cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25149108.v1
title: Gasque et al 2024_S2_For_survival_analysis from Baculovirus entry into the central nervous system of <i>Spodoptera exigua</i> caterpillars is independent of the viral protein tyrosine phosphatase

description: Neuroparasitism concerns the hostile take-over of a host's nervous system by a foreign invader, in order to alter the behaviour of the host in favour of the parasite. One of the most remarkable cases of parasite-induced host behavioural manipulation comprises the changes baculoviruses induce in their caterpillar hosts. Baculoviruses may manipulate caterpillar behaviour in two ways: hyperactivity (increased movement in the horizontal plane) and/or tree-top disease (movement to elevated levels in the vertical plane). Those behavioural changes are followed by liquefaction and death of the caterpillar. In <i>Autographa californica</i> multiple nucleopolyhedrovirus (AcMNPV)-infected <i>Spodoptera exigua</i> caterpillars, an enzymatic active form of the virally encoded protein tyrosine phosphatase (PTP) is needed for the expression of hyperactivity from 3 days post infection (dpi). Using eGFP-expressing recombinant AcMNPV strains, we show that infection of the caterpillar's central nervous system (CNS) can be observed primarily from 3 dpi onwards. In addition, we demonstrate that the structural and enzymatic function of PTP does not play a role in infection of the CNS. Instead we show that the virus entered the CNS via the trachea, progressing caudally to frontally through the CNS and that the infection progressed from the outermost cell layers towards the inner cell layers of the CNS, in a PTP independent manner. These findings help to further understand parasitic manipulation and the mechanisms by which neuroparasites infect the host nervous system to manipulate host behaviour.
DOI: 10.6084/m9.figshare.25149108
title: Gasque et al 2024_S2_For_survival_analysis from Baculovirus entry into the central nervous system of <i>Spodoptera exigua</i> caterpillars is independent of the viral protein tyrosine phosphatase

description: Neuroparasitism concerns the hostile take-over of a host's nervous system by a foreign invader, in order to alter the behaviour of the host in favour of the parasite. One of the most remarkable cases of parasite-induced host behavioural manipulation comprises the changes baculoviruses induce in their caterpillar hosts. Baculoviruses may manipulate caterpillar behaviour in two ways: hyperactivity (increased movement in the horizontal plane) and/or tree-top disease (movement to elevated levels in the vertical plane). Those behavioural changes are followed by liquefaction and death of the caterpillar. In <i>Autographa californica</i> multiple nucleopolyhedrovirus (AcMNPV)-infected <i>Spodoptera exigua</i> caterpillars, an enzymatic active form of the virally encoded protein tyrosine phosphatase (PTP) is needed for the expression of hyperactivity from 3 days post infection (dpi). Using eGFP-expressing recombinant AcMNPV strains, we show that infection of the caterpillar's central nervous system (CNS) can be observed primarily from 3 dpi onwards. In addition, we demonstrate that the structural and enzymatic function of PTP does not play a role in infection of the CNS. Instead we show that the virus entered the CNS via the trachea, progressing caudally to frontally through the CNS and that the infection progressed from the outermost cell layers towards the inner cell layers of the CNS, in a PTP independent manner. These findings help to further understand parasitic manipulation and the mechanisms by which neuroparasites infect the host nervous system to manipulate host behaviour.
DOI: 10.18419/darus-3859/65
title: WINSENT_tower.iges

description: WINSENT Wind turbine geometry, approximate, but close to reality: Laser-scan generated CAD iges file of the wind turbine tower. The tower is rotated away from the z-axis to account for the rotor shaft angle, aligning with the blade located at the bottommost position. The blade's spanwise direction is along the z-axis, and its pitch axis is at x=0, y=0. The geometry of the tower is thus maintained within the same coordinate system.
DOI: 10.6084/m9.figshare.25217628
title: Data_for_Figure 2 from Bet-hedging and variability in plant development: seed germination and beyond

description: Germination times and seedling survival measurements for data in Figure 2
DOI: 10.6084/m9.figshare.25217628.v1
title: Data_for_Figure 2 from Bet-hedging and variability in plant development: seed germination and beyond

