cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21942/uva.17218484.v1
title: Resampled Bathymetry (GEBCO 2019)

description: <b>DESCRIPTION:</b><br><br> Modern global batymetric map. The original data is GEBCO_2019. The spatial resolution was reduced to 2-minutes grid level.<br><br><b>VALUES: </b><br><br> Average elevation in meters for land and ocean<br><br><b>SPATIAL RESOLUTION:</b><br><br> 120 arc seconds<br><br><b>FILE NAMING:</b><br> <br> File naming: BATHYMETRY.tif<br> <br><br>
DOI: 10.21942/uva.17216081
title: Shelf sea extent rasters (SLW140 2019)

description: <strong>DESCRIPTION:<br> </strong><br> Global paleoreconstruction of shelf sea extent for every 500 yr time period using the global bathymetric model (GEBCO 2019) and a state-of-the-art global spatiotemporal sea level curve. The global sea level curve was generated using the software SELEN4 (10.5281/zenodo.3520451) and raster DEMSRE3a (10.5281/zenodo.1637816). <br> <strong>MAPPED CATEGORIES:</strong><br> <br> 0 = &gt; 0 m BPSL (Below Past Sea Level)<br> 1 = Between 0 and -140 m BPSL<br> <br> <strong>MAPPED NA VALUES:<br> </strong><br> No Data = &lt; -140 m BPSL<br> <br> <strong>SPATIAL RESOLUTION:</strong><br> <br> The spatial resolution of the dataset is a factor 8 of the original GEBCO.<br> <br> <strong>TEMPORAL RESOLUTION:</strong><br> <br> A reconstruction is made for every 500 years from 0 BP to 26000 BP.<br> <br> The dataset is provided in two formats:<br> <br> <strong>1. TILED IN ASCII (SLW_tiles.zip):</strong><br> <br> 53 tiles of 10x10 degrees per folder each representing shallow water for a 500 yr time period.<br> <br> Directory naming:<br> structure: //SLW..asc<br> example: 10/010-020/SLW.005.asc<br> description: Tile with shelf sea extent from 0 to 10 degrees latitude, and 10 to 20 degrees longitude, for 500 yr BP.<br> <br> <strong>2. MOSAIC IN TIF (SLW_mosaic.zip):</strong><br> <br> 53 global maps each presenting shallow water for a 500 yr time period.<br> <br> File naming:<br> structure: SLW.tif<br> example: SLW005.tif<br> description: Global shelf sea extent map for 500 yr BP.<br> <br> <br>
DOI: 10.21942/uva.17216081.v1
title: Shelf sea extent rasters (SLW140 2019)

description: <strong>DESCRIPTION:<br> </strong><br> Global paleoreconstruction of shelf sea extent for every 500 yr time period using the global bathymetric model (GEBCO 2019) and a state-of-the-art global spatiotemporal sea level curve. The global sea level curve was generated using the software SELEN4 (10.5281/zenodo.3520451) and raster DEMSRE3a (10.5281/zenodo.1637816). <br> <strong>MAPPED CATEGORIES:</strong><br> <br> 0 = &gt; 0 m BPSL (Below Past Sea Level)<br> 1 = Between 0 and -140 m BPSL<br> <br> <strong>MAPPED NA VALUES:<br> </strong><br> No Data = &lt; -140 m BPSL<br> <br> <strong>SPATIAL RESOLUTION:</strong><br> <br> The spatial resolution of the dataset is a factor 8 of the original GEBCO.<br> <br> <strong>TEMPORAL RESOLUTION:</strong><br> <br> A reconstruction is made for every 500 years from 0 BP to 26000 BP.<br> <br> The dataset is provided in two formats:<br> <br> <strong>1. TILED IN ASCII (SLW_tiles.zip):</strong><br> <br> 53 tiles of 10x10 degrees per folder each representing shallow water for a 500 yr time period.<br> <br> Directory naming:<br> structure: //SLW..asc<br> example: 10/010-020/SLW.005.asc<br> description: Tile with shelf sea extent from 0 to 10 degrees latitude, and 10 to 20 degrees longitude, for 500 yr BP.<br> <br> <strong>2. MOSAIC IN TIF (SLW_mosaic.zip):</strong><br> <br> 53 global maps each presenting shallow water for a 500 yr time period.<br> <br> File naming:<br> structure: SLW.tif<br> example: SLW005.tif<br> description: Global shelf sea extent map for 500 yr BP.<br> <br> <br>
DOI: 10.5281/zenodo.6811338
title: LEMMIv2 config files for instances and runs, July 2022

