cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25505/fiz.icsd.cc29bk07
title: CSD 2125298: Experimental Crystal Structure Determination

description: Related Article: M. Wildner, B.A. Zakharov, N.E. Bogdanov, D. Talla, E.V. Boldyreva, R. Miletich|2022|IUCrJ|9|194|doi:10.1107/S2052252521012720
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc29bk18
title: CSD 2125299: Experimental Crystal Structure Determination

description: Related Article: M. Wildner, B.A. Zakharov, N.E. Bogdanov, D. Talla, E.V. Boldyreva, R. Miletich|2022|IUCrJ|9|194|doi:10.1107/S2052252521012720
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc29bk29
title: CSD 2125300: Experimental Crystal Structure Determination

description: Related Article: M. Wildner, B.A. Zakharov, N.E. Bogdanov, D. Talla, E.V. Boldyreva, R. Miletich|2022|IUCrJ|9|194|doi:10.1107/S2052252521012720
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc29bk3b
title: CSD 2125301: Experimental Crystal Structure Determination

description: Related Article: M. Wildner, B.A. Zakharov, N.E. Bogdanov, D. Talla, E.V. Boldyreva, R. Miletich|2022|IUCrJ|9|194|doi:10.1107/S2052252521012720
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc29bk4c
title: CSD 2125302: Experimental Crystal Structure Determination

description: Related Article: M. Wildner, B.A. Zakharov, N.E. Bogdanov, D. Talla, E.V. Boldyreva, R. Miletich|2022|IUCrJ|9|194|doi:10.1107/S2052252521012720
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc27d0ym
title: CSD 2067140: Experimental Crystal Structure Determination

description: Related Article: M. Wildner, B.A. Zakharov, N.E. Bogdanov, D. Talla, E.V. Boldyreva, R. Miletich|2022|IUCrJ|9|194|doi:10.1107/S2052252521012720
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7467566
title: Source Data for the publication: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in Acute Promyelocytic Leukemia

description: Source Data for the publication: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in Acute Promyelocytic Leukemia
DOI: 10.5281/zenodo.7467565
title: Source Data for the publication: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in Acute Promyelocytic Leukemia

description: Source Data for the publication: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in Acute Promyelocytic Leukemia
DOI: 10.5281/zenodo.7467520
title: Binary LCD codes

description: LCD
DOI: 10.5281/zenodo.7467519
title: Binary LCD codes

description: LCD
DOI: 10.23708/cttfqw
title: Analyses of the root-knot nematode (Meloidogyne graminicola) transcriptome during rice (Oryza spp.) infection

description: The plant-parasitic nematode Meloidogyne graminicola causes considerable damages to rice (Oryza sativa) culture. Resistance to M. graminicola in the related species Oryza glaberrima reduces root penetration by juveniles and stops further nematode development. M. graminicola genes expressed during O. sativa (Nipponbare) and O. glaberrima (TOG5681) infection were characterized at different time after infection. M. graminicola RNA-Seq data were retrieved from 14 (7 × 2 replicates) cDNA libraries obtained from pre-parasitic M. graminicola stage-two juveniles (J2s), and from O. sativa cv Nipponbare (susceptible) or O. glaberrima TOG5681 (resistant) plants challenged with M. graminicola. Root tips and galls, when formed, were collected at 2, 4, or 8 dpi. Time points 2, 4, and 8 dpi were chosen to focus on the early stages of the interaction, when gene expression differences may determine the nature of interaction between both partners. We generated a de novo M. graminicola transcriptome composed of 44,137 sequences. We compared the M. graminicola transcriptomes before and during infection to identify M. graminicola genes differentially expressed at 2, 4 and 8 days after infection of susceptible (Nipponbare) or resistant (TOG5681) rice.
DOI: 10.6084/m9.figshare.21757325.v2
title: SITH1 figshare.xlsx

description: Data base
DOI: 10.5281/zenodo.7467196
title: Phase contrast images of bacteria and ground truth segmentations

