cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4121/6ca3d747-ac81-4571-be33-af1948b0dfba.v1
title: Data Underlying OD poster at ESSA in Glasgow in 2023

description: The data are aggregated opinion averages over time of polls on a 5-point scale concerning questions about climate change and the energy transition. This is the data repository for the poster I made for the ESSA conference in Glasgow 2023. My aim with this was to get a first grip on inverse modelling and share what I have learned with the community. I'm happy to share the poster for more context and content upon request via lschubotz@tudelft.nl. I gratefully acknowledge the support of Populytics in this research project who provided the data. Here, I provide the aggregated data as it went into the model. Column 1 is the time stamp, column 2 is the value I used, the latter being the aggregated mean value of the votes during that time stamp.
DOI: 10.5281/zenodo.10664032
title: Creuzburg Kloster Apotheke

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963[Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.5281/zenodo.10664033
title: Creuzburg Kloster Apotheke

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963[Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.5281/zenodo.10653836
title: Top quark pair production with fully hadronic final states at the LHC

description: This public dataset was used to develop HyPER (Hypergraph for Particle Event Reconstruction).

HyPER uses blended graph-hypergraph representation learning to reconstruct short-lived particles produced at the LHC.

Production

Software



Matrix Elements (ME) and NLO Matching: MadGraph5_aMC@NLO (v2.9.16 LTS) at \(\sqrt{s}=13\) TeV.

Parton Distribution Function (PDF): NNPDF3.0nlo from LHAPDF6 (v6.3.0).

Parton Shower: PYTHIA8 (v8.306).

Detector: Delphes (v3.5.0), ATLAS detector geometry.

Jet Reconstruction: Fastjet (v3.4.0), anti-\(k_t\) algorithm with \(R=0.4\)


Jet truth matching

Jets are matched to their originating particles using the \(\Delta R\) truth matching scheme. If the angular distance between a particle and its nearest jet satisfies \(\Delta R < 0.4\), then the jet is matched to the particle. We use the following integer labels in jet_truthmatch: 0, 1, 2, 3, 4, 5, 6 ("not matched", b1, W1q1, W1q2, b2, W2q1, W2q2).

Event selections



Events contain at least 6 jets, of which 2 or more are b-tagged.

At least one identifiable W boson (two jets are matched to the decays of a W boson).

Reconstructed jets have a minimum \(p_T\) of 25 GeV and an absolute pseudorapidity \(|\eta|<2.5\).


Dataset Information




 
Training
Validation
Testing
Size-reduced


Dataset name
ttbar_train.root
ttbar_val.root
ttbar_test.root
ttbar_reduced.root


Internal ID
762705-{0-53}
762705-{54-56}
762705-{57-59}
Sampled from ttbar_train.root


Number of events*
54M
3M
3M
3M


Pass selections
7,921,299
439,692
440,069
439,598


Both tops matched
2,116,231
117,487
116,960
117,812


Max number of jets
20
20
18
20




*Only events that have passed selections are saved.

Dataset structure

Events are saved in ROOT files. They have the following structure:

- Delphes
---- njet     // Int; Number or jets
---- nbTagged // Int; Number of b-tagged jets
---- allMatchedEvent  // Int; Event is fully matched (1 or 0)
---- leastOneMatchedW // Int; Event contains at least one matched W (1 or 0)
---- jet_pt         // vector<float>; Transverse momentum of jets
---- jet_eta        // vector<float>; Pseudo-rapidity of jets
---- jet_phi        // vector<float>; Azimuthal angle of jets
---- jet_e          // vector<float>; Energy of jets
---- jet_m          // vector<float>; Invariant mass of jets
---- jet_bTag       // vector<int>; B-tagging status of jets---- jet_truthmatch // vector<int>; DeltaR jet truth matching results
---- particle_pid   // vector<int>; Particle PDGID
---- particle_pt    // vector<float>; Transverse momentum of particles
---- particle_eta   // vector<float>; Pseudo-rapidity of particles
---- particle_phi   // vector<float>; Azimuthal angle of particles
---- particle_m     // vector<float>; Invariant mass of particles

jet_* branches containing information on the final-state jets. Information on short-lived particles is obtained from generator history are saved to particle_* branches.
DOI: 10.5281/zenodo.10653837
title: Top quark pair production with fully hadronic final states at the LHC

description: This public dataset was used to develop HyPER (Hypergraph for Particle Event Reconstruction).

HyPER uses blended graph-hypergraph representation learning to reconstruct short-lived particles produced at the LHC.

Production

Software



Matrix Elements (ME) and NLO Matching: MadGraph5_aMC@NLO (v2.9.16 LTS) at \(\sqrt{s}=13\) TeV.

