cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8414391
title: Raw ptychography data for manuscript with title 'Structured Illumination Ptychography and At-wavelength Characterization with an EUV diffuser at 13.5 nm Wavelength'

description: - Given are the HDF files containing the raw diffraction patterns<br> - Although some meta-data might be available in these files, these might not be correct. The following data were used for reconstruction:<br> wavelength: 13.5 nm<br> distance sample &lt;-&gt; detector: ~29.2 mm<br> sCMOS pixel size: 11 um<br> Number of incoherent modes: 4<br> Initial probe guess: 9 um<br> For the reconstruction, OPR was used (Although it might have not been necessary for all data. However, to have comparable results it was used for each reconstruction)<br> - For each scenario, there are two data sets to calculate the Fourier ring correlation (FRC)<br> - For the analysis of the diffuser the reconstructed probe of the data set "dp_diffuser_max_dynam_range.hdf5" was used - Data were measured at the Institute of Applied Physics in Jena using a Fiber Laser driven High-order harmonic source Please contact me (wilhelm.eschen@uni-jena.de) for additional support.
DOI: 10.5525/gla.researchdata.1428
title: On-chip generation of reconfigurable cylindrical vector beams

description: This dataset contains simulation results and Stokes measurements.
DOI: 10.6073/pasta/836f8bac531022a4299cdf40aaebc3c4
title: North Temperate Lakes LTER Bythotrephes longimanus spiny water flea population monitoring in Wisconsin and Minnesota 2009 - 2014

description: Three data tables are included describing population dynamics for Bythotrephes longimanus, spiny water flea, in Southern Wisconsin during invasion. General monitor took place in Lake Mendota, Lake Monona, Lake Waubesa, Lake Kegonsa, Stormy Lake, Gile Flowage, Lake Gogebic. Accompanying Bythotrephes morphological measurements from Lake Mendota monitoring efforts in 2011 and 2012. Included are individual measurements of body morphology and reproductive status for ~2,500 Bythotrephes collected from Lake Mendota in 2011 and 2012. Sediment cores from Lake Mendota were analyzed for spiny water flea evidence with age of sediment estimated.
DOI: 10.6084/m9.figshare.25233682
title: Supplementary Material for: Homozygous Paternally Inherited <i>ASPA</i> Variant in a Patient with Canavan Disease

description: <b><i>Introduction:</i></b> Canavan disease is an autosomal recessive disorder that causes accumulation of N-acetyl ASPArtic acid in the brain due to ASPArtoacylase deficiency with homozygous or compound heterozygous pathogenic variants in the <i>ASPA</i> gene located on the short arm of chromosome 17. Clinical findings are hypotonia, progressive macrocephaly, deafness, nystagmus, blindness, and brain atrophy. <b><i>Case Presentation:</i></b> A one-year-old female case was evaluated in our medical genetics clinic for hypotonia, nystagmus, and strabismus. Chromosome analysis and array-comparative genomic hybridization showed no pathology. Clinical exome sequencing by next-generation sequencing was performed and a homozygous likely pathogenic variant NM_000049.4(<i>ASPA</i>):c.857C &gt; A p.(Ala286Asp) was identified. Sanger sequencing of the parents showed that the index case had a homozygous genotype, the father was heterozygous and the mother had a wild genotype for the identified variant in <i>ASPA</i>. A single nucleotide polymorphism (SNP) array test was planned for the family to explain this homozygosity and a loss of maternal heterozygosity was determined in the 17p13.3-p13.2 region of the <i>ASPA</i> gene. <b><i>Conclusion:</i></b> In this report, we aimed to present the first case of Canavan disease with maternal loss of heterozygosity in the <i>ASPA</i> gene.
DOI: 10.6084/m9.figshare.25567248
title: Supplementary Material for: Additive Effects of Citrus Juice Flavonoid Naringenin and Statins on HERG Channels Expressed in Xenopus Oocytes

