cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15151/esrf-es-1273624588
title: Advanced Photon Source, Sector 21 - The Life Sciences Collaborative Access Team (LS-CAT) - CAT Member Macromolecular Crystallography

description: The Life Sciences Collaborative Access Team (LS-CAT) provides Macromolecular Crystallography support to our CAT members from eight Universities in the USA, including Northwestern University, University of Michigan, Wayne State University, Michigan State University, University Wisconsin, Vanderbilt University, and University of Illinois at Chicago, and also to General Users. With a one-year dark period approaching for the upgrade of the Advanced Photon Source (APS-U), we are seeking beam time for our CAT Member laboratories at ESRF by way of this Block Allocation Group, consisting of a portion of our CAT Member PIs and their laboratory members, in order to keep supporting their research and future funding. LS-CAT is organizing our CAT Members into this BAG Proposal, and other proposals we will submit, in order to streamline the process for our CAT Members, and for the Staff of Lightsources to which we are applying for access to beam time.
DOI: 10.15151/esrf-es-1117952942
title: Mechanisms of macromolecular targets involved in signaling, pathologic processes and rare diseases

description: This proposal is a collaborative effort of the Macromolecular Structural Biology Groups in Valencia –six at the Instituto de Biomedicina de Valencia (IBV-CSIC) and one at the University of Valencia– with the objective to form a strong core of scientists devoted to deciphering the structure and molecular mechanisms of proteins and protein complexes of biomedical and biotechnological interest.
DOI: 10.15151/esrf-es-1223491086
title: 3d Virtual Histology of the Human Cochlea

description: We propose post mortem 3D imaging of human cochlea by phase-contrast x-ray tomography using highly brilliant synchrotron radiation offering non-destructive investigation of the entire organ with sensitivity high enough to segment individual cells. In line with our previous research on small animal models, the biomedical research associated with this imaging campaign targets three different lines of research: (i) Age-related structural changes in the cochlea, in particular loss of auditorial nerve cells. (ii) Structural quality control of novel optogenetic technology for cochlea implants (CI). (iii) Fundamental neuroscience research with respect to structural composition of the auditorial nerve and its 3d arrangement of neurons, in particular in the spiral ganglion. In view of age-related hearing loss, we particularly aim at evaluating the number of outer and inner hair cells (OHCs, IHCs), and spiral ganglion neurons (SGNs).
DOI: 10.15151/esrf-es-1297045203
title: Scan of fossil of early shark

description: Scan of fossil of early shark
DOI: 10.15151/esrf-es-1222608976
title: Determination of nitrogen's phase diagram up to 400 GPa

description: As an archetypal diatomic molecule, the high-pressure allotropes of molecular nitrogen are an excellent testbed for refining solid-state physics models. Above 110 GPa, the physicochemical properties of nitrogen radically change as it transforms into a 3D polymeric single-bonded solid. While ab-initio calculations predict a straightforward phase diagram for the polymeric phases—with only three polymeric solids up to 2100 GPa—recent experimental investigations suggest a much greater complexity. As it stands, four polymeric nitrogen phases have been synthesized below 245 GPa, with only one matching theoretical predictions. We here aim to uncover nitrogen's phase diagram between 220 and 400 GPa, discover new polymeric phases, solve their structure with single-crystal X-ray diffraction (SCXRD) and determine their stability range. These experiments will challenge current theoretical models, providing a rare example of the behavior of simple homoatomic systems at ultrahigh pressures.
DOI: 10.6084/m9.figshare.23694214
title: Exploring the potential of FDA approved anti-diabetic drugs for repurposing against COVID-19: a core combination of multiple computational strategies and integrated artificial intelligence

description: The latest variant of coronavirus is omicron. The World Health Organization (WHO) designated variation ‘B.1.1.529’ named omicron as a variant of concern (VOC) on 26 November 2021. By September 2020, it will have infected over 16 million patients and killed over 600,000 people over the world. This very infectious viral illness still poses a danger to world health; it has also become the greatest problem the world is facing and become the main area of research. The development of vaccines is insufficient to stop their spread and serious effects. Despite several reputable pharmaceutical firms claiming to have developed a cure for COVID-19. For that purpose, the field-based 3D-QSAR model has been used to analyze a series of anti-diabetic drugs to repurpose them against COVID-19. The LOO verified partial least square (PLS) model generates satisfactory <i>q</i><sup>2</sup> (0.4) and <i>r</i><sup>2</sup> (0.5) values. By using this model 10 compounds were screened out of 55 FDA approved anti-diabetic drugs (built-up library). Additionally, these substances were examined using molecular docking screening and ADMET. Finally, the drugs <b>L8</b>, and <b>L23</b> were discovered to be the lead drugs. Density functional theory at the B3LYP/6-311G* technique was used to examine structural geometries, electronic characteristics, and molecular electrostatic potential (MEP). This work will greatly assist in the detection and development of leads for early drug development to control COVID-19. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23694214.v1
title: Exploring the potential of FDA approved anti-diabetic drugs for repurposing against COVID-19: a core combination of multiple computational strategies and integrated artificial intelligence

