cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25919/htht-2t48
title: Parkes observations for project P1050 semester 2022APRS_12

description: This is a request for observing time for the timing campaign of new pulsar discoveries from the reprocessing of the low-latitude Galactic plane section of the HTRU survey (P630). We have now completed 90 % of the survey with GPU based coherent acceleration search, template bank and fast folding algorithm pipelines, and now have discovered 107 previously unknown pulsars. Interesting science can usually only be derived from a new pulsar after confirmation and a follow-up timing campaign is carried out. One year of initial timing is the minimum timespan required to fully characterise any newly-discovered pulsars, essential for deriving pulsar parameters such as the characteristic age, magnetic field strength, spin-down rate, as well as to detect any unexpected behaviour of the pulsar which might result from emission instabilities. This timing project is necessary for the timing of millisecond pulsars discovered in the current and last semester and for following up our confirmed pulsars from the HTRU Galactic plane survey. The follow-up timing in APRS22 will produce completely new and exciting results. In addition, this timing project will allow us to measure the true Galactic plane pulsar population and the boundaries of pulsar parameter space in the galactic plane.
DOI: 10.5281/zenodo.6591647
title: Dataset for An Empirical Study of Hackathon Code Creation and Reuse

description: This dataset is corresponds to our extended analysis done for “The Secret Life of Hackathon Code Where does it come from and where does it go?” (https://doi.org/10.1109/MSR52588.2021.00020, pre-print at: https://arxiv.org/abs/2103.01145) and “Tracking Hackathon Code Creation and Reuse” (https://doi.org/10.1109/MSR52588.2021.00085, pre-print at: https://arxiv.org/pdf/2103.10167). The replication package including the scripts used for generating this dataset from the “World of Code” (https://worldofcode.org/) dataset is available in Github link https://github.com/woc-hack/track_hack. The dataset contains the blob hashes used in the scope of the analysis and the analysis outcome. The columns are as following <strong>DevpostID</strong>: Devpost identification for the hackathon project and it can be used to get the URL for the devpost.com website. Example DevpostID -q9nd5 can be translated to https://devpost.com/software/-q9nd5 <strong>ProjectID</strong>: The Github project name <strong>HackathonEndDate</strong>: Hackathon event end date <strong>BlobHash</strong>: The blob hash used in the analysis <strong>BeforeHackathon-DuringHackathon-AfterHackathon</strong>: This column represents if the blob was first introduced before/during/after the hackathon (1: before, 2: during, 3: after) <strong>SameAuthor-Contributor-OtherAuthor</strong>: This column represents if the blob was first created by someone in the hackathon team, or someone who was a contributor to a project in which one of the members of the hackathon project contributed to as well (contributor), or someone else outside of the hackathon team (1: Author is a hackathon team member, 2: Author Contributed before with a hackathon team member, 3: Author is not related to the hackathon team). <strong>UsedBySmallProject-UsedByMediumProject-UsedByLargeProject</strong>: This column represents if the hackathon blob is reused again after the hackathon event and what is the project size that reused the code (1: not reused, 3: reused in small project, 4: reused in medium project, 5: reused in large project)
DOI: 10.5281/zenodo.6591231
title: Historical IVT data of SPEAR-LE (ens04)

description: The repository contains the historical scenario simulation (4th ensemble) of GFDL SPEAR large ensemble data. The data is used to support the finding in the paper entitled "When will humanity notice its impacts on atmospheric rivers?" by Tseng et al.
DOI: 10.5281/zenodo.6591230
title: Historical IVT data of SPEAR-LE (ens04)

description: The repository contains the historical scenario simulation (4th ensemble) of GFDL SPEAR large ensemble data. The data is used to support the finding in the paper entitled "When will humanity notice its impacts on atmospheric rivers?" by Tseng et al.
DOI: 10.5281/zenodo.4892847
title: Quality assessment of open geospatial datasets NSDI in Ukraine

description: The results of assessing the quality of open geospatial datasets by the method "5 stars" for NSDI in Ukraine.
DOI: 10.5281/zenodo.4892846
title: Quality assessment of open geospatial datasets NSDI in Ukraine

description: The results of assessing the quality of open geospatial datasets by the method "5 stars" for NSDI in Ukraine.
DOI: 10.5281/zenodo.6591692
title: D1.6 release of BioExcel QM/MM Benchmark Suite

