cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5205261
title: Biogeomorphic modeling to assess resilience of tidal marsh restoration to sea level rise and sediment supply - Supporting code and data

description: Code and data to reproduce figures and analyses of the paper: Gourgue, O., van Belzen, J., Schwarz, C., Vandenbruwaene, W., Vanlede, J., Belliard, J.-P., Fagherazzi, S., Bouma, T.J., van de Koppel, J., and Temmerman, S.: Biogeomorphic modeling to assess resilience of tidal marsh restoration to sea level rise and sediment supply, Earth Surf. Dynam., submitted. Standard Python dependencies: GDAL Geopandas Matplotlib NumPy Rasterio SciPy Seaborn Shapely scikit-learn Third-party Python dependencies: Centerline (https://github.com/fitodic/centerline) pputils (https://github.com/pprodano/pputils) pysheds (https://github.com/mdbartos/pysheds) In-house Python dependencies: Demeter 1.0.5 (https://doi.org/10.5281/zenodo.5205258) OGTools 1.1 (https://doi.org/10.5281/zenodo.3994952) TidalGeoPro 0.1 (https://doi.org/10.5281/zenodo.5205285)
description: This project has received funding from the Vlaams-Nederlandse Scheldecommissie (VNSC), the European Union's Horizon 2020 research and innovation program (Marie Skłodowska-Curie Actions – global postdoctoral fellowship – grant nr. 798222) and the Research Foundation – Flanders (FWO – fundamental research project – grant nr. G060018N). The resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government. SF was partly funded by the USA National Science Foundation awards 1637630 (PIE LTER) and 1832221 (VCR LTER).
DOI: 10.6084/m9.figshare.15177561
title: Supplementary data (ES)

description: Data on genotyped samples, aphid performance and host selection experiments
DOI: 10.6084/m9.figshare.15177561.v1
title: Supplementary data (ES)

description: Data on genotyped samples, aphid performance and host selection experiments
DOI: 10.5281/zenodo.4714666
title: Datasets and movies supporting works on The Role of Along-Fault Dilatancy in Fault Slip Behavior

description: <strong>The framework of the dataset and movies:</strong><br> The data, scripts, and movies provided here support the work of Yannick Caniven, Julia K Morgan, and David G Blank on the role of the along-fault dilatancy on fault slip behavior. This work concerns discrete element modeling using the code Ricebal developed at the Rice University, Houston, Texas, USA. The approach used here allows for simulating the behavior of a strike-slip fault at the seismic time scale, investigating the nucleation processes of slow-earthquakes and fast earthquakes. <br> <strong>The dataset:</strong><br> The directory DATASET.zip provides all data and results described in Caniven et al., 2021. The data set provides files containing:<br> - particle positions (b-*.out)<br> - time-series of stress ratio and dilatancy (dy/dx) at the wall of the model (WALL-FRIC_frames_*.txt and Dilation-frames_*.txt) <br> - time-space maps folders containing stacked slip-velocity and dilatancy along-fault profiles (MAP_Dilatancy_*_*.txt) All these files can be used to plot all visualizations presented from Figure 2 to Figure 8 in the related paper. For each figure directory, we provide an example of scripts (*.sh and *.py) that can be used to display the data using the GMT software (Global Mapping Tools) or Python. The provided scripts have been developed to be used with GMT 5.4.4 and Python 3.9.2 (using Spyder 4.2.3 in Anaconda 1.10). The use of other versions may require some adjustments. All scripts from Figure 2 to Figure 6 can be launched straightforwardly without any additional setting. <br> To use the script in the Figure7-8 directory, please follow the instructions in the script header. <br> <strong>The supporting movies:</strong><br> Movie S1 shows an example of the evolution of particle displacements at the global model scale, here during the occurrence of the fast Eq4 earthquake sequence (see Figure 7 in the paper). Note the slow nucleation of slip associated with the precursory dilation (see Figure 7b in the paper) before the onset of the dynamic stage and propagation of seismic waves. Movie S2 highlights the detailed evolution of particle displacements across the regions of the isolated slow-earthquake SEq1. The nucleation zone of this event exhibits several areas close to their failure points (apex) at different states that accommodate both fault dilation and contraction in response to the far-field imposed displacement (see Figure 8a in the paper). Movie S3 highlights the detailed evolution of particle displacements across the regions of the fast earthquake Eq3. Most asperities on each side of the main narrow nucleation zone approach failure in a synchronized state leading to general dilation and fast slip (see Figure 8b in the paper).<br>
DOI: 10.5281/zenodo.4714665
title: Datasets and movies supporting works on The Role of Along-Fault Dilatancy in Fault Slip Behavior

