cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/d56358552fba5da8dde10068fa7a5b8a
title: Bonanza Creek LTER: Shrub, Seedling and Sapling Density from 1975 to Present in the Bonanza Creek Experimental Forest near Fairbanks, Alaska

description: This study is a survey of the density of tall shrubs, saplings, and seedlings at Bonanza Creek LTER Control Plots. Densities have been measured at some sites since 1975 while others began in the mid 1980's. In 2006 methodology was changed in attempt to better capture the spatial variability of shrub and tree species within the research sites. The current method, presented here, uses a 2 meter wide transect along two site boundaries covering 220m2. All seedlings, saplings, and tall shrubs &gt;1m (regardless of species) are counted by species and size class along the transect. The previous method used 4m2 circular plots at 20 points on a 10mx10m grid within the control plot for an area of 80m2. The circular method measured all seedlings, saplings, and a certain set of "tall shrubs", regardless of height. The height requirement creates an issue when comparing the old and new methods for early successional stands. For Alnus and Salix this is likely only a problem in the FP0 sites as they are the only sites with a high density of shrubs shorter than 1m. Shrub community changes at these early successional sites should be analyzed using percent cover data. At the later successional sites most Alnus and Salix shrubs are greater than 1m so the transect method likely does not underrepresent density. The metadata and raw data from the circular method can be found in Vegetation Plots of the Bonanza Creek LTER Control Plots: Species Count (1975 - 2004) .
DOI: 10.15151/esrf-es-691708609
title: Structural Biology at EMBL Grenoble, IBS-CIBB and IAB

description: The proposals covers a broad range of structural biology projects related to pathogen biology, host-pathogen interactions, RNA biology and structure-based drug development that are carried out by PIs at EMBL Grenoble, IBS-CIBB and IAB. The proposers have long-standing experience in the use, as well as the development of beam lines for macromolecular crystallography and have participated in successive BAG applications over the years, mostly at the ESRF but also at other synchrotrons (e.g. Soleil, Petra III, Diamond, SLS).
DOI: 10.15151/esrf-es-536305647
title: BAG Montpellier

description: The BAG of Montpellier gathers researchers from distinct institutes (CBS, IGF, IRIM and LPHI) affiliated to the INSERM, the CNRS and the university of Montpellier. The CBS is a node of the national infrastructure FRISBI. In this context, it is developping new methodologies for efficient ligand screening by X-ray diffraction. It is also involved in solving the structure of novel therapeutic targets to develop novel drug candidates. The IGF is involved in characterizing membrane proteins (mainly GPCRs) in order to better understand their functioning for therapeutic application. The IRIM and LPHI are focusing on several therapeutic targets related to infectious diseases in order to identify and develop novel inhibitors. CBS and IGF use SAXS to unravel the organization and behavior of various macromolecular systems in solution. Finally, we are now also turning to the use of cryo-electron microscopy to study some macromolecular assemblies.
DOI: 10.15151/esrf-es-644087931
title: SAARLAND BAG: ATOMIC MECHANISMS OF ACTION OF MEMBRANE PROTEINS AND BIOSYNTHETIC ENZYMES

description: Projects are focussed primarily within the framework of the DFG-funded excellence network program on "Ca2+signals: Molecular Mechanisms und Integrative Functions" at Saarland University and a new joint multidisciplinary initiative of the University with the Helmholtz Institute of Pharmaceutical Research Saarland on natural bioactive compounds including their interactions with their target proteins. These projects involve the structure determination of membrane proteins and soluble proteins.
DOI: 10.15151/esrf-es-644970915
title: Macromolecular crystallography at the Philipps University Marburg (MarBAG)

description: Located at the Philipps-University-Marburg and the Max-Planck-Institute for terrestrial Microbiology in Marburg, Germany, the MarBAG employs X-ray crystallography to answer fundamental questions involving synthesis and assembly of macromolecular machines and cellular structures (e.g. CO2-fixation pathways, flagellar biosynthesis, CRISPR-Cas Systems, cell-wall-related processes). Our analysis of the structural basis of CO2 fixation and the synthesis of the green-house gas methane will help to engineer these processes as tools in climate control. Furthermore, we are interested in plant-pathogen interactions and the function of nucleotide derived signalling molecules in cellular stress physiology and organization. Currently, a 200 keV cryo-electron microscope is being installed at the UMR to complement our efforts to structurally characterize macromolecular complexes, which do not readily crystallize.
DOI: 10.15151/esrf-es-645716703
title: Paris Rive-Gauche BAG: from structure to drug design

