cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5676394
title: Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies.

description: This repository contains the molecular dynamics trajectories of the SARS-CoV-2 Spike RBD bound to BD23 and B38 monoclonal antibodies. The simulations for the RBD only systems are also provided. The trajectories are available for the WT spike protein as well as for four different variants (alpha, beta, kappa and delta). The simulations of the RBD only system are propagated for 300 ns and for the RBD-Antibody complex for 500 ns. The trajectories are saved at 100 ps interval. The Steered MD simulation trajectories (WT_RBD_B38_SMD_1.dcd etc.) and collective variables files are also included (WT_RBD_B38_SMD_1.colvars.traj etc.). There are 5 SMD trajectories for each RBD antibody pair. The details of the simulation can be obtained from the preprint: https://doi.org/10.1101/2021.08.13.456317
description: Funding: NSF MCB 2028443 Computing Resources: University of California Irvine HPC3, San Diego Supercomputer Center
DOI: 10.5281/zenodo.5677137
title: Dataset: Planetary-scale waves seen in thermal infrared images of Venusian cloud top

description: The data archive contains data used in the paper "Planetary-Scale Waves Seen in Thermal Infrared Images of Venusian Cloud Top" by Kajiwara et al. The contents of the directories are as follows. "data_used_in_figures" : The table data used in the figures are given in Excel and CSV. The table format is described in the data files. An image in NetCDF format is also included. "time_series_of_brightness_temperature_gradient" : The files contain the time series of the longitudinal gradient of Venusian cloud's brightness temperature measured by LIR onboard JAXA's Venus orbiter Akatsuki. The data were derived and analyzed in the paper "Planetary-Scale Waves Seen in Thermal Infrared Images of Venusian Cloud Top" by Kajiwara et al. The filename represents the latitude for each time series (For example, "10N" means 10 degrees north, and "EQ" means the equator). In all files, the first column gives the approximate elapsed time in days from 18 May 2017: the exact dates are given in the paper (Table S1 in the Supporting Information). The second column gives the longitudinal gradient of the brightness temperature in unit of K/degree.
DOI: 10.5281/zenodo.5677136
title: Dataset: Planetary-scale waves seen in thermal infrared images of Venusian cloud top

description: The data archive contains data used in the paper "Planetary-Scale Waves Seen in Thermal Infrared Images of Venusian Cloud Top" by Kajiwara et al. The contents of the directories are as follows. "data_used_in_figures" : The table data used in the figures are given in Excel and CSV. The table format is described in the data files. An image in NetCDF format is also included. "time_series_of_brightness_temperature_gradient" : The files contain the time series of the longitudinal gradient of Venusian cloud's brightness temperature measured by LIR onboard JAXA's Venus orbiter Akatsuki. The data were derived and analyzed in the paper "Planetary-Scale Waves Seen in Thermal Infrared Images of Venusian Cloud Top" by Kajiwara et al. The filename represents the latitude for each time series (For example, "10N" means 10 degrees north, and "EQ" means the equator). In all files, the first column gives the approximate elapsed time in days from 18 May 2017: the exact dates are given in the paper (Table S1 in the Supporting Information). The second column gives the longitudinal gradient of the brightness temperature in unit of K/degree.
DOI: 10.26078/3bqs-9029
title: 2D thermo-mechanical simulations of flat subduction - supporting data for research manuscript
DOI: 10.15468/3b4ya6
title: Studies in Neotropical Apocynaceae LIV: a synopsis of Asketanthera

description: This dataset contains the digitized treatments in Plazi based on the original journal article Morales, J. Francisco (2018): Studies in Neotropical Apocynaceae LIV: a synopsis of Asketanthera. Candollea 73 (1): 7-17, DOI: 10.15553/c2018v731a2
DOI: 10.5281/zenodo.5681304
title: Unprocessed data for the "Deriving Semantics-Aware Fuzzers from Web API Schemas" paper.

description: Unprocessed data for the "Deriving Semantics-Aware Fuzzers from Web API Schemas" paper.
DOI: 10.5281/zenodo.5681303
title: Unprocessed data for the "Deriving Semantics-Aware Fuzzers from Web API Schemas" paper.