description: <strong>The framework of the dataset and movies:</strong><br> The data, scripts, and movies provided here support the work of Yannick Caniven, Julia K Morgan, and David G Blank on the role of the along-fault dilatancy on fault slip behavior. This work concerns discrete element modeling using the code Ricebal developed at the Rice University, Houston, Texas, USA. The approach used here allows for simulating the behavior of a strike-slip fault at the seismic time scale, investigating the nucleation processes of slow-earthquakes and fast earthquakes. <br> <strong>The dataset:</strong><br> The directory DATASET.zip provides all data and results described in Caniven et al., 2021. The data set provides files containing:<br> - particle positions (b-*.out)<br> - time-series of stress ratio and dilatancy (dy/dx) at the wall of the model (WALL-FRIC_frames_*.txt and Dilation-frames_*.txt) <br> - time-space maps folders containing stacked slip-velocity and dilatancy along-fault profiles (MAP_Dilatancy_*_*.txt) All these files can be used to plot all visualizations presented from Figure 2 to Figure 8 in the related paper. For each figure directory, we provide an example of scripts (*.sh and *.py) that can be used to display the data using the GMT software (Global Mapping Tools) or Python. The provided scripts have been developed to be used with GMT 5.4.4 and Python 3.9.2 (using Spyder 4.2.3 in Anaconda 1.10). The use of other versions may require some adjustments. All scripts from Figure 2 to Figure 6 can be launched straightforwardly without any additional setting. <br> To use the script in the Figure7-8 directory, please follow the instructions in the script header. <br> <strong>The supporting movies:</strong><br> Movie S1 shows an example of the evolution of particle displacements at the global model scale, here during the occurrence of the fast Eq4 earthquake sequence (see Figure 7 in the paper). Note the slow nucleation of slip associated with the precursory dilation (see Figure 7b in the paper) before the onset of the dynamic stage and propagation of seismic waves. Movie S2 highlights the detailed evolution of particle displacements across the regions of the isolated slow-earthquake SEq1. The nucleation zone of this event exhibits several areas close to their failure points (apex) at different states that accommodate both fault dilation and contraction in response to the far-field imposed displacement (see Figure 8a in the paper). Movie S3 highlights the detailed evolution of particle displacements across the regions of the fast earthquake Eq3. Most asperities on each side of the main narrow nucleation zone approach failure in a synchronized state leading to general dilation and fast slip (see Figure 8b in the paper).<br>
DOI: 10.5517/cc8kw7x
title: CCDC 255509: Experimental Crystal Structure Determination

description: Related Article: Qianrong Fang|2009|CSD Communication|||
DOI: 10.5517/ccxfn65
title: CCDC 847267: Experimental Crystal Structure Determination

description: Related Article: N.S.Weng|2005|Jiegou Huaxue|24|121|
DOI: 10.5517/ccdc.csd.cc21p3f9
title: CCDC 1897120: Experimental Crystal Structure Determination

description: Related Article: Jin-ke Jiang   Xi-Xi Li     Hui Jiang   Hua Wu  Xian-Wu Dong|2019|CSD Communication|||
DOI: 10.13016/c79z-9dcs
title: Space-time Sub-samplers for Synthetic Satellite Experiments

description: Please see attached data descriptor.
description: This dataset provides global sub-sampling for a group of hypothetical sensors employing different orbital configurations. The hypothetical sensors include one passive radiometer, two SARs, and three LiDARs. The space-time sub-samplers are simulated as a function of the orbital configuration including the orbital altitude and inclination angle as well as the swath width for each of the hypothetical sensors. Using these sub-samplers, satellite mission planners and scientists can have a better understanding of when and where the Earth surface is viewed by the sensors without incurring the actual expense of a mission launch.
DOI: 10.6084/m9.figshare.15177567
title: Supplementary Material for: Antibiotic Prophylaxis against Surgical Site Infection after Open Hernia Surgery: A Systematic Review and Meta-Analysis

