cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21954/ou.rd.7315430
title: OpenMARS ozone column database

description: The Open access to Mars Assimilated Remote Soundings (OpenMARS) database is a reanalysis product combining past spacecraft observations with a state-of-the-art Mars Global Circulation Model (GCM). The OpenMARS product is a global surface/atmosphere reference database of key variables for multiple Mars years.<br><br>Spacecraft observations of ozone column abundance from the SPICAM (Spectroscopy for the Investigation of the Characteristics of the Atmosphere of Mars) instrument on the Mars Express spacecraft are combined with a Mars GCM used at the Open University. The database includes 3-hourly output of ozone column abundance.<br>Extended details on this dataset can be found in the OpenMARS-ozone-reference-manual.pdf document included in this repository.<br>This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 633127.
DOI: 10.21954/ou.rd.7315430.v1
title: OpenMARS ozone column database

description: The Open access to Mars Assimilated Remote Soundings (OpenMARS) database is a reanalysis product combining past spacecraft observations with a state-of-the-art Mars Global Circulation Model (GCM). The OpenMARS product is a global surface/atmosphere reference database of key variables for multiple Mars years.<br><br>Spacecraft observations of ozone column abundance from the SPICAM (Spectroscopy for the Investigation of the Characteristics of the Atmosphere of Mars) instrument on the Mars Express spacecraft are combined with a Mars GCM used at the Open University. The database includes 3-hourly output of ozone column abundance.<br>Extended details on this dataset can be found in the OpenMARS-ozone-reference-manual.pdf document included in this repository.<br>This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 633127.
DOI: 10.7284/122649
title: INS (Inertial Navigation System) data collected during research cruise RR1606 using a Kongsberg Seapath 320+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.21954/ou.rd.7315418.v1
title: OpenMARS water vapour database

description: The Open access to Mars Assimilated Remote Soundings (OpenMARS) database is a reanalysis product combining past spacecraft observations with a state-of-the-art Mars Global Circulation Model (GCM). The OpenMARS product is a global surface/atmosphere reference database of key variables for multiple Mars years.<br><br>Spacecraft observations of water vapour column abundance and temperature profiles from the Thermal Emission Spectrometer (TES) instrument on the Mars Global Surveyor spacecraft are combined with a Mars GCM used at the Open University. The database includes 2-hourly output of water vapour column abundance.<br>Extended details on this dataset can be found in the OpenMARS-water-reference-manual.pdf document included in this repository.<br>This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 633127.
DOI: 10.7284/121733
title: Meteorological Station data collected during research cruise RR1606 using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121736
title: Multibeam Echosounder data collected during research cruise RR1606 using a Kongsberg EM122 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121741
title: Winch data collected during research cruise RR1606 using a Markey DUTW-9-11 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121745
title: Winch data collected during research cruise RR1606 using a Markey DUSH-5 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315343
title: Push it to the limit: comparing periodic and local approaches to density functional theory for intermolecular interactions

description: With the aim of systematically comparing two popular approaches to density functional theory – all-electron calculations with local basis sets, and periodic calculations employing plane wave basis sets and norm-conserving pseudopotentials – we have computed complete-basis binding energies across the S22 set of intermolecular interactions, a dataset consisting of noncovalent interactions of small- and medium-sized molecules containing first- and second-row atoms, using the Troullier-Martins norm-conserving pseudopotentials with SPW92, a local spin-density approximation; and PBE, a generalised gradient approximation. We have found that it is challenging to reach the basis set limit with these periodic calculations; for the methods and systems examined, a minimum vacuum distance of 30 Å between a system and its nearest images is necessary – unless some form of dipole correction is employed – as is a kinetic energy cutoff of at least 80 Ry. The trends in convergence with respect to vacuum size and kinetic energy cutoff are largely independent of the level of density functional approximation employed. A sense of the impact of each hyperparameter on basis set error provides a foundation for ensuring quality calculations in future studies and allows us to quantify the basis set errors incurred in existing studies on similar systems.
DOI: 10.7284/126033
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise RR1607 using a Hawaii UHDAS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315343.v1
title: Push it to the limit: comparing periodic and local approaches to density functional theory for intermolecular interactions

description: With the aim of systematically comparing two popular approaches to density functional theory – all-electron calculations with local basis sets, and periodic calculations employing plane wave basis sets and norm-conserving pseudopotentials – we have computed complete-basis binding energies across the S22 set of intermolecular interactions, a dataset consisting of noncovalent interactions of small- and medium-sized molecules containing first- and second-row atoms, using the Troullier-Martins norm-conserving pseudopotentials with SPW92, a local spin-density approximation; and PBE, a generalised gradient approximation. We have found that it is challenging to reach the basis set limit with these periodic calculations; for the methods and systems examined, a minimum vacuum distance of 30 Å between a system and its nearest images is necessary – unless some form of dipole correction is employed – as is a kinetic energy cutoff of at least 80 Ry. The trends in convergence with respect to vacuum size and kinetic energy cutoff are largely independent of the level of density functional approximation employed. A sense of the impact of each hyperparameter on basis set error provides a foundation for ensuring quality calculations in future studies and allows us to quantify the basis set errors incurred in existing studies on similar systems.
DOI: 10.7284/126041
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR1607 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315259
title: Supplementary Material for: Depression Symptoms Predict Worse Clinical Response to Etanercept Treatment in Psoriasis Patients

