cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23729/965084e4-1b75-4f8d-bb51-f055b2caa191
title: Reference databases for Lazypipe project

description: Reference databases for metagenomic NGS analysis. Project repository: https://bitbucket.org/plyusnin/lazypipe/src/master/ Project website: https://www2.helsinki.fi/en/projects/lazypipe NCBI NT: Database: Minimap index for NCBI NT archaea, bacteria and viruses. 17'673'705 sequences, 392'552'172'949 bp. File: minimap.nt.abv.2023_05_16.tar.gz Database: Minimap index for NCBI NT viruses. 9'326'301 sequences, 194'755'318'770 bp. File: minimap.nt.vi.2023_06_16.tar.gz Database: BLASTN index for NCBI NT archaea and bacteria. 8'347'404 sequences, 197'796'854'179 bp. File: blast.nt.ab.2023_05_16.tar.gz Database: BLASTN index for NCBI NT viruses. 9,326,301 sequences, 194,755,318,770 bp. File: blast.nt.vi.2023_05_16.tar.gz RefSeq: Database: Minimap index for RefSeq archaea (complete, reference/representative genomes), bacteria (complete, reference/representative genomes) and viruses. 27'160 sequences, 20'170'978'762 bp. File: minimap.refseq.release219.v2.tar.gz Database: Minimap index for RefSeq archaea, bacteria (complete genomes) and viruses. 202'371 sequences, 150'389'307'001 bp. File: minimap.refseq.release219.tar.gz Database: Minimap index for RefSeq viruses. 18'689 sequences, 551'600'706 bp. File: minimap.refseq.release219.tar.gz Database: BLASTN index for RefSeq archaea and bacteria (complete, reference/representative genomes). 8,472 sequences, 19,619,389,195 bp. File: blast.refseq.ab.release219.v2.tar.gz Database: BLASTN index for RefSeq archaea and bacteria. 183,682 sequences, 149,837,706,295 bp. File: blast.refseq.ab.release219.tar.gz Database: BLASTN index for RefSeq viruses. 18,689 sequences, 551,600,706 bp. File: blast.refseq.vi.release2019.tar.gz UniRef100: Database: BLASTP index for UniRef100 archaea and bacteria. 148,440,747 sequences, 47,899,033,773 bp. File: blast.uniref100.ab.2023_06_28.tar.gz Database: BLASTP index for UniRef100 viruses. 3,034,688 sequences and 1,132,717,918 bp. File: blast.uniref100.vi.2023_06_28.tar.gz Citing: Plyusnin, Ilya, Olli Vapalahti, Tarja Sironen, Ravi Kant, and Teemu Smura. “Enhanced Viral Metagenomics with Lazypipe 2.” Viruses 15, no. 2 (February 4, 2023): 431. https://doi.org/10.3390/v15020431.
DOI: 10.21227/6vrd-0002
title: 5条鱼实验数据

description: Collective intelligence in biological groups can be employed to inspire the control of artificial complex systems, such as swarm robotics. However, modeling for the social interactions between individuals is still a challenging task. Without loss of generality, we propose a deep attention network model that incorporates the principles of biological Hard Attention mechanisms, that means an individual only pay attention to one or two neighbors for collective motion decision in large group. The model is trained by the collective movement data of 5 rummy-nose tetra fish (Hemigrammus rhodostomus). The structure of the model enforces individual agents to consider information from at most two neighboring agents. Meanwhile, the model can reveal hidden locations, where highly influential neighbors frequently appear. These findings demonstrate that the proposed Hard Attention model aligns with the information processing mechanisms, which is observed in fish schooling. Experimental results indicate that the model exhibits a strong ability to decouple sparse information for collective movement with robust metrics. It can also perform excellent scalability in different group sizes. The simulation and real robots experiment show that the model provides a powerful tool for analyzing multi-level behaviors in complex systems and offers significant insights for the distributed control of swarm robotics.
DOI: 10.5281/zenodo.7897832
title: Replication package for "WIA-SZZ: Work Item Aware SZZ"

description: This dataset includes scripts and data files used to generate all analysis and results from the paper. A <strong>README.md</strong> file is included for details on using the scripts.
DOI: 10.5281/zenodo.8277864
title: Replication package for "WIA-SZZ: Work Item Aware SZZ"

