cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7156359
title: Dataset related to article "Targeted Mutational Analysis of Circulating Tumor DNA to Decipher Temporal Heterogeneity of High-Grade Serous Ovarian Cancer"

description: This record contains raw data related to article<strong> "</strong>Targeted Mutational Analysis of Circulating Tumor DNA to Decipher Temporal Heterogeneity of High-Grade Serous Ovarian Cancer<strong>".</strong> We have previously demonstrated that longitudinal untargeted analysis of plasma samples withdrawn from patients with high-grade serous ovarian cancer (HGS-EOC) can intercept the presence of molecular recurrence (TRm) earlier than the diagnosis of clinical recurrence (TRc). This finding opens a clinical important temporal window to acquire through plasma sample analysis a real-time picture of those emerging molecular lesions that will drive and sustain the growth of relapsed disease and ultimately will confer resistance. In this proof of principle study, the same genomic libraries obtained at the diagnosis (T0), TRm and TRc were further analyzed by targeted resequencing approach to sequence the coding region of a panel of 65 genes to provide longitudinal analysis of clonal evolution as a novel strategy to support clinical decisions for the second-line treatment. Experiments were performed on plasma and tumor tissues withdrawn on a selection of previously analyzed cohorts of cases (i.e., 33 matched primary and synchronous lesions and 43 plasma samples from 18 patients). At T0, the median concordance of mutations shared by each tumor tissue biopsy and its matched plasma sample was 2.27%. This finding confirms the limit of a single tumor biopsy to be representative of the entire disease, while plasma analysis can recapitulate most of the main molecular lesions of the disease. A comparable scenario was observed during longitudinal analysis, where, with the exception of the <em>TP53</em> gene and germline mutations in <em>BRCA1/2</em> genes, no other gene shared the same locus specific gene mutation across T0, TRm and TRc time points. This high level of temporal heterogeneity has important implications for planning second-line treatment. For example, in three out of 13 cases, plasma ctDNA analysis at TRm or TRc reported acquired novel variants in the <em>TP53BP1</em> gene not present at T0. In particular, patient 21564, potentially eligible for PARP-inhibitor (PARPi) treatment at the time of diagnosis (<em>BRCA1</em> c.5182delA mutation), would unlikely respond to these drugs in second-line therapy due to the presence of eight distinct <em>TP53BP1</em> variants in plasma samples collected TRc. This study demonstrates that liquid biopsy provides a real-time molecular picture to intercept those actionable genetic vulnerabilities or drug resistance mechanisms that could be used to plan a more rational second-line treatment.
DOI: 10.6084/m9.figshare.21294888
title: Table S1, ECC445 - Antibiotic resistance profile

description: Antimicrobial susceptibility was analyzed as recommended in the 2018 CA-SFM/EUCAST guideline by the disc diffusion method on Mueller-Hinton
DOI: 10.48366/r221200
title: Regional Differences of Temperature Extremes in CMIP5 and CMIP6

description: This comparison provides an overview over the predicted changes in extreme temperatures in different reference regions based on the results from CMIP5. The data shows the mean, median, total range and 5th and 95th percentile of the predictions for the hottest yearly daytime temperature at a mean global warming of 1.5 °C.
DOI: 10.6084/m9.figshare.21294903
title: Table S3, E. chengduensis metadata from NCBI and quality control criteria

description: E. chengduensis metadata from NCBI
DOI: 10.5517/ccdc.csd.cc25wtlh
title: CCDC 2022737: Experimental Crystal Structure Determination

description: Related Article: Grigory Andreev, Nina Budantseva, Aleksander Fedoseev|2022|Polyhedron|224|116003|doi:10.1016/j.poly.2022.116003
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: 10.5517/ccdc.csd.cc28phhz
title: CCDC 2106031: Experimental Crystal Structure Determination

description: Related Article: Fen Wei, Jia Tang, Zareen Zuhra, Shoushan Wang, Xiaoxia Wang, Xiufang Wang, Guanqun Xie|2022|J. CO2 Utilization|61|102048|doi:10.1016/j.jcou.2022.102048
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: 10.5517/ccdc.csd.cc28pd5k
title: CCDC 2105928: Experimental Crystal Structure Determination

