cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9084ukq
title: Data for improved understanding of the susceptibility of Lake Superior to threats from groundwater contamination

description: This data release contains a data compilation and analysis of the hydrogeology in the U.S. portion of the Lake Superior watershed, for the purpose of providing background data for future study and modeling of groundwater and contaminant movement in the watershed. The data support an analysis of groundwater contributions to the water budget of Lake Superior and provide hydrogeologic context for future modeling and sampling of groundwater in the region. The data release contains three child items: Baseflow analysis for tributaries to Lake Superior from 1946 to 2020; Geohydrology data for groundwater analysis in the Lake Superior Watershed; and Groundwater wells from Minnesota, Wisconsin, and Michigan state databases and the U.S. Geological (USGS) National Water Information System (NWIS) database with static water level data within 10km of the Lake Superior watershed.
DOI: 10.5285/637eeed6-7175-4346-9321-0c14332456c6
title: High resolution river stage and groundwater level data from Wallingford, Oxfordshire, UK

description: The borehole is located at the UK Centre for Ecology and Hydrology (UKCEH), screened between 2 and 4.5 m in the Thames gravels, and drilled to a total depth of 4.8m. It is located on an actively managed grass verge with popular and sycamore trees within 10 m. The stilling well is positioned 420 m west of the borehole in the River Thames. Both stage and groundwater level were monitored at 1-minutre frequency to investigate hydrological fractal scaling of high frequency data between 2012 and 2016. An automatic weather station is present between the borehole and stilling well and the data are available separately from UKCEH (stetur@ceh.ac.uk).
Further site description is provided in:
Habib, A. et al. 2017. Journal of Hydrology, 549, 715-730.
Habib, A. et al. 2022. Hydrological Sciences Journal
DOI: 10.18118/g6h66k
title: Preliminary Report on Engineering and Geological Effects of the July 2019 Ridgecrest Earthquake Sequence
DOI: 10.24381/cds.4bd77450
title: Climate and energy indicators for Europe from 1979 to present derived from reanalysis
DOI: 10.24381/cds.8c59054f
title: Water level change time series for the European coast from 1977 to 2100 derived from climate projections
DOI: 10.48493/wvsn-k463
title: IsoMad Modern Biological Material
DOI: 10.5066/p9yyvv7r
title: Selenium and mercury in the Kootenai River, Montana and Idaho, 2018-2019

description: Selenium loads have been increasing over time in the Elk River, British Columbia, Canada, due to coal mining operations and runoff from associate spoil piles. The Elk River is a tributary to the Kootenay/Kootenai River and Lake Koocanusa. Extensive fish tissue monitoring has been conducted in Lake Koocanusa to assess the potential impacts of selenium from the Elk River (http://deq.mt.gov/DEQAdmin/LakeKoocanusa) However, fewer data are available for the Kootenai River downstream of Lake Koocanusa (downstream of Libby Dam). This 2018-2019 study generated baseline data on selenium and mercury concentrations in fish tissue and selenium and nutrient data in the water column of the Kootenai River and principal tributaries in Montana and Idaho. This data release is organized in two parts or &quot;child items&quot; for the fish tissue and water data, respectively. In addition to this compilation, the data are also being released through the USGS National Water Information System (NWIS) http://waterdata.usgs.gov/nwis/.
DOI: 10.5281/zenodo.10879577
title: Data for: 'Microlensing optical depth and event rate toward the Large Magellanic Cloud based on 20 years of OGLE observations'

description: This repository contains data presented in the paper "Microlensing optical depth and event rate toward the Large Magellanic Cloud based on 20 years of OGLE observations".
DOI: 10.5281/zenodo.12475904
title: SNP and InDels in peanut population
DOI: 10.5281/zenodo.12735196
title: Assessing Patterns of Metazoans in the Global Ocean using Environmental DNA

description: Data for the above publication which is in RSOS. Code is available here, https://github.com/ngeraldi/Global_ocean_genome_analysis.  The 5 files include the amplicon data (Malaspina and Tara) and all metagenome data is in DMAP_biomass_apr19 (it is not biomass, it is metagenome data). Global layers contain the metadata- april18 is amplicon data and genome is the metagenome data.

