cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11871534.v1
title: Supplementary Material for: Exploratory Analysis to Identify Candidates Benefitting from Combination Therapy of Transarterial Chemoembolization and Sorafenib for First-Line Treatment of Unresectable Hepatocellular Carcinoma: A Multicenter Retrospective Observational Study

description: <b><i>Introduction:</i></b> The benefits of combining transarterial chemoembolization (TACE) and sorafenib (TACE-S) over TACE alone for treatment of unresectable hepatocellular carcinoma (HCC) remain controversial. Yet, such populations are heterogeneous in terms of baseline characteristics. <b><i>Objective:</i></b> To investigate the predictors of survival benefits from added sorafenib and identify the potential candidates for TACE-S. <b><i>Methods:</i></b> This multicenter observational study was conducted in 17 Chinese tertiary hospitals for patients with unresectable, liver-confined HCC. Eligible patients with performance status score of ≤1 and Child-Pugh score of ≤7 were treated with TACE or TACE-S. Interactions between treatment and baseline variables were evaluated to find indicators for survival benefits, based on which the patients were stratified. Multivariate models adjusted for baseline characteristics or propensity score were used to compare overall survival (OS) and time to tumor progression (TTP). <b><i>Results:</i></b> From January 2009 to December 2015, 1,719 consecutive patients received TACE (<i>n</i> = 1,406) or TACE-S (<i>n</i> = 313). Although TACE-S compared with TACE improved TTP (adjusted hazard ratio [HR] 0.75, <i>p</i> = 0.008), no difference in OS was observed (adjusted HR 0.87, <i>p</i> = 0.090). Nevertheless, the tumor burden (sum of maximum diameter of largest tumor [cm] and tumor number) and albumin-bilirubin (ALBI) score independently predicted the survival benefits from added sorafenib (interaction <i>p</i>&lt; 0.001). For patients with either moderate tumor burden (7–13) or low ALBI score (no more than –2.8) defined as candidates, TACE-S prolonged OS (adjusted HR 0.73, <i>p</i> = 0.003) and TTP (adjusted HR 0.72, <i>p</i> = 0.014) compared to TACE alone, whereas its superiority disappeared in non-candidates. <b><i>Conclusions:</i></b> Not all unresectable HCC patients but those with moderate tumor burden or low ALBI score achieve survival benefits from TACE-S compared with TACE alone. Future randomized controlled trials focusing on the subset are warranted.
DOI: 10.6084/m9.figshare.11871537.v2
title: Metadata record for: Physical activity, time use, and food intakes of rural households in Ghana, India, and Nepal

description: This dataset contains key characteristics about the data described in the Data Descriptor Physical activity, time use, and food intakes of rural households in Ghana, India, and Nepal. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br> <br>
DOI: 10.6084/m9.figshare.11871507
title: Data PVBT and morphological parameters of the flow rate 1 mlh

description: Data PVBT and morphological parameters of the flow rate 1 mlh
DOI: 10.6084/m9.figshare.11871528
title: download_00.txt

description: The data was retrieved from Web Of Scicence, which focused on the HIF reseach of kidney cancer.
DOI: 10.6084/m9.figshare.11871537.v1
title: Metadata record for: Physical activity, time use, and food intakes of rural households in Ghana, India, and Nepal

description: This dataset contains key characteristics about the data described in the Data Descriptor Physical activity, time use, and food intakes of rural households in Ghana, India, and Nepal. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11871507.v1
title: Data PVBT and morphological parameters of the flow rate 1 mlh

description: Data PVBT and morphological parameters of the flow rate 1 mlh
DOI: 10.6084/m9.figshare.11871528.v1
title: download_00.txt

description: The data was retrieved from Web Of Scicence, which focused on the HIF reseach of kidney cancer.
DOI: 10.6084/m9.figshare.11871486
title: Raw image BV0.1_2

description: Data (Row image; flow rate 0.1 ml/h in vertical configuration)<br>
DOI: 10.6084/m9.figshare.11871486.v1
title: Raw image BV0.1_2

description: Data (Row image; flow rate 0.1 ml/h in vertical configuration)<br>
DOI: 10.6084/m9.figshare.11871480
title: Raw Image BH0.1

description: Data (Raw Image; low rate 0.1 ml/h in horizontal configuration)<br>
DOI: 10.6084/m9.figshare.11871474
title: Raw image BV100