description: Objective: Naringenin, a major flavonoid found in citrus juice, has been shown to inhibit HERG channels and cause QT prolongation. Statins, the most commonly used class of cholesterol reducing drugs, have also been reported to inhibit HERG channels and prolong QT interval in patients using these drugs. However, the interaction between naringenin and statins on the function of HERG channels has not been studied. Materials and Methods: In the present study, we expressed HERG channels in Xenopus oocytes and tested the effects of naringenin and statins separately and combined on HERG channels. Results: When 30 µM naringenin was added to statins (1 µM rosuvastatin or 3 µM atorvastatin), significantly greater inhibition of HERG was demonstrated, compared to the inhibition caused by statins alone. Conclusions: The results indicate that an additive interaction occurs between naringenin and statins; this could pose an increased risk of arrhythmias by decreasing repolarization reserve.
DOI: 10.6084/m9.figshare.25574151
title: Supplementary Material for: Clinical and pathological features of pilomatrixoma in children: a retrospective study

description: Introduction Pilomatrixoma is a benign skin neoplasm that is common in children and is often misdiagnosed. This study aimed to summarize the clinical and pathological features of pilomatrixoma in children. Methods Data on demographic information, clinical and pathological features, diagnosis, and treatment of 171 patients with pilomatrixoma from Shenzhen Baoan Women's and Children's Hospital were collected and analyzed retrospectively. Results The mean age of the patients was 5.7 (standard deviation (SD) = 3.9) year-old, and there were two age peaks (≤1 year-old, 5-11 years old) and two age valleys (2-4 years old, ≥ 12 years old). The mean disease course was 9.3 (SD = 14.1) months, 69.0%, 86.5%, and 95.3% of the patients’ disease course in 6 months, 12 months, and 24 months, respectively. The mean tumor volume is 0.6 (SD = 1.0) cm3, 81.3% of the patients’ tumor volume ≤ 1.0 cm3. Tumors were distributed sequentially in the head and neck (77.2%), upper limbs (12.9%), trunk (7.6%), and lower limbs (2.3%). The correct rates of clinical and ultrasonic diagnosis were 50.9% and 38.6%, respectively. The two most common pathological features of pilomatrixoma were shadow cells (99.4%) and basaloid cells (94.7%). There were no significant differences in age, disease course, or tumor volume between the male and female patients (P &gt; 0.05). The age and tumor volume of the patients in different body parts were significantly different (P1 = 3.10E-05 and P2 = 5.60E-05, respectively). The correlation between the disease course and tumor volume was positively significant (P ≤ 0.05). There was a significantly correlation between the disease course and tumor volume in patients with tumors at upper limbs (P = 0.03). Conclusion The age of children with pilomatrixoma presented two peaks and two valleys. Most patients had disease courses in 24 months and with tumor volumes ≤ 1.0 cm3. The correct rates of clinical and ultrasonic diagnosis were relatively low. The head and neck are the most common distribution sites of pilomatrixoma, shadow cells and basaloid cells are the most common pathological features. The tumor volume is positively correlated with disease course in patients with pilomatrixoma.
DOI: 10.6084/m9.figshare.25689504
title: Supplementary Material for: Longterm erythromycin treatment alters the airway and gut microbiota：Data from COPD patients and mice with emphysema

description: Introduction: Although long-term macrolide antibiotics could reduce the recurrent exacerbation of chronic obstructive pulmonary disease (COPD), the side effect of bacterial resistance and the impact on the microbiota remain concerning. We investigated the influence of long-term erythromycin treatment on the airway and gut microbiota in mice with emphysema and patients with COPD.
Methods: We conducted 16S rRNA gene sequencing to explore the effect of erythromycin treatment on the lung and gut microbiota in mice with emphysema. Liquid chromatography–mass spectrometry was used for lung metabolomics. A randomized controlled trial was performed to investigate the effect of 48-week erythromycin treatment on the airway and gut microbiota in COPD patients. 
Results: The mouse lung and gut microbiota were disrupted after cigarette smoke exposure. Erythromycin treatment depleted harmful bacteria and altered lung metabolism. Erythromycin treatment did not alter airway or gut microbial diversity in COPD patients. It reduced the abundance of pathogens, such as Burkholderia, in the airway of COPD patients and increased levels of symbiotic bacteria, such as Prevotella and Veillonella. The proportions of Blautia, Ruminococcus and Lachnospiraceae in the gut were increased in COPD patients after erythromycin treatment. The time to the first exacerbation following treatment was significantly longer in the erythromycin-treatment group than in the COPD group.
Conclusion: Long-term erythromycin treatment reduces airway and gut microbe abundance in COPD patients but does not affect microbial diversity and restores microbiota balance in COPD patients by reducing the abundance of pathogenic bacteria.
DOI: 10.6084/m9.figshare.26335102.v1
title: Imprints of land use history and disturbance regime in phylogenetic diversity of Mediterranean plant communities