Abstract:

Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, Tara Oceans and Malaspina, that circumnavigated the oceans, and sampled down to 4000 meters to assess metazoans from eDNA extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer relative abundance of phyla using metagenome datasets, and relate these data with environmental variables. Arthropods had the greatest taxonomic richness of metazoan phyla at the surface, while cnidarians had the greatest richness in pelagic zones. Half of the marine metazoan eDNA from metagenome datasets was from arthropods, followed by cnidarians and nematodes. We found that mean surface temperature and primary productivity were positively related with metazoan taxonomic richness. Our findings concur with existing knowledge that temperature and primary productivity are important drivers of taxonomic richness for specific taxa at the ocean’s surface, but these correlations are less evident in the deep ocean. Massive sequencing of eDNA can improve understanding of animal distributions, particularly for the deep ocean where sampling is challenging.
DOI: 10.5281/zenodo.12738074
title: Dataset for "Machine Learning Driven Sensitivity Analysis of E3SM Land Model Parameters for Wetland Methane Emissions"

description: This dataset is a part of the paper "Machine Learning Driven Sensitivity Analysis of E3SM Land Model Parameters for Wetland Methane Emissions", accepted for publication in the Journal of Advances in Modeling Earth Systems (JAMES).

Contents

This dataset includes:



lhs-gen-190.csv: Training input LHS samples generated by lhsgen.py.

lhs-gen-50-test.csv: Test input LHS samples generated by lhsgen.py.

190-elm-samples.csv: Training input perturbed parameter samples for performing ELM simulations.

50-elm-test-samples.csv: Test input perturbed parameter samples for performing ELM simulations.

train_CH-CHA.csv: Contains the five ELM simulation output flux values for 240 samples (190 train + 50 test).

lhsgen.py: Script for generating Latin Hypercube Samples.

gpr-fit-new.py: Script for fitting Gaussian Process Regression (GPR) models.

sobol-new.py: Script for performing Sobol sensitivity analysis.


Usage



lhsgen.py:



Use this script to generate the Latin Hypercube Samples for parameter sampling.



gpr-fit-new.py:



This script fits GPR models using the training samples provided in lhs-gen-190.csv.

It tests the models using the input testing samples in lhs-gen-50-test.csv.

The fitted GPR models are stored as .joblib files in the gpr_models directory.

Corresponding cross-validation and R-squared values are stored in .xlsx files.



sobol-new.py:



This script performs Sobol sensitivity analysis using the fitted GPR models by reading the .joblib files.

The Sobol indices are written to .xlsx files in the results directory.
DOI: 10.5281/zenodo.13118506
title: Source data of Mirtronstructdb - A comprehensive database of mirtrons with predicted secondary structure
DOI: 10.5281/zenodo.5040068
title: PECUNIA Reference Unit Costs Compendium (PECUNIA RUC Compendium)

description: The <strong>PECUNIA Reference Unit Costs Compendium (PECUNIA RUC Compendium)</strong> is a Microsoft Excel®-based multi-sectoral, multi-country database of unit costs comparable across countries and sectors and developed using standardized and scientifically validated methods (so called <strong>Reference Unit Costs (RUCs)</strong>) by the scientific partners of the PECUNIA Consortium between 2019 and 2021 based on the preliminary conceptual and methodological work conducted in 2018. The RUCs were developed using standardized and validated PECUNIA RUC Templates to introduce a higher degree of methodological harmonization and transparency in unit costs within and across sectors and countries. They are consistent with the harmonised PECUNIA Costing Concept (PECUNIA Care Atom, PECUNIA Service Lists, PECUNIA Coding System) and therefore with other PECUNIA Costing Tools (PECUNIA RUC Templates, PECUNIA RUM Instrument) to achieve comparability by referring to content rather than linguistic equivalence of services and other resource items. In the PECUNIA RUC Compendium, each listed RUC is complemented by multiple meta-data and a <strong>summary indicator</strong> of the overall <strong>level of certainty</strong> based on the robustness of the costing approach used and the outcome of the external validation process for fully transparency. <strong>Version 1.0</strong> of the PECUNIA RUC Compendium contains <strong>RUC estimates</strong> (in Euro, for year 2019) for a core set of <strong>service and resource use items</strong> commonly occurring in <strong>health economic evaluations with a societal perspective</strong> for <strong>multiple sectors</strong>: health and social care (HSC), education (ED), (criminal) justice (CJ), employment and productivity (EP), and patient, family and informal care (PFI); for <strong>multiple European countries</strong> (Austria, Germany, Hungary, The Netherlands, England, and Spain). It is a living document planned to be regularly updated and expanded both in terms of the covered service and resource use items and the number of countries over time.
DOI: 10.5281/zenodo.7325062
title: Spectral data used in the paper "Mid-infrared laser heterodyne spectrometer by hollow optical fiber and its newly designed coupler"

