cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10802703
title: AusENDVI: A long-term NDVI dataset for Australia

description: AusENDVI (Australian Emprical NDVI) is a monthly, 5-km gridded estimate of NDVI across Australia from 1982-2022. It is built by calibrating and harmonising NOAA's Climate Data Record AVHRR NDVI data to MODIS MCD43A4 NDVI using a gradient boosting ensemble decision tree method.  Additionally, the datasets are gapfilled using a synthetic NDVI dataset.  The methods are extensively described in an Earth System Science Data publication.

AusENDVI consists of several datasets, each dataset has a description in the attributes of the NetCDF file that describes its provenance.  The naming convention is "AusENDVI_<model_type>_<year_range>_<version>.nc". 





AusENDVI-clim_gapfilled_1982_2013. Calibrated and harmonised Climate Data Record AVHRR NDVI data from Jan. 1982 to Dec. 2013. This version of the dataset used climate data in the calibration and harmonisation process and has the best agreement statistics with MODIS MCD43A4 NDVI. The dataset has been gap filled using the methods described in the accompanying publication.


AusENDVI-clim_MCD43A4_gapfilled_1982_2022. This dataset consists of calibrated and harmonised NOAA Climate Data Record AVHRR NDVI data from Jan. 1982 to Feb. 2000, joined with MODIS-MCD43A4 NDVI data from Mar. 2000 to Dec. 2022. This version of the dataset _used climate data_ in the calibration and harmonisation process. The dataset has been gapfilled using the methods described in the accompanying publication



AusENDVI-noclim_1982_2013. Calibrated and harmonised Climate Data Record AVHRR NDVI data from Jan. 1982 to Dec. 2013. This version of the dataset did not use climate data in the calibration and harmonisation process and the dataset has not been gap filled.




AusENDVI-synthetic_1982_2022. This dataset consists of synthetic NDVI data that was built by training a model on the joined _AusENDVI-clim_ and _MODIS-MCD43A4 NDVI_ timeseries using climate, woody-cover-fraction, and atmospheric CO2 as predictors. The synthetic NDVI is used for gap filling.



All datasets are in 'EPSG:4326' projection, and have a spatial resolution of 0.05 degrees. Geographic coordinate information is contained in the `spatial_ref` variable. 

A Jupyter Notebook is also provided that shows how to load, plot, QC mask, reproject, and gap-fill AusENDVI datasets. The notebook is effectively a 'readme' file.



The notebook is also available to view/download here


An open-source github repository details the methods used to create these datasets



https://github.com/cbur24/AusENDVI


 

A few small changes to the datasets were implemented in version 0.2.0:



All datasets now have their values clipped to the range 0-1

The AusENDVI-clim dataset is now gapfilled, and includes a QC layer

The merged AusENDVI-noclim_MCD43A4_1982_2022 dataset was removed to simplify the number of datasets included in the repository. Users who want to join the 'noclim' and MODIS datasets can do so by clipping out MCD43A4 from the AusENDVI-clim_MCD43A4_gapfilled_1982_2022 dataset.

The accompanying Jupyter Notebook 'readme' has been updated.
DOI: 10.5281/zenodo.11218234
title: MESA inlists for: Type Ia Supernovae from the First Generation Stars

description: MESA input files associated with the paper "Type Ia Supernovae from the First Generation Stars". This directory contains MESA inlists and run_star_extras.f used for calculations performed with MESA r12115. The MESASDK version is aarch64-macos-22.10.1. 

 

MESA simulations of Single Degnerate Channel for SNe Ia at zero metallicity. The Common Envelope Wind model (Meng,X & Podsiadlowski,Ph) is adopted.

inlist1: Evove the 1st star (primary star)

inlist2: mass point (Secondary star)

inlist_project: Inputs for binary evolution

run_binary_extras.f: The Common Envelope Wind model for WD accretion.
DOI: 10.6084/m9.figshare.23278343
title: Egalitarian cooperation linked to central oxytocin levels in communal breeding house mice

description: Data and code used in an experimental study demonstrating that the reproductive consequences of social interactions between female house mice are linked to oxytocin concentrations in the paraventricular nucleus (PVN) of the hypothalamus.
DOI: 10.6084/m9.figshare.25138118
title: Supplementary Material for: A New and Practical Model of Human-like Ascending Aorta Aneurysm in Rats