description: This dataset includes scripts and data files used to generate all analysis and results from the paper. A <strong>README.md</strong> file is included for details on using the scripts. For replication purposes, a copy of the cloned repositories from Rosa et al. (dowloaded as of to Dec. 2022) is provided through 7 Zenodo links: 1. https://zenodo.org/record/8285106 (doi: 10.5281/zenodo.8285106) 2. https://zenodo.org/record/8285119 (doi: 10.5281/zenodo.8285119) 3. https://zenodo.org/record/8285121 (doi: 10.5281/zenodo.8285121) 4. https://zenodo.org/record/8285125 (doi: 10.5281/zenodo.8285125) 5. https://zenodo.org/record/8285127 (doi: 10.5281/zenodo.8285127) 6. https://zenodo.org/record/8285138 (doi: 10.5281/zenodo.8285138) 7. https://zenodo.org/record/8285140 (doi: 10.5281/zenodo.8285140)
DOI: 10.21227/rmfj-7790
title: 100 agents move in a cluster

description: Collective intelligence in biological groups can be employed to inspire the control of artificial complex systems, such as swarm robotics. However, modeling for the social interactions between individuals is still a challenging task. Without loss of generality, we propose a deep attention network model that incorporates the principles of biological Hard Attention mechanisms, that means an individual only pay attention to one or two neighbors for collective motion decision in large group. The model is trained by the collective movement data of 5 rummy-nose tetra fish (Hemigrammus rhodostomus). The structure of the model enforces individual agents to consider information from at most two neighboring agents. Meanwhile, the model can reveal hidden locations, where highly influential neighbors frequently appear. These findings demonstrate that the proposed Hard Attention model aligns with the information processing mechanisms, which is observed in fish schooling. Experimental results indicate that the model exhibits a strong ability to decouple sparse information for collective movement with robust metrics. It can also perform excellent scalability in different group sizes. The simulation and real robots experiment show that the model provides a powerful tool for analyzing multi-level behaviors in complex systems and offers significant insights for the distributed control of swarm robotics.
DOI: 10.34740/kaggle/ds/3694504
title: Social Event Face Recognition
DOI: 10.6084/m9.figshare.23671647.v4
title: The landscape of abiotic and biotic stress-responsive splice variants using RNA-seq datasets in hot pepper

description: <b>1.Supplementary table 1.xlsx</b>: <b>Supplementary Table 1. Overview of the pepper transcriptomes used in this study</b><br><b>2.Supplementary figure.zip</b>: <b>Supplementary Figure 1. </b><b>Quality assessment of raw read preprocessing </b><b>on 129 </b><b>raw RNA-seq datasets from </b><b><i>C. annuum</i></b><b> infected with </b><b><i>P. </i></b><b><i>capsici</i></b><b>, TMV-P2, Xag8ra, and </b><b>Xcv.</b> (a-d) Quality scores of reads for <i>P. </i><i>capsici</i>, TMV-P2, Xag8ra, and Xcv, respectively. <i>X</i>-axis represents mean sequence quality (Phred score) and y-axis represents read counts.. (e-h) Graphs for quality scores per position. The <i>x</i>-axis represents the position (bp), and the <i>y</i>-axis Phred score.: <b>Supplementary Figure 2.</b><b> </b><b>P</b><b>rincipal </b><b>components analysis (PCA) for RNA-seq datasets infected with biotic stressors in hot pepper. </b>PCA plots with normalized data of (a) <i>P. </i><i>capsici</i><i>; </i>(b) TMV-P2; (c) Xag8ra; (d) Xcv1; (e) Xcv3.: <b>Supplementary Figure 3. </b><b>Proportion of alternative splicing events detected in hot pepper under different conditions. </b>The stacked bar plot indicates the number of alternative splicing events in response to biotic and abiotic stressors, developmental stages, and phytohormones. Blue, exon skipping (SE); yellow, intron retention (RI); light grey, mutually exclusive exons (MXE); green, alternative 5’ splice site (A5SS); pink, alternative 3’ splice site (A3SS).<br><b>3.Statistical summary of mapping rates.xlsx</b>: Information about mapping rates for 428 RNA-seq datasets<br><b>4.Information of AS events results.7z</b>: AS events information under environmental stressors, developmental stages, and phytohormones<br><b>5.Supplementary File 1.xlsx</b>: Gene list of shared DAS genes under different conditions.Sheet 1 (Abio&Biotic&Tissue&Phytohormone): Gene list of shared DAS genes under abiotic, biotic stressors, developmental stages, and phytohormonesSheet 2 (Abiotic&Biotic&Tissue): Gene list of shared DAS genes under abiotic, biotic stressors, and developmental stagesSheet3 (Abiotic&Tissue): Gene list of shared DAS genes under abiotic stressors and developmental stagesSheet4 (Biotic&Tissue): Gene list of shared DAS genes under biotic stressors and developmental stages<br><b>6.Code availability. zip</b>: <b>1. Annotated gene_filtering.pl</b> - Filtering code of transcripts containing two or more annotated genes: <b>2. Stop codon_filtering.pl </b>- Filtering code of transcripts that didn't have a stop codon: <b>3. AS_counting code.pl</b> - code for counting the number of AS: <b>4. </b><b>DAS_gene_counting code.pl</b> - code for counting the DAS genes
DOI: 10.6084/m9.figshare.24099345
title: Tmaps of 13 components