description: Data (Raw image; flow rate 100 ml/h in vertical configuration)<br>
DOI: 10.6084/m9.figshare.11871462
title: Raw Image BH100

description: Data (Raw image; flow rate 100 ml/h in horizontal configuration)<br>
DOI: 10.6084/m9.figshare.11871474.v1
title: Raw image BV100

description: Data (Raw image; flow rate 100 ml/h in vertical configuration)<br>
DOI: 10.6084/m9.figshare.11871480.v1
title: Raw Image BH0.1

description: Data (Raw Image; low rate 0.1 ml/h in horizontal configuration)<br>
DOI: 10.6084/m9.figshare.11871456
title: Raw image BH500

description: Data (Raw image; flow rate 500ml/h in horizontal configuration<br>
DOI: 10.6084/m9.figshare.11871459
title: Musp.txt

description: The broadband (650-1100nm) reduced scattering coefficient spectra of nine different porcine organs were obtained using time-domain diffuse optical spectroscopy. Measurements were performed on three different spatial locations of each organ, the mean value and the standard deviation over the three locations are presented here.
DOI: 10.6084/m9.figshare.11871456.v1
title: Raw image BH500

description: Data (Raw image; flow rate 500ml/h in horizontal configuration<br>
DOI: 10.6084/m9.figshare.11871459.v2
title: Musp.txt

description: The broadband (650-1100nm) reduced scattering coefficient spectra of nine different porcine organs were obtained using time-domain diffuse optical spectroscopy. Measurements were performed on three different spatial locations of each organ, the mean value and the standard deviation over the three locations are presented here.
DOI: 10.6084/m9.figshare.11871462.v1
title: Raw Image BH100

description: Data (Raw image; flow rate 100 ml/h in horizontal configuration)<br>
DOI: 10.6084/m9.figshare.11871453
title: Raw image BV500

description: Data (Raw Image; flow rate 500 ml/h in vertical configuration)<br>
DOI: 10.6084/m9.figshare.11871459.v1
title: Untitled Item

description: The broadband (650-1100nm) reduced scattering coefficient spectra of nine different porcine organs were obtained using time-domain diffuse optical spectroscopy. Measurements were performed on three different spatial locations of each organ, the mean value and the standard deviation over the three locations are presented here.
DOI: 10.6084/m9.figshare.11871453.v1
title: Raw image BV500

description: Data (Raw Image; flow rate 500 ml/h in vertical configuration)<br>
DOI: 10.6084/m9.figshare.11871420
title: The international sinonasal microbiome study (ISMS) Dataset

description: Middle meatus swabs were collected from participants' sinuses for 16S rRNA gene sequencing (V3-V4 hypervariable region) on the Illumina MiSeq platform. Thirteen centres, across five continents, participated in the study. 532 samples (194 healthy controls and 338 chronic rhinosinusitis patients) successfully went through all stages of transport and processing to be sequenced.
DOI: 10.6084/m9.figshare.11871429
title: Raw image BH1

description: Data (Raw image; Flow rate 1 ml/h in horizontal configuration)<br>
DOI: 10.6084/m9.figshare.11871441
title: Raw Image BV1

description: Data (Raw imgae; flow rate 1 ml/h in vertical configuration)<br>
DOI: 10.6084/m9.figshare.11871441.v1
title: Raw Image BV1

description: Data (Raw imgae; flow rate 1 ml/h in vertical configuration)<br>
DOI: 10.6084/m9.figshare.11871411
title: Raw Image BH10

description: Data (Raw image; Flow rate 10 ml/h in horizontal configuration)<br>
DOI: 10.6084/m9.figshare.11871411.v1
title: Raw Image BH10

description: Data (Raw image; Flow rate 10 ml/h in horizontal configuration)<br>
DOI: 10.6084/m9.figshare.11871405
title: Raw image BV10

description: Data (Raw image; Flow Rate 10 ml/h)<br>
DOI: 10.6084/m9.figshare.11871399
title: EPI0000067.ChIP.dedup.GRCh38.20200217.ZcPAX5.bw

description: Pax5 bigwig
DOI: 10.6084/m9.figshare.11871399.v1
title: EPI0000067.ChIP.dedup.GRCh38.20200217.ZcPAX5.bw

description: Pax5 bigwig
DOI: 10.6084/m9.figshare.11871369
title: Metadata record for: High-resolution mapping of spatial heterogeneity in ice wedge polygon geomorphology near Prudhoe Bay, Alaska

description: This dataset contains key characteristics about the data described in the Data Descriptor High-resolution mapping of spatial heterogeneity in ice wedge polygon geomorphology near Prudhoe Bay, Alaska. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11871372
title: Information of air quality monitoring stations adopted in the paper "Tropospheric ozone: a growing global threat and how to control it?"

