cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26188/6295c4a5d7c5c
title: Electronic Medical Records National Data Asset

description: Data from hospital Electronic Medical Record (EMR) Systems is being transformed to an international gold standard Observational Medical Outcomes Partnership (<strong>OMOP</strong>) Common Data Model (CDM). Tools, mappings and experience gained will be made openly available, and a community of practice and a roadmap for continued national implementation will be built. The Data Asset will significantly improve the quality, accessibility and feasibility of EMR data warehouses by streamlining data governance, consent and ethics. We will convert three existing data warehouses from Queensland Health, Austin Health and Western Health so that they can be accessed through a common interface. Learnings from the <strong>Cerner</strong> conversions will then be applied to the conversion of other data warehouse platforms including the <strong>EPIC</strong> EMR system which will be investigated in collaboration with the Peter MacCallum Cancer Centre and the Royal Childrens Hospital
DOI: 10.26036/cnp0004820
title: Phased genome assemblies in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae)

description: The fitness of organisms is influenced by the number of deleterious mutations in the genome. Although the distribution pattern of haplotype-specific genetic load plays an important role in shaping the evolutionary trajectory of natural and captive populations, it has been so far elusive in diploids due to mixing of haplotypes during assembly and genotyping. Herein we produce two phased genome assemblies from female and male individuals of the critically endangered fish Chinese Bahaba (Bahaba taipingensis, Sciaenidae, Teleostei). Simulations suggest that purifying selection has limited power to remove genetic load in captive breeding, calling for genotyping interventions in conservation programs, and that higher inter-haplotypic variance of genetic load predicts more efficient load removal by artificial selection.
DOI: 10.26188/19446755
title: Primary Care OMOP Dataset

description: This is an OMOP dataset based on primary care data (Patron). The data is derived from primary care Electronic Medical Records Systems. The data is <b>not open access but researchers can apply for access subject to ethics and governance approvals. </b><b><br></b><b>More information on Patron </b><br>PATRON is a human ethics approved program of research incorporating an enduring de-identified repository of Primary Care data facilitating research and knowledge generation. PATRON is a part of the 'Data for Decisions' initiative of the Department of General Practice, University of Melbourne. 'Data for Decisions' is a research initiative in partnership with general practices. It is an exciting undertaking that makes possible primary care research projects to increase knowledge and improve healthcare practices and policy. <br>Principal Researcher: Jon EmeryData Custodian: Lena SanciData Steward: Douglas BoyleManager: Roger Ward<br>
DOI: 10.26188/19446755.v1
title: Primary Care OMOP Dataset

description: This is an OMOP dataset based on primary care data (Patron). The data is derived from primary care Electronic Medical Records Systems. The data is <b>not open access but researchers can apply for access subject to ethics and governance approvals. </b><b><br></b><b>More information on Patron </b><br>PATRON is a human ethics approved program of research incorporating an enduring de-identified repository of Primary Care data facilitating research and knowledge generation. PATRON is a part of the 'Data for Decisions' initiative of the Department of General Practice, University of Melbourne. 'Data for Decisions' is a research initiative in partnership with general practices. It is an exciting undertaking that makes possible primary care research projects to increase knowledge and improve healthcare practices and policy. <br>Principal Researcher: Jon EmeryData Custodian: Lena SanciData Steward: Douglas BoyleManager: Roger Ward<br>
DOI: 10.5281/zenodo.10360518
title: "IS477 Car Evaluation

description: This dataset involves preparing, profiling, and analyzing the range of buying values for cars
DOI: 10.5281/zenodo.10360517
title: "IS477 Car Evaluation

description: This dataset involves preparing, profiling, and analyzing the range of buying values for cars
DOI: 10.25345/c5nk36g43
title: MassIVE MSV000093642 - Raw data for manuscript : "Serine synthesis via reversed SHMT2 activity drives glycine depletion and acetaminophen hepatotoxicity in MASLD"
title: Metabolic dysfunction-associated steatotic liver disease (MASLD) affects one third of the global population. Understanding metabolic pathways involved can provide insights into disease progression and treatment. Untargeted metabolomics of livers from mice with early-stage steatosis uncovered decreased methylated metabolites, suggesting altered one-carbon metabolism. The levels of glycine, a central component of one-carbon metabolism, were lower in mice with hepatic steatosis, consistent with clinical evidence. Stable-isotope tracing demonstrated that increased serine synthesis from glycine via reverse serine hydroxymethyltransferase (SHMT) is the underlying cause for decreased glycine in steatotic livers. Consequently, limited glycine availability in steatotic livers impaired glutathione synthesis under acetaminophen-induced oxidative stress, enhancing acute hepatotoxicity. Glycine supplementation or hepatocyte-specific ablation of the mitochondrial SHMT2 isoform in mice with hepatic steatosis mitigated acetaminophen-induced hepatotoxicity by supporting de novo glutathione synthesis. Thus, early metabolic changes in MASLD that limit glycine availability sensitize mice to xenobiotics even at the reversible stage of this disease.
DOI: 10.25835/8c0pvtd9
title: Procedural fairness and safety_JRR_Seidl

