cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15161886.v1
title: The evolutionary history of the HUP domain

description: Among the enzyme lineages that undoubtedly emerged prior to the last universal common ancestor is the so-called HUP, which includes Class I aminoacyl tRNA synthetases (AARSs) as well as enzymes mediating NAD, FAD, and CoA biosynthesis. Here, we provide a detailed analysis of HUP evolution, from emergence to structural and functional diversification. The HUP is a nucleotide binding domain that uniquely catalyzes adenylation via the release of pyrophosphate. In contrast to other ancient nucleotide binding domains with the αβα sandwich architecture, such as P-loop NTPases, the HUP’s most conserved feature is not phosphate binding, but rather ribose binding by backbone interactions to the tips of β1 and/or β4. Indeed, the HUP exhibits unusual evolutionary plasticity and, while ribose binding is conserved, the location and mode of binding to the base and phosphate moieties of the nucleotide, and to the substrate(s) reacting with it, have diverged with time, foremost along the emergence of the AARSs. The HUP also beautifully demonstrates how a well-packed scaffold combined with evolvable surface elements promotes evolutionary innovation. Finally, we offer a scenario for the emergence of the HUP from a seed βαβ fragment, and suggest that despite an identical architecture, the HUP and the Rossmann represent independent emergences.
DOI: 10.25345/c5m902673
title: MassIVE MSV000089101 - CoverCrop_RootExudates_LCMS/MS_DDA
title: cover crop (19) root exudate profiles analyzed by non-targeted LC-MS/MS DDA
DOI: 10.6084/m9.figshare.17056928
title: Canuel et al. - An empirical financial analysis of integrating biomass procurement in sawtimber and pulpwood harvesting in eastern Canada

description: We studied forest harvest operations for biomass in the form of trees and tree sections, along with sawtimber and pulpwood by evaluating the cost effectiveness of the supply chain with a particular focus on harvest costs, and potential silvicultural savings from decreasing needs in site preparation and reforestation. We tested four increasing wood procurement intensities (from harvesting sawtimber only to harvesting sawtimber, pulpwood and a maximum of biomass for bioenergy) within three sites in eastern Canada.
DOI: 10.6084/m9.figshare.17056928.v2
title: Canuel et al. - An empirical financial analysis of integrating biomass procurement in sawtimber and pulpwood harvesting in eastern Canada

description: We studied forest harvest operations for biomass in the form of trees and tree sections, along with sawtimber and pulpwood by evaluating the cost effectiveness of the supply chain with a particular focus on harvest costs, and potential silvicultural savings from decreasing needs in site preparation and reforestation. We tested four increasing wood procurement intensities (from harvesting sawtimber only to harvesting sawtimber, pulpwood and a maximum of biomass for bioenergy) within three sites in eastern Canada.
DOI: 10.6084/m9.figshare.17056928.v1
title: Canuel et al. - An empirical financial analysis of biomass procurement harmonized with sawtimber and pulpwood supply in Eastern Canada

description: We studied forest harvest operations for biomass in the form of trees and tree sections, along with sawtimber and pulpwood by evaluating the cost effectiveness of the supply chain with a particular focus on harvest costs, and potential silvicultural savings from decreasing needs in site preparation and reforestation. We tested four increasing wood procurement intensities (from harvesting sawtimber only to harvesting sawtimber, pulpwood and a maximum of biomass for bioenergy) within three sites in eastern Canada.
DOI: 10.25919/g7t6-r330
title: Parkes observations for project P1141 semester 2021OCTS_07

description: Radio giant pulses (GPs) have been observed since the discovery of the Crab pulsar more than 50 years ago. Nevertheless the origins of this apparently irregular form of radio emission are still not understood. While their characteristics indicate the existence of a coherent emission mechanism, the search for an incoherent emission component via multi-wavelength correlation studies provides one way to identify potential emission regions in the magnetosphere of the pulsar. With the present proposal, we address the radio GP emission from PSR J0540-6919 (the Crab twin) and seek to search for a correlation with its X-ray emission. A recent study of this kind for the Crab pulsar proved to be successful (Enoto et al.\,2021). Our proposed study is to the best of our knowledge the first of its kind together with the Neutron Star Interior Composition ExploreR (NICER) for this particular source and will shed light on the question of whether correlations with X-ray emission are a characteristic of ordinary pulsars with radio GP emission. Such knowledge will be useful in unraveling whether there are different populations of radio GPs in the case of ordinary and millisecond pulsars.
DOI: 10.5281/zenodo.5770687
title: Analytical prediction of scattering properties of spheroidal dust particles with machine learning