description: All yaml configuration files to replicate the content of the https://lemmi.ezlab.org benchmark using the standalone app. See the README.md file.
DOI: 10.5281/zenodo.6811337
title: LEMMIv2 config files for instances and runs, July 2022

description: All yaml configuration files to replicate the content of the https://lemmi.ezlab.org benchmark using the standalone app. See the README.md file.
DOI: 10.5281/zenodo.5601912
title: Biography and History [IO Islamic 2799] تحفة المجاهدين

description: <strong>Biography and History. </strong> <strong>This manuscript is now IO Islamic 2799 </strong><strong>in the India Office collections.</strong> <strong>[metadata:</strong> <strong>Otto Loth, </strong><strong><em>A Catalogue of the Arabic Manuscripts in the Library of the India Office</em>, (volume 1), no. 714 here with further notations and hyperlinks]</strong>. 714. 2799. Size 7<sup>1/2</sup> in. by 5 in. Thirteen lines in a page. Foll. 1-36. An Account of the Muḥammadans of Malabar, entitled تحفة المجاهدين , by Shaikh ZAIN AL-DÎN [al-Malībārī], who dedicated it to ‘Alî ‘Âdil Shâh of Bijâpûr. It has been translated by Lieut. [Michael John] Rowlandson (Oriental Translation Fund, 1833) . Cf. [William Hook] Morley, Catal. of hist. MSS. 13 [ed note: this MS dated 1830], and Cat. Mus. Brit. 434 [ed. note = <em>Catalogus codicum manuscriptorum orientalium qui in Museo Britannico asservantur : partem secundam codices Arabicos amplectentem</em>, p. 434, no. D CCCCXLV, Add. 22,375, the MS dated 1833]. The preface and the introductory chapter are omitted. The MS. begins: فصل فى بدأ ظهور الاسلام فى مليبار It is also imperfect at the end. Well written in Nasta’liḳ. Of the twelfth century [i.e. probably 18th century CE in the time of John Leyden] Inscribed: احوال ملك مليبار [Bibl. Leydeniana.] [<strong>ed note:</strong> Quick link to other copies of this work]. [<strong>ed note: </strong>Quick link to IO Islamic 2807, a complete copy of this work].
DOI: 10.5281/zenodo.5601911
title: Biography and History [IO Islamic 2799] تحفة المجاهدين

description: <strong>Biography and History. </strong> <strong>This manuscript is now IO Islamic 2799 </strong><strong>in the India Office collections.</strong> <strong>[metadata:</strong> <strong>Otto Loth, </strong><strong><em>A Catalogue of the Arabic Manuscripts in the Library of the India Office</em>, (volume 1), no. 714 here with further notations and hyperlinks]</strong>. 714. 2799. Size 7<sup>1/2</sup> in. by 5 in. Thirteen lines in a page. Foll. 1-36. An Account of the Muḥammadans of Malabar, entitled تحفة المجاهدين , by Shaikh ZAIN AL-DÎN [al-Malībārī], who dedicated it to ‘Alî ‘Âdil Shâh of Bijâpûr. It has been translated by Lieut. [Michael John] Rowlandson (Oriental Translation Fund, 1833) . Cf. [William Hook] Morley, Catal. of hist. MSS. 13 [ed note: this MS dated 1830], and Cat. Mus. Brit. 434 [ed. note = <em>Catalogus codicum manuscriptorum orientalium qui in Museo Britannico asservantur : partem secundam codices Arabicos amplectentem</em>, p. 434, no. D CCCCXLV, Add. 22,375, the MS dated 1833]. The preface and the introductory chapter are omitted. The MS. begins: فصل فى بدأ ظهور الاسلام فى مليبار It is also imperfect at the end. Well written in Nasta’liḳ. Of the twelfth century [i.e. probably 18th century CE in the time of John Leyden] Inscribed: احوال ملك مليبار [Bibl. Leydeniana.] [<strong>ed note:</strong> Quick link to other copies of this work]. [<strong>ed note: </strong>Quick link to IO Islamic 2807, a complete copy of this work].
DOI: 10.34740/kaggle/dsv/3933704
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.6084/m9.figshare.20291175
title: Gene expression data for genetic mode of control and inheritance identification for five strains of the two-spotted spider mite, Tetranychus urticae