description: Data of research article
DOI: 10.15156/bio/2938081
title: UNITE QIIME release for eukaryotes

description: Three sets of QIIME files are released, corresponding to the SHs resulting from clustering at the 3% distance (97% similarity) and 1% distance (99%) threshold levels. The third set of files is the result of a dynamic use of clustering thresholds, such that some SHs are delimited at the 3% distance level, some at the 2.5% distance level, some at the 2% distance level, and so on; these choices were made manually by experts of those particular lineages of fungi. The syntax is the same throughout the three sets of files.
DOI: 10.26131/irsa551
title: CatWISE2020 Catalog

description: The CatWISE2020 Catalog contains positions and brightnesses for 1,890,715,640 sources selected from combined WISE and NEOWISE all-sky survey data collected from 2010 to 2018 at 3.4 and 4.6 microns (W1 and W2). CatWISE adapts AllWISE software to measure the sources in co-added images created from six month subsets of these data, each representing one coverage of the inertial sky, or epoch. The catalog includes the measured motion of sources in 12 epochs over the 8 year span of the data. This dataset or service is made available by the Infrared Science Archive (IRSA) at IPAC, which is operated by the California Institute of Technology under contract with the National Aeronautics and Space Administration.
DOI: 10.5281/zenodo.11156917
title: GeneMAP

description: Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import


Artem Khan1, Gokhan Unlu1, Phillip Lin2, Yuyang Liu1, Ece Kilic1, Timothy C. Kenny1, Kıvanç Birsoy1*, and Eric R. Gamazon2,3*

1 Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA 2 Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA 3 Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA

*Correspondence: kbirsoy@rockefeller.edu, eric.gamazon@vumc.org

Organisms maintain metabolic homeostasis through the combined functions of small molecule transporters and enzymes. While many of the metabolic components have been well-established, a substantial number remains without identified physiological substrates. To bridge this gap, we have leveraged large-scale plasma metabolome genome-wide association studies (GWAS) to develop a multiomic Gene-Metabolite Associations Prediction (GeneMAP) discovery platform. GeneMAP can generate accurate predictions and even pinpoint genes that are distant from the variants implicated by GWAS. In particular, our analysis identified SLC25A48 as a genetic determinant of plasma choline levels. Mechanistically, SLC25A48 loss strongly impairs mitochondrial choline import and synthesis of its downstream metabolite, betaine. Integrative rare variant and polygenic score analyses provide strong evidence that the SLC25A48 causal effects on human disease may in part be mediated by the effects of choline. Altogether, our study provides a discovery platform for metabolic gene function and proposes SLC25A48 as a mitochondrial choline transporter.

 
description: Please cite: 

Khan, A., Unlu, G., Lin, P., Liu, Y., Kilic, E., Kenny, T.C., Birsoy, K., and Gamazon, E.R. (2024). Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import. Nature Genetics. In press. 