description: <b><i>Objective:</i></b> The role of antibiotic prophylaxis (AP) in the prevention of surgical site infection (SSI) after hernia repair is debated. We conducted this systematic review and meta-analysis to assess the evidence on the value of prophylactic antibiotics in reducing the risks of SSI after open hernia surgery. <b><i>Methods:</i></b> We ran an online and manual search to identify relevant randomized controlled trials that compared prophylactic antibiotics to nonantibiotic controls in patients undergoing open surgical hernia repair. Data on SSI risk were extracted and pooled as risk ratios (RRs) with 95% confidence intervals (95% CIs), using RevMan software. We further used the Cochrane risk of bias tool and GRADE assessment to evaluate the quality of generated evidence. <b><i>Results:</i></b> Twenty-nine studies (<i>N</i> = 8,616 patients) were included in the current analysis. Antibiotic prophylaxis reduced the risk of SSI in open hernia repair patients (RR = 0.65, 95% CI = 0.53, 0.79). Subgroup analysis showed a significant benefit for antibiotics in mesh repair patients (RR = 0.60, 95% CI = 0.48, 0.76) yet no significant difference in SSI risk after herniorrhaphy (RR = 0.86, 95% CI = 0.54, 1.36). In addition, AP was associated with a significant reduction in superficial SSI risk (RR = 0.56, 95% CI = 0.43, 0.72) but not deep SSI (RR = 0.70, 95% CI = 0.30, 1.62). Further analysis showed a significant reduction in SSI risk with amoxicillin/clavulanic acid and cefazolin but not with cefuroxime. <b><i>Conclusion:</i></b> The present meta-analysis suggests that AP is beneficial prior to open mesh hernia repair. However, the quality of evidence was low, and further well-designed trials are needed.
DOI: 10.6084/m9.figshare.15177540
title: Supplementary Material for: Associations between Certain Polymorphisms in Proinflammatory Cytokines and Predisposition of Alzheimer’s Disease: A Meta-Analysis

description: <b><i>Background:</i></b> Functional gene polymorphisms of proinflammatory cytokines such as tumor necrosis factor-α (<i>TNF-α</i>), interleukin-6 (<i>IL-6</i>), interleukin-8 (<i>IL-8</i>), and interleukin-18 (<i>IL-18</i>) may contribute to the onset and development of Alzheimer’s disease (AD), but the relationships between these polymorphisms and predisposition of AD remain controversial. <b><i>Objectives:</i></b> This meta-analysis was conducted to more robustly assess relationships between <i>TNF-α/IL-6/IL-8/IL-18</i> polymorphisms and predisposition of AD by pooling the findings of relevant studies. <b><i>Methods:</i></b> A comprehensive literature searching was performed in PubMed, Embase, Web of Science, Wanfang, and CNKI databases, and 63 studies were found to be eligible for quantitative analyses. <b><i>Results:</i></b> The pooled meta-analysis results showed that genotypic frequencies of <i>TNF-α</i> rs1800629, <i>IL-6</i> rs1800795, <i>IL-8</i> rs4073, and <i>IL-18</i> rs187238 polymorphisms among AD cases and controls of Asian ethnicity differed significantly. But, we did not observe such genotypic frequencies differences in Caucasians. <b><i>Conclusions:</i></b> This meta-analysis suggests that <i>TNF-α</i> rs1800629, <i>IL-6</i> rs1800795, <i>IL-8</i> rs4073, and <i>IL-18</i> rs187238 polymorphisms may affect predisposition of AD in Asians, but not in Caucasians.
DOI: 10.6084/m9.figshare.15177540.v1
title: Supplementary Material for: Associations between Certain Polymorphisms in Proinflammatory Cytokines and Predisposition of Alzheimer’s Disease: A Meta-Analysis