Parton Distribution Function (PDF): NNPDF3.0nlo from LHAPDF6 (v6.3.0).

Parton Shower: PYTHIA8 (v8.306).

Detector: Delphes (v3.5.0), ATLAS detector geometry.

Jet Reconstruction: Fastjet (v3.4.0), anti-\(k_t\) algorithm with \(R=0.4\)


Jet truth matching

Jets are matched to their originating particles using the \(\Delta R\) truth matching scheme. If the angular distance between a particle and its nearest jet satisfies \(\Delta R < 0.4\), then the jet is matched to the particle. We use the following integer labels in jet_truthmatch: 0, 1, 2, 3, 4, 5, 6 ("not matched", b1, W1q1, W1q2, b2, W2q1, W2q2).

Event selections



Events contain at least 6 jets, of which 2 or more are b-tagged.

At least one identifiable W boson (two jets are matched to the decays of a W boson).

Reconstructed jets have a minimum \(p_T\) of 25 GeV and an absolute pseudorapidity \(|\eta|<2.5\).


Dataset Information




 
Training
Validation
Testing
Size-reduced


Dataset name
ttbar_train.root
ttbar_val.root
ttbar_test.root
ttbar_reduced.root


Internal ID
762705-{0-53}
762705-{54-56}
762705-{57-59}
Sampled from ttbar_train.root


Number of events*
54M
3M
3M
3M


Pass selections
7,921,299
439,692
440,069
439,598


Both tops matched
2,116,231
117,487
116,960
117,812


Max number of jets
20
20
18
20




*Only events that have passed selections are saved.

Dataset structure

Events are saved in ROOT files. They have the following structure:

- Delphes
---- njet     // Int; Number or jets
---- nbTagged // Int; Number of b-tagged jets
---- allMatchedEvent  // Int; Event is fully matched (1 or 0)
---- leastOneMatchedW // Int; Event contains at least one matched W (1 or 0)
---- jet_pt         // vector<float>; Transverse momentum of jets
---- jet_eta        // vector<float>; Pseudo-rapidity of jets
---- jet_phi        // vector<float>; Azimuthal angle of jets
---- jet_e          // vector<float>; Energy of jets
---- jet_m          // vector<float>; Invariant mass of jets
---- jet_bTag       // vector<int>; B-tagging status of jets---- jet_truthmatch // vector<int>; DeltaR jet truth matching results
---- particle_pid   // vector<int>; Particle PDGID
---- particle_pt    // vector<float>; Transverse momentum of particles
---- particle_eta   // vector<float>; Pseudo-rapidity of particles
---- particle_phi   // vector<float>; Azimuthal angle of particles
---- particle_m     // vector<float>; Invariant mass of particles

jet_* branches containing information on the final-state jets. Information on short-lived particles is obtained from generator history are saved to particle_* branches.
DOI: 10.6084/m9.figshare.18093071
title: Additional file 3 of Genome-wide identification and expression analysis of the coronatine-insensitive 1 (COI1) gene family in response to biotic and abiotic stresses in Saccharum

description: Additional file 3: Table S1. Identification of COI1 genes in different plants. Table S2. Conserved amino acid residues of COI1 proteins among different groups. Table S3. Characterization of SbCOI1, ShCOI1, and SsCOI1 genes. Table S4. Secondary structure analysis of SbCOI1, ShCOI1, and SsCOI1 proteins. Table S5. Percentage of identity between 7 SbCOI1s, 6 ShCOI1s, and 21 SsCOI1s was calculated using DNAMAN software. Table S6. Ten conserved motifs predicted in the COI1 proteins. Table S7. The gene type of COI1 genes in Sorghum bicolor, Saccharum spp. hybrid cultivar R570, and Saccharum spontaneum. Table S8. Syntenic relationships and selection pressure among Sorghum bicolor, Saccharum spp. hybrid cultivar R570, and Saccharum spontaneum. Table S9. Promoter cis-regulatory elements analysis of SbCOI1, ShCOI1, and SsCOI1 genes. Table S10. Sources of COI1 genes from sequenced species included in this study. Table S11 Primers used in this study.
DOI: 10.6084/m9.figshare.18093071.v1
title: Additional file 3 of Genome-wide identification and expression analysis of the coronatine-insensitive 1 (COI1) gene family in response to biotic and abiotic stresses in Saccharum