Khan, A., Lin, P., Birsoy, K., & Gamazon, E.R. (2024). GeneMAP (Version v1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.11156917

 
description: GeneMAP platform can be accessed at:  https://gamazonlab.shinyapps.io/GeneMAP/
DOI: 10.5281/zenodo.12626945
title: A Dynamic, D-dimer-based Thromboprophylaxis Strategy in Patients with COVID-19
DOI: 10.5281/zenodo.7242968
title: Data for: Diversity of Functional Edaphic Macrofauna in Musa acuminata x Musa balbisiana (AAB) Agroecosystems

description: The Dataset is linked to the article  Diversity of Functional Edaphic Macrofauna in Musa acuminata x Musa balbisiana (AAB) Agroecosystems.   The collected individuals were analyzed by order, and family and quantified and identified by gender (Database (Oxford). 2020: baaa062. PubMed: 32761142 PMC: PMC7408187.), The collection and taxonomic identification phase is explained in the protocol.i (dx.doi.org/10.17504/protocols.io.rm7vzby75vx1/v1).

This dataset was a modification as was indicated for the #GlobalSoilMacroFauna | Official template to report Data to the MACROFAUNA database (#GlobalSoilMacroFauna | Official template to report Data to the MACROFAUNA database (zenodo.org)) cited by [Mathieu, J., Antunes, A. C., Barot, S., Bonato Asato, A. E. ., Bartz, M. L. C. ., Brown, G. G., Calderon-Sanou, I., Decaëns, T., Fonte, S. J., Ganault, P., Gauzens, B., Gongalsky, K. B., Guerra, C. A., Hengl, T., Lavelle, P., Marichal, R., Mehring, H., Peña-Venegas, C. P., Castro, D., Potapov, A., Thébault, E., Thuiller, W., Witjes, M., Zhang, C., & Eisenhauer, N. (2022). sOilFauna - a global synthesis effort on the drivers of soil macrofauna communities and functioning: WORKSHOP REPORT . SOIL ORGANISMS, 94(2), 111–126. https://doi.org/10.25674/so94iss2id282]
DOI: 10.5281/zenodo.8289373
title: Experimental data for a single-stage overdriven free-displacer thermocompressor

description: This repository contains experimental data sets recorded during the operation of a reciprocating thermocompressor with an overdriven free displacer designed and realized at the Laboratory of Thermodynamics of the TU Dortmund University. ln addition, all relevant dimensions and sketches of the experimental machine and the setup of the test stand are provided. For further information, please refer to the readme file and the related works.
description: This research was funded by the German Research Foundation (DFG), grant number KU 755/5-1.
DOI: 10.6084/m9.figshare.22211833
title: calibration_surface_geometrically_corrected(DICOM).zip

description: Geometric calibration surface target after geometrical correction.
DOI: 10.15468/dl.6xqc5r
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Salix suchowensis W.C.Cheng)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 58 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110359-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tendgc
title: Occurrence Download

description: A dataset containing 2387 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nicotiana attenuata Torr. ex S.Watson)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2387 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110360-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13622588
title: Thousand-year Indexed tree-ring pine (Pinus sylvestris) chronologies from the Neman basin, Belarus
DOI: 10.5281/zenodo.13622589
title: Thousand-year Indexed tree-ring pine (Pinus sylvestris) chronologies from the Neman basin, Belarus
DOI: 10.15468/dl.77wpzb
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nicotiana benthamiana Domin)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 282 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110362-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.agdjz5
title: Occurrence Download

description: A dataset containing 4816 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Salix udensis (Wimm.) Trautv. & C.A.Mey.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4816 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110361-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pa9jm3
title: Occurrence Download

description: A dataset containing 712 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Mongolia)",
 "TaxonKey is Impatiens noli-tangere L."
 ]
}

 The dataset includes 712 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110363-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7byufm
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nicotiana knightiana Goodsp.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110365-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13379143
title: Ancient Greek Oratory Ontology v.1.0

description: This is version 1.0 of a dataset created in the context  of a PhD thesis in "Semantic Annotation and Attic Oratory" that defines the primary legal proceedings in Classical Athenian courts c. 419 BC to 323 BC. A legal proceeding is defined as "a court dispute between two litigants, for which a forensic speech would be written". This work draws upon the corpus of Attic oratory as well as The Law of Ancient Athens by David D. Phillips.

This dataset is authored by Rachel Milio (TALOS Ph.D. candidate, Department of Philology, University of Crete), under the supervision of Dr. Maria Papadopoulou (Department of Philology, University of Crete) and Prof. Christophe Roche (TALOS ERA Chair Professor, University of Crete).