description: <b><i>Background:</i></b> Functional gene polymorphisms of proinflammatory cytokines such as tumor necrosis factor-α (<i>TNF-α</i>), interleukin-6 (<i>IL-6</i>), interleukin-8 (<i>IL-8</i>), and interleukin-18 (<i>IL-18</i>) may contribute to the onset and development of Alzheimer’s disease (AD), but the relationships between these polymorphisms and predisposition of AD remain controversial. <b><i>Objectives:</i></b> This meta-analysis was conducted to more robustly assess relationships between <i>TNF-α/IL-6/IL-8/IL-18</i> polymorphisms and predisposition of AD by pooling the findings of relevant studies. <b><i>Methods:</i></b> A comprehensive literature searching was performed in PubMed, Embase, Web of Science, Wanfang, and CNKI databases, and 63 studies were found to be eligible for quantitative analyses. <b><i>Results:</i></b> The pooled meta-analysis results showed that genotypic frequencies of <i>TNF-α</i> rs1800629, <i>IL-6</i> rs1800795, <i>IL-8</i> rs4073, and <i>IL-18</i> rs187238 polymorphisms among AD cases and controls of Asian ethnicity differed significantly. But, we did not observe such genotypic frequencies differences in Caucasians. <b><i>Conclusions:</i></b> This meta-analysis suggests that <i>TNF-α</i> rs1800629, <i>IL-6</i> rs1800795, <i>IL-8</i> rs4073, and <i>IL-18</i> rs187238 polymorphisms may affect predisposition of AD in Asians, but not in Caucasians.
DOI: 10.6084/m9.figshare.15177480
title: Supplementary Material for: Pediatric Acute Ischemic Stroke by Age-Group: A Systematic Review and Meta-Analysis of Published Studies and Hospitalization Records

description: <b><i>Background:</i></b> Although stroke is rare among the pediatric population, it is nevertheless associated with serious or life-threatening consequences. The etiologic factors of acute ischemic stroke (AIS) are likely to vary over the course of childhood development. The incidence rates of AIS, not previously systematically examined by pediatric age subgroup, could guide studies of its etiology. <b><i>Objective:</i></b> The aim of this study is to evaluate the incidence rate of AIS by age-group in the pediatric population (aged 0–17/18 years) and identify any common trends or sources of variability across different countries. <b><i>Methods:</i></b> Rates of pediatric AIS were collated from a systematic literature review of published studies globally (1983–2020) and hospitalization records from Europe and the USA (2015–2018). Records that were included in the analysis reported the code or description used for AIS diagnosis and age-specific data for children aged 0–17/18 years. AIS incidence rates were summarized by age-group, data source, country, and geographic region. A meta-analysis was conducted to assess the heterogeneity of AIS rates in neonates. <b><i>Results:</i></b> The pooled AIS incidence rate was 5.6 per 100,000 children across all records. When only records reporting the AIS incidence rates for children across the full age range (0–17/18 years) were analyzed, the pooled AIS incidence rate was 4.6 per 100,000 children and ranged from 7.0 per 100,000 (Germany) to 1.3 per 100,000 (Denmark). The highest pooled rates were observed in the 0–28-day age-group (24.6 per 100,000 live births), declining to the lowest rates in the 5–9-year age-group, and rising again in the 10–17/18-year age-group. AIS rates were the most heterogeneous in the 0–28-day age-group and across European countries. Significantly higher AIS rates in neonates were observed from hospital databases (35.9 per 100,000) than in the literature (19.4 per 100,000). AIS rates may be underestimated as pediatric AIS events are rare and challenging to diagnose, and limited age-specific data are available. <b><i>Conclusions:</i></b> Incidence rates of pediatric AIS by age-groups followed a consistent overall pattern of a reverse J-shaped curve, with the highest rates in neonates, across predominantly European and North American countries. Further research is warranted to examine if this pattern is observed in other geographic regions and to identify AIS risk factors specific to different phases of childhood development.
DOI: 10.6084/m9.figshare.15177480.v1
title: Supplementary Material for: Pediatric Acute Ischemic Stroke by Age-Group: A Systematic Review and Meta-Analysis of Published Studies and Hospitalization Records