description: An update to the previous D1.4 release of the BioExcel QM/MM benchmark suite (see https://doi.org/10.5281/zenodo.3885124), provided as part of deliverable D1.6. This is a snapshot of the repository available at https://github.com/bioexcel/qmmm_benchmark_suite Compared to the previous (D1.4) release, a number of additional benchmarks were included in order to facilitate systematic performance profiling, namely: Versions of the MQAE (solute-solvent), ClC (ion channel), and CBD_PHY (phytochrome) benchmarks that use the hybrid DFT functionals PBE0 and B3LYP to incorporate Hartree-Fock exchange energy (the initial release of the benchmark suite included only the GGA functionals PBE and BLYP). Versions of the MQAE and ClC benchmarks that make use of the Auxiliary Density Matrix Method (ADMM) to markedly reduce the high computational cost of the molecular environment optimized MOLOPT basis set when used in combination with hybrid functionals such as B3LYP and PBE0. Versions of the MQAE and ClC benchmarks that use the EMSL basis set in combination with the B3LYP hybrid functional.<strong> </strong> A version of the ClC-19 benchmark that uses the HFX basis set in combination with the B3LYP hybrid functional<strong>.</strong> A version of the MQAE benchmark in which the linear size of the cell defining the quantum region is increased by a factor 2, i.e. where the volume of the quantum region is enlarged by a factor 8 <br>
DOI: 10.5281/zenodo.6591675
title: CP2K biomolecular QM/MM benchmarking data

description: Dataset containing raw CP2K output logs produced by running benchmarks from the BioExcel QM/MM benchmark suite (https://doi.org/10.5281/zenodo.6591692), provided as part of BioExcel-2 project deliverable D1.6. An analysis of (a subset of) these benchmark results can be found in https://doi.org/10.5281/zenodo.6591574 <strong>Machines used for benchmarking:</strong> Cirrus@EPCC (HPE SGI ICE XA): https://www.cirrus.ac.uk Infiniband interconnect CPU compute nodes: 2 x 18-core Intel Xeon (Broadwell) E5-2695, 2.1 GHz 256GB RAM GPU compute nodes: 2 x NVIDIA Tesla V100 (Volta) SXM2-16GB 2 x 20-core Intel Xeon (Cascade Lake) Gold 6248, 2.4 GHz 384GB RAM ARCHER2@EPCC (HPE CRAY EX): https://www.archer2.ac.uk/ Interconnect: HPE Cray Slingshot Compute nodes: 2 x 64-core AMD EPYC (Zen2 Rome) 7742, 2.25GHz 256GB RAM <strong>Benchmarking protocol</strong> Repeated runs to rule out machine noise variability were performed for each benchmark on each machine for both 1 MD step and 6 MD steps. Subsequent analysis and visualisation of parallel scaling of average runtime per MD step and subroutine-level profiling was performed using our analysis script available from: https://doi.org/10.5281/zenodo.6591681 Results on Cirrus CPU nodes are for CP2K release version 8.1, whilst results on Cirrus GPU nodes and ARCHER2 are with CP2K version 8.2.
DOI: 10.34740/kaggle/dsv/3715997
title: Proprocessed Slices Data(0)
DOI: 10.6084/m9.figshare.3761562.v2233
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.17903/fk2/gatfhn
title: Vote Heterogeneity index

description: Vote heterogeneity measures the degree of diversity in vote shares across different territorial units. It is calculated by dividing the standard deviation of vote shares by the average vote share across territorial units. In other words it measures the Coefficient of Variation.
DOI: 10.5281/zenodo.6591507
title: Protein database for SAGApipeline

description: Proteins from multiple databases were used in algal genome annotation. We first downloaded the protein data of green algae (Chlorophyta) and red algae (Rhodophyta) on UniProt for 10 higher-quality assemblies gene predictions. We refer to these protein sequences for RefSeq genomes gene prediction as seed_algae_mix, whose role is to complete gene prediction of higher quality genomes quickly and accurately. These predicted results obtained in the RefSeq genomes will be used as the query sequences to query the NR (RefSeq non-redundant proteins) database, Then the searched target sequence is extracted as the NR_extract part. Subsequently, we retrieved the protein sequences on Uniprot of all lineages of algae, please note that we did not select only the protein sequences of the 17 lineages to be annotated, but all algae from the 21 lineages searched on NCBI taxonomy, a total of 2,432,633 (1.17GB) algae protein sequences named total_algae_mix were for future predictions. The plants part of OrthoDB V10.1 and BUSCO proteins of 7 lineages were also merged into pr_total_mix.
DOI: 10.5281/zenodo.6591506
title: Protein database for SAGApipeline

