cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7809232
title: Alphafold2 models of 47G4 (Hu19) scFv dimers and of VLVL dimers

description: <strong>Alphafold2 models of 47G4 (Hu19) scFv dimers show a variety of swapped VH-VL structures.</strong> Alphafold2 dimers models of scFvs formed from VH and VL domains tend to swap to form diabodies with long linkers as for short linkers. The 47G4 scFv used in this study uses a VL-to-VH scFv construct with a long linker (see sequence in Figure 1) See Supplement files for: The 5 best Alphafold2 models of a predicted 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. In PDB format. The 5 models are ranked by AF2 in files: <strong>ranked_0...4.pdb </strong> The 5 models can be compared by superimposition of the VL domain of chain A: in iCn3D using an iCn3D PNG image file. To see the models and analyze them in 3D, invoke iCn3D with the link: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html ; open “iCn3D PNG image file” using the<strong> file:</strong> <strong>5models_Hu19_scFv_AF2_icn3d_loadable.png</strong> <strong>Alphafold2 models for 47G4 (Hu19) VL-VL dimers</strong> In PDB format. The 25 models are ranked by AF2 in files: <strong>Hu19-VLVL-AF2-ranked_0…24.pdb </strong> Only one out of 25 models offers an inverted interface but offers lower confidence. All other present the canonical interface. <strong>List of PDB structures containing VL-VL quaternary interfaces (PDB accessed on 10/11/2021)</strong> See file: <strong>PDB-</strong><strong>Igs-VLVL-asu+bu-with-over-10contacts.xls</strong> The file represents PDB structures that contain contacting VL domains with more than 10 arbitrary contacts in either the first biological Unit (BU) or asymmetric unit (ASU). Both BU and ASU are used as both may contain valid dimers, as in the the inverted VLVL dimer structure (7JO8) Some <strong>iCn3D links</strong> are provided in the excel file to look and analyze a number of structures. Some links compare 7JO8 to 1REI, or other VLVL parallel vs antiparallel dimer such as 1LVE vs 5LVE. <strong>VLVL based diabody models: canonical and inverted</strong> A model predicted by Alphafold2 version 2.0 for the 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. Supplement file in PDB format: <strong>Hu19-VLVL-diabody-model.pdb</strong> Model building of a scFv dimer using the observed VLVL dimer (7JO8) <strong>Hu19-inverted VLVL-diabody-model.pdb</strong> Both models compared:<strong> VLVLDIAB_VLINVDIAB_icn3d_loadable.png </strong> <em>Where no link is specified, PDBids can be directly loaded in iCn3D using the link</em> https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html
DOI: 10.5281/zenodo.7644235
title: Alphafold2 models of 47G4 (Hu19) scFv dimers and of VLVL dimers

description: <strong>Alphafold2 models of 47G4 (Hu19) scFv dimers show a variety of swapped VH-VL structures.</strong> Alphafold2 dimers models of scFvs formed from VH and VL domains tend to swap to form diabodies with long linkers as for short linkers. The 47G4 scFv used in this study uses a VL-to-VH scFv construct with a long linker (see sequence in Figure 1) See Supplement files for: The 5 best Alphafold2 models of a predicted 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. In PDB format. The 5 models are ranked by AF2 in files: <strong>ranked_0...4.pdb </strong> The 5 models can be compared by superimposition of the VL domain of chain A: in iCn3D using an iCn3D PNG image file. To see the models and analyze them in 3D, invoke iCn3D with the link: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html ; open “iCn3D PNG image file” using the<strong> file:</strong> <strong>5models_Hu19_scFv_AF2_icn3d_loadable.png</strong> <strong>Alphafold2 models for 47G4 (Hu19) VL-VL dimers</strong> In PDB format. The 25 models are ranked by AF2 in files: <strong>Hu19-VLVL-AF2-ranked_0…24.pdb </strong> Only one out of 25 models offers an inverted interface but offers lower confidence. All other present the canonical interface. <strong>List of PDB structures containing VL-VL quaternary interfaces (PDB accessed on 10/11/2021)</strong> See file: <strong>PDB-</strong><strong>Igs-VLVL-asu+bu-with-over-10contacts.xls</strong> The file represents PDB structures that contain contacting VL domains with more than 10 arbitrary contacts in either the first biological Unit (BU) or asymmetric unit (ASU). Both BU and ASU are used as both may contain valid dimers, as in the the inverted VLVL dimer structure (7JO8) Some <strong>iCn3D links</strong> are provided in the excel file to look and analyze a number of structures. Some links compare 7JO8 to 1REI, or other VLVL parallel vs antiparallel dimer such as 1LVE vs 5LVE. <strong>VLVL based diabody models: canonical and inverted</strong> A model predicted by Alphafold2 version 2.0 for the 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. Supplement file in PDB format: <strong>Hu19-VLVL-diabody-model.pdb</strong> Model building of a scFv dimer using the observed VLVL dimer (7JO8) <strong>Hu19-inverted VLVL-diabody-model.pdb</strong> Both models compared:<strong> VLVLDIAB_VLINVDIAB_icn3d_loadable.png </strong> <em>Where no link is specified, PDBids can be directly loaded in iCn3D using the link</em> https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html
DOI: 10.5281/zenodo.7807445
title: Image Dataset