description: Raw data for the variables included in the manuscript "Procedural fairness and safety in the acceptance of nuclear waste disposal in Germany: an empirical study" to the Journal of Risk Research by Roman Sedil and Cord Drögemüller.
DOI: 10.6084/m9.figshare.24792558
title: Experimental data for Tiger cowrie larvae.xlsx

description: This dataset reports the results of 3 <i>Cypraea tigris</i> larvae experiments:1) Water quality2) Microalgae diet3) Microalgae diet and antibiotics exposure
DOI: 10.6084/m9.figshare.24792558.v1
title: Experimental data for Tiger cowrie larvae.xlsx

description: This dataset reports the results of 3 <i>Cypraea tigris</i> larvae experiments:1) Water quality2) Microalgae diet3) Microalgae diet and antibiotics exposure
DOI: 10.6084/m9.figshare.24785355
title: H1.bb

description: ATAC-seq in fibroblasts
DOI: 10.6084/m9.figshare.24785355.v1
title: H1.bb

description: ATAC-seq in fibroblasts
DOI: 10.5281/zenodo.10294826
title: Observational data and processing results
title: Data
DOI: 10.5281/zenodo.10260277
title: Observational data and processing results
title: Data
DOI: 10.5281/zenodo.10260278
title: Observational data and processing results
title: Data
DOI: 10.5281/zenodo.10294931
title: Observational data and processing results
title: Data
DOI: 10.5281/zenodo.8396175
title: Fore wings of queens and drones of honey bees (Apis mellifera)

description: The dataset consists of fore wing images of queens and drones of honey bees (Apis mellifera). In most cases, there are both left and right wings indicated with the letters L and R, respectively, at the end of the file name. The resolution of the images is 94488 pixels per meter. The wing images are compressed into zip files. The file queens-wing-images.zip contains 4117 wing images of queens, which represent 2086 individuals. The file drones-wing-images.zip contains 8006 wing images of drones, which represent 4102 individuals. Raw coordinates of 19 landmarks marked on the wings of queens and drones are in files queens-raw-coordinates.csv and drones-raw-coordinates.csv, respectively. For a subset of queens, there is also available data about wing length and body weight in the files queens-wing-length.csv and queens-weight.csv, respectively.
DOI: 10.5281/zenodo.8396176
title: Fore wings of queens and drones of honey bees (Apis mellifera)

description: The dataset consists of fore wing images of queens and drones of honey bees (Apis mellifera). In most cases, there are both left and right wings indicated with the letters L and R, respectively, at the end of the file name. The resolution of the images is 94488 pixels per meter. The wing images are compressed into zip files. The file queens-wing-images.zip contains 4117 wing images of queens, which represent 2086 individuals. The file drones-wing-images.zip contains 8006 wing images of drones, which represent 4102 individuals. Raw coordinates of 19 landmarks marked on the wings of queens and drones are in files queens-raw-coordinates.csv and drones-raw-coordinates.csv, respectively. For a subset of queens, there is also available data about wing length and body weight in the files queens-wing-length.csv and queens-weight.csv, respectively.
DOI: 10.5281/zenodo.10139451
title: VEBA Microeukaryotic Protein Database (MicroEuk100/90/50, Version 3)

description: Microeukaryotic protein database consisting of protists and fungi for VEBA.
 