description: Unprocessed data for the "Deriving Semantics-Aware Fuzzers from Web API Schemas" paper.
DOI: 10.6084/m9.figshare.16653124
title: Random Forest Adjustment for Approximate Bayesian Computation

description: We propose a novel method for regression adjustment in approximate Bayesian computation to help improve the accuracy and computational efficiency of the posterior inference. The proposed method uses random forest regression to model the connection between summary statistics and the parameters of interest. Compared with existing approaches, the proposed method bypasses the need of preselection of summary statistics in the model, and is capable of capturing the potential nonlinear relationship between the parameters of interest and summary statistics. We also introduce a measure to quantify the importance of each summary statistic used in the model. We study the asymptotic properties of the proposed estimator and show that it has an excellent finite-sample numerical performance via two simulation examples and an application to a population genetic study.
DOI: 10.6084/m9.figshare.16653124.v2
title: Random Forest Adjustment for Approximate Bayesian Computation

description: We propose a novel method for regression adjustment in approximate Bayesian computation to help improve the accuracy and computational efficiency of the posterior inference. The proposed method uses random forest regression to model the connection between summary statistics and the parameters of interest. Compared with existing approaches, the proposed method bypasses the need of preselection of summary statistics in the model, and is capable of capturing the potential nonlinear relationship between the parameters of interest and summary statistics. We also introduce a measure to quantify the importance of each summary statistic used in the model. We study the asymptotic properties of the proposed estimator and show that it has an excellent finite-sample numerical performance via two simulation examples and an application to a population genetic study.
DOI: 10.6084/m9.figshare.16653124.v1
title: Random Forest Adjustment for Approximate Bayesian Computation

description: We propose a novel method for regression adjustment in Approximate Bayesian Computation to help improve the accuracy and computational efficiency of the posterior inference. The proposed method uses random forest regression to model the connection between summary statistics and the parameters of interest. Compared with existing approaches, the proposed method bypasses the need of pre-selection of summary statistics in the model, and is capable of capturing the potential nonlinear relationship between the parameters of interest and summary statistics. We also introduce a measure to quantify the importance of each summary statistic used in the model. We study the asymptotic properties of the proposed estimator and show that it has an excellent finite-sample numerical performance via two simulation examples and an application to a population genetic study. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.16606295
title: A Relabeling Approach to Handling the Class Imbalance Problem for Logistic Regression

description: Logistic regression is a standard procedure for real-world classification problems. The challenge of class imbalance arises in two-class classification problems when the minority class is observed much less than the majority class. This characteristic is endemic in many domains. Work by Owen has shown that cluster structure among the minority class may be a specific problem in highly imbalanced logistic regression. In this article, we propose a novel relabeling approach to handle the class imbalance problem when using logistic regression, which essentially assigns new labels to the minority class observations. An expectation–maximization algorithm is formalized to serve as a tool for efficiently computing this relabeling. Modeling on such relabeled data can lead to improved predictive performance. We demonstrate the effectiveness of this approach with detailed experiments on real datasets. Supplemental materials for the article are available online.
DOI: 10.18739/a24746s61
title: Indigenous Peoples of the Arctic boundary polygons, 2021