description: Image dataset
DOI: 10.5281/zenodo.7807444
title: Image Dataset

description: Image dataset
DOI: 10.5281/zenodo.7809229
title: Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)

description: Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing.<strong> </strong>This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.
DOI: 10.5281/zenodo.7809228
title: Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)

description: Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing.<strong> </strong>This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.
DOI: 10.5066/p9h8neoy
title: Attributed North American Grid-Based Offshore Sampling Frames

description: This sampling frame is a set of grid-based, finite-area frames spanning the offshore areas surrounding Canada, the United States, and Mexico, and is intended for use with the North American Bat Monitoring Program (NABat). A Generalized Random-Tessellation Stratified (GRTS) Survey Design draw was added to the sample units from the raw sampling grids (https://doi.org/10.5066/P9XBOCVV). The GRTS survey design algorithm assigns a spatially balanced and randomized ordering (GRTS order) to each cell within its respective framework. Grid cells are prioritized numerically; the lower the number, the higher the sampling priority. Cells can then be selected for monitoring following the GRTS order, ensuring both randomization and spatial balance. Monitoring within this standardized framework allows statistical inference to non-surveyed locations and ensures the validity of analyses at regional and range-wide scales. NABat is a continental collaboration including state and provincial, federal, and local agencies intended to standardize the collection and storage of bat data. Alaskan and Canadian waters are combined into a single grid. There are 5 grids in total: Alaska/Canada (AKCAN) Offshore grid, Continental United States (CONUS) Offshore grid, Mexico Offshore grid, Hawaii Offshore Grid, and Caribbean Offshore grid. Grid boundaries are based on World Exclusive Economic Zone oceanic political boundaries and extend into the shoreline 30 kilometers.
DOI: 10.3886/e120570v1-135800
title: Data and Code for: The Legacy of Colonial Medicine in Central Africa

description: Between 1921 and 1956, French colonial governments organized medical campaigns to treat and prevent sleeping sickness. Villagers were forcibly examined and injected with medications with severe, sometimes fatal, side effects. We digitized thirty years of archival records to document the locations of campaign visits at a granular geographic level for five central African countries. We find that greater campaign exposure reduces vaccination rates and trust in medicine -- as measured by willingness to consent to a blood test. We examine relevance for present day health initiatives; World Bank projects in the health sector are less successful in areas with greater exposure.
DOI: 10.5517/ccdc.csd.cc2fk5ls
title: CCDC 2250835: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Marcel Henkelmann, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5mt
title: CCDC 2250836: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Marcel Henkelmann, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5nv
title: CCDC 2250837: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Marcel Henkelmann, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5pw
title: CCDC 2250838: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Marcel Henkelmann, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5qx
title: CCDC 2250839: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Marcel Henkelmann, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5ry
title: CCDC 2250840: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Marcel Henkelmann, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5sz
title: CCDC 2250841: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Marcel Henkelmann, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5t0
title: CCDC 2250842: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Marcel Henkelmann, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5v1
title: CCDC 2250843: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Timo Trageser, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5w2
title: CCDC 2250844: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Timo Trageser, Matthias Wagner|2023|CSD Communication|||
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.cc2fk5x3
title: CCDC 2250845: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte, Timo Trageser, Matthias Wagner|2023|CSD Communication|||
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: 10.5281/zenodo.7809319
title: balearica_pavonina_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7809318
title: balearica_pavonina_decontaminated_gx.fasta.gz