description: <strong>Name</strong>: Phase contrast images of bacteria <strong>Data type</strong>: Paired microscopy images and corresponding labels/masks used for model training, organized as recommended by the DenoiSeg documentation. <strong>Microscopy data type</strong>: Light microscopy (Phase Contrast) <strong>Manual annotations</strong>: Labels/masks obtained via manual segmentation. For each region, all cells were annotated manually. Uncertain objects were left unannotated. <strong>Microscope</strong>: Zeiss Axio Imager M2 epi-fluorescence microscope with a Zeiss Plan-Apochromat; 100x/1.4 oil DIC objective <strong>File format</strong>: .tif (float 32-bits for phase contrast and 16-bit for mask images) <strong>Image size</strong>: 256x256 pixels (Pixel size: 64.5 nm) Content: train - raw (33 files) - masks (33 files) test - raw (11 files) - masks (11 files) All images available in the raw folders were normalized by dividing the original images with a gaussian blurred version or the original image (200 pixels). A groovy code working within ImageJ/Fiji corresponding to this operation is as follow: <pre><code class="language-java">ImagePlus normalize(ImagePlus input_image) { flatfield = (new Duplicator()).run(input_image) (new GaussianBlur()).blur(flatfield.getProcessor(), 200) return ImageCalculator.run(input_image, flatfield, "Divide create 32-bit") } import ij.ImagePlus import ij.plugin.Duplicator import ij.plugin.ImageCalculator import ij.plugin.filter.GaussianBlur</code></pre>
description: NOTE : This dataset was used to train a DenoiSeg model (https://zenodo.org/record/7467554#.Y6L0sBXMJD8)
DOI: 10.5281/zenodo.7467195
title: Phase contrast images of bacteria and ground truth segmentations

description: <strong>Name</strong>: Phase contrast images of bacteria <strong>Data type</strong>: Paired microscopy images and corresponding labels/masks used for model training, organized as recommended by the DenoiSeg documentation. <strong>Microscopy data type</strong>: Light microscopy (Phase Contrast) <strong>Manual annotations</strong>: Labels/masks obtained via manual segmentation. For each region, all cells were annotated manually. Uncertain objects were left unannotated. <strong>Microscope</strong>: Zeiss Axio Imager M2 epi-fluorescence microscope with a Zeiss Plan-Apochromat; 100x/1.4 oil DIC objective <strong>File format</strong>: .tif (float 32-bits for phase contrast and 16-bit for mask images) <strong>Image size</strong>: 256x256 pixels (Pixel size: 64.5 nm) Content: train - raw (33 files) - masks (33 files) test - raw (11 files) - masks (11 files) All images available in the raw folders were normalized by dividing the original images with a gaussian blurred version or the original image (200 pixels). A groovy code working within ImageJ/Fiji corresponding to this operation is as follow: <pre><code class="language-java">ImagePlus normalize(ImagePlus input_image) { flatfield = (new Duplicator()).run(input_image) (new GaussianBlur()).blur(flatfield.getProcessor(), 200) return ImageCalculator.run(input_image, flatfield, "Divide create 32-bit") } import ij.ImagePlus import ij.plugin.Duplicator import ij.plugin.ImageCalculator import ij.plugin.filter.GaussianBlur</code></pre>
description: NOTE : This dataset was used to train a DenoiSeg model (https://zenodo.org/record/7467554#.Y6L0sBXMJD8)
DOI: 10.6084/m9.figshare.21757325
title: Relationship between Human herpesvirus 6 infection and inflammatory bowel disease using novel biomarker

description: Antibody titers to SITH-1, a protein specific to HHV-6 latent infection, were measured in 163 patients with IBD (107 with ulcerative colitis [UC] and 56 with Crohn's disease [CD]); clinical scores and depression scores of UC and CD were analyzed to examine the relationship between SITH-1 and IBD.
DOI: 10.6084/m9.figshare.21757325.v4
title: Relationship between Human herpesvirus 6 infection and inflammatory bowel disease using novel biomarker

description: Antibody titers to SITH-1, a protein specific to HHV-6 latent infection, were measured in 163 patients with IBD (107 with ulcerative colitis [UC] and 56 with Crohn's disease [CD]); clinical scores and depression scores of UC and CD were analyzed to examine the relationship between SITH-1 and IBD.
DOI: 10.6084/m9.figshare.21757325.v3
title: Relationship between Human herpesvirus 6 infection and inflammatory bowel disease using novel biomarker