description: This respository includes the data used in the paper "Analytical prediction of scattering properties of spheroidal dust particles with machine learning". "alldata.zip" represents the extinction and absorption coefficients, and phase matrix elements of spheroids dust particles for both training and test data. These data comes from the Oleg Dubovik's group: https://www.grasp-open.com/products/spheroid-package-release/. "tmat_Jacall_norm_intg.pickle" contains the Jacobians simulated from linearized T-matrix model used for training in the paper and "tmat_fine_n_intg.pickle" involves Jacobians used for testing.
DOI: 10.5281/zenodo.5768632
title: Analytical prediction of scattering properties of spheroidal dust particles with machine learning

description: This respository includes the data used in the paper "Analytical prediction of scattering properties of spheroidal dust particles with machine learning". "alldata.zip" represents the extinction and absorption coefficients, and phase matrix elements of spheroids dust particles for both training and test data. These data comes from the Oleg Dubovik's group: https://www.grasp-open.com/products/spheroid-package-release/. "tmat_Jacall_norm_intg.pickle" contains the Jacobians simulated from linearized T-matrix model used for training in the paper and "tmat_fine_n_intg.pickle" involves Jacobians used for testing.
DOI: 10.6084/m9.figshare.19401089
title: CR 2210 relaxation

description: The results of a relaxation with PLUTO for CR 2210
DOI: 10.6084/m9.figshare.19401089.v1
title: CR 2210 relaxation

description: The results of a relaxation with PLUTO for CR 2210
DOI: 10.18112/openneuro.ds003592.v1.0.8
title: Neurocognitive aging data release with behavioral, structural, and multi-echo functional MRI measures
DOI: 10.6084/m9.figshare.19391684.v2
title: Annual dose

description: response to annual dose
DOI: 10.6073/pasta/fd1ca25545df476a605f37ed9a514f29
title: MCR LTER: Coral Reef: Population Dynamics: Symbiodinium population initial sampling conditions in corals of Moorea

description: These data consist of sample collection locations and conditions only, not the results of sequencing. These data were an initial collection of an expected time series which was not repeated. Clade data derived from the sample collection described here are archived on GeoSymbio. Coral are symbiotic with photosynthetic dinoflagellates from the genus Symbiodinium. There are eight divergent clades (A-H) within the genus which each contain many genetic varieties. Different types of Symbiodinium have been shown to affect the growth rate and thermal tolerance of the coral. The diversity and population structure of Symbiodinium on a reef and how it changes over time is therefore critical to the stability and resilience of coral reefs. Our research conducted through the MCR LTER project aims at defining the population structure of Symbiodinium present in the corals of Moorea and documenting changes over time. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2022). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
DOI: 10.5281/zenodo.6377927
title: Control Network for Ganymede Images from JunoCam Perijove 34

description: Delivered is a photogrammetric control network for four images of Ganymede collected by the Juno- Cam instrument during the Juno mission’s perijove 34 encounter on 2021-06-07. The network has 184,659 control points and 369,318 control measures (2 measures per control point). The network is a PVL formatted text file for use in ISIS (Integrated Software for Imagers and Spectrometers). When control points are merged with an image distance tolerance of 1.0 pixel the resulting network has 83,096 control points and 233,598 control measures. Extracting control points with 4 or more measures yields a network with 16,709 control points and 75,197 control measures. The initial network is produced with novel code implemented in Mathematica. In the “Initial Network” 98% of residuals are less than 1.72 pixels. Median residual is .40 pixels. There are 54 control points with residuals greater than 3 pixels, and 1544 with greater than 2. See ControlNetworkJunoCamV16j.pdf for details.
description: {"references": ["Hansen, C. J., Caplinger, M. A., Ingersoll, A., Ravine, M. A., Jensen, E., Bolton, S., & Orton, G. (2017). Junocam: Juno's outreach camera. Space Science Reviews, 213(1), 475-506. https://- doi.org/10.1007/s11214-014-0079-x", "Bolton, S. J., Lunine, J., Stevenson, D., Connerney, J. E. P., Levin, S., Owen, T. C., ... & Thorpe, R. (2017). The juno mission. Space Science Reviews, 213(1), 5-37. https://doi.org/10.1007/s11214-017-0429-6", "Laura, Jason, Acosta, Alex, Addair, Travis, Adoram-Kershner, Lauren, Alexander, James, Alexandrov, Oleg, et al. (2022, March 4). Integrated So\ufffdware for Imagers and Spectrometers (Version 7.0.0_RC1). Zenodo. https://doi.org/10.5281/zenodo.6329951", "Acton, C., Bachman, N., Semenov, B., & Wright, E. (2018). A look towards the future in the handling of space science mission geometry. Planetary and Space Science, 150, 9-12. https://- doi.org/10.1016/j.pss.2017.02.013"]}
DOI: 10.5281/zenodo.6377926
title: Control Network for Ganymede Images from JunoCam Perijove 34