description: Germination times and seedling survival measurements for data in Figure 2
DOI: 10.6084/m9.figshare.25217631
title: Code_for_Figure 2 from Bet-hedging and variability in plant development: seed germination and beyond

description: R code to generate plots in Figure 2
DOI: 10.6084/m9.figshare.25217631.v1
title: Code_for_Figure 2 from Bet-hedging and variability in plant development: seed germination and beyond

description: R code to generate plots in Figure 2
DOI: 10.5517/ccdc.csd.cc2dm1tx
title: CCDC 2222849: Experimental Crystal Structure Determination

description: Related Article: Takuya Kodama, Kenta Uchida, Chihiro Nakasuji, Ryohei Kishi, Yasutaka Kitagawa, Mamoru Tobisu|2023|Inorg.Chem.|62|7861|doi:10.1021/acs.inorgchem.3c00583
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.cc2dm1vy
title: CCDC 2222850: Experimental Crystal Structure Determination

description: Related Article: Takuya Kodama, Kenta Uchida, Chihiro Nakasuji, Ryohei Kishi, Yasutaka Kitagawa, Mamoru Tobisu|2023|Inorg.Chem.|62|7861|doi:10.1021/acs.inorgchem.3c00583
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.cc2frf0n
title: CCDC 2256831: Experimental Crystal Structure Determination

description: Related Article: Takuya Kodama, Kenta Uchida, Chihiro Nakasuji, Ryohei Kishi, Yasutaka Kitagawa, Mamoru Tobisu|2023|Inorg.Chem.|62|7861|doi:10.1021/acs.inorgchem.3c00583
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: 10.25345/c5fq9qg9h
title: MassIVE MSV000094077 - Proteomics profiling of bilirubin nanoparticle treatment against myocardial ischemia-reperfusion injury
title: In myocardial infarction, ischemia-reperfusion injury (IRI) poses a significant challenge due to a lack of effective treatments. Bilirubin, a natural compound known for its anti-inflammatory and antioxidant properties, has been identified as a potential therapeutic agent for IRI. The Biology/Disease-driven Human Proteome Project (B/D-HPP) of the Human Proteome Project (HPP) has conducted proteomic research on various diseases and phenomena using human samples as well as model animals, however there is no report about the proteomic studies related to IRI and bilirubin treatment. In this study, we explored the effects of bilirubin nanoparticles in a rat model of myocardial IRI. A total of 3,621 protein groups comprising 76,681 distinct peptides were identified using LC-MS/MS, where, we distinguished two kinds of protein groups: those showing increased expression in IRI and decreased expression in IRI with bilirubin treatment, and vice versa, accounting for 202 and 35 proteins, respectively. Our proteomic analysis identified significant upregulation in the Wnt and insulin signaling pathways and increased Golgi markers, indicating their role in mediating bilirubin nanoparticle's protective effects. This research contributes to the proteomic understanding of myocardial IRI and suggests bilirubin nanoparticles as a promising strategy for cardiac protection, warranting further investigation in human models.
DOI: 10.6084/m9.figshare.25217762
title: Benue South Computer Knowledge and Utilization Dataset

description: Data collected for a quantitative cross-sectional study in 120 health facilities, involving 430 healthcare workers in Benue South, Nigeria targeted at measuring computer knowledge and utilization and factors that influence both.
DOI: 10.6084/m9.figshare.25217762.v1
title: Benue South Computer Knowledge and Utilization Dataset

description: Data collected for a quantitative cross-sectional study in 120 health facilities, involving 430 healthcare workers in Benue South, Nigeria targeted at measuring computer knowledge and utilization and factors that influence both.
DOI: 10.6084/m9.figshare.23585301
title: <b>An urban cellular automata model based on a spatiotemporal non-stationary neighborhood</b>

description: This project is intended to publicly disclose the data and code of this study after the publication of the paper.
DOI: 10.6084/m9.figshare.23585301.v1
title: <b>基于时空非平稳邻域的城市元胞自动机模型</b>

description: 本项目用于在论文发表后公开披露本研究的数据和代码。
DOI: 10.6084/m9.figshare.25039971
title: Ustekinumab safety and effectiveness in patients with ulcerative colitis: results from a large real-life study

