cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25540396
title: Supplementary Material for: Deep Brain Stimulation of the Globus Pallidus Internus In a Child With Refractory Dystonia Due To L2-Hydroxyglutaric Aciduria

description: Introduction
L-2-Hydroxyglutaric aciduria (L2HGA) is a rare neurometabolic disorder marked by progressive and debilitating psychomotor deficits. Here, we report the first patient with L2HGA-related refractory dystonia that was managed with deep brain stimulation to the bilateral globus pallidus internus (GPi-DBS). 

Case Presentation
We present a 17-year-old female with progressive decline in cognitive function, motor skills, and language ability which significantly impaired activities of daily living. Neurological exam revealed generalized dystonia, significant choreic movements in the upper extremities, slurred speech, bilateral dysmetria, and a wide-based gait. Brisk deep tendon reflexes, clonus, and bilateral Babinski signs were present. Urine 2-OH-glutaric acid level was significantly elevated. Brain MRI showed extensive supratentorial subcortical white matter signal abnormalities predominantly involving the U fibers and bilateral basal ganglia. Genetic testing identified a homozygous pathogenic mutation in the L-2-hydroxyglutarate dehydrogenase gene c. 164G&gt;A (p. Gly55Asp). Following minimal response to pharmacotherapy, GPi-DBS was performed. Significant increases in mobility and decrease in dystonia were observed at 3 weeks, 6 months, and 12 months postoperatively. 

Conclusion
This is the first utilization of DBS as treatment for L2HGA-related dystonia. The significant improvement seen indicates that pallidal neuromodulation may be a viable option for pharmaco-resistant cases, and possibly in other secondary metabolic dystonias.
DOI: 10.6084/m9.figshare.25908823.v1
title: 3D model time series of a coastal dike in Ouistreham, France

description: Structure from Motion 3D photogrammetric model time series of a coastal dike acquired as part of the Cherloc project and used as case studies to train machine learning models in the cLASpy_T software. These 3D models were acquired in Ouistreham in Normandy, France by the M2C laboratory and processed using the OpenMVG/MVS software. A time series of 4 dates are included: April 28th, May 11th, June 30th and November 3rd 2021. For each date, a "dataset.las" with the necessary features is provided as well as a "TrainSet.las" including a reference classification to be used for machine learning model design.
DOI: 10.6084/m9.figshare.26113933
title: Prediction of plant complex traits via integration of multi-omics data

description: The preprocessed omics data and intermediate result files for our manuscript, including genomic, transcriptomic, and gene-body and single site methylomic data matrix. A Readme file including the invetory of uploaded data was also provided.
DOI: 10.6084/m9.figshare.26130010
title: Supplementary Material for: The Impact of Drug Interactions on the results of DAT-SPECT Imaging in a Specialty Movement Disorders Practice: A Retrospective Analysis of Outcomes

description: Introduction: DAT-SPECT imaging is approved as a diagnostic tool for the evaluation of suspected Parkinsonian syndromes, but the FDA approved package insert lists 16 potential drugs that may interfere with the image obtained. The clinical impact of these drugs upon imaging results has not been established. This study aims to determine the accuracy of DAT-SPECT imaging in assessing presynaptic dopaminergic denervation in the setting of these drugs.

Methods: This is a retrospective chart review of patients at a single center who underwent DAT-SPECT imaging while taking “contraindicated” drugs between December 2012 to December 2022. 

Results: A total of 1224 charts were screened, and 153 (12.5%) charts met the inclusion criteria. Bupropion (32%, n=49) and sertraline (26%, n=40) were the most common contraindicated drugs. The false positive rate was 9.2%. 

Conclusion: This retrospective analysis supports the concern that certain drugs may interfere with DAT-SPECT imaging results, leading to potential false positives. This has implications for how clinicians interpret DAT-SPECT imaging in patients taking these medications and whether they should advise patients to stop these medications before a scan is performed.
DOI: 10.5067/terra/ceres/ssf1degmonth_l3.004a
title: CERES Level 3 SSF1deg-Month Terra-MODIS HDF file - Edition 4A
DOI: 10.5281/zenodo.10028178
title: PKZILLA candidate domains of unknown function (cDUFs) analysis

