cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/fydgyx
title: astericsreport UnivariateDataset_14e662256625.html

description: univariate analysis report obtained from ASTERICS (UID: piglet_usecase)
DOI: 10.57745/itwmnc
title: astericsreport bivariateAnalysis4e66909c8ac.html

description: bivariate analysis report obtained from ASTERICS (UID: piglet_usecase)
DOI: 10.57745/nzvtxs
title: Infos_444.tab

description: Metadata on the 444 piglets
DOI: 10.57745/uafn1i
title: Plasma_Over90df0525b552.csv

description: metabolites under-concentrated in plasma at 110 days obtained from ASTERICS (UID: piglet_usecase)
DOI: 10.57745/hxq59c
title: astericsreport MFAobj_14e63b2a70b9.html

description: MFA report obtained from ASTERICS (UID: piglet_usecase)
DOI: 10.57745/thnxk9
title: Metabolome_Urine_444.csv

description: ASICS quantification for urine 1H NMR
DOI: 10.57745/vh5zfj
title: Metabolome_LAmniot_444.csv

description: ASICS quantification for amniotic fluid 1H NMR
DOI: 10.57745/wmprrj
title: Plasma_Under110_MetaboAnalystNames.txt

description: corrected metabolite names for MetaboAnalyst analysis (metabolites under-concentrated at 110 days)
DOI: 10.5281/zenodo.8144427
title: Bases de Dados acerca do poder conclusivo no Brasil

description: Bases de dados retirada das plataformas "Dados Abertos" da Câmara dos Deputados e Senado Federal do Brasil, de forma a entender a relevância da apreciação conclusiva das matérias nas Casas.
DOI: 10.5281/zenodo.8144426
title: Bases de Dados acerca do poder conclusivo no Brasil

description: Bases de dados retirada das plataformas "Dados Abertos" da Câmara dos Deputados e Senado Federal do Brasil, de forma a entender a relevância da apreciação conclusiva das matérias nas Casas.
DOI: 10.15454/domehb/2wipei
title: Rep2-90-160223_500000.longest18chr.tab

description: individual matrix (Rep2 at 90 days of gestation)
DOI: 10.15454/domehb/ub01ih
title: Rep2-110-160308_500000.longest18chr.tab

description: individual matrix (Rep2 at 110 days of gestation)
DOI: 10.15454/domehb/ewf2n1
title: merged.500000.longest18chr.tab

description: merged HiC matrix (over the 6 samples), 500kb
DOI: 10.15454/domehb/l3dcn3
title: Rep3-90-160308_500000.longest18chr.tab

description: individual matrix (Rep3 at 90 days of gestation)
DOI: 10.15454/domehb/t6myva
title: tads_juicer_50000.tar.gz

description: TADs (8 files from the 6 individual matrices and the two merged matrices corresponding to the two gestational age).
DOI: 10.15454/domehb/vva8uw
title: Rep1-90-160216_500000.longest18chr.tab

description: individual matrix (Rep1 at 90 days of gestation)
DOI: 10.15454/domehb/xhnkeq
title: Rep1-110-160307_500000.longest18chr.tab

description: individual matrix (Rep1 at 110 days of gestation)
DOI: 10.15454/domehb/xqjdyo
title: index.500000.longest18chr.abs.bed

description: common index to all HiC matrices, 500kb
DOI: 10.15454/domehb/8axpu3
title: Rep3-110-160517_500000.longest18chr.tab

description: individual matrix (Rep3 at 110 days of gestation)
DOI: 10.15454/domehb/eg50s4
title: ABcompartments.tar.gz

description: A/B compartments (8 files from the 6 individual matrices and the two merged matrices corresponding to the two gestational age).
DOI: 10.15454/domehb/hfs3nm
title: chr_matrices4viz.tar.gz

description: chromosome specific matrices used for the visualization script in https://forgemia.inra.fr/nathalie.villa-vialaneix/pighic
DOI: 10.15454/8blmnq/0rnt4u
title: index.200000.longest18chr.abs.bed