Number of sequences:
 * MicroEuk100 = 79,920,431 (19 GB)
 * MicroEuk90  = 51,767,730 (13 GB)
 * MicroEuk50  = 29,898,853 (6.5 GB)
 
Number of source organisms per dataset:
* MycoCosm = 2503
* PhycoCosm = 174
* EnsemblProtists = 233
* MMETSP = 759
* TARA_SAGv1 = 8
* EukProt = 366
* EukZoo = 27
* TARA_SMAGv1 = 389
* NR_Protists-Fungi = 48217
 
Files:
MicroEuk_v3.tar.gz = 25 GB
-rw-rw---- 1 jespinoz jcl110  19G Nov 15 14:57 MicroEuk100.faa.gz - Main fasta file with 79,920,431 protein sequences from 52,676 source organisms.  Uses md5 hash identifiers.
-rw-rw---- 1 jespinoz jcl110 2.0G Nov 15 14:59 identifier_mapping.proteins.tsv.gz - Protein identifier mappings between datasets, original identifiers, source organisms, and md5 hash identifiers.
-rw-rw---- 1 jespinoz jcl110 1.7G Nov 15 16:10 MicroEuk90_clusters.tsv.gz - MMSEQS2 clustering MicroEuk100
-rw-rw---- 1 jespinoz jcl110 1.5G Nov 15 14:57 MicroEuk100.list.gz - List of md5 hash protein identifiers in MicroEuk100
-rw-rw---- 1 jespinoz jcl110 1.1G Nov 15 16:10 MicroEuk50_clusters.tsv.gz - MMSEQS2 clustering MicroEuk90
-rw-rw---- 1 jespinoz jcl110  13M Nov 15 23:39 MicroEuk100.eukaryota_odb10.list.gz - MicroEuk100 protein identifier hits to BUSCO's eukaryota_odb10 marker using the provided score thresholds
-rw-rw---- 1 jespinoz jcl110 1.5M Nov 15 14:58 source_taxonomy.tsv.gz - Source taxonomy, lineage, dataset, and notes for each source organism
 
For more information and citations, please visit the main GitHub repository: 
https://github.com/jolespin/veba
DOI: 10.5281/zenodo.10139450
title: VEBA Microeukaryotic Protein Database (MicroEuk100/90/50, Version 3)

description: Microeukaryotic protein database consisting of protists and fungi for VEBA.
 
Number of sequences:
 * MicroEuk100 = 79,920,431 (19 GB)
 * MicroEuk90  = 51,767,730 (13 GB)
 * MicroEuk50  = 29,898,853 (6.5 GB)
 
Number of source organisms per dataset:
* MycoCosm = 2503
* PhycoCosm = 174
* EnsemblProtists = 233
* MMETSP = 759
* TARA_SAGv1 = 8
* EukProt = 366
* EukZoo = 27
* TARA_SMAGv1 = 389
* NR_Protists-Fungi = 48217
 
Files:
MicroEuk_v3.tar.gz = 25 GB
-rw-rw---- 1 jespinoz jcl110  19G Nov 15 14:57 MicroEuk100.faa.gz - Main fasta file with 79,920,431 protein sequences from 52,676 source organisms.  Uses md5 hash identifiers.
-rw-rw---- 1 jespinoz jcl110 2.0G Nov 15 14:59 identifier_mapping.proteins.tsv.gz - Protein identifier mappings between datasets, original identifiers, source organisms, and md5 hash identifiers.
-rw-rw---- 1 jespinoz jcl110 1.7G Nov 15 16:10 MicroEuk90_clusters.tsv.gz - MMSEQS2 clustering MicroEuk100
-rw-rw---- 1 jespinoz jcl110 1.5G Nov 15 14:57 MicroEuk100.list.gz - List of md5 hash protein identifiers in MicroEuk100
-rw-rw---- 1 jespinoz jcl110 1.1G Nov 15 16:10 MicroEuk50_clusters.tsv.gz - MMSEQS2 clustering MicroEuk90
-rw-rw---- 1 jespinoz jcl110  13M Nov 15 23:39 MicroEuk100.eukaryota_odb10.list.gz - MicroEuk100 protein identifier hits to BUSCO's eukaryota_odb10 marker using the provided score thresholds
-rw-rw---- 1 jespinoz jcl110 1.5M Nov 15 14:58 source_taxonomy.tsv.gz - Source taxonomy, lineage, dataset, and notes for each source organism
 
For more information and citations, please visit the main GitHub repository: 
https://github.com/jolespin/veba
DOI: 10.6084/m9.figshare.24792612
title: supp_file.zip

description: Natal down is a crucial aspect of a bird's reproductive success. These downy feathers vary considerably across species, both in terms of their distribution across the body regions and their density. In this study, we embarked on an extensive exploration of natal down's evolutionary patterns across 178 avian families and the potential factors that correlate with its variation, especially for their breeding characteristics and nestling features. We first characterized the natal down diversity according to its density in different body regions. Ancestral state reconstruction was then conducted for each body region. Remarkably, these reconstructions revealed a consistent evolutionary pattern across all pterylae (feather tracts) in different body regions and pinpointed two significant episodes in avian evolution where species exhibited a loss of natal down. We then analyzed the correlated evolution of natal down with variables like nest attendance, nest characteristics, geographical location, and climatic conditions. We revealed that bird species that benefit from the relative safety of the local environment are more likely to exhibit reduced natal down. Our study contributes valuable perspectives to our understanding of avian evolutionary history, behavioral ecology, and the distinct conservation needs of bird species.
DOI: 10.6084/m9.figshare.24792612.v1
title: supp_file.zip