description: We assessed expression using RNAseq for five strains of the two spotted spider mite, Tetranychus urticae (inbred strains SOL-BEi, ROS-ITi, JP-RRi, MR-VPi, and MAR-ABi). In the experimental design, four of the strains (ROS-ITi, JP-RRi, MR-VPi, and MAR-ABi) were crossed to the SOL-BEi strain, and RNA for RNAseq was collected from adult females of the parental strains and respective F1s. Using parental strain and F1 data, including allele-specific expression in F1s, we determined the mode of genetic control for gene expression variation in the respective contrasts. We also used the data to determine the mode of genetic inheritance. The analysis was based on RNAseq data and genomic DNAseq data released to NCBI under accessions PRJNA801103 and PRJNA799176 respectively. Datasets released here include (1) parent of origin RNA-seq read counts per gene for ASE analyses, (2) total RNAseq read counts per gene (no filters base on allelic states) used for assessing inheritance, and (3) variant data for pairwise comparisons of each of the four strains to SOL-BEi (the variant data was used in assessing ASE). The respective data is provided in three archives (a README file is provided in each archive).
DOI: 10.6084/m9.figshare.20291175.v1
title: Gene expression data for genetic mode of control and inheritance identification for five strains of the two-spotted spider mite, Tetranychus urticae

description: We assessed expression using RNAseq for five strains of the two spotted spider mite, Tetranychus urticae (inbred strains SOL-BEi, ROS-ITi, JP-RRi, MR-VPi, and MAR-ABi). In the experimental design, four of the strains (ROS-ITi, JP-RRi, MR-VPi, and MAR-ABi) were crossed to the SOL-BEi strain, and RNA for RNAseq was collected from adult females of the parental strains and respective F1s. Using parental strain and F1 data, including allele-specific expression in F1s, we determined the mode of genetic control for gene expression variation in the respective contrasts. We also used the data to determine the mode of genetic inheritance. The analysis was based on RNAseq data and genomic DNAseq data released to NCBI under accessions PRJNA801103 and PRJNA799176 respectively. Datasets released here include (1) parent of origin RNA-seq read counts per gene for ASE analyses, (2) total RNAseq read counts per gene (no filters base on allelic states) used for assessing inheritance, and (3) variant data for pairwise comparisons of each of the four strains to SOL-BEi (the variant data was used in assessing ASE). The respective data is provided in three archives (a README file is provided in each archive).
DOI: 10.15151/esrf-es-781088676
title: The Iberian cryoEM community BAG

description: The Iberian cryoEM BAG is a large consortium (&gt; 30 groups) composed of Portuguese and Spanish groups working in biologically relevant problems including disease-related metabolic enzymes, antibiotic resistance, DNA replication and DNA maintenance, protein synthesis, virus structure and mechanisms, and macromolecular complexes involved in the control of key cellular processes like protein folding and degradation.
DOI: 10.15151/esrf-es-807929331
title: Synthesis of single-bonded crystalline polymeric carbon monoxide upon laser heating at megabar pressures

description: Among a variety of simple molecules that undergo high pressure polymerization, carbon monoxide (CO) represents an intriguing case, and the formation of polymeric CO (pCO) at few GPa has been studied in a great number of experimental and theoretical works. Our group recently extended the pressure range where XRD and IR measurements on pCO were reported up to 50 GPa, obtaining results that suggest the stabilization of an amorphous, extended 3D network of mostly single-bonded carbon atoms, in good agreement with the previous theoretical calculations. These calculations predict the stability of crystalline pCO phases that were never experimentally attained, probably because of the kinetic hindrance of this transformation. Here we propose to deepen the knowledge on the high pressure, high temperature phase diagram of pCO by studying the potential conversion of amorphous pCO to the predicted polymeric crystalline parents following laser heating (1000-4000 K) at 100-150 GPa.
DOI: 10.15151/esrf-es-857439127
title: iNEXT Discovery: Structural biology for translational research and discovery.

description: The aim of this proposal is to provide user access to Online crystallography and fragment screening pipelines based on the combination of EMBL’s HTX Lab services and the CrystalDirect Technology and automated data collection at ESRF’s MX beamlines, supported through the collaborative EMBL-ESRF Joint Structural Biology Group (JSBG). This will include three different user access modalities: 1) Large-Scale Fragment Screening, 2) Structural characterization of ligand-target complexes and 3) Online Crystallography (automated protein-to-structure pipeline). This work will be carried out in the context of international collaborative projects. Access to these modalities will require competitive application and peer-review through projects like the E.C. funded iNEXT Discovery or the recently awarded ISIDORe.
DOI: 10.15151/esrf-es-847479780
title: Study by nano-XRD of the coalescence of GaN nanopillars grown by Nano-Pendeo Epitaxy