Acknowledgement: We gratefully acknowledge the generous funding of the European Commission under the ERA Chair Project TALOS AI for SSH (Grant agreement ID: 101087269).

Contact: Rachel.Milio@outlook.com
description: This version includes:

1. The .otb file. To view it, please import it in  Tedi ontoTerminology Editor

2. The .rdf file. To view it, please import it in Protégé ontology editor

3. The .html file that includes the terms (in English) 

5. The .html file that includes the terms (in Ancient Greek) 

Software:

This dataset was built with Tedi ontoTerminology Editor. Tedi ontoTerminology Editor is a software platform for the creation and management of ontoterminologies. Tedi software platform is distributed by the University of Crete (free for academic use, contact: christophe.roche@uoc.gr).

The .rdf file is queryable via a SPARQL endpoint.

Downloads:

Download the RDF/OWL file; to view the ontology metrics import this file in Protégé (open access ontology editor); to visualize the ontology import this file in VOWL

To view the .html files in your browser download them and rename them using the .html extension.
description: Metrics:

Tedi



Number of concepts: 39

Number of terms: 80


RDF/Protégé:



 Axiom: 3, 752

Logical axiom count: 1,879       

Declaration axioms count: 72    

Class count: 53

Object property count: 13         

Individual count: 367    

Annotation Property count: 34

Sub class of: 246            

Disjoint Classes: 231

Object Property Domain: 12      

Object Property Range: 12

Class Assertion: 486      

Object Property Assertion: 892

Annotation Assertion: 1779

Annotation Property Domain: 12            

Annotation Property Range Of: 10
DOI: 10.5281/zenodo.13379144
title: Ancient Greek Oratory Ontology v.1.0

description: This is version 1.0 of a dataset created in the context  of a PhD thesis in "Semantic Annotation and Attic Oratory" that defines the primary legal proceedings in Classical Athenian courts c. 419 BC to 323 BC. A legal proceeding is defined as "a court dispute between two litigants, for which a forensic speech would be written". This work draws upon the corpus of Attic oratory as well as The Law of Ancient Athens by David D. Phillips.

This dataset is authored by Rachel Milio (TALOS Ph.D. candidate, Department of Philology, University of Crete), under the supervision of Dr. Maria Papadopoulou (Department of Philology, University of Crete) and Prof. Christophe Roche (TALOS ERA Chair Professor, University of Crete).

Acknowledgement: We gratefully acknowledge the generous funding of the European Commission under the ERA Chair Project TALOS AI for SSH (Grant agreement ID: 101087269).

Contact: Rachel.Milio@outlook.com
description: This version includes:

1. The .otb file. To view it, please import it in  Tedi ontoTerminology Editor

2. The .rdf file. To view it, please import it in Protégé ontology editor

3. The .html file that includes the terms (in English) 

5. The .html file that includes the terms (in Ancient Greek) 

Software:

This dataset was built with Tedi ontoTerminology Editor. Tedi ontoTerminology Editor is a software platform for the creation and management of ontoterminologies. Tedi software platform is distributed by the University of Crete (free for academic use, contact: christophe.roche@uoc.gr).

The .rdf file is queryable via a SPARQL endpoint.

Downloads:

Download the RDF/OWL file; to view the ontology metrics import this file in Protégé (open access ontology editor); to visualize the ontology import this file in VOWL

To view the .html files in your browser download them and rename them using the .html extension.
description: Metrics:

Tedi



Number of concepts: 39

Number of terms: 80


RDF/Protégé:



 Axiom: 3, 752

Logical axiom count: 1,879       

Declaration axioms count: 72    

Class count: 53

Object property count: 13         

Individual count: 367    

Annotation Property count: 34

Sub class of: 246            

Disjoint Classes: 231

Object Property Domain: 12      

Object Property Range: 12

Class Assertion: 486      

Object Property Assertion: 892

Annotation Assertion: 1779

Annotation Property Domain: 12            

Annotation Property Range Of: 10