description: Our BAG was created in 2006 to federate well-established structural biology laboratories from south Paris. At present, several projects are investigated by different teams from 5 Institutes: (1) I2BC (Institut de Biologie Intégrative de la Cellule), (2) IBPC (Institut de Biologie Physico-Chimique), (3) INSERM (Institut National de la Santé et de la Recherche Médicale), (4) LBPA (Laboratoire de Biologie et Pharmacologie Appliquée) and (5) CiTCoM (Cibles Thérapeutiques et Conception de Médicaments, ex-name LCRB). Our research area focuses on many important biological systems involved in human pathology or infectious diseases, including molecular chaperones, DNA recombination, RNA maturation, ribosome biogenesis, telomerase assembly, bacterial toxins, malaria disease, neurodegenerative disease, drugs resistance and cell-signalling.
DOI: 10.15151/esrf-es-649492524
title: Italian CryoEM Bag (ICB)

description: This BAG application builds on the development of single particle cryoEM in the Italian Structural Biology community, as in Italy there is no top-end instrument is yet available. The groups in this application have acquired know-how in cryoEM through international collaborations or by acquiring medium-level in-house equipment. Access to the CM01 beamline at the ESRF from August 2020 has allowed the development of projects from groups that do not have in-house equipment that will most likely result in high top level publications in 2021. The three screening microscopes presently installed in Italy boosted sample production in 2020 in spite of the Covid-19 pandemic and the number of samples foreseen for 2021 has greatly increased. The BAG from Italian institutions is nurturing the expansion of the field in Italy and will result in a high-level scientific production.
DOI: 10.15151/esrf-es-652448489
title: ZnV2O4: On the Border of Disorder

description: The frustrated spinel ZnV2O4 is a material where chemical and magnetic (dis)orders are deeply intertwined. We have prepared two powder samples, one via a sintering method and the other via a microwave-assisted route (MW). Previously, we performed a high-resolution diffraction measurement on ID22 which revealed that the MW sample remained cubic down to 4 K whereas the sintered sample underwent a phase transition below 35 K. We also observed significant diffuse scattering below the Bragg peaks of both samples, and that the peaks of our sintered sample are inherently broad (at least 2x broader than the MW sample), both of which indicate local structural disorder. Following on from these results, we now wish to perform a full total scattering experiment on ID22. Together with our high-resolution data, this will allow us to explore the average and local structures of our two samples, and understand why only one has a phase transition, and the impact this has on the magnetic ground state.
DOI: 10.15151/esrf-es-660041967
title: Pressure-induced transitions in ACrF3 (A = Na, K, NH4) fluoroperovskites

description: The aim of the proposed experiment is to utilize the large-volume press at ESRF to elucidate the pressure-induced structural phase transitions we recently observed in NaCrF3 by x-ray diffraction, and further expand this research to the KCrF3 and NH4CrF3 fluoroperovskites. Through the experiments, we foresee that new insight into Cr(II) fluoroperovskites and the rich structural chemistry of fluorides and fluoroperovskites will be gained, including the discovery of new polymorphs. We hope to encounter interesting magnetic and/or electronic properties in the high-pressure polymorphs. The experiment is a part of an initiative to investigate Cr(II) fluoroperovskites. Neither KCrF3 nor NH4CrF3 are investigated under high-pressure before.
DOI: 10.15151/esrf-es-654230635
title: FInnish National Protein Crystallography Consortium