description: Indigenous Peoples of the Arctic boundary polygons Greg Fiske at Woodwell Climate Research Center (gfiske@woodwellclimate.org) April 2021 Created for Figure 1.1 in Chapter 1: Introduction: Building Common Interests with Informed Decisionmaking for Sustainability (Paul Arthur Berkman, Oran R. Young, Alexander N. Vylegzhanin, David A. Balton and Ole Øvretveit). IN: Berkman, P.A., Young, O.R., Vylegzhanin, A.N., Balton, D.A. and Øvretveit, O. (eds.). 2022. Building Common Interests in the Arctic Ocean with Global Inclusion. Volume 2. Informed Decisionmaking for Sustainability. Original data created by GRID Arendal, shared by Levi Westerveld (levi.westerveld@grida.no). Updates applied by gereferencing the map at this location: https://www.grida.no/resources/13341 based on advice by Westerveld. Additional spatial edits to each shapefile were based on conversation with Anna Degteva (anna.d.ips@arctic-council.org) at the Arctic Council Indigenous Peoples' Secretariat (https://www.arcticpeoples.com/) who personally requested updates from the six Indigenous Peoples’ Organizations. All but Russian Association of Indigenous Peoples Organization of the North (RAIPON) responded with map edit requests that were incorporated into the shape files that are herein submitted for open access. The edit requests came in the format of hand drawn polygons on top of existing jpg images and/or lists of placenames that should (or should not) be included in each boundary file. Lastly, additional resource maps were shared by Lars Kellerud at GRID Aredal. All efforts were made to accommodate comments and resources provided while editing these layers. These shapefiles were updated with support from the United States National Science Foundation (NSF) through the Arctic/Pan-Arctic Options projects (Award Nos. NSF-OPP 1263819, NSF-ICER 1660449, NSF-ICER 2103490).
DOI: 10.15468/yzsm3v
title: A new species of Halisaurus from the Late Cretaceous phosphates of Morocco, and the phylogenetical relationships of the Halisaurinae (Squamata: Mosasauridae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Bardet, Nathalie, Suberbiola, Xabier Pereda, Iarochene, Mohamed, Bouya, Baadi, Amaghzaz, Mbarek (2005): A new species of Halisaurus from the Late Cretaceous phosphates of Morocco, and the phylogenetical relationships of the Halisaurinae (Squamata: Mosasauridae). Zoological Journal of the Linnean Society 143 (3): 447-472, DOI: 10.1111/j.1096-3642.2005.00152.x, URL: https://academic.oup.com/zoolinnean/article-lookup/doi/10.1111/j.1096-3642.2005.00152.x
DOI: 10.6084/m9.figshare.9894431.v1
title: Effect of Ephedrae Herba methanol extract on high-fat diet-induced hyperlipidaemic mice

description: <b>Context:</b> Ephedrae Herba (EH), the dried stems and leaves of <i>Ephedra sinica</i> Stapf., <i>E. intermedia</i> Schrenk et C. A. Mey., or <i>E. equisetina</i> Bge. (Ephedraceae [Ephedra]) is used to treat respiratory diseases. Recently, especially in the Republic of Korea, EH has also been used for weight reduction. <b>Objective:</b> We evaluated the effects and molecular targets of methanol EH extract (EHM) on high-fat diet (HFD)-induced hyperlipidemic ICR mice. <b>Materials and methods:</b> EHM was orally administered (100 mg/kg body weight/day) for 3 weeks. We observed changes in body weight (BW), total cholesterol (TC), high-density lipoprotein–cholesterol, and triglycerides to evaluate the physiological changes induced by HFD or EHM administration. To evaluate lipid peroxidation and liver toxicity, malondialdehyde and blood alanine aminotransferase levels were measured. In addition to analyzing liver gene expression profiles, EHM target proteins were identified using a protein interaction database. <b>Results:</b> EHM administration for 3 weeks significantly (<i>p</i> <b>Discussion and conclusions:</b> EHM regulated hyperlipidaemia by decreasing total blood lipid and triglyceride levels in hyperlipidaemic mice. EHM showed preventive effects against hyperlipidaemia in mice, possibly via the regulation of DNA repair and the expression of energy metabolism-related genes and proteins.
DOI: 10.6084/m9.figshare.9894431
title: Effect of Ephedrae Herba methanol extract on high-fat diet-induced hyperlipidaemic mice