description: Additional file 3: Table S1. Identification of COI1 genes in different plants. Table S2. Conserved amino acid residues of COI1 proteins among different groups. Table S3. Characterization of SbCOI1, ShCOI1, and SsCOI1 genes. Table S4. Secondary structure analysis of SbCOI1, ShCOI1, and SsCOI1 proteins. Table S5. Percentage of identity between 7 SbCOI1s, 6 ShCOI1s, and 21 SsCOI1s was calculated using DNAMAN software. Table S6. Ten conserved motifs predicted in the COI1 proteins. Table S7. The gene type of COI1 genes in Sorghum bicolor, Saccharum spp. hybrid cultivar R570, and Saccharum spontaneum. Table S8. Syntenic relationships and selection pressure among Sorghum bicolor, Saccharum spp. hybrid cultivar R570, and Saccharum spontaneum. Table S9. Promoter cis-regulatory elements analysis of SbCOI1, ShCOI1, and SsCOI1 genes. Table S10. Sources of COI1 genes from sequenced species included in this study. Table S11 Primers used in this study.
DOI: 10.6084/m9.figshare.19665972
title: Exclusive Enteral Nutrition Exerts Anti-Inflammatory Effects Through Modulating Microbiota, Bile Acid Metabolism, and Immune Activities

description: Data sets include:
1. Gut microbiota relative abundance table (generated from metaphlan3)
2. Quantification of bile acids in the stool samples of pediatric CD patients.
3. Flow cytometry result figures for each PBMC sample.
DOI: 10.6084/m9.figshare.12850229
title: Differential DNA methylomes of clinical MDR, XDR and XXDR <i>Mycobacterium tuberculosis</i> isolates revealed by using single-molecule real-time sequencing

description: Post-replicative DNA methylation is essential for diverse biological processes in both eukaryotes and prokaryotes. <i>Mycobacterium tuberculosis</i> (<i>M. tuberculosis</i>), the causative agent of tuberculosis, remains one of the most formidable threats worldwide. Although DNA methylation of <i>M. tuberculosis</i> has been documented, little information is available for clinical drug-resistant <i>M. tuberculosis</i>. Single-molecule real-time (SMRT) sequencing was used to profile the core methylome of three clinical isolates, namely multidrug-resistant (MDR), extensively drug-resistant (XDR) and extremely drug-resistant (XXDR) strains. 3812, 6808 and 6041 DNA methylated sites were identified in MDR-MTB, XDR-MTB and XXDR-MTB genome, respectively. There are two types of methylated motifs, namely N<sup>6</sup>-methyladenine (m6A) and N<sup>4</sup>-methylcytosine (m4C). A novel widespread 6 mA methylation motif 5′-CACGCAG-3′ was found in XDR-MTB and XXDR-MTB. The methylated genes are involved in multiple cellular processes, especially metabolic enzymes engaged in glucose metabolism, fatty acid and TCA cycle. Many methylated genes are involved in mycobacterial virulence, antibiotic resistance and tolerance. This provided a comprehensive list of methylated genes in drug-resistant clinical isolates and the basis for further functional elucidation.
DOI: 10.6084/m9.figshare.12850229.v1
title: Differential DNA methylomes of clinical MDR, XDR and XXDR <i>Mycobacterium tuberculosis</i> isolates revealed by using single-molecule real-time sequencing

description: Post-replicative DNA methylation is essential for diverse biological processes in both eukaryotes and prokaryotes. <i>Mycobacterium tuberculosis</i> (<i>M. tuberculosis</i>), the causative agent of tuberculosis, remains one of the most formidable threats worldwide. Although DNA methylation of <i>M. tuberculosis</i> has been documented, little information is available for clinical drug-resistant <i>M. tuberculosis</i>. Single-molecule real-time (SMRT) sequencing was used to profile the core methylome of three clinical isolates, namely multidrug-resistant (MDR), extensively drug-resistant (XDR) and extremely drug-resistant (XXDR) strains. 3812, 6808 and 6041 DNA methylated sites were identified in MDR-MTB, XDR-MTB and XXDR-MTB genome, respectively. There are two types of methylated motifs, namely N<sup>6</sup>-methyladenine (m6A) and N<sup>4</sup>-methylcytosine (m4C). A novel widespread 6 mA methylation motif 5′-CACGCAG-3′ was found in XDR-MTB and XXDR-MTB. The methylated genes are involved in multiple cellular processes, especially metabolic enzymes engaged in glucose metabolism, fatty acid and TCA cycle. Many methylated genes are involved in mycobacterial virulence, antibiotic resistance and tolerance. This provided a comprehensive list of methylated genes in drug-resistant clinical isolates and the basis for further functional elucidation.
DOI: 10.6084/m9.figshare.18093182
title: Additional file 2 of Membrane tension sensing molecule-FNBP1 is a prognostic biomarker related to immune infiltration in BRCA, LUAD and STAD