description: <b><i>Background/Aims:</i></b> This study aimed to investigate the predicting values of depression and anxiety symptoms for clinical response to etanercept treatment in psoriasis patients. <b><i>Methods:</i></b> A total of 85 psoriasis patients who received 6 months of etanercept treatment were consecutively enrolled in this prospective cohort study. The Psoriasis Area and Severity Index (PASI) score was evaluated at month 0 (M0), M1, M3, and M6, and the corresponding PASI 75/90 response at each visit was assessed. Also, anxiety and depression symptoms were assessed by the Hospital Anxiety and Depression Scale (HADS) at M0, M1, M3, and M6. <b><i>Results:</i></b> Depression symptoms were observed to correlate with female gender (<i>p</i> = 0.004), longer disease duration (<i>p</i> = 0.018), and higher PASI score (<i>p</i> &lt; 0.001), and anxiety symptoms were seen to be associated with female gender (<i>p</i> = 0.017), larger psoriasis-affected body surface area (<i>p</i> = 0.049), and higher PASI score (<i>p</i> = 0.017) in psoriasis patients. After etanercept treatment, HADS-Depression (HADS-D) and HADS-Anxiety (HADS-A) scores were both decreased at M1, M3, and M6 (all <i>p</i> &lt; 0.001) compared with M0. Most importantly, baseline depressed patients presented with a lower PASI 75 response rate at M3 (<i>p</i> = 0.014) and M6 (<i>p</i> = 0.005), and a reduced PASI 90 response rate at M6 (<i>p</i> = 0.045) compared with baseline non-depressed patients. Furthermore, multivariate logistic regression analyses revealed that depression symptoms at baseline were an independent predictive factor for the lower possibility of both PASI 75 response (<i>p</i> = 0.048) and PASI 90 response (<i>p</i> = 0.048) achievements at M6 in psoriasis patients. However, no correlation of baseline anxiety symptoms with PASI 75/90 responses was observed. <b><i>Conclusion:</i></b> Depression symptoms at baseline independently predict a worse clinical response to etanercept treatment in psoriasis patients.
DOI: 10.7284/126045
title: Expendable Probe data collected during research cruise RR1607 using a Turo Quoll instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315241
title: Supplementary Material for: Exosomes from Thymic Stromal Lymphopoietin-Activated Dendritic Cells Promote Th2 Differentiation through the OX40 Ligand

description: <b><i>Objectives:</i></b> Exosomes are extracellular vesicles released from various inflammatory cells, such as T cells, B cells, dendritic cells (DCs), and mast cells, which have been implicated in the modulation of immune response in asthma. This study aimed to investigate whether exosomes from DCs activated by thymic stromal lymphopoietin (TSLP) play a role in T-helper cell differentiation through the OX40 ligand (OX40L). <b><i>Methods:</i></b> Serum samples from patients with asthma were collected to measure the levels of OX40L, T-helper type 1 (Th1) cytokine interferon (IFN)-γ, and T-helper type 2 (Th2) cytokine interleukin (IL)-4 by enzyme-linked immunosorbent assay (ELISA). Exosomes were isolated from TSLP-activated DCs and co-cultured with CD4+ T cells. Western blot and ELISA assays were used to measure the levels of OX40L, IFN-γ, and IL-4 in DCs and CD4+ T cells. Flow cytometry was applied to detect Th1 and Th2 cells. <b><i>Results:</i></b> OX40L and IL-4 were increased and IFN-γ was decreased in serum from asthmatic patients compared with healthy controls. TSLP induced DCs to express OX40L in released exosomes, which could promote proliferation of CD4+ T cells, elevate the level of IL-4, and promote Th2 differentiation. <b><i>Conclusion:</i></b> Blockade of OX40L in DC-derived exosomes could inhibit exosome-mediated CD4+ T proliferation and Th2 differentiation.
DOI: 10.6084/m9.figshare.7315238
title: Supplementary Material for: Hospital Volume and Mortality following Diagnostic Bronchoscopy in Lung Cancer Patients: Data from a National Inpatient Database in Japan