description: An original method has been developed for achieving low dislocation density gallium nitride (GaN) and managing the strain in the nitride layers. It is based on the self-realignment of Si(111) nano-pillars (NP) during nitride layer coalescence. This study has several goals: (i) determine the degree of tilt and twist of the individual Si NP induced by coalescence; (ii) obtain the in-plane and out-of-plane strain distribution for the GaN layer, which will give us further information about the threading dislocation density (TDD) in our platelets. We will study the coalescence process with the variation of the pitch (center-to-center distance) by testing samples with varied pitches but the same NP diameter. We also intend to study the layers for various GaN growth times in order to better comprehend each step of the GaN pyramid coalescence. These observations will provide a clear picture of the coalescence process which will be beneficial to grow GaN platelets with low TDD.
DOI: 10.15151/esrf-es-771373161
title: ITABAG: 3D structures of macromolecules related to human health

description: The ITABAG includes structural biologists from Universities, National Research Council and Hospital research centres in Italy. The laboratories apply various diffraction methods to study the structure-function relationships in various macromolecules. A unifying factor for the vast majority of the macromolecules under study is that they are related to human health, either directly, being human proteins involved in some disease, or indirectly, as proteins expressed by human pathogens and validated as potential pharmacological targets. Other projects investigate basic chemical processes, such as crystal growth and polymer association and formation of nanostructures.
DOI: 10.15151/esrf-es-771371926
title: Austrian Crystallographic Diffraction Consortium

description: This proposed Austrian Crystallographic Diffraction Consortium (ACDC) BAG is to support various macromolecular structural biology groups across Austria (totally 15 research groups at 8 institutions in 5 cities). We employ mainly the technique of X-ray crystallography to characterize macromolecular biological complexes. Approval of this BAG will be absolutely essential for researchers in all these groups to carry out their structural studies on various health-related subjects, which are targeted at characterizing large molecular assemblies or proteins currently under-represented in the PDB, including membrane proteins. Corresponding high-resolution diffraction data are only obtainable through the use of synchrotron radiation sources. Thus regular synchrotron access is highly desirable to maintain a competitive advantage in our individual research fields.
DOI: 10.15151/esrf-es-771376485
title: BAG BARCELONA

description: BAG Barcelona is constituted by 9 groups that belong to the Institute of Molecular Biology Barcelona from the Spanish Research Council (IBMB-CSIC), the Institute for Research in Biomedicine (IRB), and the Research Institute from Hospital Santa Creu i Sant Pau (HSCSP-IR). The main subjects of research are protein/DBA complexes, molecular machines, compounds of viruses, and the molecular mechanisms of proteases and other enzymes. Our Scientific results strongly rely on the high quality data and excellent performance and support of ESRF macromolecular crystallography beamlines.
DOI: 10.15151/esrf-es-756417574
title: High-speed X-ray phase contrast imaging of cavitation bubble cloud dynamics in a high-intensity focused ultrasound field

description: Exploiting X-ray phase contrast imaging, this proposal aims to extend our physical description of the cavitation bubble cloud dynamics in a high-intensity focused ultrasound (HIFU) field to the internal cloud dynamics. The expected comprehensive description will contribute to improve the use of HIFU in multiple medical applications. More specifically, we intend to conduct HIFU-cavitation bubble cloud experiments in (1) a boundary-free environment to describe the canonical dynamics of bubble clouds and (2) in a human body environment (using phantoms) to address the effect of boundaries on the cloud dynamics mimicking conditions in HIFU-based clinical therapies.
DOI: 10.15151/esrf-es-799263100
title: Structural Biology in Marseille

description: Our BAG groups 8 teams from 4 Marseille laboratories. Research themes deal with infection, health and biotechnology. For 107 projects within this proposal we foresee 10 MX and 2 SAXS shifts for the next beam time allocation period. This amount of beam time reflects what we had asked for in the previous proposal round. Two teams of the BAG combine structural biology with medicinal chemistry and beam time at MASSIF for large ligand-screening campaigns will mostly suit their research purposes. Access to beamlines with tuneable energy will be instrumental for projects requiring phasing by MAD or MIRAS. One team uses exclusively Bio-SAXS and allocation of one shift/session would be welcomed. Remote access for MX sessions has become very popular whereas scientists prefer to be on-site for Bio-SAXS experiments. We are grateful to the ESRF staff for always being forthcoming with regard to scheduling, logistics and experiments, allowing the BAG to produce good Science in a comfortable setting.
DOI: 10.15151/esrf-es-771372332
title: Southampton, Bristol, Exeter, KCL, Portsmouth, UCL Royal Free Block Allocation Group (BAG)

description: This BAG coordinates activities of groups from the South-West of the UK. The focus is on projects in Immunology, transcriptional regulation, and enzymology. A particular strength are the macromolecular complexes that several of the groups target. The activities in rational protein design (Bristol) and enzyme design (Portsmouth) are particular highlight and have enriched the portfolio of projects of this ag since joining in 2020.
DOI: 10.15151/esrf-es-799085531
title: Demonstration of proof-of-concept experiment for x-ray quantum interferometers