description: Delivered is a photogrammetric control network for four images of Ganymede collected by the Juno- Cam instrument during the Juno mission’s perijove 34 encounter on 2021-06-07. The network has 184,659 control points and 369,318 control measures (2 measures per control point). The network is a PVL formatted text file for use in ISIS (Integrated Software for Imagers and Spectrometers). When control points are merged with an image distance tolerance of 1.0 pixel the resulting network has 83,096 control points and 233,598 control measures. Extracting control points with 4 or more measures yields a network with 16,709 control points and 75,197 control measures. The initial network is produced with novel code implemented in Mathematica. In the “Initial Network” 98% of residuals are less than 1.72 pixels. Median residual is .40 pixels. There are 54 control points with residuals greater than 3 pixels, and 1544 with greater than 2. See ControlNetworkJunoCamV16j.pdf for details.
description: {"references": ["Hansen, C. J., Caplinger, M. A., Ingersoll, A., Ravine, M. A., Jensen, E., Bolton, S., & Orton, G. (2017). Junocam: Juno's outreach camera. Space Science Reviews, 213(1), 475-506. https://- doi.org/10.1007/s11214-014-0079-x", "Bolton, S. J., Lunine, J., Stevenson, D., Connerney, J. E. P., Levin, S., Owen, T. C., ... & Thorpe, R. (2017). The juno mission. Space Science Reviews, 213(1), 5-37. https://doi.org/10.1007/s11214-017-0429-6", "Laura, Jason, Acosta, Alex, Addair, Travis, Adoram-Kershner, Lauren, Alexander, James, Alexandrov, Oleg, et al. (2022, March 4). Integrated So\ufffdware for Imagers and Spectrometers (Version 7.0.0_RC1). Zenodo. https://doi.org/10.5281/zenodo.6329951", "Acton, C., Bachman, N., Semenov, B., & Wright, E. (2018). A look towards the future in the handling of space science mission geometry. Planetary and Space Science, 150, 9-12. https://- doi.org/10.1016/j.pss.2017.02.013"]}
DOI: 10.25451/flinders.16545477
title: Genetic data of little penguins collected at eight colonies in South Australia between 2011 and 2014

description: Genetic data of little penguins analysed with next generation sequencing. The data were obtained from 75 penguins across eight colonies in South Australia.<br><br>Date coverage: 2011 - 2014<br>Location: South Australia, Australia<br>Related dataset: <i>Little Penguin (Eudyptula minor) RADseq illumina sequencing RAW output</i>https://doi.org/10.25451/flinders.19288226
DOI: 10.25451/flinders.16545477.v1
title: Genetic data of little penguins collected at eight colonies in South Australia between 2011 and 2014

description: Genetic data of little penguins analysed with next generation sequencing. The data were obtained from 75 penguins across eight colonies in South Australia.<br><br>Date coverage: 2011 - 2014<br>Location: South Australia, Australia<br>Related dataset: <i>Little Penguin (Eudyptula minor) RADseq illumina sequencing RAW output</i>https://doi.org/10.25451/flinders.19288226
DOI: 10.25451/flinders.19288226
title: Little Penguin (Eudyptula minor) RADseq illumina sequencing RAW output