description: Ustekinumab (UST) is an interleukin-12/interleukin-23 receptor antagonist recently approved for treating ulcerative colitis (UC) but with limited real-world data. Therefore, we evaluated the effectiveness and safety of UST in patients with UC in a real-world setting. This is a multicenter, retrospective, observational cohort study. The primary endpoints were the clinical remission rate (partial Mayo score, PMS, ≤1) and the safety of UST. Other endpoints were corticosteroid-free remission (CSFR) rate, clinical response rate (PMS reduction of at least 2 points), and fecal calprotectin (FC) reduction at week 24. We included 256 consecutive patients with UC (M/F 139/117, median age 52). The clinical remission and clinical response rates at eight weeks were 18.7% (44/235) and 53.2% (125/235), respectively, and 27.6% (42/152) and 61.8% (94/152) at 24 weeks, respectively. At 24 weeks, CSFR was 20.3% (31/152), and FC significantly dropped at week 12 (<i>p</i> = 0.0004) and 24 (<i>p</i> = 0.038). At eight weeks, patients naïve or with one previous biologic treatment showed higher remission (<i>p</i> = 0.002) and clinical &gt;response rates (<i>p</i> = 0.018) than patients previously treated with ≥ 2. Adverse events occurred in six patients (2.3%), whereas four patients (1.6%) underwent colectomy. This real-world study shows that UST effectively and safely treats patients with UC.
DOI: 10.6084/m9.figshare.25039971.v1
title: Ustekinumab safety and effectiveness in patients with ulcerative colitis: results from a large real-life study

description: Ustekinumab (UST) is an interleukin-12/interleukin-23 receptor antagonist recently approved for treating ulcerative colitis (UC) but with limited real-world data. Therefore, we evaluated the effectiveness and safety of UST in patients with UC in a real-world setting. This is a multicenter, retrospective, observational cohort study. The primary endpoints were the clinical remission rate (partial Mayo score, PMS, ≤1) and the safety of UST. Other endpoints were corticosteroid-free remission (CSFR) rate, clinical response rate (PMS reduction of at least 2 points), and fecal calprotectin (FC) reduction at week 24. We included 256 consecutive patients with UC (M/F 139/117, median age 52). The clinical remission and clinical response rates at eight weeks were 18.7% (44/235) and 53.2% (125/235), respectively, and 27.6% (42/152) and 61.8% (94/152) at 24 weeks, respectively. At 24 weeks, CSFR was 20.3% (31/152), and FC significantly dropped at week 12 (<i>p</i> = 0.0004) and 24 (<i>p</i> = 0.038). At eight weeks, patients naïve or with one previous biologic treatment showed higher remission (<i>p</i> = 0.002) and clinical &gt;response rates (<i>p</i> = 0.018) than patients previously treated with ≥ 2. Adverse events occurred in six patients (2.3%), whereas four patients (1.6%) underwent colectomy. This real-world study shows that UST effectively and safely treats patients with UC.
DOI: 10.5281/zenodo.8403177
title: Simulation dataset and plotting scripts used for journal article "Impact of acidity and surface modulated acid dissociation on cloud response to organic aerosol" by Sengupta et al. (2024)

description: Simulation data underlying all figures presented in "Impact of acidity and surface modulated acid dissociation on cloud response to organic aerosol" by Sengupta et al. (2024). DOI: 10.5194/acp-24-1467-2024

The data for each figure and the plotting scripts are included in a zip file labelled by the figure number as presented in the paper and accompanying supplement.
DOI: 10.5281/zenodo.8403178
title: Simulation dataset and plotting scripts used for journal article "Impact of acidity and surface modulated acid dissociation on cloud response to organic aerosol" by Sengupta et al. (2024)

description: Simulation data underlying all figures presented in "Impact of acidity and surface modulated acid dissociation on cloud response to organic aerosol" by Sengupta et al. (2024). DOI: 10.5194/acp-24-1467-2024

The data for each figure and the plotting scripts are included in a zip file labelled by the figure number as presented in the paper and accompanying supplement.
DOI: 10.5281/zenodo.10652084
title: Training Data for "From reads to (pseudo) counts : guided step by step exploration" tutorial (Galaxy Training Material)

description: A sampled subset of reads, used in the 'From Reads to (Pseudo) Counts: Guided Step-by-Step Exploration' GNT tutorial, which covers RNA-seq analysis including:



Qualitative analysis

Quantification of genes and transcripts (counts and pseudo-counts)

Assembly with reference

Local assembly


This subset is extracted from:

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny, David Monnin, Adil El Filali, Claudia Marcia Carareto, Cristina Vieira, Franck Picard, Natacha Kremer, Fabrice Vavre, Marie-France Sagot, Vincent Lacroix, SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence, Nucleic Acids Research, Volume 44, Issue 19, 2 November 2016, Page e148, https://doi.org/10.1093/nar/gkw655
DOI: 10.5281/zenodo.10652085
title: Training Data for "From reads to (pseudo) counts : guided step by step exploration" tutorial (Galaxy Training Material)

description: A sampled subset of reads, used in the 'From Reads to (Pseudo) Counts: Guided Step-by-Step Exploration' GNT tutorial, which covers RNA-seq analysis including:



Qualitative analysis

Quantification of genes and transcripts (counts and pseudo-counts)

Assembly with reference

Local assembly


This subset is extracted from:

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny, David Monnin, Adil El Filali, Claudia Marcia Carareto, Cristina Vieira, Franck Picard, Natacha Kremer, Fabrice Vavre, Marie-France Sagot, Vincent Lacroix, SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence, Nucleic Acids Research, Volume 44, Issue 19, 2 November 2016, Page e148, https://doi.org/10.1093/nar/gkw655
DOI: 10.5281/zenodo.10601333
title: Code of The certainty mirage in water modelling
DOI: 10.5281/zenodo.10606734
title: Code of The certainty mirage in water modelling
DOI: 10.15151/esrf-es-1470891890
title: CryoEM structure of human MICAL1, the novel multidomain flavoenzyme participating in actin cytoskeleton dynamics

description: MICALs form a family of mainly cytosolic multidomain enzymes that control actin cytoskeleton dynamics. They are peculiar actin-binding proteins as they cause F-actin depolymerisation by oxidation of actin residues thanks to the H2O2-producing NADPH oxidase activity of the N-terminal flavoprotein domain, which is enhanced in the MICAL-F-actin complex. The catalytic domain is followed by several domains, responsible of the control of the activity upon interaction with regulating small molecules and proteins. MICALs participate in cell differentiation, migration, division, vesicle trafficking and even gene expression through their actin depolymerising activity or H2O2 production leading to oxidation of largely unknown target proteins. Elucidating the 3D structure of MICAL1 by cryoEM, will clarify the hypothesised peculiar mode of regulation of the activity, and will be key to devise ways to modulate the enzyme activity in the context of diseases like cancer and neurological disorders.
DOI: 10.14279/depositonce-19824
title: Event-based Background-Oriented Schlieren

description: Schlieren imaging is an optical technique to observe the flow of transparent media, such as air or water, without any particle seeding. However, conventional frame-based techniques require both high spatial and temporal resolution cameras, which impose bright illumination and expensive computation limitations. Event cameras offer potential advantages (high dynamic range, high temporal resolution, and data efficiency) to overcome such limitations due to their bio-inspired sensing principle. This paper presents a novel technique for perceiving air convection using events and frames by providing the first theoretical analysis that connects event data and schlieren. We formulate the problem as a variational optimization one combining the linearized event generation model with a physically-motivated parametrization that estimates the temporal derivative of the air density. The experiments with accurately aligned frame- and event camera data reveal that the proposed method enables event cameras to obtain on par results with existing frame-based optical flow techniques. Moreover, the proposed method works under dark conditions where frame-based schlieren fails, and also enables slow-motion analysis by leveraging the event camera’s advantages. Our work pioneers and opens a new stack of event camera applications, as we publish the source code as well as the first schlieren dataset with high-quality frame and event data.
DOI: 10.5281/zenodo.10656358
title: SOTitle+: Automatic Bi-modal Question Title Generation for Stack Overflow with Prompt Learning

description: Dataset and trained model for our manuscript "SOTitle+: Automatic Bi-modal Question Title Generation for Stack Overflow with Prompt Learning".

The GitHub repository is https://github.com/shaoyuyoung/SOTitlePlus.