description: MRI statistic dataVoxel-based intergroup comparisons of FC were performed in 13 RSNs (ICs) within their respective mask, and age, sex, and education were controlled. Here are the case-control T maps obtained by using two-sample T-tests.
DOI: 10.6084/m9.figshare.24099345.v1
title: Tmaps of 13 components

description: MRI statistic dataVoxel-based intergroup comparisons of FC were performed in 13 RSNs (ICs) within their respective mask, and age, sex, and education were controlled. Here are the case-control T maps obtained by using two-sample T-tests.
DOI: 10.21227/ebzh-dh30
title: Robot experimental data

description: Collective intelligence in biological groups can be employed to inspire the control of artificial complex systems, such as swarm robotics. However, modeling for the social interactions between individuals is still a challenging task. Without loss of generality, we propose a deep attention network model that incorporates the principles of biological Hard Attention mechanisms, that means an individual only pay attention to one or two neighbors for collective motion decision in large group. The model is trained by the collective movement data of 5 rummy-nose tetra fish (Hemigrammus rhodostomus). The structure of the model enforces individual agents to consider information from at most two neighboring agents. Meanwhile, the model can reveal hidden locations, where highly influential neighbors frequently appear. These findings demonstrate that the proposed Hard Attention model aligns with the information processing mechanisms, which is observed in fish schooling. Experimental results indicate that the model exhibits a strong ability to decouple sparse information for collective movement with robust metrics. It can also perform excellent scalability in different group sizes. The simulation and real robots experiment show that the model provides a powerful tool for analyzing multi-level behaviors in complex systems and offers significant insights for the distributed control of swarm robotics.
DOI: 10.15151/esrf-es-1299129381
title: IBS BAG

description: The IBS BAG includes in this proposal IBS teams and external groups from CEA-Cadarache (St Paul lez Durance) and IRBA (Brétigny-sur-Orge). We study structure-function relationships of proteins emphasizing in human health, biotechnology and methodology. Most of the projects are a continuation of the MX-2398 proposal and can be grouped into different topics as follows: host-pathogen interaction, new drug targets, fundamental cellular mechanisms, membrane proteins, biotechnological applications and methodology. Some of these projects use integrative approaches (X-ray crystallography, SAXS, NMR (and cryo-EM), together with other biophysical studies) with the aim to fully understand the complexity of the biological macromolecular systems on study.
DOI: 10.15151/esrf-es-1299170379
title: Heidelberg BAG (HeidelBAG)