description: index file for bins: chr | start | end | id
DOI: 10.15454/8blmnq/vc36cj
title: Rep3-90-160308_200000.longest18chr.tab

description: corresponding BioSamples accession number: ERS5298956 raw read files on ENA with accession number: SAMEA7390800 count file: bin1 id | bin2 id | count
DOI: 10.15454/8blmnq/kzgmta
title: Rep1-90-160216_200000.longest18chr.tab

description: corresponding BioSamples accession number: ERS5298954 raw read files on ENA with accession number: SAMEA7390796 count file: bin1 id | bin2 id | count
DOI: 10.15454/8blmnq/outtjg
title: diffbins_200000.txt

description: Results of differential analysis performed in 3 steps from the Rep* files between conditions d90 and d110 1) A filtering step, in which low count interactions were removed from the dataset: this step is used to leverage the effect of multiple testing correction (and to improve the testing procedure power) by removing low count interactions that have a very low chance to be found differentially expressed. We chose to use a fixed threshold based on the total number of reads, across the 6 samples, associated to a given interaction (30, which corresponded to a minimum of 5 reads per sample on average), to filter out irrelevant bin pairs from the differential analysis. 2) A normalization step (between interaction matrix normalization), to make the different matrices comparable. As stressed in (Lun and Smyth, 2015), contrary to RNA-seq data, a normalization based on the (potentially corrected) library size is not sufficient for Hi-C data. Indeed, the complexity of the protocol generally generates additional biases that result in trended differences between libraries (as visible on MA plots). To correct such biases, we used the method proposed in (Ballman et al., 2004) and implemented in the R / Bioconductor package csaw (Lun and Smyth, 2016) that performs a non-linear normalization based on a fast cyclic loess algorithm. Gene and sample specific offsets were computed and incorporated in the Generalized Linear Model (GLM) described in the next step, to correct trended differences. The efficiency of the normalization was controlled using PCA and MA plots on pseudo counts (log2transformed counts), before and after normalization. 3) A differential analysis step: this step was performed using a Generalized Linear Model (GLM) based on the Negative Binomial (NB) distribution with a group fixed effect (two-level factor: 90/110 days). The model was estimated with the implementation of the R / Bioconductor package edgeR (Robinson et al., 2010) and log ratio tests were used to assess the significativity of the group effect on each bin pair interaction. p-values were genome wide corrected using (Benjamini and Hochberg, 1995) procedure to control the False Discovery Rate (FDR).
DOI: 10.15454/8blmnq/vg6u3a
title: Rep2-110-160308_200000.longest18chr.tab

description: corresponding BioSamples accession number: ERS5298953 raw read files on ENA with accession number: SAMEA7390797 count file: bin1 id | bin2 id | count
DOI: 10.15454/8blmnq/wgzqjp
title: Rep1-110-160307_200000.longest18chr.tab

description: corresponding BioSamples accession number: ERS5298955 raw read files on ENA with accession number: SAMEA7390795 count file: bin1 id | bin2 id | count
DOI: 10.15454/8blmnq/x2phkv
title: Rep3-110-160517_200000.longest18chr.tab

description: corresponding BioSamples accession number: ERS5298957 raw read files on ENA with accession number: SAMEA7390799 count file: bin1 id | bin2 id | count
DOI: 10.15454/8blmnq/xo8ab2
title: Rep2-90-160223_200000.longest18chr.tab

description: corresponding BioSamples accession number: ERS5298958 raw read files on ENA with accession number: SAMEA7390798 count file: bin1 id | bin2 id | count
DOI: 10.7284/154852
title: Expendable Probe data collected during research cruise NA143 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/154826
title: INS (Inertial Navigation System) data collected during research cruise NA143 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/154853
title: INS (Inertial Navigation System) data collected during research cruise NA143 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.20079697
title: Transition-potential coupled cluster II: optimisation of the core orbital occupation number