description: PEN_C5N7WANXX_s_7_fastq.txt.gz - compressed RAW read data from illumina Hiseq 2000 generated from a RADseq library digested with Pst1 and Msp1 and sequenced with SE 100bp reads.<br>PEN_key.txt - contains metadata associated with the RAW data. This is a list of samples including one blank and four duplicate samples which were included in the sequencing. It also includes the unique library barcode for each sample and the location of the sample on the sequencing plate. For other sample related metadata see Supplementary material 1 from publication.<br>PEN_SNPcallingOUTPUT.zip - Remaining folders and files containing other output associated with SNP calling using the UNEAK Tassel pipeline version 3.0.169. SNP calling was performed using a default error rate, a minor allele frequency cut-off of &gt; 0.05 and a minimum call rate of 80% (Supplementary material S2). Inferred loci with a read depth of&lt;10 or that did not occur in at least 90% of individuals were removed. We only selected a single SNP per fragment and SNPs with a minor allele ratio of &lt; 0.2 were called as homozygotes for the major allele.<br>hapMap.zip - Post SNP calling files contains genotypes, tag pair sequences (HapMap.fas.txt), number of allele calls for each locus for each sample (HapMap.hmc.txt) and locus specific information (HapMap.hmp.txt)<br><br>This project was approved by the Flinders University Ethics Committee (E388) and supported by a scientific permit to conduct the research (Y26040).<br>Colombelli-Négrel, D., Slender, A., Bradford, T. <i>et al.</i> Subtle genetic clustering among South Australian colonies of little penguins (<i>Eudyptula minor</i>). <i>Conserv Genet</i> <b>21, </b>747–756 (2020). https://doi.org/10.1007/s10592-020-01284-4<br>Related dataset: <i>Genetic data of little penguins collected at eight colonies in South Australia between 2011 and 2014</i>DOI: https://doi.org/10.25451/flinders.16545477
DOI: 10.25451/flinders.19288226.v1
title: Little Penguin (Eudyptula minor) RADseq illumina sequencing RAW output

description: PEN_C5N7WANXX_s_7_fastq.txt.gz - compressed RAW read data from illumina Hiseq 2000 generated from a RADseq library digested with Pst1 and Msp1 and sequenced with SE 100bp reads.<br>PEN_key.txt - contains metadata associated with the RAW data. This is a list of samples including one blank and four duplicate samples which were included in the sequencing. It also includes the unique library barcode for each sample and the location of the sample on the sequencing plate. For other sample related metadata see Supplementary material 1 from publication.<br>PEN_SNPcallingOUTPUT.zip - Remaining folders and files containing other output associated with SNP calling using the UNEAK Tassel pipeline version 3.0.169. SNP calling was performed using a default error rate, a minor allele frequency cut-off of &gt; 0.05 and a minimum call rate of 80% (Supplementary material S2). Inferred loci with a read depth of&lt;10 or that did not occur in at least 90% of individuals were removed. We only selected a single SNP per fragment and SNPs with a minor allele ratio of &lt; 0.2 were called as homozygotes for the major allele.<br>hapMap.zip - Post SNP calling files contains genotypes, tag pair sequences (HapMap.fas.txt), number of allele calls for each locus for each sample (HapMap.hmc.txt) and locus specific information (HapMap.hmp.txt)<br><br>This project was approved by the Flinders University Ethics Committee (E388) and supported by a scientific permit to conduct the research (Y26040).<br>Colombelli-Négrel, D., Slender, A., Bradford, T. <i>et al.</i> Subtle genetic clustering among South Australian colonies of little penguins (<i>Eudyptula minor</i>). <i>Conserv Genet</i> <b>21, </b>747–756 (2020). https://doi.org/10.1007/s10592-020-01284-4<br>Related dataset: <i>Genetic data of little penguins collected at eight colonies in South Australia between 2011 and 2014</i>DOI: https://doi.org/10.25451/flinders.16545477
DOI: 10.25345/c5gh9bd3d
title: MassIVE MSV000089102 - Lung Adenocarcinoma Confirmatory: Phosphoproteome
title: Gillette MA, Satpathy S, Kane MH, Avanessian SC, Clauser KR, Mani DR, Carr SA. Broad Institute of MIT and Harvard, Cambridge, MA USA. The proteomic and phosphoproteomic analyses of lung cancer samples were structured as two sets nominally termed the Discovery set and the Confirmatory set. The Confirmatory set is further divided into two processing tranches, deemed C1 and C2. To facilitate quantitative comparison between all samples across experiments, a common reference sample was included in each TMT plex. A common physical, rather than in silico reference was used for this purpose for optimal quantitative precision between TMT-10 or TMT-11 experiments.
DOI: 10.25345/c5br8mk7p
title: MassIVE MSV000089103 - Lung Adenocarcinoma Confirmatory: Proteome
title: Gillette MA, Satpathy S, Kane MH, Avanessian SC, Clauser KR, Mani DR, Carr SA. Broad Institute of MIT and Harvard, Cambridge, MA USA. The proteomic and phosphoproteomic analyses of lung cancer samples were structured as two sets nominally termed the Discovery set and the Confirmatory set. The Confirmatory set is further divided into two processing tranches, deemed C1 and C2. To facilitate quantitative comparison between all samples across experiments, a common reference sample was included in each TMT plex. A common physical, rather than in silico reference was used for this purpose for optimal quantitative precision between TMT-10 or TMT-11 experiments.
DOI: 10.17632/pdpmwtpmpx.1
title: A SERIAL MEDIATION EFFECT Data set