description: This dataset consisits of the source data, code, and derived data for an analysis of regions of the PKZILLA polypeptides that were not annotated by InterProScan, and thus are candidates to be domains of unknown function (cDUFs). See Manuscript for more details.
DOI: 10.5281/zenodo.10028238
title: Prymnesium parvum 12B1 polyketide synthase (PKS) domain and module analysis

description: The .zip file contains source data and code for an analysis that determines the modular structure from the domain structure of type I modular polyketide synthases (PKSs) in the Prymnesium parvum strain 12B1 gene annotation. In brief, a regex is used against a string representation of the PKS domain structures to determine the module structure. Some manual modifications for calling modules were performed where they deviated. Resulting data is available in the .zip file as .bed, .FASTA, .xlsx files. See Manuscript for further details.
DOI: 10.5281/zenodo.12146560
title: Domain phylogenetics for the PKZILLAs

description: Source data files, executable code, and results for A-type PKZILLA PKS domain phylogenetic analysis.

Difference from previous version:

Difference between v1.0 to v1.1 of this Zenodo item series: is that KR11f0, KR20f0 were renamed in the plots to K11*, KR20*, respectively, based on new interpretations.  

Difference between v1.1 to v1.2: Trees were recalculated to include bootstrap node support values (Felsenstein bootstrap proportions)

Domain phylogenetics method:

See manuscript for full details. 

Plots were generated from the resulting newick files using ete3.
DOI: 10.5281/zenodo.12147198
title: PKZILLA domain phylogenies with outgroup representatives from Uniprot

description: Source data files, executable code, and results for PKZILLA domain phylogenetic analysis, with inclusion of representative PKS domain outgroups from Uniprot.

Difference from previous version:

Difference between v1.0 to v1.1 of this Zenodo item series: is the text in the final plots has highlighting to allow the reader to quickly appreciate it without having to look closely at each taxonomic identifier, and KR11f0, KR20f0 were renamed in the plots to K11*, KR20*, respectively, based on new interpretations.  

Difference between v1.1 to v1.2: 

Domain phylogenetics method:

Representative PKS domains from bacteria, fungi, dinoflagellates, haptophytes, and human FAS were downloaded from the InterPro API using high level queries for taxonomically restricted polypeptides with the presence of PKS domains, and their Uniprot reviewed (Swiss-Prot) or unreviewed (TrEMBL) status, and then further filtered based on the presence of well known polyketide names in the metadata of the matching Uniprot entry (see impactful_polyketides.tsv):

erythromycinrapamycinsirolimusdoxorubicinamphotericintacrolimusfk506mupirocinnystatinivermectinsalinomycinmonensintetracyclinedoxorubicinplicamycindaunorubicinepothilonediscodermolidebrefeldinnarasinpikromycinactinorhodinaflatoxinlovastatinsaxitoxinquinolidomicincuracin

The PKS domains of the PKZILLAs and those PKS domains from the representative Uniprot PKS polypeptides were then multiple sequence aligned with kalign2 v2.0.4 and maximum likelihood phylograms calculated with RAxML-NG v. 1.2.2 (see manuscript for details)

Plots were generated from the resulting newick files using ete3 v3.1.3 (Huerta-Cepas et al. 2016). Text within PDF plots was highlighted with color using PyMuPDF v1.23.19.

References:





J. Huerta-Cepas, F. Serra, and P. Bork, “ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data,” Molecular Biology and Evolution, vol. 33, no. 6, pp. 1635–1638, Jun. 2016, doi: 10.1093/molbev/msw046.
DOI: 10.18140/flx/1440032
title: FLUXNET2015 BR-Sa1 Santarem-Km67-Primary Forest

description: This is the FLUXNET2015 version of the carbon flux data for the site BR-Sa1 Santarem-Km67-Primary Forest.
DOI: 10.25318/9810038601-eng
title: Highest level of education by geography: Canada, provinces and territories

description: Compares distribution of highest certificate, diploma or degree between provinces and territories. Allows sorting/ranking of provinces and territories by percentage.
DOI: 10.5066/f76w992g
title: Sentinel