description: Antibody titers to SITH-1, a protein specific to HHV-6 latent infection, were measured in 163 patients with IBD (107 with ulcerative colitis [UC] and 56 with Crohn's disease [CD]); clinical scores and depression scores of UC and CD were analyzed to examine the relationship between SITH-1 and IBD.
DOI: 10.17632/6996v22hm5.1
title: LINF_340018500

description: protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.17632/h7c23gbncy.1
title: LINF_340018600

description: protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.17632/d3k72vkgp2.1
title: Factores relevantes del emprendimiento

description: El emprendimiento es un modelo social y económico que tiene como propósito impulsar la creación de empresas. Montar un negocio no es emprendimiento, se requiere de un producto, servicio o proceso innovador para ser catalogado como verdadero emprendimiento. A partir de la identificación de factores relevantes, se puede definir el emprendimiento, como la iniciativa personal de idear, montar y poner en marcha una nueva empresa, y para lograrlo requiere de educación, persistencia, motivación, contactos, habilidades en mercadeo, recursos de capital, apoyo del Estado, de la familia y de la universidad, afrontando riesgos y dificultades como el desánimo y la soledad. El espíritu empresarial es la fuerza interior del emprendedor que lo impulsa a lograr el objetivo de materializar su sueño de ser independiente económicamente mediante la creación y puesta en marcha de su propia nueva empresa.
DOI: 10.17632/kxjv328wmk.1
title: LINF_340019600

description: PTP1-interacting protein
Leishmania infantum (strain JPCM5)
DOI: 10.17632/4yxm85s8yt.1
title: LINF_340020700

description: protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.17632/87g26cddkk.1
title: UEC TEL project

description: NVivo file from TEL welfare project
DOI: 10.5281/zenodo.7271067
title: Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus

description: This repository contains associated datasets and accession numbers for a study entitled '<strong>Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus'</strong>. The scripts for this project can be found on the GitHub project page. Expected composition tsv files are the OTU tables for each simulation performed (001-010). OTU IDs in this case are the expected taxonomy with the associated accession numbers. Samples are numbered 1-40, including the simulation number. Expected sequences fasta files contain the sequences used as input for each simulation, without primers or Illumina adapter sequences. Amplicons were generated using the following primers: <strong>GI Primers </strong><br> GISKF: CTG CCC GAA TTY GTA AAT GA 4<br> GISKR: CCA ACC CAR CCA TTR TAC A 5<br> <br> <strong>GII Primers </strong><br> G2SKF: CNT GGG AGG GCG ATC GCAA 8<br> G2SKR: CCR CCN GCA TRH CCR TTR TAC AT In this study, three databases and multiple classifiers were compared. Here we include the taxonomy and fasta files for each database; noronet =NoroNet RIVM, calicinet= HuCat CDC and custom, randomly generated database. Fasta files for the classifiers include the GI/GII primers listed above in a 5-3 orientation. The tags.txt file contains the Illumina adapters used for the simulation component of the study.
description: {"references": ["lant in Tokyo, Japan. Water Sci Technol. 2006;54(11\u201312):301\u20138. 37.\tKitajima M, Haramoto E, Phanuwan C, Katayama H, Ohgaki S. Detection of genogroup IV norovirus in wastewater and river water in Japan. Lett Appl Microbiol. 2009;49(5):655\u20138.", "Gourl\u00e9 H, Karlsson-Lindsj\u00f6 O, Hayer J, Bongcam-Rudloff E. Simulating Illumina metagenomic data with InSilicoSeq. Bioinformatics. 2019 Feb 1;35(3):521\u20132.", "Kroneman A, Vennema H, Deforche K, Avoort H v. d., Pe\u00f1aranda S, Oberste MS, et al. An automated genotyping tool for enteroviruses and noroviruses. J Clin Virol. 2011;51(2):121\u20135.", "Tatusov RL, Chhabra P, Diez-Valcarce M, Barclay L, Cannon JL, Vinj\u00e9 J. Human Calicivirus Typing tool: A web-based tool for genotyping human norovirus and sapovirus sequences. J Clin Virol. 2020 Dec 13;104718."]}
DOI: 10.17632/f5xc69gjd3.1
title: LINF_340021400