description: Natal down is a crucial aspect of a bird's reproductive success. These downy feathers vary considerably across species, both in terms of their distribution across the body regions and their density. In this study, we embarked on an extensive exploration of natal down's evolutionary patterns across 178 avian families and the potential factors that correlate with its variation, especially for their breeding characteristics and nestling features. We first characterized the natal down diversity according to its density in different body regions. Ancestral state reconstruction was then conducted for each body region. Remarkably, these reconstructions revealed a consistent evolutionary pattern across all pterylae (feather tracts) in different body regions and pinpointed two significant episodes in avian evolution where species exhibited a loss of natal down. We then analyzed the correlated evolution of natal down with variables like nest attendance, nest characteristics, geographical location, and climatic conditions. We revealed that bird species that benefit from the relative safety of the local environment are more likely to exhibit reduced natal down. Our study contributes valuable perspectives to our understanding of avian evolutionary history, behavioral ecology, and the distinct conservation needs of bird species.
DOI: 10.15151/esrf-es-1371493554
title: Is amorphous calcium sulfate a common precursor phase to bassanite and gypsum?

description: Calcium sulfate minerals (i.e. gypsum, anhydrite and bassanite) are ubiquitous on Earth and they are highly relevant chemical compounds for a wide variety of industrial processes. The current consensus based on state-of-the-art synchrotron and electron microscopy data, is that the formation of crystalline phases in the CaSO4-H2O system is non-classical involving several steps, including an intermediate amorphous
phase. The overarching issue that remains to be resolved is whether all three phases of CaSO4, and in particular gypsum and bassanite,
follow the same non-classical pathway entailing a common precursor amorphous phase? With this proposal we aim to use SAXS/WAXS to
follow in situ and in a time-resolved manner the evolution of species forming from aqueous solutions containing calcium and sulfate ions. We propose an experiment in which bassanite or gypsum are formed selectively under directly comparable, thermodynamic conditionsdiffering only slightly in temperature.
DOI: 10.15151/esrf-es-1371497379
title: Structural analysis of historical materials

description: This proposal is a continuation of the HG-172 BAG experiment, a new access route to the ESRF structural analysis capacities for the Heritage Science community. The upgrade to the ESRF-EBS was the triggering element to propose a single block allocation group (BAG). Two complementary analytical configurations are used in the BAG: High angular resolution XRD (ID22) and High lateral resolution XRD (ID13). The combination of these two beamlines generates precious clues on the origin, processing and degradation of historical materials. By relying on the new analytical capacities of the EBS combined with optimized access route, sample preparation procedures and processing pipelines, the Heritage BAG has proven to be a very efficient way to increase the output of the Cultural Heritage community, to reinforce a scientific network of expert users structured around the ESRF, and to initiate new European collaborations in Heritage Science.
DOI: 10.15151/esrf-es-1369819176
title: Subcellular-Level Physiological Cisplatin Distribution in the Cochlea

description: Cisplatin ototoxicity (CO) contributes to ~0.5 million hearing impairment cases among cancer patients globally each year. The lack of understanding of cisplatin distribution in the cochlea and the mechanism of CO hinders the development of effective prevention and treatment strategies. Recently, our group reported a promising candidate, honokiol, for treating CO during chemotherapy. Whether honokiol works through affecting cisplatin distribution is neither clear. 2D sections of cochleas can provide some clues on Pt distributions, however, we need a comprehensive understanding on the three-dimensional (3D) cisplatin distributions within the cochlea internal network.Therefore, we want to perform correlative holographic nanotomography and 3D XRF scanning on vitrified cochleas for precise and comprehensive observation on Pt targeted subcellular compartments. This research will provide crucial insights for understanding the mechanism of CO and the protective effect of honokiol.
DOI: 10.15151/esrf-es-1368350050
title: Systematic mapping of the excited quintet state potentials in model Fe-based molecular photoswitches