description: <b><i>Background:</i></b> Recent advances in bronchoscopy utilizing endobronchial ultrasound (EBUS) as well as lung cancer therapy may have driven physicians to perform diagnostic bronchoscopy (DB) for high-risk patients. <b><i>Objectives:</i></b> The aim of this study was to clarify the relationship between hospital volume (HV) and outcomes of DB. <b><i>Methods:</i></b> We collected data on inpatients with lung cancer who underwent DB from July 2010 to March 31, 2014. The annual HV of DB was classified as “very low” (≤50 cases/year), “low” (51–100 cases/year), “high” (101–300 cases/year), or “very high” (&gt; 300 cases/year). The primary outcome was all-cause 7-day mortality after DB. Multivariable logistic regression fitted with a generalized estimation equation was performed to evaluate the association between HV and all-cause 7-day mortality after DB, adjusted for patient background factors. <b><i>Results:</i></b> We identified a total of 77,755 eligible patients in 954 hospitals. All-cause 7-day mortality was 0.5%. Compared with the low-volume group, 7-day mortality was significantly lower in the high-volume group (odds ratio [OR] = 0.69, 95% confidence interval [CI]: 0.52–0.92, <i>p</i> = 0.010), and a similar trend was shown in the very-high-volume group (OR = 0.67; 95% CI: 0.43–1.05, <i>p</i> = 0.080). Radial EBUS with the guide sheath method and EBUS-guided transbronchial needle aspiration showed a significantly lower 7-day mortality. <b><i>Conclusions:</i></b> All-cause 7-day mortality was inversely associated with HV. The risk of DB in patients with lung cancer should be recognized, and the exploitation of EBUS may help reduce mortality after DB.
DOI: 10.6084/m9.figshare.7315241.v1
title: Supplementary Material for: Exosomes from Thymic Stromal Lymphopoietin-Activated Dendritic Cells Promote Th2 Differentiation through the OX40 Ligand

description: <b><i>Objectives:</i></b> Exosomes are extracellular vesicles released from various inflammatory cells, such as T cells, B cells, dendritic cells (DCs), and mast cells, which have been implicated in the modulation of immune response in asthma. This study aimed to investigate whether exosomes from DCs activated by thymic stromal lymphopoietin (TSLP) play a role in T-helper cell differentiation through the OX40 ligand (OX40L). <b><i>Methods:</i></b> Serum samples from patients with asthma were collected to measure the levels of OX40L, T-helper type 1 (Th1) cytokine interferon (IFN)-γ, and T-helper type 2 (Th2) cytokine interleukin (IL)-4 by enzyme-linked immunosorbent assay (ELISA). Exosomes were isolated from TSLP-activated DCs and co-cultured with CD4+ T cells. Western blot and ELISA assays were used to measure the levels of OX40L, IFN-γ, and IL-4 in DCs and CD4+ T cells. Flow cytometry was applied to detect Th1 and Th2 cells. <b><i>Results:</i></b> OX40L and IL-4 were increased and IFN-γ was decreased in serum from asthmatic patients compared with healthy controls. TSLP induced DCs to express OX40L in released exosomes, which could promote proliferation of CD4+ T cells, elevate the level of IL-4, and promote Th2 differentiation. <b><i>Conclusion:</i></b> Blockade of OX40L in DC-derived exosomes could inhibit exosome-mediated CD4+ T proliferation and Th2 differentiation.
DOI: 10.6084/m9.figshare.7315235
title: Table S1 Information on the species and the sequences used for evolutionary analyses in primates (A), rodents (B) and in bats (C).

description: <b>Table S1 Information on the species and the sequences used for evolutionary analyses in primates (A), rodents (B) and in bats (C).</b> <br>The NTCP sequences retrieved from public databases and their corresponding accession numbers are given. The species that were sequenced in this study are highlighted in bold, with their associated accession number deposited in GenBank. The species from which HBV has been previously detected are indicated.
DOI: 10.7284/126034
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1607 using a Furuno GP-150 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315136
title: Mappability resources for GRCh38 using Gencode v26 annotation

description: This item contains mappability resources computed for human genome GRCh38 using gene annotations from GENCODE v26. 75-mers from exons and 36-mers from UTRs were used to compute gene mappability and cross-mappability.
DOI: 10.6084/m9.figshare.7315235.v1
title: Table S1 Information on the species and the sequences used for evolutionary analyses in primates (A), rodents (B) and in bats (C).