description: Related Article: Fen Wei, Jia Tang, Zareen Zuhra, Shoushan Wang, Xiaoxia Wang, Xiufang Wang, Guanqun Xie|2022|J. CO2 Utilization|61|102048|doi:10.1016/j.jcou.2022.102048
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: 10.5517/ccdc.csd.cc28phj0
title: CCDC 2106032: Experimental Crystal Structure Determination

description: Related Article: Fen Wei, Jia Tang, Zareen Zuhra, Shoushan Wang, Xiaoxia Wang, Xiufang Wang, Guanqun Xie|2022|J. CO2 Utilization|61|102048|doi:10.1016/j.jcou.2022.102048
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: 10.5517/ccdc.csd.cc28phm3
title: CCDC 2106035: Experimental Crystal Structure Determination

description: Related Article: Fen Wei, Jia Tang, Zareen Zuhra, Shoushan Wang, Xiaoxia Wang, Xiufang Wang, Guanqun Xie|2022|J. CO2 Utilization|61|102048|doi:10.1016/j.jcou.2022.102048
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: 10.6084/m9.figshare.21294915
title: Table S4, ECC445 - PathogenFinder summary

description: PathogenFinder summary
DOI: 10.6084/m9.figshare.21294915.v1
title: Table S4, ECC445 - PathogenFinder summary

description: PathogenFinder summary
DOI: 10.6084/m9.figshare.21294924
title: Table S5, ECC445 - CrisprCasFinder_summary

description: CrisprCasFinder summary
DOI: 10.6084/m9.figshare.21294924.v1
title: Table S5, ECC445 - CrisprCasFinder_summary

description: CrisprCasFinder summary
DOI: 10.6084/m9.figshare.20477256
title: Spatial dynamic metabolomics identifies metabolic trajectories during human kidney epithelium development

description: Accumulating evidence demonstrates important roles for metabolism in cell fate determination. However, It is a challenge to assess metabolism at a spatial resolution that acknowledges both heterogeneity and cellular dynamics in its tissue microenvironment. Using a multi-omics platform to study cell-type specific dynamics in metabolism in complex tissues, we describe the metabolic trajectories during nephrogenesis in the developing human kidney. Exploiting <em>in situ </em>analysis of isotopic labeling, a shift from glycolysis towards fatty acid β-oxidation was observed during the differentiation from the renal vesicle, towards the S-shaped body and the proximal tubules. In addition, we show that hiPSC-derived kidney organoids are characterized by a metabolic immature phenotype, that fails to use mitochondrial long-chain fatty acids for energy metabolism. Furthermore, supplementation of butyrate enhances tubular epithelial differentiation and maturation in cultured kidney organoids. Our findings highlight the relevance of understanding metabolic trajectories to efficiently guide stem cell differentiation.
DOI: 10.6084/m9.figshare.21294933
title: Table S6, CRISPR spacers comparison

description: CRISPR spacers comparison from CRISPR Comparison ToolKit
DOI: 10.5258/soton/d2389
title: Dataset supporting an article "Evaluation of a spring-finger based, magnetic connector concept for reliable E-textile interconnects"

description: The data supports a publication of "Evaluation of a spring-finger based, magnetic connector concept for reliable E-textile interconnects", by T. Greig, K. Yang and R. Torah, in IEEE Transactions on Components, Packaging and Manufacturing Technology, 2022, doi: 10.1109/TCPMT.2022.3209591. The data folder contains csv files holding the time / voltage data from the experiment described in above article. In those files, a voltage of 0V means that a connection was being made, 1V means it wasn't. Anything in between means it's probably coming or going. It also has connector reliability data for the article and a script for the graphing thereof.
DOI: 10.5281/zenodo.7157221
title: Available Wireless Sensor Network and Internet of Things testbed facilities: dataset

description: In this data set, we present data collected for the purpose of carrying out a systematic review of the available Wireless Sensor Network and Internet of Things testbed facilities. The data was collected through multiple stages and in each stage the pre-defined criteria were applied. We provide a dataset describing the hardware and software aspects of Wireless Sensor Network and Internet of Things testbed facilities available in the market and scientific community. The data were gathered through an extensive systematic review process of scientific articles published between the years 2011 and 2021. The review aims to obtain good quality data for people who are actively researching the Internet of Things facilities or anyone who is interested in that field.
DOI: 10.5281/zenodo.7157220
title: Available Wireless Sensor Network and Internet of Things testbed facilities: dataset