description: The Finnish BAG encompasses 25 groups active in crystallography in Finland. The projects vary widely and include membrane proteins such as membrane pyrophosphatases, and various protein complexes and receptors (growth factor receptors, integrins), signaling proteins such as kinases, other proteins involved in disease and antibiotics development (neuronal adhesion and myelin proteins, PP2A, ADP-ribosylation and biocatalytic enzymes) and several pathogen proteins (e.g. viral proteins) and various enzyme targets and e.g. studies on phytochrome photoreceptors and complexes involved in actin and cytoskeleton dynamics and regulation. Overall the BAG serves the national needs for highly variable projects, with different biological and biotechnological applications. Several project will benefit from microfocus beam lines and tunable wavelength options for phasing, others benefit from quick robust screening by MASSIF. Biology lab is needed for SAXS experiments.
DOI: 10.15151/esrf-es-650704790
title: Coherent, bright and focused light to resolve neural circuits
DOI: 10.15151/esrf-es-652445140
title: The effect of vacancies distribution on network flexibility and switching properties of Prussian Blue Analogues

description: We will study two Prussian Blue Analogues (PBAs) CsxCoy[Fe(CN)6] and RbxMny[Fe(CN)6] which show temperature- or light-controlled magnetic switching due to the spin-crossover present in this materials. The previous studies have identified the presence of hexacyanoferrate vacancies as a key condition for observing the spin-crossover, as the vacancies provide the structural flexibility allowing to accommodate atomic rearrangements required for charge transfer. In our previous work, we have shown that vacancy distribution Prussian Blue Analogues is not random and can be affected by the crystal growth conditions. Thus, the goal for this work is twofold: first, to identify the chemical parameters that affect local structure in the most significant way; second, to exploit the effect of different types of disorder on spin-crossover, in particular, the temperature of the phase transition.
DOI: 10.15151/esrf-es-652447868
title: Phylogeny of Coleoptera Staphylinoidea through fossils morphology

description: The aim of this project is an external and internal morphological study of key amber beetle fossils by direct observation (for external morphology) and virtual dissection (for internal structures) using propagation phase contrast synchrotron X-ray microtomography. Critical data obtained from fossils by these methods will be integrated into the interdisciplinary investigation of the biggest animal evolutionary radiation, the phylogeny of Coleoptera Staphylinoidea. This is a continuation of EC530 and LS 2248.
DOI: 10.15151/esrf-es-652454550
title: Gold nanoparticles in natural paleo fluids from Kola superdeep borehole

description: The Kola superdeep borehole (SG-3) is the result of a scientific drilling project (realized in 1970-1992) in the Pechengsky District, near the Russian border with Norway, on the Kola Peninsula. This borehole of 12,262 meters retains the deepest artificial point on Earth. This project is the first attempt to characterize Au nanoparticles in natural fluid inclusions inside quartz from this borehole using micro-beam scanning small-angle/wide angle X-ray scattering (SAXS/WAXS) techniques combined with simultaneous X-ray fluorescence (XRF), anomalous SAXS (ASAXS) and X-ray near edge structure (XANES). These new data are indispensable for the knowledge of Au behavior in deep fluid systems and the mechanism of its accumulation in the Earth’s crust.
DOI: 10.15151/esrf-es-690854603
title: Bridging the gap between cellular and whole body imaging using Hierarchical Phase-Contrast Tomography: HiP-CT

description: Humans and other large organisms are three-dimensional multiscale biological systems where large scale function and structure are dependent on the macrostructure’s interconnectivity down to the cellular and subcellular level. Using the exceptional coherence provided by the ESRF-EBS, we have demonstrated that propagation-based phase-contrast can effectively decouple resolution from specimen size in soft tissue, obtaining 1.4 micron voxel resolution in 150 mm diameter human organs. Through this Long Term Proposal (LTP) we will develop the techniques required to image whole human and animal bodies ex vivo at 25 micron resolution, zooming to sub-micron voxels (0.7micron) locally, resolving sub-cellular structures through hard- and soft-tissue. Resolving how the micro (sub-cellular) interacts with the macro (whole organism) across length scales will provide all new insights into biological and biomedical function. This is true for both healthy and pathological system level behaviour.
DOI: 10.15151/esrf-es-705433153
title: Inhouse research

description: Self-assembly processes of a variety of amphiphilic systems will be studied by millisecond resolved SAXS combined with stopped flow mixing.
DOI: 10.15151/esrf-es-651612221
title: Juvenile coral night and day growth: 3D tomographies of Sr distribution imaging both below and above the absorption edge