description: The Sentinel fleet of satellites is designed to deliver land remote sensing data that are central to the European Commissions Copernicus program. The Sentinel-2 mission is the result of close collaboration between the European Space Agency (ESA), the European Commission, industry, service providers, and data users. The mission has been designed and built by a consortium of around 60 companies led by Airbus Defence and Space, and supported by the CNES French space agency to optimize image quality and by the DLR German Aerospace Centre to improve data recovery using optical communications. The Sentinel-2 mission consists of two satellites developed to support vegetation, land cover, and environmental monitoring. The Sentinel-2A satellite was launched by ESA on June 23, 2015, and operates in a sun-synchronous orbit with a 10-day repeat cycle. The current Sentinel-2A acquisition priorities are focused primarily on Europe. A second identical satellite (Sentinel-2B) was launched March 7, 2017 and is expected to be operational for data acquisitions in 3 - 4 month. Together they will cover all Earths land surfaces, large islands, and inland and coastal waters every five days. The Sentinel-2 MultiSpectral Instrument (MSI) acquires 13 spectral bands ranging from Visible and Near Infrared (VNIR) to Shortwave Infrared (SWIR) wavelengths along a 290-km orbital swath. The MSI sensor data are complementary to data acquired by the U.S. Geological Survey (USGS) Landsat 8 Operational Land Imager (OLI) and Landsat 7 Enhanced Thematic Mapper Plus (ETM+). A collaborative effort between ESA and the USGS provides for the public access and redistribution of global acquisitions of ESAs Sentinel-2 data at no cost through secondary U.S. based portals, in addition to direct user access from ESA.
DOI: 10.5067/aqua/airs/data303
title: Aqua AIRS Level 3 Standard Daily Product using AIRS IR-only V6
DOI: 10.5281/zenodo.10552071
title: U.K. N2O top-down emissions: Results from InTEM and RHIME 2013-2022

description: U.K. top-down nitrous oxide (N2O) emissions estimates for 2013-2022

Top-down emissions were derived using the InTEM (Manning et al., 2021) and RHIME (Ganesan et al., 2014) inverse models with atmospheric N2O mole fraction measurements from the U.K. DECC network (O'Doherty et al., 2020). This dataset provides monthly top-down emissions estimates for the U.K. (land-only, sea-only, land+sea components) with 68% confidence interval ranges. A priori total monthly N2O emissions created by the U.K. Emissions Model are also provided. This dataset was used in the publication "Combining top-down and bottom-up approaches to evaluate recent trends and seasonal patterns in U.K. N2O emissions" that has been submitted to JGR: Atmospheres by Saboya et al. 

Further information about the generation of this dataset and its implications can be found in Saboya et al. (2024). Please note InTEM emissions data hold a Crown Copyright.
DOI: 10.5281/zenodo.10868050
title: Dataset for manuscript: How energy dissipation mode controls the evolution of multiple plane-strain hydraulic fractures

description: Numerical results and codes to generate the figures for the manuscript "How energy dissipation mode controls the evolution of multiple plane-strain hydraulic fractures".
DOI: 10.5281/zenodo.11459715
title: Products for "Hydrogen sulfide and metal-enriched atmosphere for a Jupiter-mass exoplanet"

description: Data and model for JWST transit observation of HD 189733b using NIRCam (GO 1633, PI: Drake Deming) from paper "Hydrogen sulfide and metal-enrichedatmosphere for a Jupiter-mass exoplanet" (Fu et al. 2024).
DOI: 10.5281/zenodo.3759712
title: Data for Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

description: <strong>Description of the datasets</strong> Data are organized as folders and compressed with tar.gz. There are two compressed data folder: <strong>data </strong>which used for cattle genome graphs experiment and <strong>data_human</strong> which we used for human genome graphs experiment. <strong>Cattle genome graphs experiments</strong> First you need to unzip the file using command <em>tar -xvzf data.tar.gz</em>. After unzipping, the data folder is organized as follows: Utilities: contain bovine ARS-UCD 1.2 fasta reference with the accompanying index. Bin: contain the softwares used in the paper (vg, liftover, vcf2diploid) Part1: data for analysis in variant prioritization section, further subdivided into: vcf_sim: variant files from four animal in each breed used to simulate reads reads_sim: simulated short reads used for read mapping vcf_freq: variants augmented to graphs filtered based on allele frequency Part2: data used for analysis in the section of graph mapping with breeds-filtered variants, further subdivided into: vcf_breed: variant files used to graphs construction. Part3: data used for analysis in the section of consensus genome, further subdivided into: read_sims: simulated reads as in the part1, but the coordinates are liftovered to the new consensus genomes. reference: contain the original reference and consensus references. vcf_consensus: contain major allele variants to construct consensus genomes. Part4: data analysis in the section of whole genome graph construction and variant genotyping. vcf_construct: variants from chromosome 1-29 from 82 Brown Swiss used to construct BSW whole genome graph. BSW_graph: whole genome Brown Swiss graph with the three accompanying indexes (xg,gcsa, and gbwt). <strong>Human genome graphs experiments</strong> First you need to unzip the <em>data_human</em> file using command <em>tar -xvzf data</em><em>_hum.tar.gz</em>. After unzipping, the data folder is organized as follows: reference: the g1k_v37 reference used as a graph backbone vcf_sim: variant files from four individuals in each population used to simulate reads reads_sim: simulated short reads used for read mapping vcf_freq: variants augmented to graphs filtered based on allele frequency
DOI: 10.5281/zenodo.7523058
title: Database of physicochemical and optical properties of black carbon fractal aggregates