description: The issue of orbital relaxation in computational core-hole spectroscopy, specifically x-ray absorption, has been a major problem for methods such as equation-of-motion coupled cluster with singles and doubles (EOM-CCSD). The transition-potential coupled cluster (TP-CC) method is utilised to address this problem by including an explicit treatment of orbital relaxation via the use of reference orbitals with a fractional core occupation number. The value of the fractional occupation parameter <i>λ</i> was optimised for both TP-CCSD and XTP-CCSD methods in an element-specific manner due to the differences in atomic charge and energy scale. Additionally, TP-CCSD calculations using the optimised parameters were performed for the K-edge absorption spectra of gas-phase adenine and thymine. TP-CCSD reproduces the valence region well and requires smaller overall energy shifts in comparison to EOM-CCSD, while also improving on the relative position and intensities of several absorption peaks.
DOI: 10.6084/m9.figshare.20449069
title: Pursuing the basis set limit of CCSD(T) non-covalent interaction energies for medium-sized complexes: case study on the S66 compilation

description: Our recently developed conventional, explicitly correlated, and local natural orbital (LNO) based coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] methods are utilised to closely approach the basis set limit of interaction energies between medium-sized molecular complexes. The study is partly motivated by our previous finding that state-of-the-art diffusion Monte Carlo and CCSD(T) interaction energies are not in complete agreement even for some of the dimers in the popular S66 compilation [Al-Hamdani and Nagy et al. Nat. Commun. (2021) 12:3927]. We improve upon the previous S66 CCSD(T) reference by using up to the quadruple-<i>ζ</i> (QZ) level CCSD(T) contributions, utilising our recent (T+) approach and suggesting a more robust explicitly correlated CCSD reference. Our efficient LNO-CCSD(T) method allowed us to also compute tightly converged, quintuple-<i>ζ</i> level interaction energies for the S66 set. Moreover, the new CCSD(T)/QZ references enabled the so far most rigorous benchmark of the LNO and other popular local correlation approaches on the S66 set. The accuracy of local approximations was found in the few 10 to few 100 cal/mol interaction energy error range, assuming sufficiently tight settings, such as the Tight and the Normal settings of LNO-CCSD(T) threshold combinations, respectively.
DOI: 10.6084/m9.figshare.20079697.v1
title: Transition-potential coupled cluster II: optimisation of the core orbital occupation number

description: The issue of orbital relaxation in computational core-hole spectroscopy, specifically x-ray absorption, has been a major problem for methods such as equation-of-motion coupled cluster with singles and doubles (EOM-CCSD). The transition-potential coupled cluster (TP-CC) method is utilised to address this problem by including an explicit treatment of orbital relaxation via the use of reference orbitals with a fractional core occupation number. The value of the fractional occupation parameter <i>λ</i> was optimised for both TP-CCSD and XTP-CCSD methods in an element-specific manner due to the differences in atomic charge and energy scale. Additionally, TP-CCSD calculations using the optimised parameters were performed for the K-edge absorption spectra of gas-phase adenine and thymine. TP-CCSD reproduces the valence region well and requires smaller overall energy shifts in comparison to EOM-CCSD, while also improving on the relative position and intensities of several absorption peaks.
DOI: 10.6084/m9.figshare.20449069.v2
title: Pursuing the basis set limit of CCSD(T) non-covalent interaction energies for medium-sized complexes: case study on the S66 compilation