description: <b>Context:</b> Ephedrae Herba (EH), the dried stems and leaves of <i>Ephedra sinica</i> Stapf., <i>E. intermedia</i> Schrenk et C. A. Mey., or <i>E. equisetina</i> Bge. (Ephedraceae [Ephedra]) is used to treat respiratory diseases. Recently, especially in the Republic of Korea, EH has also been used for weight reduction. <b>Objective:</b> We evaluated the effects and molecular targets of methanol EH extract (EHM) on high-fat diet (HFD)-induced hyperlipidemic ICR mice. <b>Materials and methods:</b> EHM was orally administered (100 mg/kg body weight/day) for 3 weeks. We observed changes in body weight (BW), total cholesterol (TC), high-density lipoprotein–cholesterol, and triglycerides to evaluate the physiological changes induced by HFD or EHM administration. To evaluate lipid peroxidation and liver toxicity, malondialdehyde and blood alanine aminotransferase levels were measured. In addition to analyzing liver gene expression profiles, EHM target proteins were identified using a protein interaction database. <b>Results:</b> EHM administration for 3 weeks significantly (<i>p</i> <b>Discussion and conclusions:</b> EHM regulated hyperlipidaemia by decreasing total blood lipid and triglyceride levels in hyperlipidaemic mice. EHM showed preventive effects against hyperlipidaemia in mice, possibly via the regulation of DNA repair and the expression of energy metabolism-related genes and proteins.
DOI: 10.6073/pasta/2a2d0f0557a813cefeb4e26feeea75d7
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 10 meteorological station: 30-minute summary data: 2017 - ongoing

description: This data package contains 30-minute air temperature, relative humidity, and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-1 met station. Average air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively. This is an ONGOING dataset.
DOI: 10.34740/kaggle/dsv/2804350
title: Egypt High School Grades (Sanwya Amma)
DOI: 10.34740/kaggle/ds/1712469
title: Egypt High School Grades (Sanwya Amma)
DOI: 10.3886/e153001v1-101440
title: COVID Behavioral Health Data

description: Electronic data collection through a Qualtrics survey link, was utilized to explore pathways of COVID-19 behavioral health and quality of life. This cross-sectional study included responses from April 2020-July 2020 from adults ages 18–65. Participants gave virtual consent by continuing the online survey and were informed they could skip any questions or stop at any time—there was no compensation for time. Tulane University Institutional Review Board approved study protocol.
DOI: 10.5281/zenodo.5683564
title: Mechanism of Praziquantel action at a parasitic flatworm ion channel

description: Data supporting Park <em>et al.</em> [Mechanism of praziquantel action at a parasitic flatworm ion channel]
DOI: 10.5281/zenodo.5683563
title: Mechanism of Praziquantel action at a parasitic flatworm ion channel

description: Data supporting Park <em>et al.</em> [Mechanism of praziquantel action at a parasitic flatworm ion channel]
DOI: 10.6073/pasta/2b221d57634e04cd6144bbe27fb11d03
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 10 meteorological station: 1-hour summary data: 2017 - ongoing

description: This data package contains hourly air temperature, relative humidity, wind speed, wind direction, and precipitation summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-10 met station. Air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.5517/ccdc.csd.cc24c8yr
title: CCDC 1977054: Experimental Crystal Structure Determination

description: Related Article: Sambasivarao Kotha,  Subba Rao Cheekatla|2020|Indian J.Chem.,Sect.B:Org.Chem.Incl.Med.Chem.|59|1556|
DOI: 10.5517/ccdc.csd.cc24cbd8
title: CCDC 1977099: Experimental Crystal Structure Determination

description: Related Article: Fayaz Ali Larik, Lucy L. Fillbrook, Sandra S. Nurttila, Adam D. Martin, Rhiannon P. Kuchel, Karrar Al Taief, Mohan Bhadbhade, Jonathon E. Beves, Pall Thordarson|2021|Angew.Chem.,Int.Ed.|60|6764|doi:10.1002/anie.202015703
DOI: 10.5517/ccdc.csd.cc24cbf9
title: CCDC 1977100: Experimental Crystal Structure Determination

description: Related Article: Fayaz Ali Larik, Lucy L. Fillbrook, Sandra S. Nurttila, Adam D. Martin, Rhiannon P. Kuchel, Karrar Al Taief, Mohan Bhadbhade, Jonathon E. Beves, Pall Thordarson|2021|Angew.Chem.,Int.Ed.|60|6764|doi:10.1002/anie.202015703
DOI: 10.5517/ccdc.csd.cc24cbgb
title: CCDC 1977101: Experimental Crystal Structure Determination