description: .
DOI: 10.25345/c5nv99m64
title: MassIVE MSV000091662 - Molecular dissection and testing of PRSS37 function through LC-MS/MS and the generation of a PRSS37 humanized mouse model
title: LC-MS/MS of Prss37 WT and KO mice male reproductive tract.
DOI: 10.5281/zenodo.7809350
title: cacatua_sulphurea_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7809349
title: cacatua_sulphurea_decontaminated_gx.fasta.gz

description: .
DOI: 10.7278/s50d-40cy-rkf5
title: Dataset for: Panther Tongue - outcrop analog - metric database
DOI: 10.6084/m9.figshare.14267219
title: Tabula Sapiens Single-Cell Dataset

description: v5 of the dataset fixes a bug with the previous versions where the 'sublingual' salivary gland anatomical location was incorrectly labeled 'submandibular'
DOI: 10.7278/s50d-njws-r7tz
title: Panther Tongue virtual outcrop study - Model Files
DOI: 10.3886/e114567v1-135820
title: Replication data for: Adaptation to Climate Change: Evidence from US Agriculture

description: Understanding the potential impacts of climate change on economic outcomes requires knowing how agents might adapt to a changing climate. We exploit large variation in recent temperature and precipitation trends to identify adaptation to climate change in US agriculture, and use this information to generate new estimates of the potential impact of future climate change on agricultural outcomes. Longer run adaptations appear to have mitigated less than half--and more likely none--of the large negative short-run impacts of extreme heat on productivity. Limited recent adaptation implies substantial losses under future climate change in the absence of countervailing investments.
description: United States Farms.
DOI: 10.18112/openneuro.ds004551.v1.0.1
title: testMIproject
DOI: 10.5281/zenodo.7809374
title: geukensia_granosissima_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7809373
title: geukensia_granosissima_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7747335
title: Centrifuge SANBAFPH database for SOVAP

description: <strong>Centrifuge database for Sar, Nematode, Bacteria, Archaea, Fungi, Protozoa, and Human reference and representative genomes (SANBAFPH)</strong> Database type: Centrifuge database Centrifuge version: 1.0.4 Label: 17032023 Sequences: 32,318 Sum length: 25,415,962,902 Assembly summary entries: 4,668 <strong>Summary</strong> In module 2 of the SOVAP pipeline, which is dedicated to the decontamination step, we used Centrifuge software to filter out reads originating from non-viral sources. To achieve this, we created a custom database for Centrifuge called SANBAFPH, which includes reference and representative genomes of <strong>SA</strong>R (Stramenopila, Alveolata, and Rhizaria) <strong>N</strong>ematodes, <strong>B</strong>acteria, <strong>A</strong>rchaea, <strong>F</strong>ungi, <strong>P</strong>rotozoa, and <strong>H</strong>uman. This custom database enables Centrifuge to accurately identify and remove non-viral reads from the virome datasets, resulting in more accurate and reliable viral detection and analysis. -------------------------------------------------------- <strong>SOVAP v.1.3: </strong>GitHub <strong><em>Soil Virome Analysis Pipeline</em></strong> Description The study of viral communities in complex environmental samples, such as <strong>soil</strong>, can provide valuable insights into the diversity and functions of viral communities in the ecosystem. However, processing and analyzing of virome data can be a challenging task that requires the integration of various computational tools and techniques. To address these challenges, we have developed <strong>SOVAP</strong> pipeline that utilizes a suite of state-of-the-art tools for processing, analysis, and annotation viromics and metagenomics data. It utilizes various tools such as <strong>Fastp</strong> and <strong>Centrifuge</strong> for preprocessing and contamination removal, <strong>geNomad</strong>, <strong>Diamond</strong> and <strong>Megan</strong> for identification and annotation of viral contigs which are assembled and clustered using <strong>Megahit</strong> and <strong>CD-HIT</strong>. Additionally, this pipeline provides an <strong>estimate of the abundance</strong> of viral contigs, allowing for a more comprehensive understanding of the virome within the sample. The integration of these tools offers a reliable and effective means of taxonomy classification and annotation of viral contigs, aiding researchers in gaining insight into the composition and function of the virome within the analyzed sample. By integrating the SOVAP pipeline with <strong>IMG/VR</strong> and <strong>geNomad</strong>, it is possible to identify a wider range of viruses, including those that were previously unknown. The <strong>batch-mode</strong> script allows for the processing of multiple datasets using the SOVAP pipeline. This feature is particularly useful for <strong>large-scale</strong> analyses, such as those involving multiple environmental samples or large sequencing datasets.
DOI: 10.5281/zenodo.7747334
title: Centrifuge SANBAFPH database for SOVAP