description: Our recently developed conventional, explicitly correlated, and local natural orbital (LNO) based coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] methods are utilised to closely approach the basis set limit of interaction energies between medium-sized molecular complexes. The study is partly motivated by our previous finding that state-of-the-art diffusion Monte Carlo and CCSD(T) interaction energies are not in complete agreement even for some of the dimers in the popular S66 compilation [Al-Hamdani and Nagy et al. Nat. Commun. (2021) 12:3927]. We improve upon the previous S66 CCSD(T) reference by using up to the quadruple-<i>ζ</i> (QZ) level CCSD(T) contributions, utilising our recent (T+) approach and suggesting a more robust explicitly correlated CCSD reference. Our efficient LNO-CCSD(T) method allowed us to also compute tightly converged, quintuple-<i>ζ</i> level interaction energies for the S66 set. Moreover, the new CCSD(T)/QZ references enabled the so far most rigorous benchmark of the LNO and other popular local correlation approaches on the S66 set. The accuracy of local approximations was found in the few 10 to few 100 cal/mol interaction energy error range, assuming sufficiently tight settings, such as the Tight and the Normal settings of LNO-CCSD(T) threshold combinations, respectively.
DOI: 10.7284/154854
title: Meteorological Station data collected during research cruise NA143 using a Campbell Weatherpak-2000 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.21317426
title: On the UV spectroscopy and photodynamics of octatetraene

description: The UV absorption spectrum of all-<i>trans</i>-octatetraene is reinvestigated theoretically, focussing on the strongly dipole-allowed 1Ag–1Bu transition. The dynamical calculations rely on <i>ab initio</i> multistate CASPT2 (MS-CASPT2) computations of the underlying potential energy surfaces and coupling elements, and the multiconfiguration time-dependent Hartree (MCTDH) method for solving the time-dependent Schrödinger equation for the nuclear motion. The vibronic structure of the absorption band near 2700 Å is well reproduced, better than ever before by a purely <i>ab initio</i> approach. The C–C single bond and C=C double bond stretching modes dominate the vibrational structure of the transition. While the latter resembles nearly harmonic motion on weakly coupled potential energy surfaces, the time-dependent calculations reveal a subpicosecond electronic population transfer from the 1Bu state to the lower-lying 2Ag state proceeding on a time scale of ∼50fs. The details of this internal conversion process and its relation to the conical intersection between the two excited states are discussed, paying particular attention to the impact of the 1Bu –2Ag energy gap on the dynamics.
DOI: 10.7284/154838
title: Multibeam Echosounder data collected during research cruise NA143 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.21317426.v1
title: On the UV spectroscopy and photodynamics of octatetraene

description: The UV absorption spectrum of all-<i>trans</i>-octatetraene is reinvestigated theoretically, focussing on the strongly dipole-allowed 1Ag–1Bu transition. The dynamical calculations rely on <i>ab initio</i> multistate CASPT2 (MS-CASPT2) computations of the underlying potential energy surfaces and coupling elements, and the multiconfiguration time-dependent Hartree (MCTDH) method for solving the time-dependent Schrödinger equation for the nuclear motion. The vibronic structure of the absorption band near 2700 Å is well reproduced, better than ever before by a purely <i>ab initio</i> approach. The C–C single bond and C=C double bond stretching modes dominate the vibrational structure of the transition. While the latter resembles nearly harmonic motion on weakly coupled potential energy surfaces, the time-dependent calculations reveal a subpicosecond electronic population transfer from the 1Bu state to the lower-lying 2Ag state proceeding on a time scale of ∼50fs. The details of this internal conversion process and its relation to the conical intersection between the two excited states are discussed, paying particular attention to the impact of the 1Bu –2Ag energy gap on the dynamics.
DOI: 10.7284/154845
title: Multibeam Echosounder data collected during research cruise NA143 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/154850
title: Singlebeam Echosounder data collected during research cruise NA143 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/154855
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA143 using a AML AML-3 RT instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152412
title: Anemometer data collected during research cruise OC2108C using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152428
title: Anemometer data collected during research cruise OC2109B using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152433
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC2109B using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152461
title: Anemometer data collected during research cruise OC2111A using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151221
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SR2213 using a Hawaii UHDAS instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17037/data.00003555
title: PharmacoTXA: Pharmacokinetics of Tranexamic Acid after oral, intramuscular or intravenous administration: a prospective, randomised, cross-over trial in healthy volunteers