description: Corals incorporate Sr in the CaCO3 aragonitic skeleton, when Sr2+ ions are available in the environment. We are using in-situ pulse-labeling by strontium, to map growth of the early stages of coral larva shortly after settlement. We propose to image the ~2% Sr-enriched layers added to the skeleton by the young organisms by day or night. We propose to use tomographic imaging at energies both above and below the Sr edge of 16.105 eV as well as by high-energy phase contrast enhanced microCT. We will create Sr-edge difference tomographis to visualize and study juvenile growth patterns across diel cycles. This information will help elucidate fundamental aspects of mineral accretion in these ecologically critical animals
DOI: 10.15151/esrf-es-651037872
title: Quantifying Microscale Stress and Strain Fields in Concrete and Cementitious Composites

description: We will quantify the microscale stress and strain fields generated during the macroscopic compression of concrete. Currently, the macroscopic modulus and strength of concrete are predicted accurately by “mean-field” micromechanics theories and numerical models based on the postulate that each sand particle (aggregate) in the microstructure experiences the same stress state during macroscale loading and is perfectly bonded to the surrounding cement-paste matrix. Recent work by the proposers demonstrates that the aggregates instead experience significant stress variability. Our proposed experiments will exploit combined 3DXRD, scanning 3DXRD and x-ray computed tomography, with digital volume correlation, to quantify stress variability and aggregate-matrix debonding during elastic and inelastic stages of compression in-situ. Results will improve micromechanics theories and provide first-of-its-kind information on aggregate-matrix interface mechanisms previously inaccessible in-situ.
DOI: 10.15151/esrf-es-703631186
title: Mobilization of rhenium in magmatic fluids with implications for its exploration

description: Rhenium (Re) is one of the rarest elements on Earth (average abundance &lt; 1 ppb) and is of fundamental importance for our modern high-tech industry due to its high thermal stability (melting temperature beyond 3100 °C). Yet the enrichment process of Re in ore deposits is little understood mainly due to the difficulties to perform experiments at extremely high dilution levels and simultaneously at high P/T conditions. The new ESRF-extremely brilliant source capabilities and several recent technical developments at the ESRF beamline BM23 allow overcoming these limitations. We therefore propose to study systematically the solubility and speciation of Re in fluids as a function of P/T and fluid composition using X-ray fluorescence spectroscopy. The new data will improve our understanding of Re mobilization in magmatic systems and its enrichment process with implications for the exploration of Re.
DOI: 10.15151/esrf-es-650700384
title: Imaging structural transitions of a non-Newtonian fluid using time-resolved X-ray diffraction computed tomography

description: Non-Newtonian fluids change viscosity under the application of stress, and understanding the properties and phase transitions of these fluids are important to create models of their flow behaviour in porous media. Certain non-Newtonian fluids crystallize in the absence of stress, and behave like an approximate Bingham fluid. When sufficient stress is applied, the viscosity drops significantly so that the material flows like a fluid with minimal shear forces. The spatial dynamic behaviour of these complex fluids in complicated geometries is surprisingly unknown. Here, we propose time-resolved X-ray diffraction computed tomography to spatially and chemically map the interplay between flow regimes, crystallization, and the local geometrical constraints on complex fluids in several distinct sample environments, to better understand the physical behaviour of complex fluids flowing in complex porous media.
DOI: 10.15151/esrf-es-650701185
title: Ceria nanoparticles distribution and oxidation state in Drosophila model organism for NP-based antioxidant treatment in degenerative disease

description: Cerium oxide (CeO2) and, in particular, ceria nanoparticles (CNPs) have recently emerged for their unique regenerative antioxidant activity due to their ability to reduce either reactive oxygen species (ROS), and reactive nitrogen species (RNS) . The antioxidant ability of the CNPs has been proven in vitro but it is not clear whether these nanoparticles could be effective also in vivo. In the case of a whole organism, CNPs have to be able to cross various biological barriers (i.e. blood brain barrier) in order to be effective on-site (i.e. endothelial cell or brain cells). Drosophila melanogaster is one of the most common animal models used to test potential therapeutic strategies: we here propose to assess whether the CNPs, ingested by the Drosophila fly, are distributed in different tissues/organs of this live model organism, and how the Ce oxidation state changes based on its distribution, by means of Ce-LIII-edge μXANES spectroscopy at ID21.
DOI: 10.15151/esrf-es-650701946
title: Operando investigation of the gas sensing mechanism of SnO2 materials by modulation excitiation HERFD-XAS at the Sn L1 edge