description: <b>Table S1 Information on the species and the sequences used for evolutionary analyses in primates (A), rodents (B) and in bats (C).</b> <br>The NTCP sequences retrieved from public databases and their corresponding accession numbers are given. The species that were sequenced in this study are highlighted in bold, with their associated accession number deposited in GenBank. The species from which HBV has been previously detected are indicated.
DOI: 10.7284/126036
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1607 using a Ashtech ADU2 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315136.v1
title: Cross_Mappability_grch38_gencode26

description: This item contains cross-mappability resources computed on human genome GRCh38 using gene annotations from GENCODE v26. 75-mers from exons and 36-mers from UTRs were used to compute gene mappability and cross-mappability.
DOI: 10.7284/126043
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1607 using a Trimble SPS351 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315136.v2
title: Mappability resources for GRCh38 using Gencode v26 annotation

description: This item contains cross-mappability resources computed on human genome GRCh38 using gene annotations from GENCODE v26. 75-mers from exons and 36-mers from UTRs were used to compute gene mappability and cross-mappability.
DOI: 10.6084/m9.figshare.7315079
title: Supplementary Material for: The Effects of Direct Oral Anticoagulants, Warfarin, Aspirin and Thienopyridine on the Performance of Immunochemical, Faecal, Occult Blood Tests

description: <b><i>Aim:</i></b> To clarify whether antithrombotic drugs affect diagnosis using the immunochemical faecal occult blood test ­(iFOBT) of colorectal neoplasia. <b><i>Methods:</i></b> Using the Japan Endoscopy Database from 8 centres between 2015 and 2017, we analyzed data about patients who were iFOBT positive and had received direct oral anticoagulants (DOAC), warfarin, aspirin or thienopyridine. One-to-one matching-analogue propensity score weighted analyses were performed to compare the positive predictive value (PPV) of all neoplasms, invasive and non-invasive colorectal cancers and adenomas between drug users and non-users. All neoplasms included invasive and non-invasive colorectal cancer, and adenomas. <b><i>Results:</i></b> We analyzed 197 DOAC users and 196 non-users, 153 warfarin users and 153 non-users, 408 aspirin users and 415 non-users, and 97 thienopyridine users and 97 non-users. No significant differences were observed in the PPV for all neoplasms (56.67 vs. 50.43%), invasive cancer (4.32 vs. 3.53%), non-invasive cancer (15.58 vs. 15.56%) or adenoma (53.13 vs. 48.09%) between the DOAC user and non-user groups. No significant differences were observed in the PPV for all neoplasia, invasive and non-invasive cancer, or adenoma between warfarin, aspirin and thienopyridine use and non-users. <b><i>Conclusions:</i></b> DOAC, warfarin, aspirin and thienopyridine use did not decrease the PPVs of the iFOBT used to evaluate all colorectal neoplasia.
DOI: 10.7284/126039
title: INS (Inertial Navigation System) data collected during research cruise RR1607 using a iXSea Phins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315079.v1
title: Supplementary Material for: The Effects of Direct Oral Anticoagulants, Warfarin, Aspirin and Thienopyridine on the Performance of Immunochemical, Faecal, Occult Blood Tests

description: <b><i>Aim:</i></b> To clarify whether antithrombotic drugs affect diagnosis using the immunochemical faecal occult blood test ­(iFOBT) of colorectal neoplasia. <b><i>Methods:</i></b> Using the Japan Endoscopy Database from 8 centres between 2015 and 2017, we analyzed data about patients who were iFOBT positive and had received direct oral anticoagulants (DOAC), warfarin, aspirin or thienopyridine. One-to-one matching-analogue propensity score weighted analyses were performed to compare the positive predictive value (PPV) of all neoplasms, invasive and non-invasive colorectal cancers and adenomas between drug users and non-users. All neoplasms included invasive and non-invasive colorectal cancer, and adenomas. <b><i>Results:</i></b> We analyzed 197 DOAC users and 196 non-users, 153 warfarin users and 153 non-users, 408 aspirin users and 415 non-users, and 97 thienopyridine users and 97 non-users. No significant differences were observed in the PPV for all neoplasms (56.67 vs. 50.43%), invasive cancer (4.32 vs. 3.53%), non-invasive cancer (15.58 vs. 15.56%) or adenoma (53.13 vs. 48.09%) between the DOAC user and non-user groups. No significant differences were observed in the PPV for all neoplasia, invasive and non-invasive cancer, or adenoma between warfarin, aspirin and thienopyridine use and non-users. <b><i>Conclusions:</i></b> DOAC, warfarin, aspirin and thienopyridine use did not decrease the PPVs of the iFOBT used to evaluate all colorectal neoplasia.
DOI: 10.6084/m9.figshare.7315064
title: R Analytical code

description: R analytical code for this systematic review
DOI: 10.7284/126044
title: INS (Inertial Navigation System) data collected during research cruise RR1607 using a Kongsberg Seapath 320+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315064.v1
title: R Analytical code

description: R analytical code for this systematic review
DOI: 10.7284/126032
title: Meteorological Station data collected during research cruise RR1607 using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7315049
title: Mappability resources for hg19 using Gencode v19 annotation

description: This dataset contains mappability resources computed on human genome hg19 using gene annotations from GENCODE v19.