description: Proteins from multiple databases were used in algal genome annotation. We first downloaded the protein data of green algae (Chlorophyta) and red algae (Rhodophyta) on UniProt for 10 higher-quality assemblies gene predictions. We refer to these protein sequences for RefSeq genomes gene prediction as seed_algae_mix, whose role is to complete gene prediction of higher quality genomes quickly and accurately. These predicted results obtained in the RefSeq genomes will be used as the query sequences to query the NR (RefSeq non-redundant proteins) database, Then the searched target sequence is extracted as the NR_extract part. Subsequently, we retrieved the protein sequences on Uniprot of all lineages of algae, please note that we did not select only the protein sequences of the 17 lineages to be annotated, but all algae from the 21 lineages searched on NCBI taxonomy, a total of 2,432,633 (1.17GB) algae protein sequences named total_algae_mix were for future predictions. The plants part of OrthoDB V10.1 and BUSCO proteins of 7 lineages were also merged into pr_total_mix.
DOI: 10.34740/kaggle/dsv/3716024
title: Proprocessed Slices Data(0.4)
DOI: 10.34740/kaggle/dsv/3716042
title: Proprocessed Slices Data(0.6)
DOI: 10.5281/zenodo.6591520
title: Global aerodynamic parameters in 1982-2017 based on GLASS LAI (v1.1 update to 2020)

description: The bulk surface properties, including canopy height (ht), zero-plane displacement height (d), and roughness length (z0) are crucial biophysical parameters that influence momentum, energy, and mass exchanges at the land-atmosphere interface. Here we provide a global estimate of bulk aerodynamic parameters during 1982-2017 at 0.05-degree spatial resolution and monthly temporal interval, using remote-sensed leaf area index, canopy height, and a turbulent transfer model. Two separate datasets are generated using GLASS LAI and GIMMS LAI. This dataset includes the products based on GLASS LAI. Details can be found: Liu, Y., Guo, W., Huang, H., Ge, J., Qiu, B., 2021. Estimating global aerodynamic parameters in 1982–2017 using remote-sensing data and a turbulent transfer model. Remote Sens. Environ. 260, 112428. https://doi.org/https://doi.org/10.1016/j.rse.2021.112428
DOI: 10.5281/zenodo.4662149
title: Global aerodynamic parameters in 1982-2017 based on GLASS LAI (v1.1 update to 2020)

description: The bulk surface properties, including canopy height (ht), zero-plane displacement height (d), and roughness length (z0) are crucial biophysical parameters that influence momentum, energy, and mass exchanges at the land-atmosphere interface. Here we provide a global estimate of bulk aerodynamic parameters during 1982-2017 at 0.05-degree spatial resolution and monthly temporal interval, using remote-sensed leaf area index, canopy height, and a turbulent transfer model. Two separate datasets are generated using GLASS LAI and GIMMS LAI. This dataset includes the products based on GLASS LAI. Details can be found: Liu, Y., Guo, W., Huang, H., Ge, J., Qiu, B., 2021. Estimating global aerodynamic parameters in 1982–2017 using remote-sensing data and a turbulent transfer model. Remote Sens. Environ. 260, 112428. https://doi.org/https://doi.org/10.1016/j.rse.2021.112428
DOI: 10.5281/zenodo.4662150
title: Global aerodynamic parameters in 1982-2017 based on GLASS LAI

description: ************************************************************************************ May 29, 2022 <strong>Version 1.1 updates to 2020. https://doi.org/10.5281/zenodo.6591520</strong> ************************************************************************************ The bulk surface properties, including canopy height (ht), zero-plane displacement height (d), and roughness length (z0) are crucial biophysical parameters that influence momentum, energy, and mass exchanges at the land-atmosphere interface. Here we provide a global estimate of bulk aerodynamic parameters during 1982-2017 at 0.05-degree spatial resolution and monthly temporal interval, using remote-sensed leaf area index, canopy height, and a turbulent transfer model. Two separate datasets are generated using GLASS LAI and GIMMS LAI. This dataset includes the products based on GLASS LAI. Details can be found: Liu, Y., Guo, W., Huang, H., Ge, J., Qiu, B., 2021. Estimating global aerodynamic parameters in 1982–2017 using remote-sensing data and a turbulent transfer model. Remote Sens. Environ. 260, 112428. https://doi.org/https://doi.org/10.1016/j.rse.2021.112428
DOI: 10.6084/m9.figshare.19919606
title: Ropivacaine with intraspinal administration alleviates preeclampsia-induced kidney injury via glycocalyx /alpha 7 nicotinic acetylcholine receptor pathway