description: Anonymised dataset, protocol, published manuscript, data dictionary and other relevant trial documents for a Phase 1 study to determine the pharmacokinetics and local and systemic tolerance of tranexamic acid in healthy volunteers using a population approach after oral, intramuscular or intravenous administration, and the feasibility of measuring tranexamic acid in spots of dry capillary blood.
DOI: 10.48567/9z82-1188
title: Antarctic satellite composite imagery animations, 2009.
DOI: 10.5281/zenodo.8144454
title: Configuration optimization with limited functional impact

description: This dataset contains the validation and replication data for the paper Configuration Optimization with limited functional impact.
DOI: 10.5281/zenodo.8144453
title: Configuration optimization with limited functional impact

description: This dataset contains the validation and replication data for the paper Configuration Optimization with limited functional impact.
DOI: 10.5281/zenodo.8144438
title: AssistTaxi: v1.1

description: We present AssistTaxi, a robust dataset specifically curated to address the critical need for high-quality data in the field. AssistTaxi is designed to capture real-world scenarios and encompasses data collected from Melbourne Orlando International Airport (KMLB) and Grant-Valkaria (X59) general aviation airport.
DOI: 10.5281/zenodo.8144439
title: AssistTaxi: v1.1

description: We present AssistTaxi, a robust dataset specifically curated to address the critical need for high-quality data in the field. AssistTaxi is designed to capture real-world scenarios and encompasses data collected from Melbourne Orlando International Airport (KMLB) and Grant-Valkaria (X59) general aviation airport.
DOI: 10.48567/5g4d-zs40
title: Antarctic satellite composite imagery animations, 2010.
DOI: 10.5517/ccdc.csd.cc2fm104
title: CCDC 2252615: Experimental Crystal Structure Determination

description: Related Article: Johannes Schneider, Ivo Krummenacher, Holger Braunschweig, Holger Helten|2023|Chem.Commun.|59|8408|doi:10.1039/d3cc01825c
description: Related Article: Johannes S. Schneider, Ivo Krummenacher, Holger Braunschweig, Holger Helten|2023|Chem.Commun.|59|8408|doi:10.1039/D3CC01825C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fm115
title: CCDC 2252616: Experimental Crystal Structure Determination

description: Related Article: Johannes Schneider, Ivo Krummenacher, Holger Braunschweig, Holger Helten|2023|Chem.Commun.|59|8408|doi:10.1039/d3cc01825c
description: Related Article: Johannes S. Schneider, Ivo Krummenacher, Holger Braunschweig, Holger Helten|2023|Chem.Commun.|59|8408|doi:10.1039/D3CC01825C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fm126
title: CCDC 2252617: Experimental Crystal Structure Determination

description: Related Article: Johannes Schneider, Ivo Krummenacher, Holger Braunschweig, Holger Helten|2023|Chem.Commun.|59|8408|doi:10.1039/d3cc01825c
description: Related Article: Johannes S. Schneider, Ivo Krummenacher, Holger Braunschweig, Holger Helten|2023|Chem.Commun.|59|8408|doi:10.1039/D3CC01825C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fm137
title: CCDC 2252618: Experimental Crystal Structure Determination

description: Related Article: Johannes Schneider, Ivo Krummenacher, Holger Braunschweig, Holger Helten|2023|Chem.Commun.|59|8408|doi:10.1039/d3cc01825c
description: Related Article: Johannes S. Schneider, Ivo Krummenacher, Holger Braunschweig, Holger Helten|2023|Chem.Commun.|59|8408|doi:10.1039/D3CC01825C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.48567/qhqc-rw41
title: Antarctic satellite composite imagery animations, 2011.
DOI: 10.48567/n6h7-aa74
title: Antarctic satellite composite imagery animations, 2012.
DOI: 10.5281/zenodo.7994488
title: IEA PVPS Task 16 Satellite nowcasting benchmark : Dataset of animated satellite images for the selection of case studies

description: This dataset contains animated satellite images used for the selection of case studies in the framework of the IEA PVPS task 16 satellite nowcasting benchmark. The animated images contains images from the channel 12 of MSG as well as NWC SAF products (cloud types and cloud top height) over France over the year 2020.