description: In this data set, we present data collected for the purpose of carrying out a systematic review of the available Wireless Sensor Network and Internet of Things testbed facilities. The data was collected through multiple stages and in each stage the pre-defined criteria were applied. We provide a dataset describing the hardware and software aspects of Wireless Sensor Network and Internet of Things testbed facilities available in the market and scientific community. The data were gathered through an extensive systematic review process of scientific articles published between the years 2011 and 2021. The review aims to obtain good quality data for people who are actively researching the Internet of Things facilities or anyone who is interested in that field.
DOI: 10.5255/ukda-sn-855992
title: Provincial Autonomy in Pakistan, 1956-2020

description: This dataset produces annual codes through expert analysis levels of de/centralization in Pakistan's federation between 1956 and 2020 (also covering East Pakistan until 1971). It includes three politico-institutional measures -'constitutional autonomy’, the ‘provinces’ institutional autonomy’ and the ‘central manipulation of provincial elections’. It also separately codes the legislative and administrative autonomy of 22 policy areas - Agriculture, Citizenship and immigration, Culture, Currency and money supply, Defence, Economic activity, Education - pre-tertiary, Education - tertiary, Elections and voting, Employment relations, Environmental protection, external affairs, Finance and securities, Health care, Language, Law - civil, Law - criminal, Law enforcement, Media, Natural resources, Social welfare and Transport. Finally, it codes five fiscal areas ‘proportion of own-source revenues out of total provincial revenues’, ‘restrictions on own-source revenues’, ‘proportion of federal conditional transfers out of total provincial revenues’, ‘degree of conditionality (for conditional grants only)’ and ‘provincial public sector borrowing autonomy’.
DOI: 10.5281/zenodo.7157241
title: geranium_maculatum_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.7157240
title: geranium_maculatum_zanfona_1.fasta.gz

description: .
DOI: 10.34740/kaggle/dsv/4294385
title: Indian Car Dataset
DOI: 10.5258/soton/d2353
title: Dataset to support the Southampton Doctoral thesis 'An Exploration of Factors that Impact Black, Indigenous and People of Colour (BIPOC) Healthcare Professionals at Work'

description: Qualitative data was analysed in chapter 1 of the thesis, using NVivo. Only the results of the studies were analysed (attached below). Quantitative and qualitative data was collected via Qualtrics (in collaboration with co-investigators Sarah Beattie and Leanne Timings) for the empirical part of the thesis Chapter 2). The quantitative data was analysed using SPSS and is attached below. The qualitative text was analysed using NVivo and is attached below. A participant information and consent form was required (and ethically approved) for chapter 2 and is also attached below.
DOI: 10.5281/zenodo.7156317
title: Dataset for SPCAM TC paper

description: The dataset contains processed data and codes for analyzing and producing figures. Each sub-experiment is classified by its initial date. The SPCAM code is available at https://svn-ccsm-release.cgd.ucar.edu/model_development_releases/spcam2_0-cesm1_1_1. The tracking algorithm for identifying an individual TC event is available at https://github.com/christophermoseley/iterative_raincell_tracking. The code for CWV PDFs is available at https://github.com/NOAA-GFDL/MDTF-diagnostics/tree/main/diagnostics/convective_transition_diag. The raw data of simulation outputs are available for online sharing upon request, due to the large volume of the dataset.
DOI: 10.34740/kaggle/dsv/4294437
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.5066/f7k64g7d
title: Soil chemistry adjacent to roads treated with dust control products at Loess Bluffs National Wildlife Refuge