description: <strong>Centrifuge database for Sar, Nematode, Bacteria, Archaea, Fungi, Protozoa, and Human reference and representative genomes (SANBAFPH)</strong> Database type: Centrifuge database Centrifuge version: 1.0.4 Label: 17032023 Sequences: 32,318 Sum length: 25,415,962,902 Assembly summary entries: 4,668 <strong>Summary</strong> In module 2 of the SOVAP pipeline, which is dedicated to the decontamination step, we used Centrifuge software to filter out reads originating from non-viral sources. To achieve this, we created a custom database for Centrifuge called SANBAFPH, which includes reference and representative genomes of <strong>SA</strong>R (Stramenopila, Alveolata, and Rhizaria) <strong>N</strong>ematodes, <strong>B</strong>acteria, <strong>A</strong>rchaea, <strong>F</strong>ungi, <strong>P</strong>rotozoa, and <strong>H</strong>uman. This custom database enables Centrifuge to accurately identify and remove non-viral reads from the virome datasets, resulting in more accurate and reliable viral detection and analysis. -------------------------------------------------------- <strong>SOVAP v.1.3: </strong>GitHub <strong><em>Soil Virome Analysis Pipeline</em></strong> Description The study of viral communities in complex environmental samples, such as <strong>soil</strong>, can provide valuable insights into the diversity and functions of viral communities in the ecosystem. However, processing and analyzing of virome data can be a challenging task that requires the integration of various computational tools and techniques. To address these challenges, we have developed <strong>SOVAP</strong> pipeline that utilizes a suite of state-of-the-art tools for processing, analysis, and annotation viromics and metagenomics data. It utilizes various tools such as <strong>Fastp</strong> and <strong>Centrifuge</strong> for preprocessing and contamination removal, <strong>geNomad</strong>, <strong>Diamond</strong> and <strong>Megan</strong> for identification and annotation of viral contigs which are assembled and clustered using <strong>Megahit</strong> and <strong>CD-HIT</strong>. Additionally, this pipeline provides an <strong>estimate of the abundance</strong> of viral contigs, allowing for a more comprehensive understanding of the virome within the sample. The integration of these tools offers a reliable and effective means of taxonomy classification and annotation of viral contigs, aiding researchers in gaining insight into the composition and function of the virome within the analyzed sample. By integrating the SOVAP pipeline with <strong>IMG/VR</strong> and <strong>geNomad</strong>, it is possible to identify a wider range of viruses, including those that were previously unknown. The <strong>batch-mode</strong> script allows for the processing of multiple datasets using the SOVAP pipeline. This feature is particularly useful for <strong>large-scale</strong> analyses, such as those involving multiple environmental samples or large sequencing datasets.
DOI: 10.5281/zenodo.7809376
title: carcharhinus_longimanus_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7809375
title: carcharhinus_longimanus_decontaminated_gx.fasta.gz

description: .
DOI: 10.25346/s6/uepjma
title: trusted remote storage test

description: test the trusted remote storage option
DOI: 10.5281/zenodo.7809378
title: carduelis_carduelis_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7809377
title: carduelis_carduelis_decontaminated_gx.fasta.gz

description: .