description: In order to estimate the climate impact of highly absorbing black carbon (BC) aerosols, it is necessary to know their optical properties. The Lorentz-Mie theory, often used to calculate the optical properties of BC under the spherical morphological assumption, produces discrepancies when compared to measurements. In light of this, researchers are currently investigating the possibility of computing the optical properties of BC using a realistic fractal aggregate morphology. To determine the optical properties of such BC fractal aggregates, the Multiple Sphere T-Matrix method (MSTM) is used, which can take more than 24 hours for a single simulation depending on the aggregate properties. This study provides a highly accurate benchmark machine-learning algorithm that can be used to generate the optical properties of BC fractal aggregate in a fraction of a second. The machine learning algorithm was trained over an extensive database of physicochemical and optical properties of BC fractal aggregates. The extensive training data helped develop an ML algorithm that can accurately predict the optical properties of BC fractal aggregates with an average deviation of less than one percent from their actual values. Specifically, the ML algorithm provides the option to generate the optical properties in the visible spectrum using either kernel ridge regression (KRR) or artificial neural networks (ANN) for a BC fractal aggregate of desired physicochemical properties like size, morphology, and organic coating. The dataset of physicochemical and optical properties of BC fractal aggregates are provided here. The developed ML algorithm for predicting the optical properties of BC fractal aggregates (https://github.com/jaikrishnap/Machine-learning-for-prediction-of-BCFAs) is highly useful for real-world applications due to its wide parameter range, high accuracy, and low computational cost. <strong>Contents</strong> database_optical_properties_black_carbon_fractal_aggregtates.csv, data file, comma-separated values database_header.txt, metadata, text <strong>Citation for the database: </strong> B., Romshoo, T., Müller, B., Patil, J., Michels, T., Kloft, M., and Pöhlker, M.: Database of physicochemical and optical properties of black<br> carbon fractal aggregates, Dataset, https://doi.org/10.5281/zenodo.7523058, 2023.
DOI: 10.5523/bris.fpl32oat0vjh25eoao7llprz3
title: Raw planktic foraminifera assemblage size data accompanying Filippi et al. 2024. Impacts of the Early Eocene Climatic Optimum (EECO, ~53-49 Ma) on planktic foraminiferal resilience

description: This dataset contains raw foraminiferal assemblage size data for ODP Sites 1209 and 1210
DOI: 10.6073/pasta/7486a33ab8549c262233ad3e4a8b42a3
title: Hubbard Brook Experimental Forest: Daily Solar Radiation Measurements, 1959 - present

description: Daily solar radiation has been measured at Hubbard Brook Experimental
 Forest Headquarters since 1959, using several different sensors.
 Radiation was recorded continuously first by a Belfort pyranograph and
 later by a Weather Measure pyranograph. The pyranograph has been at
 its current Headquarter location since 1960 and before that at weather
 station 1, near weir 1. With the installation of the automatic weather
 station in 1981, a LiCor pyranometer was collocated with the
 pyranograph and used as the primary radiation sensor. After the LiCor
 sensor came online the pyranograph charts were only read for the
 purpose of gapfilling. The pyranograph remained in operation until
 2005 for this purpose but was discontinued when the charts were no
 longer available. In April, 2018 the LiCor sensor was exchanged for an
 Apogee SP230 light sensor. Data checking was done on the entire record
 and values flagged when changes were made to previously posted,
 erroneous or missing data.