description: ////////// GENERAL INFORMATION ///////// 1. Title of Dataset: MIR hollow optical fiber coupler (HOPC) heterodyne spectral data 2. Authors: Hiromu Nakagawa, hiromu.nakagawa.c1@tohoku.ac.jp 3. Contact information: Hiromu Nakagawa, hiromu.nakagawa.c1@tohoku.ac.jp 4. Measurement dates: ///////////// FOLDER & FILE OVERVIEW ///////////// There are three data files for spectral data in Figures 6 and 7. (1) "MIR_HOPC_Heterodyne_spectral_data_QCL_Figure6.txt": The quantum cascade laser (QCL) emission spectral data in Figure 6: The first line is the intermediate frequency, the second line is the relative intensity of the QCL emission spectrum. (2) "MIR_HOPC_Heterodyne_tsys_Figure7_wFiber.txt" and "MIR_HOPC_Heterodyne_tsys_Figure7_woFiber.txt": The individual spectral data of system noise temperature in Figure 7. The first line is the intermediate frequency, the second and the third lines are the system noise temperature [K] of CO2 gas laser-based heterodyne spectrometer at 10.3 micron led through a hollow fiber (second) and led through in free space (third) in Figure 7. The file name of the individual spectrum includes "w" and "wo". "w" means the spectral data measured with fiber to led CO2 laser; while, "wo" means the spectral data measured without fiber (free space) to led CO2 laser. ///////////// POINT OF ATTENTION ///////////// The spectra were taken at the laboratory measurements in Tohoku University, Sendai, Japan. The data in this archive are relevant for the revised manuscript.
DOI: 10.5281/zenodo.7896106
title: Global uptake of CO2 by lime from 1930 to 2020

description: This dataset is associated with the publication on Earth System Science Data, with the same title. It includes three sections lime material production and uses, the simulation results of global lime CO<sub>2</sub> emission and uptake by year, the variables and ranges considered in the uncertainty analyses of the lime carbon emission and uptake estimation, and the corresponding confidence intervals from the comments. For detailed explanations of these datasets, one should refer to the original manuscript.
DOI: 10.5287/bodleian:jnw5n8od5
title: [Data] Multi-resonant open-access microcavity arrays for light matter interaction

description: Data presented and analysed in arXiv:2207.03676 [physics.optics] [https://arxiv.org/abs/2207.03676].
DOI: 10.5441/001/1.7vr1k987
title: Data from: Wolf ecology and caribou-primary prey-wolf spatial relationships in low productivity peatland complexes in northeastern Alberta

description: Woodland caribou (Rangifer tarandus caribou) in northeastern Alberta have historically been provided a refuge from wolf (Canis lupus) predation by using habitats not typically occupied by moose (Alces alces), which are the primary prey species for wolves in this region. However, in recent years most caribou populations in northeastern Alberta have declined, suggesting that they no longer have a refuge from wolf predation. I tested the hypotheses that (1) primary prey densities have increased since recent industrial expansion into caribou range, resulting in a numeric response by wolves; and (2) an altered wolf-primary prey system has reduced the ability of caribou to spatially separate from other prey - and consequently wolves - in this system. My results showed that wolf densities in the region have increased from approximately 6/1,000 km2 to approximately 11/1,000 km2. Based on my estimates, there has also been a corresponding increase in ungulate biomass, which appears to be primarily due to the recent increase in white-tailed deer (Odocoileus virginianus). My results suggest that wolf use and selection of this novel prey species has also increased dramatically, particularly during the snow season. Similarly, I found that wolf use and selection for beaver (Castor canadensis) was substantively higher than suggested by previous studies in this region. Wolf use of beaver was highest in the snow-free season, and could result in increased wolf-caribou encounters at this time of year. Moose were an important prey species for wolves throughout the year. These results suggest that wolves within caribou range in northeastern Alberta currently utilize multiple primary prey species. The spatial overlap between wolves and caribou has increased substantively within the past decade; however, caribou still attempt to avoid high predation risk by spatially separating from areas that tend to be selected by primary prey species and wolves. Despite differential habitat selection, the proportion of caribou in wolf diet appears to have increased in the past decade, suggesting that bog-fen habitat provides only a partial refuge from predation. These findings are integral to the effective management of primary prey and wolves in caribou ranges in northeastern Alberta, and will help inform caribou landscape planning teams in decision making processes.
DOI: 10.5523/bris.5nky6wq0wh4a2hy88qa2zs7ef
title: High-performance, adiabatically nanotapered fibre-chip couplers in silicon at 2 microns wavelength