description: <b><i>Background:</i></b> Although stroke is rare among the pediatric population, it is nevertheless associated with serious or life-threatening consequences. The etiologic factors of acute ischemic stroke (AIS) are likely to vary over the course of childhood development. The incidence rates of AIS, not previously systematically examined by pediatric age subgroup, could guide studies of its etiology. <b><i>Objective:</i></b> The aim of this study is to evaluate the incidence rate of AIS by age-group in the pediatric population (aged 0–17/18 years) and identify any common trends or sources of variability across different countries. <b><i>Methods:</i></b> Rates of pediatric AIS were collated from a systematic literature review of published studies globally (1983–2020) and hospitalization records from Europe and the USA (2015–2018). Records that were included in the analysis reported the code or description used for AIS diagnosis and age-specific data for children aged 0–17/18 years. AIS incidence rates were summarized by age-group, data source, country, and geographic region. A meta-analysis was conducted to assess the heterogeneity of AIS rates in neonates. <b><i>Results:</i></b> The pooled AIS incidence rate was 5.6 per 100,000 children across all records. When only records reporting the AIS incidence rates for children across the full age range (0–17/18 years) were analyzed, the pooled AIS incidence rate was 4.6 per 100,000 children and ranged from 7.0 per 100,000 (Germany) to 1.3 per 100,000 (Denmark). The highest pooled rates were observed in the 0–28-day age-group (24.6 per 100,000 live births), declining to the lowest rates in the 5–9-year age-group, and rising again in the 10–17/18-year age-group. AIS rates were the most heterogeneous in the 0–28-day age-group and across European countries. Significantly higher AIS rates in neonates were observed from hospital databases (35.9 per 100,000) than in the literature (19.4 per 100,000). AIS rates may be underestimated as pediatric AIS events are rare and challenging to diagnose, and limited age-specific data are available. <b><i>Conclusions:</i></b> Incidence rates of pediatric AIS by age-groups followed a consistent overall pattern of a reverse J-shaped curve, with the highest rates in neonates, across predominantly European and North American countries. Further research is warranted to examine if this pattern is observed in other geographic regions and to identify AIS risk factors specific to different phases of childhood development.
DOI: 10.6084/m9.figshare.15177633
title: Count data and normalization code

description: TCGA Breast cancer count data and normalization code
DOI: 10.5281/zenodo.5211186
title: AMIP-data

description: "PUBLISH AS IS".
DOI: 10.5281/zenodo.4708618
title: AMIP-data

description: "PUBLISH AS IS".
DOI: 10.5281/zenodo.5142299
title: AMIP-data

description: "Publish AS IS"
DOI: 10.5281/zenodo.5205494
title: AMIP-data

description: "Publish AS IS"
DOI: 10.6084/m9.figshare.15177594.v1
title: dataset of the sampling information and biogeochemical parameters.xlsx

description: The dataset contains the basic sampling information and biogeochemical parameters like Nutrients, DOC and Chl-a in the SCS and Kuroshio<br><br>
DOI: 10.5281/zenodo.5211204
title: Downsampling of CT-Lymph-Node Dataset for Body Part Regression Tutorial

description: Down sampling of the CT Lymph Node dataset from the TCIA.<br> The files were down sampled to a pixel spacing of 7 mm/pixel. Through zero padding and cropping, all images are provided in the size of 64px x 64 px. Moreover, the HU values were clipped between -1000 HU and 1500 HU and rescaled to -1 and 1. To avoid aliasing effects, an additional Gaussian smoothing filter was applied before down sampling. This dataset was created for a Body Part Regression tutorial.
description: {"references": ["Roth, H., Lu, L., Seff, A., Cherry, K. M., Hoffman, J., Wang, S., Liu, J., Turkbey, E., & Summers, R. M. (2015). A new 2.5 D representation for lymph node detection in CT [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2015.AQIIDCNM", "Roth, H. R., Lu, L., Seff, A., Cherry, K. M., Hoffman, J., Wang, S., Liu, J., Turkbey, E., & Summers, R. M. (2014). A New 2.5D Representation for Lymph Node Detection Using Random Sets of Deep Convolutional Neural Network Observations. In Medical Image Computing and Computer-Assisted Intervention \u2013 MICCAI 2014 (pp. 520\u2013527). Springer International Publishing. https://doi.org/10.1007/978-3-319-10404-1_65", "Seff, A., Lu, L., Cherry, K.M., Roth, H.R., Liu, J., Wang, S., Hoffman, J., Turkbey, E.B., & Summers, R.M. 2D view aggregation for lymph node detection using a shallow hierarchy of linear classifiers. Medical Image Computing and Computer-Assisted Intervention--MICCAI 2014, p544-552, 2014. (http://arxiv.org/abs/1408.3337)", "Please cite the following paper when using the segmentation masks: Seff, A., Lu, L., Barbu, A., Roth, H., Shin, H.-C., & Summers, R. M. (2015). Leveraging Mid-Level Semantic Boundary Cues for Automated Lymph Node Detection. In Lecture Notes in Computer Science Medical Image Computing and Computer-Assisted Intervention\u2013MICCAI 2015 (pp. 53\u201361). Springer International Publishing. https://doi.org/10.1007/978-3-319-24571-3_7", "Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. Journal of Digital Imaging, 26(6), 1045\u20131057. https://doi.org/10.1007/s10278-013-9622-7"]}