description: The health of soils along roadways is critical for maximizing habitat quality and minimizing negative ecological effects of roads. Adjacent to unpaved roads, soil chemistry may be altered by the deposition of dust, as well as by road treatment with dust suppressants or soil stabilizer products. If present in roadside soils, these product residues may be available to plants, terrestrial invertebrates, or small mammals. Unfortunately, very few studies have attempted to track the transport of dust suppressants after application. As part of a larger ongoing study on the environmental effects of dust suppressant products on roadside plants and animals, we sampled roadside soils at Loess Bluff National Wildlife Refuge in 2015. Replicated road sections at Loess Bluff National Wildlife Refuge had been previously treated with two road productscalcium chloride-based durablend-C and synthetic iso-alkane EnviroKleen. In order to quantify the effect of dust suppressant treatment on roadside soils, we took replicated composite soil samples one year after treatment at 1m and 4m from the roads edge, and analyzed samples for a suite of soil chemistry variables (pH, conductivity, NO3-N, P, K, Ca, Mg, Na and S). We also assessed dust suppressant product residues in the soil. For durablend-C, we used soil conductivity as an indicator. For EnviroKleen, we developed a method for extraction and isolation, followed by analysis with gas chromatography/mass spectrometry to look for a specific EnviroKleen signature. Surprisingly, soil conductivity was not elevated adjacent to road sections treated with durablend-C, relative to other sections. EnviroKleen was detectable at both 1m and 4m from treated sections at concentrations from 1 to 1500 mg/kg, and was non-detectable in soils adjacent to the untreated section. The most notable characteristic of soils across all treated and untreated sections at 1m was elevated calcium (up to 30,000 mg/kg), likely as a result of dust deposition from the limestone surface aggregate. These results indicate that, at least in some cases, soil chemistry may be more influenced by proximity to the road itself than by treatment with a dust suppressant product. Importantly, this study is the first to detect and quantify a synthetic fluid product in soils adjacent to a treated roadway. In addition to informing ecological risk assessments for dust suppressants, these results can help practitioners make informed choices about environmentally responsible unpaved road management.
DOI: 10.5281/zenodo.6606486
title: Local explanation SHAP approach applied to MIROC5,RCP8.5-forced multi-model ensemble study of GrIS future sea-level contributions

description: The repository contains materials for analysing the results of the Local explanation named SHAP-CTREE (Redelmeier et al., 2020) approach applied to the MIROC5,RCP8.5-forced multi-model ensemble study of GrIS future sea-level contributions from Goelzer et al. (2020). The available files are:<br> - run_SupplMat.R: the main R script to perform the diagnostics and the different analyses (levels 1 - 3)<br> - utilsPLOT.R: functions for plotting<br> - Diagnostics.zip: the zip file with the png figures, named 'GrIS_CaseXXX_yYYY.png', that depict the diagnostic for case XXX for prediction time YYY<br> - SupplementaryMaterials.zip<br> - RData files for each prediction time YYY "Shapley_yYYY" with:<br> S: matrix N=55 cases x d+1: SHAP values for the d inputs (+ average sea level value at time YYY)<br> YHAT: ML-based predictions of the sea level for the 55 cases<br> YTRUE: true values for the 55 cases<br> mae: mean absolute error<br> - RData file containing the design of experiments "DOE_GrIS_MIROC5-RCP85.RData"<br> doe: matrix with values of the d=9 inputs These constitute the supplementary materials of Rohmer et al. (2022, The Cryosphere). All technical details are provided in this reference.
description: {"references": ["Goelzer, H., Nowicki, S., Payne, A., Larour, E., Seroussi, H., Lipscomb, W. H., et al.: The future sea-level contribution of the Greenland ice sheet: a multi-model ensemble study of ISMIP6, The Cryosphere, 14(9), 3071-3096, 2020.", "Rohmer, J., Thieblemont, R., Le Cozannet, G., Goelzer, H. Durand, G.: Improving interpretation of sea-level projections through a machine-learning-based local explanation approach, The Cryosphere, submitted.", "Redelmeier, A., Jullum, M., and Aas, K.: Explaining predictive models with mixed features using Shapley values and conditional inference trees, in International Cross-Domain Conference for Machine Learning and Knowledge Extraction (pp. 117-137). Springer, Cham, 2020."]}
DOI: 10.5281/zenodo.6606487
title: Local explanation SHAP approach applied to MIROC5,RCP8.5-forced multi-model ensemble study of GrIS future sea-level contributions