description: Experimental measurements, simulation files and simulation data, and data analysis to accompany the manuscript by the same name.
DOI: 10.6084/m9.figshare.23656623
title: Data File 1_AO.zip

description: Data underlying the results presented in the paper "Alignment and Characterisation of Remote-Refocusing Systems"
DOI: 10.6084/m9.figshare.25662924
title: Supplementary Material for: Intrathecal anesthesia prevents ventricular arrhythmias in rats with myocardial ischemia/reperfusion

description: Introduction: Ventricular arrhythmia is commonly provoked by acute cardiac ischemia through sympathetic exaggeration and is often resistant to antiarrhythmic therapies. Thoracic epidural anesthesia has been reported to terminate fatal ventricular arrhythmia; however, its underlying mechanism is unknown. 
Methods: Rats were randomly divided into four groups: sham, sham plus bupivacaine, ischemia/reperfusion (IR), and IR plus bupivacaine groups. Bupivacaine (1 mg/mL, 0.05 mL/100 g body weight) was injected intrathecally into the L5-L6 intervertebral space prior to establishing a myocardial ischemia/reperfusion rat model. Thereafter, cardiac arrhythmia, cardiac function, myocardial injury, and electrical activities of the heart and spinal cord were evaluated.
Results: Intrathecal bupivacaine inhibited spinal neural activity, improved heart rate variability, reduced ventricular arrhythmia score, and ameliorated cardiac dysfunction in IR rats. Furthermore, intrathecal bupivacaine attenuated cardiac injury and myocardial apoptosis and regulated cardiomyocyte autophagy and connexin-43 distribution during myocardial IR.
Conclusion: Our results indicate that intrathecal bupivacaine blunts spinal neural activity to prevent cardiac arrhythmia and dysfunction induced by IR and that this antiarrhythmic activity may be associated with regulation of autonomic balance, myocardial apoptosis and autophagy, and cardiac gap junction function.
DOI: 10.6084/m9.figshare.25721169.v3
title: Microbe_surveillance_in_the_amphibian_pet_trade_results_from_a_pilot_study.xlsx

description: Anonymized data reported in the manuscript "<b>Microbe surveillance in the amphibian pet trade: results from a pilot study." </b>Spreadsheet includes surveillance sample information (e.g., species, life-stage, qPCR results) as well as participant responses to questions regarding basic biosecurity practices.
DOI: 10.6084/m9.figshare.26004421.v1
title: Datasets generated for O'Mara et al. (2024), Constraining Plio-Pleistocene shifts in Northwest African hydroclimate, ecosystem distributions, and marine productivity: new paleo-records across the Mid-Pleistocene Transition. <i>Paleoceanography and Paleoclimatology (accepted)</i>.

description: Organic and inorganic geochemical paleo-proxy measurements from marine sediment core MD03-2705 taken from the Northwest African margin. New samples dating to the Mid-Pleistocene Transition (1.1 – 1.0 Ma) are presented here. Data include plant-wax hydrogen (dD) and carbon (d13C) isotopes; plant-wax concentrations; and constant flux (extraterrestrial 3He) normalized estimates of mass accumulation rates of bulk sediment, dust, opal, and calcium carbonate. Plant-wax concentrations were made via gas chromatography-mass spectrometry at the Lamont-Doherty Earth Observatory (LDEO) Organic Geochemistry Lab using an Agilent 7890A GC coupled to an Agilent 5975C MS, plant-wax isotope measurements were made at the LDEO Stable Isotope Lab using A Thermo Delta V Advantage isotope ratio mass spectrometer coupled to a Thermo Trace GC Ultra and Isolink through a ConFlo IV, helium isotope measurements were made in the LDEO Noble Gas Lab using a MAP-215 mass spectrometer, and carbonate and opal fractions were measured at the LDEO Noble Gas Lab and the Bradtmiller Lab at Macalester College using coulometry and alkaline extraction and molybdate blue spectrophotometry respectively.<b>File descriptions</b>: inorg_table.xlsx includes the inorganic geochemical measurements of helium isotopes, and mass accumulation rates of multiple sedimentary components of each sample.org_iso_table.xlsx includes the isotope measurements of plant-wax n-alkane carbon and hydrogen isotopes (including ice-volume corrections for hydrogen), calculated landscape fraction C4 plants, and precipitation hydrogen isotopes estimated from the C31 n-alkane.alk_conc_table.xlsx includes the concentration of C25-C35 odd chain length n-alkanes in micrograms per gram of dry sediment.All data tables have core depth (cm) and associated age estimates for each sample. event_metadata.xlsx includes the core metadata. meas_metadata.xlsx includes units for each variable across the three data tables.
DOI: 10.6084/m9.figshare.26087554
title: Amplicon data of 80 soil bacteria from the Pamir Plateau