description: Data for Research Paper
DOI: 10.17632/r5g4zgwpnr.1
title: Sea-level oscillations data from Fundão Island Tide Station, RJ-Brazil

description: Sea-level oscillations data from Fundão Island Tide Station.
Lat: -22.86
Lon: -43.21 
It is a observed series of sea-level oscillations in the inner of Guanabara Bay, in the state of Rio de Janeiro, Brazil. 
The data has been reduced to zero and starts on December 12, 2013 at 11:10 AM local time (GMT/UTC-3), with a sampling interval every 10 minutes and ends on August 20, 2014 at 11:40 AM
DOI: 10.17632/tww8sm8t6s.1
title: 2017 Survey of US Neuroradiologists

description: 2017 Survey Data of United States’ Neuroradiology Workforce including work environment, clinical and call workload, burnout measures, subjective interpretive errors and intention to retire early or change careers
DOI: 10.17632/67k5byngdx.1
title: A study of Yali Zhang et al

description: Cross-species tropism and antigenic landscapes of circulating SARS-CoV-2 variants
DOI: 10.17632/fs839x372j.2
title: Supplemental Figure 1

description: Naranjo’s algorithm
DOI: 10.17632/6pyjjwmngd.3
title: Protective Effects of Intestinal Gallic Acid in Neonatal Dairy Calves against Extended-Spectrum β-lactamase Producing Enteroaggregative Escherichia coli Infection:  Modulating Intestinal Homeostasis and Colitis

description: Metabolomics preprocessed data, the data set is related to figure 2, Extended Data figure S3.
DOI: 10.21227/h5e9-m398
title: Quantum Volume in Practice: What Users Can Expect from NISQ Devices Dataset

description: Quantum volume (QV) has become the de-facto standard benchmark to quantify the capability of Noisy Intermediate-Scale Quantum (NISQ) devices. While QV values are often reported by NISQ providers for their systems, we perform our own series of QV calculations on more than 20  NISQ devices currently (2021/2022) offered by IBM Q, IonQ, Rigetti, Oxford Quantum Circuits, and Quantinuum (formerly Honeywell). Our approach characterizes the performances that an advanced user of these NISQ devices can expect to achieve with a reasonable amount of optimization, but without white-box access to the device. In particular, we compile QV circuits to standard gate sets of the vendor using compiler optimization routines where available, and we perform experiments across different initial qubit mappings. We find that running QV tests requires very significant compilation cycles, QV values achieved in our tests typically lag behind officially reported results and also depend significantly on the classical compilation effort invested. This dataset is comprised of the compiled (and un-compiled) circuits generated for this analysis.
DOI: 10.6084/m9.figshare.19401131
title: Corrections to the literature: Three recently published records for Nicrophorus (Coleoptera: Staphylinidae: Silphinae) deemed erroneous

description: Occurrence data in decimal longitude, decimal latitude format for the species Nicrophorus guttula and Nicrophorus hybridus in support of niche model analyses in "Corrections to the literature: Three recently published records for Nicrophorus (Coleoptera: Staphylinidae: Silphinae) deemed erroneous"<br>
DOI: 10.5517/ccdc.csd.cc28kb4b
title: CCDC 2102021: Experimental Crystal Structure Determination

description: Related Article: Lin Wang, Shuyan Li, Xiaozhou Xu, Xiaoyan Xu, Qing Wang, Duanxiu Li, Hailu Zhang|2022|Journal of Drug Delivery Science and Technology|70|103228|doi:10.1016/j.jddst.2022.103228
DOI: 10.15131/shef.data.17081228
title: Data for 'Low-voltage SEM of air-sensitive powders: From sample preparation to micro/nano analysis with secondary electron hyperspectral imaging'

description: SEHI data volumes included in 10.1016/j.micron.2022.103234.For methodology of preparation, collection and data processing see section 5 of the published article.<br>Corresponding SEHI data volume metadata in .json format.
DOI: 10.15131/shef.data.17081228.v1
title: Data for 'Low-voltage SEM of air-sensitive powders: From sample preparation to micro/nano analysis with secondary electron hyperspectral imaging'

description: SEHI data volumes included in 10.1016/j.micron.2022.103234.For methodology of preparation, collection and data processing see section 5 of the published article.<br>Corresponding SEHI data volume metadata in .json format.