description: The dataset provides information of 2,935 air quality monitoring stations over the world. The geographical coordinates, categories of the sites and data sources are documented
DOI: 10.6084/m9.figshare.11871369.v1
title: Metadata record for: High-resolution mapping of spatial heterogeneity in ice wedge polygon geomorphology near Prudhoe Bay, Alaska

description: This dataset contains key characteristics about the data described in the Data Descriptor High-resolution mapping of spatial heterogeneity in ice wedge polygon geomorphology near Prudhoe Bay, Alaska. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11871372.v1
title: Information of air quality monitoring stations adopted in the paper "Tropospheric ozone: a growing global threat and how to control it?"

description: The dataset provides information of 2,935 air quality monitoring stations over the world. The geographical coordinates, categories of the sites and data sources are documented
DOI: 10.6084/m9.figshare.11871303
title: Cytological and Molecular Screening of Chlamydia trachomatis in infertile women-Sudan .xlsx

description: This data set includes demographic, clinical data, result of Giemsa staining and molecular test for urine and high vaginal swab of infertile Sudanese women screened for <i>Chlamydia trachomatis.</i><b>participants in data were classified into two groups as follow: </b><b>primary infertile women those failed to get pregnant (and no abortion </b><b>exposure</b><b>) for at least one year after marriage, and the secondary infertile women those exposed to abortion/s and/or successful pregnancy/ies before but now they fail to get pregnant</b><i><br></i>
DOI: 10.6084/m9.figshare.11871303.v2
title: Cytological and Molecular Screening of Chlamydia trachomatis in infertile women-Sudan .xlsx

description: This data set includes demographic, clinical data, result of Giemsa staining and molecular test for urine and high vaginal swab of infertile Sudanese women screened for <i>Chlamydia trachomatis.</i><b>participants in data were classified into two groups as follow: </b><b>primary infertile women those failed to get pregnant (and no abortion </b><b>exposure</b><b>) for at least one year after marriage, and the secondary infertile women those exposed to abortion/s and/or successful pregnancy/ies before but now they fail to get pregnant</b><i><br></i>
DOI: 10.6084/m9.figshare.11871303.v1
title: CYTOLOGICAL AND MOLECULAR SCREENING OF CT IN INFERTILE WOMEN-SUDAN.xlsx

description: This data set includes demographic, clinical data, result of Giemsa staining and molecular test for urine and high vaginal swab of infertile Sudanese women screened for <i>Chlamydia trachomatis.</i>
DOI: 10.6084/m9.figshare.11871189
title: Extraction of Moving Areas in Random-Dot Animation with Parallel Computation

description: The observation of random-dot animations requires the motion detection techniques of moving objects from the background, allowing the boundary of the moving areas to be perceived despite that each frame consists of random-dot patterns with no boundaries. The present study aims to extract the moving parts as well as its moving direction on the random-dot animations based on the local parallel computation of the pixel level. Assuming motion is captured in high frame rate, the variable range of an optical flow is restricted within a finite discretized area of pixels. Then, the system is constructed to select the suitable optical flow among the finite possibilities according to the reaction-diffusion equation dynamics, computed in a distributed manner. This process is one of the regularization methods and is described as the minimization process of the potential functional. Using the computation result of the previous frames, we attempted to reduce the computational iterations and to detect the plural objects moving at different speeds. These effects are demonstrated by computer simulations using actual random-dot animations.
DOI: 10.6084/m9.figshare.11871189.v1
title: Extraction of Moving Areas in Random-Dot Animation with Parallel Computation

description: The observation of random-dot animations requires the motion detection techniques of moving objects from the background, allowing the boundary of the moving areas to be perceived despite that each frame consists of random-dot patterns with no boundaries. The present study aims to extract the moving parts as well as its moving direction on the random-dot animations based on the local parallel computation of the pixel level. Assuming motion is captured in high frame rate, the variable range of an optical flow is restricted within a finite discretized area of pixels. Then, the system is constructed to select the suitable optical flow among the finite possibilities according to the reaction-diffusion equation dynamics, computed in a distributed manner. This process is one of the regularization methods and is described as the minimization process of the potential functional. Using the computation result of the previous frames, we attempted to reduce the computational iterations and to detect the plural objects moving at different speeds. These effects are demonstrated by computer simulations using actual random-dot animations.
DOI: 10.6084/m9.figshare.11871174
title: Information & data files concerning a study of the Confinement of Ultrarelativistic Electron Remnant Belts to Low L-shells