description: Additional file 2. Supplementary Tables.
DOI: 10.6084/m9.figshare.18093182.v1
title: Additional file 2 of Membrane tension sensing molecule-FNBP1 is a prognostic biomarker related to immune infiltration in BRCA, LUAD and STAD

description: Additional file 2. Supplementary Tables.
DOI: 10.6084/m9.figshare.12850310
title: MiR-200a and miR-200b restrain inflammation by targeting ORMDL3 to regulate the ERK/MMP-9 pathway in asthma

description: Asthma is one of the most frequent and serious diseases worldwide. Inflammation has been reported to correlate with airway remodeling, which is critical for the progression of asthma. Better understanding of novel molecules modulating asthma and the underlying mechanism will benefit explorations of new treatments. <b>Method:</b> To explore the role of miR-200a and miR-200b in asthma, miR-200a mimics/inhibitor and miR-200b mimics/inhibitor were employed in A549 cells, respectively. Expression levels of inflammatory cytokines, including TNF-α, IL-4, IL-5, IL-13 and IL-1β, were measured by quantitative real time polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA). A dual luciferase reporter assay was performed to identify whether miR-200a/200b directly bound to Orosomucoid 1-like 3 (ORMDL3). ERK, p-ERK and MMP-9, involved in downstream pathways of ORMDL3, were detected using qRT-PCR and western blotting. <b>Results:</b> MiR-200a/200b silencing significantly increased the expression of inflammatory cytokines, including TNF-α, IL-4, IL-5, IL-13 and IL-1β, in A549 cells. ORMDL3 was the target gene of miR-200a/200b, with high expression levels in miR-200a inhibitor and miR-200b inhibitor groups. MiR-200a and miR-200b played synergistic roles in the regulation of the inflammatory effect in A549 cells. Expression levels of p-ERK and MMP-9 were significantly increased in miR-200a inhibitor and miR-200b inhibitor groups and were rescued by ERK inhibitor and MMP-9 inhibitor, respectively. <b>Conclusion:</b> These findings suggest that miR-200a and miR-200b are required to regulate asthma inflammation. Reduction in miR-200a/200b promotes the development of asthma inflammation by targeting ORMDL3 to activate the ERK/MMP-9 pathway. Therefore, elevating miR-200a and miR-200b and decreasing ORMDL3 might be potential strategies for inhibition of the asthma process.
DOI: 10.6084/m9.figshare.12850310.v1
title: MiR-200a and miR-200b restrain inflammation by targeting ORMDL3 to regulate the ERK/MMP-9 pathway in asthma

description: Asthma is one of the most frequent and serious diseases worldwide. Inflammation has been reported to correlate with airway remodeling, which is critical for the progression of asthma. Better understanding of novel molecules modulating asthma and the underlying mechanism will benefit explorations of new treatments. <b>Method:</b> To explore the role of miR-200a and miR-200b in asthma, miR-200a mimics/inhibitor and miR-200b mimics/inhibitor were employed in A549 cells, respectively. Expression levels of inflammatory cytokines, including TNF-α, IL-4, IL-5, IL-13 and IL-1β, were measured by quantitative real time polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA). A dual luciferase reporter assay was performed to identify whether miR-200a/200b directly bound to Orosomucoid 1-like 3 (ORMDL3). ERK, p-ERK and MMP-9, involved in downstream pathways of ORMDL3, were detected using qRT-PCR and western blotting. <b>Results:</b> MiR-200a/200b silencing significantly increased the expression of inflammatory cytokines, including TNF-α, IL-4, IL-5, IL-13 and IL-1β, in A549 cells. ORMDL3 was the target gene of miR-200a/200b, with high expression levels in miR-200a inhibitor and miR-200b inhibitor groups. MiR-200a and miR-200b played synergistic roles in the regulation of the inflammatory effect in A549 cells. Expression levels of p-ERK and MMP-9 were significantly increased in miR-200a inhibitor and miR-200b inhibitor groups and were rescued by ERK inhibitor and MMP-9 inhibitor, respectively. <b>Conclusion:</b> These findings suggest that miR-200a and miR-200b are required to regulate asthma inflammation. Reduction in miR-200a/200b promotes the development of asthma inflammation by targeting ORMDL3 to activate the ERK/MMP-9 pathway. Therefore, elevating miR-200a and miR-200b and decreasing ORMDL3 might be potential strategies for inhibition of the asthma process.
DOI: 10.6084/m9.figshare.12850316
title: Bile acids, lipid and purine metabolism involved in hepatotoxicity of first-line anti-tuberculosis drugs