description: Tin dioxide is the benchmark for modern gas sensing materials. Despite its significance, the fundamental mechanisms remains under discussion. The proposed investigation will study synthesisstructure-function-relationships of differently prepared gas sensing materials by operando modulation excitation X-ray absorption spectroscopy the Sn L1 edge. This approach ensures to detect even minimal changes of the active Sn sites at the surface. By carefully selecting a representative set of samples the role of intrinsic oxygen vacancies, foreign dopants and added loadings will be studied to provide fundamental insights in the gas sensing mechanism and how it is changed by these factors.
DOI: 10.15151/esrf-es-651037666
title: In situ and operando coherent diffraction imaging of nanostructures during chemical reactions: towards atomic resolution and time-resolved e
DOI: 10.15151/esrf-es-705433552
title: CXDI on test samples

description: Coherent X-ray Diffraction Imaging will be applied on a series of test samples to optimize the experimental protocol for the highest spatial resolution.
DOI: 10.15151/esrf-es-705833525
title: Magnetic excitations in LaCo2P2

description: Magnetic excitations in LaCo2P2
DOI: 10.15151/esrf-es-650388810
title: Tracking structural changes of Ni/Fe3O4 model electrodes during the Oxygen Evolution Reaction (OER) using High Energy Surface X-ray Diffract

description: The aim of this experiment is to use HESXRD for the operando study of atomic-scale structural changes of Fe3O4(001) and Fe3O4(111) thin film model electrodes decorated by Ni nanoparticles of varying size during potentiostatic and potentiodynamic OER conditions. Special focus will be put on the expected strain effects in the the oxide films during pulse electrolysis conditions. The systematically probed parameter space (different Ni nanoparticle sizes and different surface orientations) will yield new insight into the correlation between the potential-dependent Ni nanoparticle sintering, the strain/stress effects in the Fe3O4 thin films, the synergy effects between Fe and Ni toward the catalytic properties, and the model electrode stability, both under potentiostatic and potentiodynamic OER conditions. The results will pave the way to a knowledge-based synthesis of improved and robust precious-metal free electrode materials for the water-splitting reaction.
DOI: 10.5281/zenodo.3842597
title: Survival curves using Cox proportional hazards model for CLEC4A on TCGA and GSE39582

description: Survival curves obtained using Cox proportional hazards model on Clec4A in TCGA (READ and COAD) as well as the published data set GSE39582.
DOI: 10.5281/zenodo.3842596
title: Survival curves using Cox proportional hazards model for CLEC4A on TCGA and GSE39582

description: Survival curves obtained using Cox proportional hazards model on Clec4A in TCGA (READ and COAD) as well as the published data set GSE39582.
DOI: 10.15151/esrf-es-735816212
title: SAARLAND BAG: ATOMIC MECHANISMS OF ACTION OF MEMBRANE PROTEINS AND BIOSYNTHETIC ENZYMES

description: Projects are focussed primarily within the framework of the DFG-funded excellence network program on "Ca2+signals: Molecular Mechanisms und Integrative Functions" at Saarland University and a new joint multidisciplinary initiative of the University with the Helmholtz Institute of Pharmaceutical Research Saarland on natural bioactive compounds including their interactions with their target proteins. These projects involve the structure determination of membrane proteins and soluble proteins.
DOI: 10.15151/esrf-es-670012634
title: The Hydrothermal Geochemistry of Tantalum

description: Tantalum (Ta) is recognized as one of the so-called ‘critical minerals’, with wide applications in the electronics and green energy industry but limited supply chain. An understanding of the speciation and solubility of Ta in hydrothermal solutions is key in helping both Ta exploration and mineral processing. High-resolution X-ray absorption spectroscopy (XAS) can reveal fine features of the XANES spectra, thus help identifying important Ta aqueous complexes (with O, F and Cl) that are hard to identify using conventional XAS detection techniques. This study plans to measure the coordination structure and solubility of Ta in hydrothermal fluoride and chloride solutions at up to 500 °C and 800 bar to better understand the transport and deposition properties of Ta and its fractionation from its geochemical twin niobium (Nb) in hydrothermal systems.