description: The HeidelBAG unites macromolecular crystallography of EMBL Heidelberg and the Heidelberg University Biochemistry Center (BZH). Central to all projects are large assemblies involved in chromosome organization and transcription control, in nuclear and cytoplasmic RNA regulation and modification, in translational control by ribosome associated factors or further in protein targeting, membrane protein insertion or post-translational modification. While O. Barabas from EMBL has left the BAG, Svetlana Dodonova and Sebastian Eustermann at EMBL will join and add projects on chromatin organization. Nearly all projects make use of integrated structural biology techniques (MX, SAXS/SANS, NMR, cryo-EM, AI approaches) that are combined with complementary methods, a strategy that warranties the continuous success of the BAG. More and more the detailed architecture and mechanistic description of entire macromolecular machines come into focus. The BAG reports on 17 publications and 30 PDB entries.
DOI: 10.15151/esrf-es-1303533524
title: Structural Biology of macromolecules and macromolecular complexes from India

description: Structural biology research groups located in India constitute the INDIA-BAG and will utilize MX, SAXS and CryoEM to study different biological macromolecules. The non-proprietary agreement signed between ESRF and the Regional Centre for Biotechnology (RCB), on behalf of the Department of Biotechnology (DBT) enables studies that provide fundamental insight regarding different biological processes . About 50 groups are part of this BAG and the allocated beamtime will be available for over 500 young researchers. A brief description of all the research groups is provided in the global summary. The ESRF-India partnership is supported by a grant provided by the DBT. Please note that a comprehensive annual report has to be sent to the DBT to obtain release of funds to pay ESRF membership dues. Consequently, all the structural biologists from India are grouped in a single BAG to enable smooth allocation of beamtime and monitoring of progress to collect the required statistics.
DOI: 10.15151/esrf-es-1302901770
title: Aquatic particulate organic matter: assembly, growth, and global structure

description: Particulate Organic Matter (POM), forms and grows in the oceans from colloidal-size precursors, and its sedimentation to the ocean floor represent a major sink of the global carbon cycle. For a more accurate modeling of POM formation, a better insight in its structure, formation rates and underlying aggregation mechanisms is needed. To this end, we propose USAXS experiments covering the sub-micron to micron length scale regime to monitor the structural evolution of nascent POM from model precursors over time, as a function of solution conditions.
DOI: 10.15151/esrf-es-1302902268
title: Eigenstrain Analysis of Residual Stress Relaxation due to Heat Treatment of Additively Manufactured Bodies

description: In this study, highly accurate experimental data obtained from post printing heat treated LPBF additively manufactured body using the strain tomography technique, that was developed using the measurements in ESRF in 2006, will be used for the determination of creep properties, the eigenstrain reconstruction of full-field residual strains, strain relaxation and creep strain, and the analysis of PPHT parameters. The proposed experiment is the continuation of previous successful experiment that was performed using as-printed LPBF additively manufactured body at the beam-time of Proposal MA5208 awarded by ESRF. Full field eigenstrain reconstruction of residual stresses will be conducted after diffraction data collected from 5 planes and processed using the strain tomography technique. The data collection of this technique is similar to the conventional absorption tomography, but the set-up used for strain tomography quantifies lattice spacing rather than density.
DOI: 10.15151/esrf-es-1302904542
title: Resolving the mechanism of ferroelectricity in hexagonal barium titanate

description: Ferroelectric ceramics form critical components of contemporary electronic devices due to their technologically appealing electromechanical properties. The cubic perovskite BaTiO3 comprises one of the most renowned ferroelectrics, where co-operative displacements of the Ti4+ cations along the &lt;111&gt; lattice direction produce the macroscopic polarisation. BaTiO3 can also exist in a hexagonal polymorph (h-BaTiO3), which – despite also being ferroelectric – has attracted surprisingly little attention. Moreover, the mechanism of ferroelectricity in this material has remained contentious owing to its insufficient structural characterisation. We seek to resolve the controversy regarding its ferroelectric ground state by performing a variable-temperature synchrotron X-ray diffraction (S-XRD) study. This will inform how ferroelectric properties can be engineered into similar structural architectures, informing the design of multifunctional ceramic materials for future electronic devices.
DOI: 10.15151/esrf-es-1259505667
title: Multi-scale Multi-techniques investigations of Li-ion batteries: towards a European Battery Hub