description: protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.7271066
title: Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus

description: This repository contains associated datasets and accession numbers for a study entitled '<strong>Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus'</strong>. The scripts for this project can be found on the GitHub project page. Expected composition tsv files are the OTU tables for each simulation performed (001-010). OTU IDs in this case are the expected taxonomy with the associated accession numbers. Samples are numbered 1-40, including the simulation number. Expected sequences fasta files contain the sequences used as input for each simulation, without primers or Illumina adapter sequences. Amplicons were generated using the following primers: <strong>GI Primers </strong><br> GISKF: CTG CCC GAA TTY GTA AAT GA 4<br> GISKR: CCA ACC CAR CCA TTR TAC A 5<br> <br> <strong>GII Primers </strong><br> G2SKF: CNT GGG AGG GCG ATC GCAA 8<br> G2SKR: CCR CCN GCA TRH CCR TTR TAC AT In this study, three databases and multiple classifiers were compared. Here we include the taxonomy and fasta files for each database; noronet =NoroNet RIVM, calicinet= HuCat CDC and custom, randomly generated database. Fasta files for the classifiers include the GI/GII primers listed above in a 5-3 orientation. The tags.txt file contains the Illumina adapters used for the simulation component of the study.
description: {"references": ["lant in Tokyo, Japan. Water Sci Technol. 2006;54(11\u201312):301\u20138. 37.\tKitajima M, Haramoto E, Phanuwan C, Katayama H, Ohgaki S. Detection of genogroup IV norovirus in wastewater and river water in Japan. Lett Appl Microbiol. 2009;49(5):655\u20138.", "Gourl\u00e9 H, Karlsson-Lindsj\u00f6 O, Hayer J, Bongcam-Rudloff E. Simulating Illumina metagenomic data with InSilicoSeq. Bioinformatics. 2019 Feb 1;35(3):521\u20132.", "Kroneman A, Vennema H, Deforche K, Avoort H v. d., Pe\u00f1aranda S, Oberste MS, et al. An automated genotyping tool for enteroviruses and noroviruses. J Clin Virol. 2011;51(2):121\u20135.", "Tatusov RL, Chhabra P, Diez-Valcarce M, Barclay L, Cannon JL, Vinj\u00e9 J. Human Calicivirus Typing tool: A web-based tool for genotyping human norovirus and sapovirus sequences. J Clin Virol. 2020 Dec 13;104718."]}
DOI: 10.17632/7t2xj9zfhk.1
title: LINF_340022100

description: protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.17632/89y3v4y424.1
title: LINF_340021300

description: D-isomer specific 2-hydroxyacid dehydrogenase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/cv4y7fmsh3.1
title: LINF_340021200

description: D-isomer specific 2-hydroxyacid dehydrogenase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/cw549y4cz7.1
title: LINF_340021100

description: D-isomer specific 2-hydroxyacid dehydrogenase
Leishmania infantum (strain JPCM5)
DOI: 10.22008/fk2/fw9wfv/km8i9g
title: Supplementary file_Sliwinska_et_al.20211117.xlsx

description: :unav
DOI: 10.17632/x2skst5jg7.1
title: zircon U-Pb geochronlogical and Ar-Ar thermochronlogical data in Gyaca county, NE Himalaya