description: Introduction: Ascending aortic aneurysm is a serious health risk. In order to study ascending aortic aneurysms, elastase and calcium ion treatment for aneurysm formation are mainly used, but their aneurysm formation time is long, the aneurysm formation rate is low. Thus, this study aimed to construct a rat model of ascending aorta aneurysm with a short modeling time and high aneurysm formation rate, which may mimic the pathological processes of human ascending aorta aneurysm. 
Methods: Cushion needles with different pipe diameters (1.0, 1.2, 1.4 and 1.6 mm) were used to establish a human-like rat model of ascending aortic aneurysm by narrowing the ascending aorta of rats and increasing the force of blood flow on the vessel wall. The vascular diameters were evaluated using color Doppler ultrasonography after two weeks. The characteristics of ascending aortic aneurysm in rats were detected by Masson’s trichrome staining, Verhoeff’s Van Gieson staining and hematoxylin and eosin staining while RT-PCR were utilized to assess the total RNA of cytokine interleukin-1β, interleukin 6, transforming growth factor-beta1 and metalloproteinase 2.
Results: Two weeks after surgery, the ultrasound images and the statistical analysis demonstrated that the diameter of the ascending aorta in rats increased more than 1.5 times, similar to that in humans, indicating the success of animal modeling of ascending aortic aneurysm. Moreover, the optimal constriction diameter of the ascending aortic aneurysm model is 1.4 mm by the statistical analysis of the rate of ascending aortic aneurysm and mortality rate in rats with different constriction diameters. 
Conclusions: The human-like ascending aortic aneurysm model developed in this study can be used for the studies of the pathological processes and mechanisms in ascending aortic aneurysm in a more clinically relevant fashion.
DOI: 10.6084/m9.figshare.26370721
title: Supplementary Material for: Clinical implications of C2 lesion in IgA nephropathy: A cohort study

description: Introduction: In 2016, the Oxford Classification of IgA Nephropathy(IgAN) updated its scoring system for the glomerular crescents. Despite this, the clinical significance of crescentic lesions in the updated Oxford classification is still unexplored through prospective cohort studies.
Methods: 134 patients diagnosed with IgAN accompanied with C2 lesions at Peking University First Hospital were consecutively enrolled and prospectively followed up for analysis. Multivariate Cox regression in combination with LASSO regression was used to analyze risk factors associated with end stage kidney disease (ESKD).
Results: During biopsy, the average mean eGFR was 39.3 mL/min/1.73 m2, and the average mean proteinuria was 4.4 g/day. The proportion of kidney failure at 1 year, 2 years, and 3 years were 24%, 34%, and 47%, respectively. The results of LASSO in combination with Cox regression showed that mean arterial pressure (MAP) (Hazard ratio [HR]=1.035, 95% Confidence interval[95%CI] 1.013-1.056, P=0.001), glomerular filtration rate(eGFR) at biopsy (HR=0.968, 95%CI [0.948-0.990], P&lt;0.004) and T2 lesions (HR=2.490, 95%CI [1.179-5.259], P=0.017) were independent risk factor associated with ESKD in patients with C2 lesions. Furthermore, based on univariate analyses, we found that patients with kidney function declined more than 50% within 3 months prior to biopsy or pathological findings indicated a proportion of crescents exceeding 50% were both associated with a poor kidney prognosis. Lastly, when the proportion of the crescent was less than 50%, patients receiving combined steroid and immunosuppressant treatment did not exhibit a better renal prognosis than those receiving steroid only.
Conclusion: Patients diagnosed with IgAN and concurrent C2 lesions exhibited a poor clinical prognosis, necessitating more effective treatment strategies.
DOI: 10.6084/m9.figshare.3423695
title: To the Maintenance of Balinese Culture

description: This paper discusses cultural maintenance and the role of Balinese taboos. Today, the influence of outside societies cannot be avoided because of tourism development in Bali. From the topic concerned, the subjects of the study are taken from professional tourist guides and their family—wives and children. Ideally, Balinese people must be familiar with their own culture and outside societies must be hoped too. However, most of them didn’t know clearly what the culture is. Culture must be maintained by people in general because culture is embodied in religion. The problems are: first, what are the conditions that should be understood by the community to maintain the culture? Second, what are the necessary things that should be known by the community to avoid the Balinese taboos? To solve these problems, the research employed with the cognitive approach. By the cognitive approach data are taken from the informant’s knowledge. Thus, the research revealed new values toward the understanding of Balinese culture because the information came from the insiders’ view.
DOI: 10.17632/wyfdm5ysh6.1
title: Slug Liquid Holdup 