description: Related Article: Fayaz Ali Larik, Lucy L. Fillbrook, Sandra S. Nurttila, Adam D. Martin, Rhiannon P. Kuchel, Karrar Al Taief, Mohan Bhadbhade, Jonathon E. Beves, Pall Thordarson|2021|Angew.Chem.,Int.Ed.|60|6764|doi:10.1002/anie.202015703
DOI: 10.5517/ccdc.csd.cc24cbhc
title: CCDC 1977102: Experimental Crystal Structure Determination

description: Related Article: Fayaz Ali Larik, Lucy L. Fillbrook, Sandra S. Nurttila, Adam D. Martin, Rhiannon P. Kuchel, Karrar Al Taief, Mohan Bhadbhade, Jonathon E. Beves, Pall Thordarson|2021|Angew.Chem.,Int.Ed.|60|6764|doi:10.1002/anie.202015703
DOI: 10.5517/ccdc.csd.cc24cbjd
title: CCDC 1977103: Experimental Crystal Structure Determination

description: Related Article: Fayaz Ali Larik, Lucy L. Fillbrook, Sandra S. Nurttila, Adam D. Martin, Rhiannon P. Kuchel, Karrar Al Taief, Mohan Bhadbhade, Jonathon E. Beves, Pall Thordarson|2021|Angew.Chem.,Int.Ed.|60|6764|doi:10.1002/anie.202015703
DOI: 10.5281/zenodo.5678009
title: Dataset for "Changes in mechanisms and characteristics of Western U.S. floods over the last sixty years"

description: This is the data prepared for submission of "Changes in mechanisms and characteristics of Western U.S. floods over the last sixty years." Four types of data are included: 1) daily streamflow on 119 basins from USGS and the selected AM and POT events (time and magnitude) during 1960-2018; 2) basin-averaged Livneh-VIC outputs during 1960-2018; 3) the corresponding FGM for each AMS and POT event on 119 basins, and 4) AR catalog developed by Guan and Waliser (2015)
DOI: 10.5281/zenodo.5678008
title: Dataset for "Changes in mechanisms and characteristics of Western U.S. floods over the last sixty years"

description: This is the data prepared for submission of "Changes in mechanisms and characteristics of Western U.S. floods over the last sixty years." Four types of data are included: 1) daily streamflow on 119 basins from USGS and the selected AM and POT events (time and magnitude) during 1960-2018; 2) basin-averaged Livneh-VIC outputs during 1960-2018; 3) the corresponding FGM for each AMS and POT event on 119 basins, and 4) AR catalog developed by Guan and Waliser (2015)
DOI: 10.6084/m9.figshare.17003329
title: mock human and microbe fasta

description: mock human and microbe fasta created as described here: https://hackmd.io/@astrobiomike/making-mock-human-and-microbe-fasta
DOI: 10.6084/m9.figshare.17003329.v1
title: mock human and microbe fasta

description: mock human and microbe fasta created as described here: https://hackmd.io/@astrobiomike/making-mock-human-and-microbe-fasta
DOI: 10.6073/pasta/5bd887a28378b805886efc6d9db2cc41
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 10 meteorological station: 5-minute summary wind and air temperature data: 2013 - ongoing

description: This data package contains 5-minute air temperature and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-10 met station. Average air temperature, wind speed, and wind direction are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. This is a subset of baseline weather data collected at the 15 Jornada Basin LTER CSIS study blocks, New Mexico. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.6073/pasta/589385a4ca582adb1c0df8ff799d69b0
title: Porewater nutrient concentrations from control plots and fertilized plots at Spartina alterniflora, S.patens and Typha sp. marshes, Plum Island Ecosystem LTER, MA.

description: Nutrient concentrations from porewater samples at marsh sites in the Plum Island Ecosystems (PIE) LTER site. There are three long term marsh fertilization experimental research sites. The fertilization sites include one Typha-dominated brackish marsh, one Spartina alterniflora-dominated salt marsh, one S. patens-dominated salt marsh on the Rowley and upper Parker Rivers and two non-fertilized marsh sites on the Parker River National Wildlife Refuge.