description: In this science-driven Long-Term proposal, we propose a 3-years multi-beamline program tackling grand challenges for actual, emerging and future battery technologies. We will deploy advanced methodologies for accelerating research by setting new cooperation modes for multi-techniques multi-scale studies. Three chemistry-neutral scientific cases have been identified to fulfil this LTP: bulk-to-surface mechanisms, high energy system and smart sensing. Multiple, time-coordinated, interoperable spectroscopic, imaging & scattering techniques will be implemented. This proposal is the Pilot Phase towards a European Battery Hub aiming at accelerating workflows in battery research by optimizing the exceptional diversity of means available at ESRF. We expect to demonstrate the added value of a new “proposal” mechanism, e.g. science-driven beamtime allocation group, serving the fast growing, highly competitive and rapidly evolving European battery community.
DOI: 10.15151/esrf-es-1317654864
title: Nanoscale X-ray fluorescence and phase contrast imaging of diverse materials

description: Nanoscale X-ray fluorescence and phase contrast imaging of diverse materials
DOI: 10.34740/kaggle/dsv/6428526
title: Indian Food 16
DOI: 10.5517/ccdc.csd.cc2dbzrh
title: CCDC 2215097: Experimental Crystal Structure Determination

description: Related Article: Soňa Kohúteková, Irena Matulková, Martin Zábranský, Jaime Lledó Martín, Ivana Císařová, Róbert Gyepes, Petr Němec, Marlena Gryl, Tomasz Seidler, Ivan Němec|2023|J.Solid State Chem.|327|124288|doi:10.1016/j.jssc.2023.124288
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.cc2dbzsj
title: CCDC 2215098: Experimental Crystal Structure Determination

description: Related Article: Soňa Kohúteková, Irena Matulková, Martin Zábranský, Jaime Lledó Martín, Ivana Císařová, Róbert Gyepes, Petr Němec, Marlena Gryl, Tomasz Seidler, Ivan Němec|2023|J.Solid State Chem.|327|124288|doi:10.1016/j.jssc.2023.124288
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.cc2dbztk
title: CCDC 2215099: Experimental Crystal Structure Determination

description: Related Article: Soňa Kohúteková, Irena Matulková, Martin Zábranský, Jaime Lledó Martín, Ivana Císařová, Róbert Gyepes, Petr Němec, Marlena Gryl, Tomasz Seidler, Ivan Němec|2023|J.Solid State Chem.|327|124288|doi:10.1016/j.jssc.2023.124288
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.cc2dbzvl
title: CCDC 2215100: Experimental Crystal Structure Determination

description: Related Article: Soňa Kohúteková, Irena Matulková, Martin Zábranský, Jaime Lledó Martín, Ivana Císařová, Róbert Gyepes, Petr Němec, Marlena Gryl, Tomasz Seidler, Ivan Němec|2023|J.Solid State Chem.|327|124288|doi:10.1016/j.jssc.2023.124288
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.cc2dbzwm
title: CCDC 2215101: Experimental Crystal Structure Determination

description: Related Article: Soňa Kohúteková, Irena Matulková, Martin Zábranský, Jaime Lledó Martín, Ivana Císařová, Róbert Gyepes, Petr Němec, Marlena Gryl, Tomasz Seidler, Ivan Němec|2023|J.Solid State Chem.|327|124288|doi:10.1016/j.jssc.2023.124288
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.cc2dbzxn
title: CCDC 2215102: Experimental Crystal Structure Determination

description: Related Article: Soňa Kohúteková, Irena Matulková, Martin Zábranský, Jaime Lledó Martín, Ivana Císařová, Róbert Gyepes, Petr Němec, Marlena Gryl, Tomasz Seidler, Ivan Němec|2023|J.Solid State Chem.|327|124288|doi:10.1016/j.jssc.2023.124288
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.cc2dbzyp
title: CCDC 2215103: Experimental Crystal Structure Determination

description: Related Article: Soňa Kohúteková, Irena Matulková, Martin Zábranský, Jaime Lledó Martín, Ivana Císařová, Róbert Gyepes, Petr Němec, Marlena Gryl, Tomasz Seidler, Ivan Němec|2023|J.Solid State Chem.|327|124288|doi:10.1016/j.jssc.2023.124288
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.