SOTitlePlusData.zip includes all the train/valid/test datasets in our experiments which contain eight programming languages.

SOTitlePlusModel.zip includes the .bin model which is trained by Pytorch in RQ1.
DOI: 10.5281/zenodo.10656359
title: SOTitle+: Automatic Bi-modal Question Title Generation for Stack Overflow with Prompt Learning

description: Dataset and trained model for our manuscript "SOTitle+: Automatic Bi-modal Question Title Generation for Stack Overflow with Prompt Learning".

The GitHub repository is https://github.com/shaoyuyoung/SOTitlePlus.

SOTitlePlusData.zip includes all the train/valid/test datasets in our experiments which contain eight programming languages.

SOTitlePlusModel.zip includes the .bin model which is trained by Pytorch in RQ1.
DOI: 10.6084/m9.figshare.22757304
title: Additional file 3 of Integrative multi-omics analysis depicts the methylome and hydroxymethylome in recurrent bladder cancers and identifies biomarkers for predicting PD-L1 expression

description: Additional file 3: Table S2. Significant 5mC differentially methylated regions in bladder cancers, recurrent bladder cancers and PD-L1 highly expressed bladder cancers.
DOI: 10.6084/m9.figshare.22757304.v1
title: Additional file 3 of Integrative multi-omics analysis depicts the methylome and hydroxymethylome in recurrent bladder cancers and identifies biomarkers for predicting PD-L1 expression

description: Additional file 3: Table S2. Significant 5mC differentially methylated regions in bladder cancers, recurrent bladder cancers and PD-L1 highly expressed bladder cancers.
DOI: 10.6084/m9.figshare.22757307
title: Additional file 4 of Integrative multi-omics analysis depicts the methylome and hydroxymethylome in recurrent bladder cancers and identifies biomarkers for predicting PD-L1 expression

description: Additional file 4: Table S3. Significant 5hmC differentially methylated regions in bladder cancers, recurrent bladder cancers and PD-L1 highly expressed bladder cancers.
DOI: 10.6084/m9.figshare.22757307.v1
title: Additional file 4 of Integrative multi-omics analysis depicts the methylome and hydroxymethylome in recurrent bladder cancers and identifies biomarkers for predicting PD-L1 expression

description: Additional file 4: Table S3. Significant 5hmC differentially methylated regions in bladder cancers, recurrent bladder cancers and PD-L1 highly expressed bladder cancers.
DOI: 10.6084/m9.figshare.6504449
title: Analytical Strain-softening Solutions of a spherical cavity

description: ABSTRACT This paper deals with a spherical cavity excavated in infinite homogeneous and isotropic strain-softening rock mass subjected to a hydrostatic initial stresses. By simplifying the strain-softening process of the post-failure region as a Multi-step Brittle-Plastic model (MBPM), analytical solutions of the spherical cavity are derived with the consideration of the deterioration of elastic parameters. Meanwhile, critical deterioration conditions of elastic parameters are established theoretically. Both Mohr-Coulomb (M-C) and Hoek-Brown (H-B) criteria are included in the analysis. The results are compared with those obtained by former numerical methods, and the solutions are validated. Moreover, the presented results show that deteriorated elastic parameters for post-failure rock mass only has a little influence on stresses, softening radius and residual radius, but influences the deformation significantly.
DOI: 10.6084/m9.figshare.6504449.v1
title: Analytical Strain-softening Solutions of a spherical cavity

description: ABSTRACT This paper deals with a spherical cavity excavated in infinite homogeneous and isotropic strain-softening rock mass subjected to a hydrostatic initial stresses. By simplifying the strain-softening process of the post-failure region as a Multi-step Brittle-Plastic model (MBPM), analytical solutions of the spherical cavity are derived with the consideration of the deterioration of elastic parameters. Meanwhile, critical deterioration conditions of elastic parameters are established theoretically. Both Mohr-Coulomb (M-C) and Hoek-Brown (H-B) criteria are included in the analysis. The results are compared with those obtained by former numerical methods, and the solutions are validated. Moreover, the presented results show that deteriorated elastic parameters for post-failure rock mass only has a little influence on stresses, softening radius and residual radius, but influences the deformation significantly.