description: Experimentally measured HLS data from 22 different studies are made available as a dataset for the present study. Each data point consists of the measured HLS for a given set of VSG, VSL, µL, D, Ø, σL, ρL and ρG. The dataset covers flow direction from horizontal to vertical, liquid viscosity from 1 mPa.s to 5300 mPa.s and surface tension from 27.5 to 72 mN/m. The ranges of the other flow parameter are: VSG (0.046-15.308) m/s, VSL (0.0155-3.048) m/s, D (0.0254-0.1) m, ρL (800-1000) kg/m4 and ρG (1-4) kg/m3. The HLS was measured using capacitance sensors, which were dynamically calibrated by using quick closing ball valves. Two types of capacitance sensors were adopted in the included studies, namely: two-wire and ring type sensors. Most of the experimental studies included in the present paper preferred using two-wire sensor due to its easy static calibration as compared to the ring type sensor.
DOI: 10.6073/pasta/0d591da0aff8bbcc8ec07c160d83d36e
title: PVC02 Plant species composition on selected watersheds at Konza Prairie

description: Canopy coverage of all vascular plant species were estimated in 20 circular 10 sq m plots for each of the topographic positions within each included watershed at Konza Prairie.
DOI: 10.15131/shef.data.26869993
title: Multiscale topological analysis of kinetoplast DNA via high-resolution AFM

description: High-resolution atomic force microscopy of single kinetoplast DNA molecules reveals structural heterogeneity and complex catenation behaviour across several length scales.Data analysis is described in the accompanying publication.
DOI: 10.5281/zenodo.10685297
title: Seismograms for deep-focus earthquakes in the Peru-Brazil region

description: Description

Seismograms used to determine focal mechanisms for a sequence of 42 deep-focus earthquakes that occurred at the Peru-Brazil region from 2014 to 2022.



Data from the Brazilian Seismographic Network (RSBR), including network codes BL, BR, NB and ON, are open and available at http://rsbr.on.br

Data from the temporary 3-basins Project (XC) can be requested through the USP Seismological Center (USPSC) FDSNWS server (http://seisrequest.iag.usp.br/fdsnws/dataselect/1/) (Assumpção & Bianchi, 2016)

Data from the other networks* used in this study were all collected through the EarthScope Consortium (formerly IRIS) Wilber 3 at https://ds.iris.edu/wilber3/.


*Network codes: 

IU (Albuquerque Seismological Laboratory/USGS, 2014), II (Scripps Institution of Oceanography, 1986), G (Institut de Physique du Globe de Paris (IPGP) and École et Observatoire des Sciences de la Terre de Strasbourg (EOST), 1982), GE (GEOFON Data Centre, 1993), C (Chilean National Seismic Network), C1 (Universidad de Chile, 2012), CX (GFZ German Research Centre for Geosciences; Institut des Sciences De l’Univers-Centre National de la Recherche CNRS-INSU, 2006), CM (Servicio Geológico Colombiano, 1993) and EC (Ecuador Seismic Network).

References

Albuquerque Seismological Laboratory/USGS. (2014). Global Seismograph Network (GSN - IRIS/USGS) [Dataset]. International Federation of Digital Seismograph Networks. https://doi.org/10.7914/SN/IU

Assumpção, M. S., & Bianchi, M. B. (2016). Pantanal, Chaco and Paraná (PCPB) structural studies network [Dataset]. USP Seismological Center (USPSC). https://doi.org/10.7914/8scf-yd39

GEOFON Data Centre (1993). GEOFON Seismic Network [Dataset]. Deutsches GeoForschungsZentrum GFZ. https://doi.org/10.14470/TR560404

GFZ German Research Centre for Geosciences; Institut des Sciences De l’Univers-Centre National de la Recherche CNRS-INSU (2006). IPOC Seismic Network [Dataset]. Integrated Plate boundary Observatory Chile – IPOC. https://doi.org/10.14470/PK615318

Institut de Physique du Globe de Paris (IPGP) and École et Observatoire des Sciences de la Terre de Strasbourg (EOST) (1982). GEOSCOPE, French Global Network of Broad Band Seismic Stations [Dataset]. Institut de Physique du Globe de Paris (IPGP), Université de Paris. https://doi.org/10.18715/GEOSCOPE.G

Scripps Institution of Oceanography (1986). Global Seismographic Network – IRIS/IDA [Dataset]. International Federation of Digital Seismograph Networks.  https://doi.org/10.7914/SN/II

Servicio Geológico Colombiano (1993). Red Sismologica Nacional de Colombia [Dataset]. International Federation of Digital Seismograph Networks. https://doi.org/10.7914/SN/CM

Universidad de Chile (2012). Red Sismologica Nacional [Dataset]. International Federation of Digital Seismograph Networks. https://doi.org/10.7914/SN/C1
DOI: 10.5281/zenodo.10866729
title: Combined RSEI Water Scores and American Community Survey, 2011–2021

description: This dataset was created for a master's thesis in geography at the University of Utah. County-level RSEI scores and county demographics were combined for a spatiotemporal regression analysis. Counties in the contiguous United States and years 2011–2021 are included.