description: These Information files and data files should be considered with our paper "On the Confinement of Ultrarelativistic Electron Remnant Belts to Low L-shells" by V. Pinto, X.-J. Zhang, D. Mourenas, et al., to appear the Journal of Geophysical Research-Space Physics. They include a PDF file "Information..." that details the 18 considered events of remnant belts of ultra-relativistic electrons observed in 2012-2017 by the Van Allen Probes and the method of production of the data files, There are also data files of ULF wave power as a function of time for the different pairs of stations provided in "date-power-new+" dat files (in the "ULFWavePower.zip" file). LANL* LCDS calculations for the considered periods are provided in "Lmax-date-Txx" txt files (in the "LANL-LCDS.zip" file) for T96 and T05 magnetic field models (xx in file name indicating the UT hour of start and LCDS being calculated in steps of 5 min). The electron PSD profiles obtained from the Van Allen Probes during/nearby each event are provided in the "PSD-VanAllenProbes" PDF file.<br>All the data used here are freely available from different repositories (see below). We gratefully acknowledge Van Allen Probes ECT-REPT/MagEIS and EMFISIS data freely available from https://www.rbsp-ect.lanl.gov/ and https://emfisis.physics.uiowa.edu/data/. We are also grateful to S. Mende and C.T. Russell for the Prince George and Athabasca magnetometer data from the THEMIS GMAG network freely available at http://themis.igpp.ucla.edu/gmag_desc.shtml (where magnetometer data from the following stations are also available), the AUTUMNX magnetometer network funded through the Canadian Space Agency Geospace Observatory for the Athabasca University magnetometer data at http://autumn.athabascau.ca/, the Tromso Geophysical Observatory, University of TromsoÂž Norway, for the Dombas magnetometer data at http://flux.phys.uit.no/geomag.html, the Geophysical Institute of the University of Alaska at http://magnet.asf.alaska.edu/ for the Trapper Creek magnetometer data, and the Canadian Magnetic Observatory Network maintained and operated by the Geological Survey of Canada at https://www.geomag.nrcan.gc.ca/index-en.php for the Meanook magnerometer data used in this study. We also thank I.R. Mann, D.K. Milling, and the CARISMA team for the PINA and LCL magnetometer data obtained from http://data.carisma.ca, provided by the University of Alberta with founding from the Canadian Space Agency. We acknowledge the CXD team at LANL for GPS electron flux measurements freely available from NOAA at https://www.ngdc.noaa.gov/stp/spaceweather/satellite-data/satellitesystems/gps/. OMNI data is freely available from CDAWeb https://cdaweb.gsfc.nasa.gov<br><br>
DOI: 10.6084/m9.figshare.11871147
title: Transcriptional profiling of human macrophages during infection with <i>Bordetella pertussis</i>

description: <i>Bordetella pertussis</i>, a strictly human re-emerging pathogen and the causative agent of whooping cough, exploits a broad variety of virulence factors to establish efficient infection. Here, we used RNA sequencing to analyse the changes in gene expression profiles of human THP-1 macrophages resulting from <i>B. pertussis</i> infection. In parallel, we attempted to determine the changes in intracellular <i>B. pertussis</i>-specific transcriptomic profiles resulting from interaction with macrophages. Our analysis revealed that global gene expression profiles in THP-1 macrophages are extensively rewired 6 h post-infection. Among the highly expressed genes, we identified those encoding cytokines, chemokines, and transcription regulators involved in the induction of the M1 and M2 macrophage polarization programmes. Notably, several host genes involved in the control of apoptosis and inflammation which are known to be hijacked by intracellular bacterial pathogens were overexpressed upon infection. Furthermore, <i>in silico</i> analyses identified large temporal changes in expression of specific gene subsets involved in signalling and metabolic pathways. Despite limited numbers of the bacterial reads, we observed reduced expression of majority of virulence factors and upregulation of several transcriptional regulators during infection suggesting that intracellular <i>B. pertussis</i> cells switch from virulent to avirulent phase and actively adapt to intracellular environment, respectively.
DOI: 10.6084/m9.figshare.11871147.v1
title: Transcriptional profiling of human macrophages during infection with <i>Bordetella pertussis</i>