 
 These data were gathered as part of the Hubbard Brook Ecosystem Study
 (HBES). The HBES is a collaborative effort at the Hubbard Brook
 Experimental Forest, which is operated and maintained by the USDA
 Forest Service, Northern Research Station.
DOI: 10.6073/pasta/7a070aab134c1add4f239fab6318b4d7
title: Carbon Dynamics in the Hyporheic Zone of a Headwater Mountain Stream in the Cascade Mountains, Oregon – Watershed 1 at HJA – June 2013 to March 2014

description: This study investigated carbon dynamics in the hyporheic zone of a steep, forested catchment in the Cascade Mountains of western Oregon, USA. Water samples were collected monthly from a headwater stream and well network during baseflow conditions from July to December 2013 and again in March 2014. We also sampled during one fall storm event, collecting pre-storm, rising leg, and extended high flow samples. The well network is located at the base of Watershed 1 (WS1) of the H.J. Andrews Experimental Forest and spans the full width of the floodplain (~14 m) along a 29 m reach of stream. We measured pH, temperature, water level, major anions, major cations, DOC, DIC, and total alkalinity. Flow paths, travel time to wells and hydraulic conductivity were available from previous studies.
DOI: 10.6084/m9.figshare.25772358
title: Supplementary Material for: Frailty in midlife as a predictor of changes in body composition from midlife into old age: a longitudinal birth cohort study

description: Introduction: Few studies have investigated the association between frailty and subsequent body composition.

Methods: We performed separate linear mixed model analyses to study the associations between changes in the participants frailty status assessed by a frailty index (FI) and subsequent body mass index (BMI), lean mass index (LMI), fat mass index (FMI), and FMI to LMI-ratio values assessed on three occasions over 17 years. The analyses were carried out among 996 participants spanning from age 57 to 84 years.

Results: With advancing age, LMI and BMI decreased, whereas FMI and FMI to LMI -ratio increased. Participants with ‘stable frailty’, followed by those with ‘increasing frailty’ experienced faster decreases in LMI and faster increases in FMI and FMI to LMI -ratio values from midlife into old age relative to those in the group ‘stable not frail’. Contrastingly, those in the highest third of absolute annual increase in FMI and FMI to LMI -ratio became more frail faster from midlife into old age relative to those in the lowest third.

Conclusions: We found evidence of an adverse health outcome of frailty where lean indices declined faster and fat indices and fat to lean -ratios increased faster from midlife into old age. The changes resembled those that occurred with aging, but at a faster pace. The relationship between body composition and frailty is likely bidirectional, where high or increasing levels of fat are associated with the risk of becoming more frail earlier, but where a longer duration of frailty may increase the risk of faster age-related changes to body composition.
DOI: 10.6084/m9.figshare.26029756
title: Supplementary Material for: Tachycardia and acute kidney injury among critically ill patients with sepsis: a prospective observational study

description: Introduction: Tachycardia caused by sympathetic overactivity impairs myocardial function and raises septic patient mortality. This study examined whether tachycardia is associated with acute kidney injury (AKI) period-prevalence among critically ill patients with and without sepsis. 
Methods: In 328 patients (119 sepsis and 209 non-sepsis) admitted to our intensive care unit (ICU), we assessed heart rate at ICU admission, plasma neutrophil gelatinase-associated lipocalin (NGAL) and N-terminal pro-B-type natriuretic peptide, and urinary L-type fatty acid-binding protein and N-acetyl-β-D-glucosaminidase (NAG) at 0 and 48 hours after admission. Tachycardia was defined as a heart rate of above 100 beats/min.
Results: Tachycardia was independently correlated with AKI prevalence during the first week after ICU admission in the septic patients, but not in the non-septic patients. A dose-dependent increase in AKI period-prevalence was observed across ascending heart rate ranges. Furthermore, we discovered a dose-dependent increase of renal biomarker-positive patients regarding plasma NGAL and urinary NAG over increasing heart rate ranges 48 hours after admission.
Conclusion: The findings revealed an independent relationship between tachycardia and AKI prevalence during the first week of ICU in septic patients. Heart rate was found to have a dose-dependent effect on AKI prevalence and renal insult monitored by biomarkers.
DOI: 10.6084/m9.figshare.26046277
title: Audited reports data

description: Audited reports data for 20 banks in India for the period 2014 to 2017Quarterly performance efficiency scores
DOI: 10.15468/dl.2qjve9
title: Occurrence Download

description: A dataset containing 5143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Year 2018-2020",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Cercis canadensis L."
 ]
}

 The dataset includes 5143 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052707-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.