description: The data include zircon U-Pb age of a intermediate dike (Table S1-sample STV01-mendeley), and 39Ar-40Ar thermochronology result of mica quartz phyllite (Table S2-Ar-Ar data-mendeley) from the Gyaca mélange zone in Gyaca county, NE Himalaya. Sample STV01 was collected from the intermediate dikes and parrlleled to the replaced cleavages of folds, while sample DX2085 was collected from the matrix of Gyaca mélanges near the dikes. The intermediate dikes intruded the Gyaca mélange along the foliation S2 (axial plane cleavage) and remoulded each other, indiacating the syntectonic relationship and the deformation timing of folding. Fourteen zircons among twenty two dated grains obtained from sample STV01 (Appendix 2) show concordance of >95% yielded weighted mean 206Pb/238U age of 55.29±0.54 Ma (MSWD=0.85), suggesting that the folding deformation happened nearly simultaneous in the Early Eocene. Steps 2 to 5 of muscovite 39Ar-40Ar data from sample DX2085 yileded a plateau age of 55.78±0.14 Ma (81.73% of the 39Ar gas release, MSWD=2.38) and an inverse isochron age of 55.62±0.15 Ma (MSWD=4.2). The sub-particle rotation recrystallization and bulging recrystallization of quartz particles from sample DX2085 indicate a deformation temperature range of 380°~420°, exceeding the closure temperature of muscovite(~350°), which implies the 39Ar-40Ar age can be used to constrain the timing of the contraction deformation in the Gyaca mélange zone. The positive flower structural style in the upper Triassic tectonostratigraphy in NE Himalaya implies intense contraction deformation and contemporaneous folding between the Gyaca mélange zone and the Langjiexue fold-thrust belt. Combined with the regional geological background, consequently, the dramatical contraction deformation in the NE Tethyan Himalaya should begin after the Early Cretaceous, and it’s most likely to take place in the Early Eocene (55~56 Ma) through the India-Asia collision rather than in the Early Cretaceous by the collision of the “Longzi block” and an intra-oceanic arc.
DOI: 10.17632/x2skst5jg7.2
title: zircon U-Pb geochronlogical and Ar-Ar thermochronlogical data in Gyaca county, NE Himalaya

description: The data include zircon U-Pb age of a intermediate dike (Table S1-sample STV01-mendeley), and 39Ar-40Ar thermochronology result of mica quartz phyllite (Table S2-Ar-Ar data-mendeley) from the Gyaca mélange zone in Gyaca county, NE Himalaya. Sample STV01 was collected from the intermediate dikes and parrlleled to the replaced cleavages of folds, while sample DX2085 was collected from the matrix of Gyaca mélanges near the dikes. The intermediate dikes intruded the Gyaca mélange along the foliation S2 (axial plane cleavage) and remoulded each other, indiacating the syntectonic relationship and the deformation timing of folding. Fourteen zircons among twenty two dated grains obtained from sample STV01 (Appendix 2) show concordance of >95% yielded weighted mean 206Pb/238U age of 55.29±0.54 Ma (MSWD=0.85), suggesting that the folding deformation happened nearly simultaneous in the Early Eocene. Steps 2 to 5 of muscovite 39Ar-40Ar data from sample DX2085 yileded a plateau age of 55.78±0.14 Ma (81.73% of the 39Ar gas release, MSWD=2.38) and an inverse isochron age of 55.62±0.15 Ma (MSWD=4.2). The sub-particle rotation recrystallization and bulging recrystallization of quartz particles from sample DX2085 indicate a deformation temperature range of 380°~420°, exceeding the closure temperature of muscovite(~350°), which implies the 39Ar-40Ar age can be used to constrain the timing of the contraction deformation in the Gyaca mélange zone. The positive flower structural style in the upper Triassic tectonostratigraphy in NE Himalaya implies intense contraction deformation and contemporaneous folding between the Gyaca mélange zone and the Langjiexue fold-thrust belt. Combined with the regional geological background, consequently, the dramatical contraction deformation in the NE Tethyan Himalaya should begin after the Early Cretaceous, and it’s most likely to take place in the Early Eocene (55~56 Ma) through the India-Asia collision rather than in the Early Cretaceous by the collision of the “Longzi block” and an intra-oceanic arc.
DOI: 10.17632/7rsxyfsnd5.1
title: Early childhood caries development

description: Early childhood caries development
DOI: 10.17632/8kctvy79pd.1
title: LINF_340020900

description: protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.17632/64vzwdcm2p.1
title: AMAMENTAÇÃO

description: Fontes e referências para capítulo de Equipamentos e Tecnologias em amamentação do Manual de Casas de Parto do município de São Paulo