los MDTs de 25 m de resolución y recortado para la España peninsular. El objetivo final de este archivo es su descarga e implementación en la nueva versión del plugin de QGIS "EasyBasin". Para ello, es necesario descargarlo y extraerlo en la carpeta:  C:/EasyBasin/Rasters/MDT/
DOI: 10.6084/m9.figshare.25257136
title: Table S10.csv

description: Genes set of mitochondrial factors and biogenesis.
DOI: 10.6084/m9.figshare.13507687
title: A Factor-Based Estimation of Integrated Covariance Matrix With Noisy High-Frequency Data

description: This article studies a high-dimensional factor model with sparse idiosyncratic covariance matrix in continuous time, using asynchronous high-frequency financial data contaminated by microstructure noise. We focus on consistent estimations of the number of common factors, the integrated covariance matrix and its inverse, based on the flat-top realized kernels introduced by Varneskov. Simulation results illustrate the satisfactory performance of our estimators in finite samples. We apply our methodology to the high-frequency price data on a large number of stocks traded in Shanghai and Shenzhen stock exchanges, and demonstrate its value for capturing time-varying covariations and portfolio allocation.