description: <i>Bordetella pertussis</i>, a strictly human re-emerging pathogen and the causative agent of whooping cough, exploits a broad variety of virulence factors to establish efficient infection. Here, we used RNA sequencing to analyse the changes in gene expression profiles of human THP-1 macrophages resulting from <i>B. pertussis</i> infection. In parallel, we attempted to determine the changes in intracellular <i>B. pertussis</i>-specific transcriptomic profiles resulting from interaction with macrophages. Our analysis revealed that global gene expression profiles in THP-1 macrophages are extensively rewired 6 h post-infection. Among the highly expressed genes, we identified those encoding cytokines, chemokines, and transcription regulators involved in the induction of the M1 and M2 macrophage polarization programmes. Notably, several host genes involved in the control of apoptosis and inflammation which are known to be hijacked by intracellular bacterial pathogens were overexpressed upon infection. Furthermore, <i>in silico</i> analyses identified large temporal changes in expression of specific gene subsets involved in signalling and metabolic pathways. Despite limited numbers of the bacterial reads, we observed reduced expression of majority of virulence factors and upregulation of several transcriptional regulators during infection suggesting that intracellular <i>B. pertussis</i> cells switch from virulent to avirulent phase and actively adapt to intracellular environment, respectively.
DOI: 10.6084/m9.figshare.11871123
title: Row Data Day 0_2.fq.gz

description: Row data for mRNA sequensing of sample from radiation wounds before treatment.
DOI: 10.6084/m9.figshare.11871123.v1
title: Row Data Day 0_2.fq.gz

description: Row data for mRNA sequensing of sample from radiation wounds before treatment.
DOI: 10.6084/m9.figshare.11871111
title: Experimental data from Practical parameter identifiability for spatio-temporal models of cell invasion

description: We examine the practical identifiability of parameters in a spatio-temporal reaction–diffusion model of a scratch assay. Experimental data involve fluorescent cell cycle labels, providing spatial information about cell position and temporal information about the cell cycle phase. Cell cycle labelling is incorporated into the reaction–diffusion model by treating the total population as two interacting subpopulations. Practical identifiability is examined using a Bayesian Markov chain Monte Carlo (MCMC) framework, confirming that the parameters are identifiable when we assume the diffusivities of the subpopulations are identical, but that the parameters are practically non-identifiable when we allow the diffusivities to be distinct. We also assess practical identifiability using a profile likelihood approach, providing similar results to MCMC with the advantage of being an order of magnitude faster to compute. Therefore, we suggest that the profile likelihood ought to be adopted as a screening tool to assess practical identifiability before MCMC computations are performed.
DOI: 10.6084/m9.figshare.11871111.v2
title: Experimental data from Practical parameter identifiability for spatio-temporal models of cell invasion

description: We examine the practical identifiability of parameters in a spatio-temporal reaction–diffusion model of a scratch assay. Experimental data involve fluorescent cell cycle labels, providing spatial information about cell position and temporal information about the cell cycle phase. Cell cycle labelling is incorporated into the reaction–diffusion model by treating the total population as two interacting subpopulations. Practical identifiability is examined using a Bayesian Markov chain Monte Carlo (MCMC) framework, confirming that the parameters are identifiable when we assume the diffusivities of the subpopulations are identical, but that the parameters are practically non-identifiable when we allow the diffusivities to be distinct. We also assess practical identifiability using a profile likelihood approach, providing similar results to MCMC with the advantage of being an order of magnitude faster to compute. Therefore, we suggest that the profile likelihood ought to be adopted as a screening tool to assess practical identifiability before MCMC computations are performed.
DOI: 10.6084/m9.figshare.11871102
title: Row Data Day 20-Plasminogen_2.fq.gz

description: Row data for mRNA sequensing of sample from radiation wounds treated with plasminogen for 20 days.
DOI: 10.6084/m9.figshare.11871099
title: Row Data Day 20-Plasminogen_1.fq.gz

description: Row data for mRNA sequensing of sample from radiation wounds treated with plasminogen for 20 days.
DOI: 10.6084/m9.figshare.11871096
title: Row Data Day 20-PBS_1.fq.gz

description: Row data for mRNA sequensing of sample from radiation wounds treated with PBS for 20 days.