description: The ASV tables, fasta sequences, and taxonomy data for bacteria
DOI: 10.6084/m9.figshare.26087566
title: Amplicon data of 80 soil fungi from the Pamir Plateau

description: The ASV tables, fasta sequences, and taxonomy data for fungi.
DOI: 10.6084/m9.figshare.26362588
title: Supplementary Material for: Diagnostic utility of preserved dried umbilical cord PCR in intrauterine herpes simplex virus infection: A case report and literature review

description: Introduction: Intrauterine herpes simplex virus (HSV) infection is uncommon and challenging to diagnose, requiring detection of HSV in skin lesions within 48 hours post-birth. Case Presentation: A preterm female infant presented with the typical triad of blisters, microcephaly, and chorioretinitis, but the initial diagnostic approach was elusive due to negative results for TORCH pathogens from vesicles/serum. Referred at 7 months for developmental delay and epilepsy, her brain imaging showed calcification and cortical dysplasia. Polymerase chain reaction (PCR) of her preserved dried umbilical cord detected HSV-2 DNA, diagnosing intrauterine HSV infection. HSV-2 was later found in relapsed blisters at 8 months but not in cerebrospinal fluid or brain tissue. A literature review identified 104 congenital/intrauterine HSV cases; 28.8% presented the typical triad, and 50% were diagnosed using specimens collected 48 hours post-birth. Conclusion: This case marks the first retrospective diagnosis of intrauterine HSV infection via PCR on preserved umbilical cord, underscoring its diagnostic value.
DOI: 10.6084/m9.figshare.26525959
title: Supplementary Material for: M2BPGi Correlated with Immunological Biomarkers and Further Stratified Recurrence Risk in Patients with Hepatocellular Carcinoma

description: Introduction
Novel biomarkers reflecting liver fibrosis and the immune microenvironment may correlate with the risk of hepatocellular carcinoma (HCC) recurrence. This study aimed to evaluate the prognostic value of serum biomarkers in predicting HCC recurrence.
Methods
Serum biomarkers, including M2BPGi, IL-6, IL-10, CCL5, VEGF-A, soluble PD-1, PD-L1, TIM-3, and LAG-3, were measured in 247 patients with HCC undergoing surgical resection. Factors associated with recurrence-free survival (RFS) and overall survival (OS) were evaluated. The ERASL-post model and IMbrave050 criteria were used to define HCC recurrence risk groups.
Results
Serum M2BPGi levels significantly correlated with FIB-4 score, APRI, ALBI score, AFP, ALT, AST, IL-10, CCL5, VEGF-A, soluble PD-1, PD-L1, TIM-3, and LAG-3 levels. M2BPGi, VEGF-A, soluble PD-1, and TIM-3 levels significantly correlated with RFS. In multivariate analysis, M2BPGi &gt;1.5 COI (hazard ratio (HR) = 2.100, p &lt; 0.001), tumor size &gt;5 cm (HR = 1.859, p = 0.002), multiple tumors (HR = 2.562, p &lt; 0.001), AFP &gt;20 ng/mL (HR = 2.141, p &lt; 0.001), and microvascular invasion (HR = 1.954, p = 0.004) were independent predictors of RFS. M2BPGi levels significantly stratified the recurrence risk in ERASL-post and IMbrave050 risk groups. An M2BPGi-based model could significantly discriminate RFS in the overall cohort as well as in the IMbrave050 low- and high-risk groups. M2BPGi &gt;1.5 COI was also an independent predictor of OS after resection (HR = 2.707, p &lt; 0.001).
Conclusion
Serum M2BPGi levels significantly correlated with surrogate markers of liver fibrosis, liver function, and immunology. M2BPGi is a significant predictor of HCC recurrence and survival after resection and could be incorporated into recurrence-prediction models.