description: We propose a proof-of-concept experiment to demonstrate the ability to use x-ray quantum nonlinear interferometers for precise phase sensing. The interferometer is based on the effect of parametric down conversion (PDC) in a monolithic double Laue silicon structure. Quantum interferometers have much higher sensitivity than classical interferometers as has been demonstrated by experiments with visible light and predicted by theory, hence can lead to the development of phase contrast imaging methods for the measurements of samples with refractive index contrasts much smaller than the capabilities today. The experiment will advance the field of x-ray quantum optics and open possibilities for the development of quantum technologies with x-rays.
DOI: 10.15151/esrf-es-806483731
title: Bragg Coherent X-ray Diffraction Imaging (BCDI) of nanoscale strain evolution in a single crystal under high pressure.

description: Measuring and understanding the internal strain changes in response to the external pressure produces critical information to unveil the origin of unconventional behavior of crystalline materials in high-pressure environments. Moreover, defects in nano-crystals have a critical influence on the properties of nanocrystals where a single defect can completely modify the properties. Because of the close proximity of surfaces the energy and mobility of defects in nano-objects are borne to be very different from what they are in the bulk. The primary goal is the understanding of the defect behavior (creation, stability, annihilation, defect defect interaction) including the strain fields surrounding them in nano-objects under high-pressure. We propose to perform in-situ experiments combining High pressure and Bragg Coherent Diffraction Imaging, which has become the most effective technique for imaging the 3D structure of individual crystals.
DOI: 10.15151/esrf-es-817883673
title: PROTEINS RELATED TO PATHOGENESIS OF DISEASES, VIRAL PROTEINS, CELL DIVISION, SIGNALLING AND CHROMATIN PROCESSES

description: Our BAG is composed of eight PIs at six different institutions in Italy and Austria. We focus on a large variety of human, bacterial, viral and synthetic protein targets and address diverse biological contexts by combining structural biology with biochemistry, biophysics, cellular and in vivo investigations.
DOI: 10.15151/esrf-es-812471821
title: Test on single optic fibers

description: In this experiment we will assess the capability of the beamline to collect XAS data on samples smaller than the beam focal spot. In particular we will analyze optic fibers (diameter 150um) whose core (diameter 10 um) is composed of Er-doped glass. Er-LIII edge spectra will be collected.
DOI: 10.15151/esrf-es-735689292
title: Structural studies of metalloenzymes and proteins involved in metalloenzyme maturation

description: Our interests are the study of natural or artificial redox metalloenzymes involved in green processes for the synthesis of biofuels or high-value added molecules. To do that, structural studies are required to understand the maturation of complex metalloenzymes or their reaction mechanism. Our objectives are i) the determination of crystal structures of of several intermediates of the reactions catalyzed by artificial metalloenzymes as well as the structures of hybrids in complex with their substrates. Different aboitic reactions will be studied: sulfoxidation, hydroxylation and carbonation ; ii) the determination of the crystal structure of carbon monoxide dehydrogenas (CODH) and its chaperones, involved in nickel insertion into CODH, as well as the interaction of the enzymes with its gaseous substrates (CO, CO2)
DOI: 10.15151/esrf-es-744177234
title: The Netherlands BAG

description: The Netherlands BAG includes groups situated at five Dutch universities (Utrecht, Groningen, Amsterdam, Wageningen and Eindhoven) and at the Netherlands Cancer Institute in Amsterdam, with a total of twelve PIs. The structural biology research carried out in these groups is highly diverse, including prokaryotic and eukaryotic proteins with a strong focus on targets and processes of biomedical relevance. Central to many projects are protein receptors and their interactions with other proteins and with small molecule modulators. An additional major research area concerns structure-based protein engineering and design aiming at the characterization and engineering of new enzymes for green chemistry and new-to-nature reactions. Projects deal with membrane and soluble proteins, cell surface receptors, and protein-protein, protein-ribonucleotide, protein-drug and enzyme-ligand complexes.
DOI: 10.5281/zenodo.6821771
title: Aquila audax SPAdes preassembly

description: .
DOI: 10.17199/brightness/mb0001
title: Sample Data from Multiblade

description: This data was collected as part of BrightnESS, funded by the European Union                         Framework Programme for Research and Innovation Horizon 2020, under grant                         agreement 676548. It consists of test data for the detector.
DOI: 10.5281/zenodo.6821770
title: Aquila audax SPAdes preassembly

description: .