description: Rifampin (RIF), isoniazid (INH) and pyrazinamide (PZA) are essential components of the short-term first-line anti-tuberculosis (anti-TB) chemotherapy regimen and can cause hepatotoxicity. However, the mechanism of anti-TB drug-induced hepatotoxicity (ATDH) is currently unclear. We investigate the relevant contributions to liver injury and the pathway of the above-mentioned drugs administered alone or in combination. UPLC-Q-TOF/MS-based metabolomics, bile acids (BAs) analysis and FXR/SHP detection were used to evaluate the toxicity of these drugs and clarify the underlying metabolism-related pathway. In C57BL/6 mice administered the corrected clinical doses, RIF, INH and PZA could induced hepatotoxicity; with less toxicity in the combination therapy than RIF. The pathological biochemistry, BAs concentration and metabolically regulated FXR/SHP gene expression analyzes in mice were consistent with the metabolomics results. FXR played a role in the hepatotoxicity of anti-tuberculosis drugs in the obeticholic acid treated and FXR<sup>-/-</sup> mice. Additionally, the purine and lipid metabolic pathways were involved in ATDH. ATDH was involved in bile acids and lipid and purine metabolism. The BAs metabolic pathway involvement in mice was validated in TB patients. The noninvasive metabolomics approach is more systemic than routine toxicity evaluation and can be used to assess compound toxicity and the underlying mechanism.
DOI: 10.6084/m9.figshare.12850316.v1
title: Bile acids, lipid and purine metabolism involved in hepatotoxicity of first-line anti-tuberculosis drugs

description: Rifampin (RIF), isoniazid (INH) and pyrazinamide (PZA) are essential components of the short-term first-line anti-tuberculosis (anti-TB) chemotherapy regimen and can cause hepatotoxicity. However, the mechanism of anti-TB drug-induced hepatotoxicity (ATDH) is currently unclear. We investigate the relevant contributions to liver injury and the pathway of the above-mentioned drugs administered alone or in combination. UPLC-Q-TOF/MS-based metabolomics, bile acids (BAs) analysis and FXR/SHP detection were used to evaluate the toxicity of these drugs and clarify the underlying metabolism-related pathway. In C57BL/6 mice administered the corrected clinical doses, RIF, INH and PZA could induced hepatotoxicity; with less toxicity in the combination therapy than RIF. The pathological biochemistry, BAs concentration and metabolically regulated FXR/SHP gene expression analyzes in mice were consistent with the metabolomics results. FXR played a role in the hepatotoxicity of anti-tuberculosis drugs in the obeticholic acid treated and FXR<sup>-/-</sup> mice. Additionally, the purine and lipid metabolic pathways were involved in ATDH. ATDH was involved in bile acids and lipid and purine metabolism. The BAs metabolic pathway involvement in mice was validated in TB patients. The noninvasive metabolomics approach is more systemic than routine toxicity evaluation and can be used to assess compound toxicity and the underlying mechanism.
DOI: 10.6084/m9.figshare.18093158
title: Additional file 2 of Iodine-125 seed represses the growth and facilitates the apoptosis of colorectal cancer cells by suppressing the methylation of miR-615 promoter

description: Additional file 2..
DOI: 10.6084/m9.figshare.12850373
title: The risk factors for delayed bleeding after endoscopic resection of colorectal tumors: a meta-analysis

description: The most common complication of post-colorectal endoscopic resection is delayed bleeding. The assessment of risk factors for delayed bleeding provides important and useful information in standard clinical operations. The risk factors have been previously reported; however, they remain inconsistent across different studies. In this meta-analysis, the patient conditions, lesion-related factors, and operation-related factors were compared between delayed bleeding and no bleeding. PubMed, Cochrane, Embase, China National Knowledge Infrastructure (CNKI), and Wanfang Database were searched to identify eligible studies. Pooled odds ratio (OR) and 95% confidence intervals (CI) were calculated along with heterogeneity. This study is the first meta-analysis to investigate risk factors for colorectal delayed bleeding. We found several risk factors contributing to this condition: colorectal tumors located in the proximal colon, a history of antithrombotic drug use, high-grade intraepithelial neoplasia or early cancer, piecemeal resection, intraoperative hemorrhage, no clip placement, and severe submucosal fibrosis. Despite our findings, we also conclude that more high-quality, large-scale clinical randomized controlled studies are needed due to limited retrospective studies at present. Future therapeutic colonoscopies should focus on precise diagnosis, treatment safety, and management during the perioperative period.