description: The rational design of efficient light-activated functional molecules requires the understanding of their potential energy surfaces (PES), but the ones obtained with quantum chemical (QC) tools are hard to verify with available spectroscopy tools. The combination of X-ray spectroscopy and scattering has been shown to reveal intricate details of the PES, and this is the approach we wish to exploit here. We propose to study modified Fe(II)-polypyridine complexes, model systems for light-switchable molecular magnets, for which QC calculations suggest the feasibility of altering the excited state PES by ligand substitution. Transient optical absorption shows that the lifetime of the excited quintet state changes upon substitution, suggesting variation of the energy landscape. The proposed experiment will test the quintet-singlet energy gap (beyond the molecular structures). Such confirmation of the systematically varied PES shall help us to design molecules with optimized functionality.
DOI: 10.15151/esrf-es-1368350202
title: Unravel the interfacial structures of plant-based proteins at the air-water interface

description: The transition towards sustainable, plant-based protein sources for food systems requires knowledge on how plant-based proteins interact with food-relevant microstructures. In particular, in the formulation of aerated food systems (e.g. foams), the mechanism by which plant-based proteins stabilise the interfaces is considerably different than that of traditional animal-based protein. This proposal aims to investigate the in situ structures and formation dynamics of plant-based proteins at the air-water interface, using grazing incidence small angle X-ray scattering (GISAXS). The structural information provided by GISAXS forms the missing link between (in house) state of the art interfacial rheology and high resolution but ex situ and static atomic force microscopy (AFM). The experiment will provide a major step forward towards a general understanding of the interfacial stabilisation mechanisms of plant-based proteins.
DOI: 10.25919/wdzt-1v33
title: Parkes observations for project P1171 semester 2023OCTS_04

description: The origin of Fast Radio Bursts (FRBs) is still unclear with a plethora of theoretical models for their origin. Several models predict associated multi-wavelength emission, but previous searches for optical, X-ray or gamma-ray counterparts of FRBs have not led to any detection. The Galactic magnetar SGR 1935+2154A has been observed to simultaneously emit FRB-like bursts and X-ray flares, which suggests that also extragalactic FRB sources may exhibit X-ray counterparts.
 
 Because of the high cost of X-ray satellites and in face of the relatively low FRB detection probability in their small field of view, coordinated radio and X-ray observations are logistically very difficult to set up. We propose a new approach using the X-ray satellite XMM-Newton and the Parkes/Murriyang radio telescope to put constraints on the theoretical models: We aim to conduct shadowing observations with the Parkes telescope to search for new FRBs in fields that are simultaneously covered by XMM-Newton. We hereby target regular XMM observations of nearby (low-z) galaxies, to increase our detection chances of possibly associated X-ray emission. In case of an FRB detection in the radio band, we will have guaranteed simultaneous X-ray coverage and will get detailed information about the associated X-ray spectrum and light curve since all XMM-Newton data will become public a year after the observation.
DOI: 10.6084/m9.figshare.24408319.v2
title: Chromosomal-level genome assembly of the reef gardener long-spine urchin, Diadema setosum

description: The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific and can cause severe bioerosion on the reef community.<b> </b>Nevertheless, the lack of genomic information has hindered the study its ecology and evolution. Here, we report the chromosomal-level genome (885.8 Mb) of the long-spined sea urchin D. setosum using a combination of PacBio long-read sequencing and Omni-C scaffolding technology. The assembled genome contained scaffold N50 length of 38.3 Mb, 98.1 % of BUSCO (Geno, metazoa_odb10) genes, and with 98.6% of the sequences anchored to 22 pseudo-molecules/chromosomes. A total of 27,478 genes including 23,030protein-coding genes were annotated. The high-quality genome of D. setosum presented here provides a significant resource for further understanding on the ecological and evolutionary studies of this coral reef associated sea urchin.
DOI: 10.6084/m9.figshare.24792660
title: The annotation file of genome assembly of Trachinotus_blochii

description: The genome assembly project of Trachinotus blochii.
DOI: 10.6084/m9.figshare.24792660.v1
title: The annotation file of genome assembly of Trachinotus_blochii

description: The genome assembly project of Trachinotus blochii.
DOI: 10.25592/uhhfdm.13852
title: EASIER translation pipeline DGS test sentences

description: 20 movies based on 10 German sentences to test the EASIER translation pipeline DGS -&gt; German. Variations concern some lexical items as well as affect as explained in the accompanying pdf.
DOI: 10.25592/uhhfdm.13851
title: EASIER translation pipeline DGS test sentences

description: 20 movies based on 10 German sentences to test the EASIER translation pipeline DGS -&gt; German. Variations concern some lexical items as well as affect as explained in the accompanying pdf.