description: The repository contains materials for analysing the results of the Local explanation named SHAP-CTREE (Redelmeier et al., 2020) approach applied to the MIROC5,RCP8.5-forced multi-model ensemble study of GrIS future sea-level contributions from Goelzer et al. (2020).<br> - run_Suppl.R: the main R script to perform the diagnostics and the different analyses (levels 1 - 3);<br> - utils.R: functions for plotting;<br> - GrIS_SHAP_AllTime.RData: A R data object with <br> xinput0: list of T=18 matrices N=55 cases x d=6inputs: design of experiments<br> S0: list of T=18 matrices N=55 cases x d+1: SHAP values for the d inputs<br> Ypred: list of T=18 vectors of N=55 cases: ML-based predictions of sea level change<br> Ytrue: list of T=18 vectors of N=55 cases: Sea level change computed within MIROC5,RCP8.5,GrIS MME<br> mu0: vector of 18 values: time evolution of GrIS MME mean<br> - Diagnostics.zip: the zip file with the png figures, named 'GrIS_time_YYYcaseXXX.png', that depict the diagnostic for case XXX and prediction time YYY These constitute the supplementary materials of Rohmer et al. (2022, The Cryosphere, submitted). All technical details are provided in this reference.
description: {"references": ["Goelzer, H., Nowicki, S., Payne, A., Larour, E., Seroussi, H., Lipscomb, W. H., et al.: The future sea-level contribution of the Greenland ice sheet: a multi-model ensemble study of ISMIP6, The Cryosphere, 14(9), 3071-3096, 2020.", "Rohmer, J., Thieblemont, R., Le Cozannet, G., Goelzer, H. Durand, G.: Improving interpretation of sea-level projections through a machine-learning-based local explanation approach, The Cryosphere, submitted.", "Redelmeier, A., Jullum, M., and Aas, K.: Explaining predictive models with mixed features using Shapley values and conditional inference trees, in International Cross-Domain Conference for Machine Learning and Knowledge Extraction (pp. 117-137). Springer, Cham, 2020."]}
DOI: 10.5281/zenodo.7157302
title: Local explanation SHAP approach applied to MIROC5,RCP8.5-forced multi-model ensemble study of GrIS future sea-level contributions

description: The repository contains materials for analysing the results of the Local explanation named SHAP-CTREE (Redelmeier et al., 2020) approach applied to the MIROC5,RCP8.5-forced multi-model ensemble study of GrIS future sea-level contributions from Goelzer et al. (2020). The available files are:<br> - run_SupplMat.R: the main R script to perform the diagnostics and the different analyses (levels 1 - 3)<br> - utilsPLOT.R: functions for plotting<br> - Diagnostics.zip: the zip file with the png figures, named 'GrIS_CaseXXX_yYYY.png', that depict the diagnostic for case XXX for prediction time YYY<br> - SupplementaryMaterials.zip<br> - RData files for each prediction time YYY "Shapley_yYYY" with:<br> S: matrix N=55 cases x d+1: SHAP values for the d inputs (+ average sea level value at time YYY)<br> YHAT: ML-based predictions of the sea level for the 55 cases<br> YTRUE: true values for the 55 cases<br> mae: mean absolute error<br> - RData file containing the design of experiments "DOE_GrIS_MIROC5-RCP85.RData"<br> doe: matrix with values of the d=9 inputs These constitute the supplementary materials of Rohmer et al. (2022, The Cryosphere). All technical details are provided in this reference.
description: {"references": ["Goelzer, H., Nowicki, S., Payne, A., Larour, E., Seroussi, H., Lipscomb, W. H., et al.: The future sea-level contribution of the Greenland ice sheet: a multi-model ensemble study of ISMIP6, The Cryosphere, 14(9), 3071-3096, 2020.", "Rohmer, J., Thieblemont, R., Le Cozannet, G., Goelzer, H. Durand, G.: Improving interpretation of sea-level projections through a machine-learning-based local explanation approach, The Cryosphere, submitted.", "Redelmeier, A., Jullum, M., and Aas, K.: Explaining predictive models with mixed features using Shapley values and conditional inference trees, in International Cross-Domain Conference for Machine Learning and Knowledge Extraction (pp. 117-137). Springer, Cham, 2020."]}
DOI: 10.5281/zenodo.7155466
title: data

description: The data and run-scripts used in the manuscript entitled Reconstructing and Nowcasting of Rainfall Fields by a CML Network.
DOI: 10.5281/zenodo.7155467
title: data

description: The data used in the manuscript entitled Reconstructing and Nowcasting of Rainfall Fields by a CML Network.
DOI: 10.5281/zenodo.7155469
title: data

description: The data and run-scripts used in the manuscript entitled Reconstructing and Nowcasting of Rainfall Fields by a CML Network.
DOI: 10.34740/kaggle/dsv/4294464
title: Indian Cars Dataset part 2