Risk-Screening Environmental Indicators. Annual, county-level RSEI risk scores for surface water were obtained from the EPA RSEI model through the EasyRSEI Dashboard. RSEI scores are defined as the relative potential for health risks, given the estimated exposure calculated by the EPA. A binary risk indicator was created, signifying whether the county had any risk in a given year.

American Community Survey 5-year estimates. County-level population characteristics were collected as five-year estimates from the American Community Survey, with annual estimates for the survey end year applying to each year from 2011–2021. We used the R tidycensus package to collect variables and geometry from the US Census Bureau API. Variables included total population (scaled by 10,000), percent racial composition (American Indian or Alaska Native, or AIAN; Asian; Black or African American; Native Hawaiian or Other Pacific Islander, or NHPI; Some Other Race; Two or More Races; and White), and percent ethnic composition (Hispanic or Latinx). Each census-defined racial category was collected as non-Hispanic or Latinx, such that each group was mutually exclusive.
DOI: 10.5281/zenodo.11187761
title: Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought

description: Plants are colonized by distinct pathogenic and commensal microbiomes across different regions of the globe, but the factors driving their geographic variation are largely unknown. Using 16S rDNA and shotgun sequencing, we characterized the associations of the Arabidopsis thaliana leaf microbiome with host genetics and climate variables from 267 populations in the species’ native range across Europe. Comparing the distribution of the 575 major bacterial amplicon variants (phylotypes), we discovered that microbiome composition in A. thaliana segregates along a latitudinal gradient. The latitudinal clines in microbiome composition are predicted by metrics of drought, but also by the spatial genetics of the host. To validate the relative effects of drought and host genotype we conducted a common garden field study, finding 10% of the core bacteria to be affected directly by drought, and 20% to be affected by host genetic associations with drought. These data provide a valuable resource for the plant microbiome field, with the identified associations suggesting that drought can directly and indirectly shape genetic variation in A. thaliana via the leaf microbiome.
description: all_metagenome_metadata_9_2020_reads.tsv: This is the metadata file for the collected samples.

 OTUtab_GP1000.rds: ASV phyloseq object (to be read into R) with samples subsampled to 1000 reads.

OTUtab_GP1000_at15.rds: ASV phyloseq object (to be read into R) with samples subsampled to 1000 reads then filtered for common A. thaliana ASVs

plant_clim.rds: Adapted (non-phyloseq) object used for random forest modeling and other regression methods.

metadata_carnegie_drought_experiment_2022_final_submitted: metadata file for plants in the Carnegie experiment in 2022. Corresponding 16S ASV data found in carnegie_field_exp_asvs.rds.

carnegie_field_exp_asvs.rds: ASV phyloseq object (to be read into R) with ASVs found in the Carnegie field experiment in Stanford CA in 2022. No filtering has been applied to this phyloseq object.

Supplementary_data.xls: excel file with the raw data for the Arabiodpsis infection experiments in the growth chamber in drought and control conditions in Utah when infected with p25.C2. Used to generate figure S10 in manuscript.
DOI: 10.5281/zenodo.12565023
title: Analysis of public single-cell sequencing database of COVID lung samples

description: Lung endothelial cells from three published scRNA-seq datasets (GSE122960, GSE149878, GSE171668) of healthy subjects and COVID-19 patients were collected for further integrative analyses. The endothelial cells were classified into three sub-groups according to their distinguished expression of IL7R, DKK2, and EDNRB. For differential analysis of gene expression, counts per million of aggregated UMIs in each group were adopted in Wilcoxon rank-sum test.
DOI: 10.5281/zenodo.13123649
title: Ephemeral Piscivory in a Mesopredator Sunfish: Implications for Pond Food Webs
DOI: 10.6084/m9.figshare.10505021
title: Supplementary Material for: Blended Psychotherapy: Treatment Concept and Case Report for the Integration of Internet- and Mobile-Based Interventions into Brief Psychotherapy of Depressive Disorders