description: Preeclampsia is characterized by hypertension and proteinuria, which is associated with kidney injury. Glycocalyx (GCX) degradation mediated endothelial injury can result in proteinuria and kidney damage. alpha 7 nicotinic acetylcholine receptor (α7nAChR) connects nervous and immune systems to respond to stress or injury. We aimed to explore the protective effect and mechanism of intraspinal analgesia on maternal kidney injury in preeclampsia. Endotoxin-induced preeclampsia rats treated with ropivacaine via intraspinal administration. Renal histopathological examination was performed, cell apoptosis in the kidney, the levels of Glycocalyx markers of Syndecan-1 and heparin sulfate (HS) in maternal serum, Syndecan-1 along with α7nAChR in the kidney were measured. Our results showed that kidney injury was obviously in preeclampsia rats with proteinuria, endothelial damage, higher apoptosis rate, increasing levels of Syndecan-1 and HS in serum, upregulated Syndecan-1 expression but downregulated α7nAChR expression in kidney. Preeclampsia rats treated with intraspinal injected ropivacaine attenuated preeclampsia-induced kidney injury as Syndecan-1 and HS were decreased in serum, Syndecan-1 expression was suppressed as well as α7nAChR was activated in the kidney. Our results suggested that Ropivacaine administered through the spinal canal may protect preeclampsia-induced renal injury by decreasing GCX and α7nAChR activation.
DOI: 10.6084/m9.figshare.19919606.v1
title: Ropivacaine with intraspinal administration alleviates preeclampsia-induced kidney injury via glycocalyx /alpha 7 nicotinic acetylcholine receptor pathway

description: Preeclampsia is characterized by hypertension and proteinuria, which is associated with kidney injury. Glycocalyx (GCX) degradation mediated endothelial injury can result in proteinuria and kidney damage. alpha 7 nicotinic acetylcholine receptor (α7nAChR) connects nervous and immune systems to respond to stress or injury. We aimed to explore the protective effect and mechanism of intraspinal analgesia on maternal kidney injury in preeclampsia. Endotoxin-induced preeclampsia rats treated with ropivacaine via intraspinal administration. Renal histopathological examination was performed, cell apoptosis in the kidney, the levels of Glycocalyx markers of Syndecan-1 and heparin sulfate (HS) in maternal serum, Syndecan-1 along with α7nAChR in the kidney were measured. Our results showed that kidney injury was obviously in preeclampsia rats with proteinuria, endothelial damage, higher apoptosis rate, increasing levels of Syndecan-1 and HS in serum, upregulated Syndecan-1 expression but downregulated α7nAChR expression in kidney. Preeclampsia rats treated with intraspinal injected ropivacaine attenuated preeclampsia-induced kidney injury as Syndecan-1 and HS were decreased in serum, Syndecan-1 expression was suppressed as well as α7nAChR was activated in the kidney. Our results suggested that Ropivacaine administered through the spinal canal may protect preeclampsia-induced renal injury by decreasing GCX and α7nAChR activation.
DOI: 10.6084/m9.figshare.19919609.v1
title: Circ_0008068 facilitates the oral squamous cell carcinoma development by microRNA-153-3p/acylgycerol kinase (AGK) axis

description: Oral squamous cell carcinoma (OSCC) is a common cancer with high recurrence, metastasis rates and poor prognosis. Circular RNAs (circRNAs) take part in regulating OSCC. Herein, we examined the role of circ_0008068 in OSCC. The circ_0008068, Katanin p60 ATPase-containing subunit A-like 1 (KATNAL1) mRNA, microRNA-153-3p (miR-153-3p) and acylgycerol kinase (AGK) contents were indicated by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot. Moreover, in vitro and in vivo assays were conducted to scrutinize the effects of circ_0008068 on OSCC. Additionally, the contact between miR-153-3p and circ_0008068 or AGK was assessed by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. Thereafter, we found that the appearance of circ_0008068 and AGK was increased, and miR-153-3p content was diminished in OSCC. Circ_0008068 lack subdued cell proliferation, migration, invasion, tube formation and glycolysis metabolism, but stimulated cell apoptosis in OSCC. In addition, circ_0008068 bound to miR-153-3p to modulate the expression of its target AGK. Besides, miR-153-3p was validated to act as a tumor suppressor in OSCC tumorigenesis by suppressing AGK. Additionally, circ_0008068 knockdown also attenuated tumor growth in nude mice. In all, circ_0008068 expedited the growth of OSCC by miR-153-3p/AGK axis. <b>Abbreviations:</b> OSCC: Oral squamous cell carcinoma; AGK: Acylgycerol kinase; CircRNA: Circular RNA; KATNAL1: Katanin p60 ATPase-containing subunit A-like 1; qRT-PCR: Quantitative real-time polymerase chain reaction; miRNAs/miRs: MicroRNAs; RIP: RNA immunoprecipitation; 3′UTR3’: -untranslated region; HK2: Hexokinase 2; LDHA Lactate dehydrogenase A; IHC: Immunohistochemistry; CCK8: Cell counting kit-8; GAPDH: Glyceraldehyde-3-phosphate dehydrogenase
DOI: 10.6084/m9.figshare.19919609
title: Circ_0008068 facilitates the oral squamous cell carcinoma development by microRNA-153-3p/acylgycerol kinase (AGK) axis