description: <b><i>Background:</i></b> Blended psychotherapy (bPT) is a treatment that integrates internet- and mobile-based interventions into out-/inpatient psychotherapy. It can enrich the therapy by using online-based treatment modules as therapeutic extension that patients use time- and location-independently between face-to-face sessions. It could potentially improve the efficacy of psychotherapy and increase the number of treated persons through saved therapist time. The case report aims to facilitate the understanding of the blended treatment components. <b><i>Case Report:</i></b> A 4-month short-time depression treatment with six face-to-face therapy sessions, six online lessons, and app ratings of a 48-year-old female patient is presented based on the CARE guidelines and quantitative and qualitative measures (treatment documentation). Depressive symptoms were clinically significantly reduced (PHQ-9, 0–27: T0 = 17; T1 = 7) from a moderately severe to a subclinical-mild degree, and no diagnostic criteria were met in the 12-month follow-up diagnostic interview. The patient showed a maximum treatment satisfaction (ZUF-8, 8–32: T1 = 32) and adherence and rated the therapeutic working alliance (WAI, 12–60: T1 = 57) highly positive. <b><i>Conclusion:</i></b> bPT reduced depressive symptoms for this patient. Strengths of the treatment were the facilitated use of the internet-based elements with a full-time job and the individualization within the face-to-face sessions through the therapist. Treatment success was limited by the predetermined six sessions, which hindered addressing all topics and conducting relapse prevention.
DOI: 10.6084/m9.figshare.23906130
title: Phylogenetic analysis files for RNA viruses of parasitic nematodes.

description: Sequence alignment of the Brugia malayi RNA Virus 1 and Onchocerca volvulus RNA Virus 1 groups, using the "Hepe-Virga" and "Mono-Chu" clade alignments from Shi et al. 2016 as a base respectively. Both alignments were supplemented by sequences from Dheilly et al. 2022. The identified RdRP sequences from this study were then added to these alignments based on their putative virus orders. Additional RdRP sequences from viruses of flatworms that were more than 50% complete (less than 50% of identified amino acids were ‘X’) were also added for completeness, with all sequences re-aligned using MAFFT (v.7.505) using the E-INS-I strategy. Uninformative parts of the sequence were then removed using Trimal (v1.2rev59), with the gappyout strategy specified. The final alignment was then used for phylogenetic analysis using IQTree (v.1.6.1) at 1000 non-parametric bootstraps. ModelFinder was also used to identify the best evolutionary model for BMRV1 and OVRV1 (LG+F+I+G4 for all).The above method was also used to generate full phylogenetic trees for viruses identified as part of the Bunyavirales (best-determined evolutionary model LG+F+I+G4), Durnavirales (LG+F+G4), Flavivirus (LG+I+G4), Ghabrivirales (LG+G4), Jingchu-Monovirales (LG+F+I+G4), Martellivrales (LG+F+I+G4), Picornavirales (LG+F+I+G4), Qinviridae (LG+I+G4), and Reovirales (LG+F+I+G4) groups.The uploaded sequence alignments (fasta file format) are those used by IQTree to build the final phylogenetic tree. The newick-formatted treefiles for all aforementioned viruses are also available (nwk file format).
DOI: 10.6084/m9.figshare.24805881
title: Supplementary Material for: Clinical characteristics of pathogenic ACAN variants and 3-year response to growth hormone treatment: real-world data

description: Introduction 
Heterozygous variants in the ACAN gene may underlie disproportionate short stature with characteristically accelerated bone age (BA) maturation and/or early-onset osteoarthritis (OA).
Methods
To describe phenotype, analyze genotype-phenotype correlations and assess the response of growth hormone (GH) treatment in children with a heterozygous ACAN variant. Thirty-six subjects (23 boys, 13 girls) with ACAN-deficiency and treated for ≥1 year with GH were identified in the Dutch National Registry of GH treatment in children.
Results
We identified 25 different heterozygous ACAN variants in 36 subjects. Median (IQR) height SDS at start of GH was -2.6 SDS (-3.2 to -2.2). Characteristic features such as disproportion, advanced BA, early-onset OA and dysmorphic features like midface hypoplasia and brachydactyly were present in the majority of children, but in ~20% no specific features were reported. Subjects with a truncating ACAN variant had a shorter height SDS compared to subjects with a non-truncating variant (-2.8 SDS and -2.1 SDS respectively, P=0.002). After 3 years of GH, height gain SDS in prepubertal children was 1.0 SDS (0.9 to 1.4). In pubertal children, height SDS remained relatively stable. 
Conclusion
The phenotype of subjects with pathogenic heterozygous ACAN variants is highly variable and genetic testing for ACAN-deficiency should be considered in any child with significant short stature, even in the absence of disproportion, specific dysmorphic features or bone-age advancement. Furthermore, children with ACAN-deficiency may benefit from GH with a modest but significant response, which is sustained during 3 years of treatment.