description: Oral squamous cell carcinoma (OSCC) is a common cancer with high recurrence, metastasis rates and poor prognosis. Circular RNAs (circRNAs) take part in regulating OSCC. Herein, we examined the role of circ_0008068 in OSCC. The circ_0008068, Katanin p60 ATPase-containing subunit A-like 1 (KATNAL1) mRNA, microRNA-153-3p (miR-153-3p) and acylgycerol kinase (AGK) contents were indicated by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot. Moreover, in vitro and in vivo assays were conducted to scrutinize the effects of circ_0008068 on OSCC. Additionally, the contact between miR-153-3p and circ_0008068 or AGK was assessed by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. Thereafter, we found that the appearance of circ_0008068 and AGK was increased, and miR-153-3p content was diminished in OSCC. Circ_0008068 lack subdued cell proliferation, migration, invasion, tube formation and glycolysis metabolism, but stimulated cell apoptosis in OSCC. In addition, circ_0008068 bound to miR-153-3p to modulate the expression of its target AGK. Besides, miR-153-3p was validated to act as a tumor suppressor in OSCC tumorigenesis by suppressing AGK. Additionally, circ_0008068 knockdown also attenuated tumor growth in nude mice. In all, circ_0008068 expedited the growth of OSCC by miR-153-3p/AGK axis. <b>Abbreviations:</b> OSCC: Oral squamous cell carcinoma; AGK: Acylgycerol kinase; CircRNA: Circular RNA; KATNAL1: Katanin p60 ATPase-containing subunit A-like 1; qRT-PCR: Quantitative real-time polymerase chain reaction; miRNAs/miRs: MicroRNAs; RIP: RNA immunoprecipitation; 3′UTR3’: -untranslated region; HK2: Hexokinase 2; LDHA Lactate dehydrogenase A; IHC: Immunohistochemistry; CCK8: Cell counting kit-8; GAPDH: Glyceraldehyde-3-phosphate dehydrogenase
DOI: 10.6084/m9.figshare.19919651
title: Long non-coding RNA ZNFX1 antisense 1 (ZFAS1) suppresses anti-oxidative stress in chondrocytes during osteoarthritis by sponging microRNA-1323

description: LncRNAs play a regulatory role in osteoarthritis (OA); however, the detailed mechanism remains to be elucidated. This study aimed to investigate the role of lncRNA zinc finger NFX1-type containing 1 (ZNFX1) antisense 1 (ZFAS1) in OA progression and explore its possible mechanismsagainst oxidative stress. Human cartilage specimens were obtained from 10 patients without OA who underwent traumatic amputation and 25 patients with OA who underwent total knee replacement surgery. Chondrocytes were prepared from harvested articular cartilage. ZFAS1, nuclear factor erythroid 2-related factor 2 (Nrf2), and heme oxygenase 1 (HO-1) expression levels were analyzed using quantitative reverse transcription PCR and WB. The chondrocyte growth was indicated by MTT and colony formation assays. Chondrocyte apoptosis, reactive oxygen species generation, and anti-oxidative enzymes activities were also measured. ZFAS1 expression was reduced in OA samples and lipopolysaccharide (LPS)-treated chondrocytes used as an OA cell model mimic. ZFAS1 overexpression facilitated proliferation and repressed oxidative stress, inflammation, and apoptosis in LPS-induced chondrocytes. ZFAS1 also activated the anti-oxidative Nrf2-HO-1 pathway. ZFAS1 directly targeted miR-1323, which partially reversed the effects of ZFAS1 on chondrocyte proliferation, oxidative stress, inflammation, and apoptosis. Furthermore, Nrf2 was negatively regulated by miR-1323. The effect of miR-1323 inhibition was partly abrogated by the administration of brusatol, an Nrf2 inhibitor. Collectively, the results showed that ZFAS1 promoted chondrocyte proliferation and repressed oxidative stress, possibly by regulating the novel miR-1323-Nrf2 axis of the inflammation and apoptosis triggered by LPS, indicating that ZFAS1 is a promising therapeutic target for OA.