description: The latest variant of coronavirus is omicron. The World Health Organization (WHO) designated variation ‘B.1.1.529’ named omicron as a variant of concern (VOC) on 26 November 2021. By September 2020, it will have infected over 16 million patients and killed over 600,000 people over the world. This very infectious viral illness still poses a danger to world health; it has also become the greatest problem the world is facing and become the main area of research. The development of vaccines is insufficient to stop their spread and serious effects. Despite several reputable pharmaceutical firms claiming to have developed a cure for COVID-19. For that purpose, the field-based 3D-QSAR model has been used to analyze a series of anti-diabetic drugs to repurpose them against COVID-19. The LOO verified partial least square (PLS) model generates satisfactory <i>q</i><sup>2</sup> (0.4) and <i>r</i><sup>2</sup> (0.5) values. By using this model 10 compounds were screened out of 55 FDA approved anti-diabetic drugs (built-up library). Additionally, these substances were examined using molecular docking screening and ADMET. Finally, the drugs <b>L8</b>, and <b>L23</b> were discovered to be the lead drugs. Density functional theory at the B3LYP/6-311G* technique was used to examine structural geometries, electronic characteristics, and molecular electrostatic potential (MEP). This work will greatly assist in the detection and development of leads for early drug development to control COVID-19. Communicated by Ramaswamy H. Sarma
DOI: 10.15151/esrf-es-1221766658
title: Evolution of the ray-finned fish brain revealed through exceptional fossil preservation

description: Ray-finned fishes (actinopterygians) today account for over half of all living vertebrates, and their origins date back over 300 million years. With over 30,000 species, they represent the largest vertebrate group and encompass everything from goldfish to seahorses and tuna to sunfish. Ray-finned fishes display an array of morphological innovations, key among which are features of the brain. There are several challenges to understanding how—and when—these innovations evolved, not least that living ray-finned fishes are evolutionarily remote from their early ancestors, and soft tissue structures rarely fossilise. Propagation phase contrast synchrotron X-ray μCT of 319-million-year fossil fish that exceptionally preserve neural tissues within the skull – such as the brain and cranial nerves – will open a window into brain evolution early in the group’s history. The findings from this work will clarify patterns of evolution and innovation outside of the living group.
DOI: 10.15151/esrf-es-1221768304
title: XAS-XRD investigations on the effect of different synthetic routes and annealing conditions on the design of inorganic materials

description: The aim of this proposal is to investigate to which extent different synthetic routes, i.e. inverse miniemulsion (wet-chemistry) and ball milling (solid state-chemistry) affect the local structure of photoluminescent materials, e.g. calcium molybdate (CaMoO4) doped with Eu3+ ions, and correlate these findings with the observed optical and chemico-physical properties. We aim to evaluate the dopant-induced variations on the structure (electronic, short- and long-range) through a combination of X-ray absorption spectroscopy measurements (at Eu L3-edge and Mo K-edge) and X-ray diffraction. In particular. experiments will be performed in situ while annealing at 900 °C, both in vacuum and in air. With these, we further focus on understanding the details of the annealing process, in either vacuum or air, since the atmosphere of the process was found to affect the final photoluminescent and conductivity properties of calcium molybdate to a different extent depending on the synthetic route.
DOI: 10.15151/esrf-es-1221770075
title: Cu-exchanged Hydroxyapatites: understanding the ionic exchange mechanism and potential towards selective redox catalysis by in situ XAS

description: Hydroxyapatites (HA) are versatile materials that can substitute any of their basic units by ionic species possessing similar characteristics while maintaining their structural entity. Commonly, a cationic exchange at a superficial level is performed by substituting the Ca2+ by a similar metal cation (M2+). The substitution of the Ca2+ by Cu2+ ions is particularly interesting, due to the versatility of Cu in many different applicative fields, including heterogeneous catalysis. Yet, the knowledge of the nature of the Cu substituents at a molecular level is still scarce. Driven by encouraging findings about the red-ox activity of Cu-HA, we propose to study by in situ XAS a batch of Cu-HA with a Cu loading of 2-7 wt. % and high surface area. The proposed study will provide a full characterization of Cu-HA in terms of Cu oxidation state and coordination environment, under model conditions designed to explore the potential of these materials towards selective oxidation catalysis.
DOI: 10.15151/esrf-es-1221772561
title: CO2 direct air capture (DAC) by zeolites: the importance of structural flexibility

description: In this project the adsorption capacity for CO2 and the selectivity of zeolites with CHA topology will be evaluated in relation to the framework flexibility and to the molecules-cations interactions. Different CHA type zeolites containing various counter balancing cations (Cs, Na, K) will be tested for CO2 adsorption in the presence of competing molecule (i.e. N2, H2O) at different temperatures. Mixed CO2 + N2 systems will be tested to mimic the CHA behavior as phisysorbent in direct air capture (DAC). The project aims to unveil the relation among CO2 adsorption and structural flexibility by highlighting the role of the host-guests interactions at atomistic level.
DOI: 10.15151/esrf-es-1221776186
title: Elucidating Cu Reactive Site Structure in Selective Biomass Electrooxidation Catalysts using in-situ XAS

description: The ability to electrooxidize biomass compounds efficiently and selectively can serve as source of both renewable hydrocarbons and H2 under electrolysis conditions. Although a host of common anode electrocatalysts have been implemented in biomass oxidation reactions, our group has recently discovered that Cu-based materials, notoriously bad catalyst for water electrooxidation, exhibit enhanced reactivity and selectivity toward biomass. With this beamtime proposal, we aim to resolve the Cu active site structure in layered double hydroxide (LDH) catalysts using in-situ XAS, providing insights into the design of future catalyst with improved biomass electrolysis properties.
DOI: 10.15151/esrf-es-1276518342
title: Localization of fibrillar polymorphs in human brain tissue

description: Fibrillar aggregates of Abeta peptides and tau protein are defining features of Alzheimer's disease (AD) but the role these structures play in the etiology of disease remains uncertain. Outstanding questions remain as to the distribution of polymorphs between and within cases. The proposed work will apply x-ray scanning micro- and nano-diffraction to histological sections of human brain tissue in order to map the distribution and arrangement of fibrillar aggregates of these proteins in plaques and tangles. The central hypothesis of the proposed work is that the spatial distribution of structural polymorphs in brain tissue will provide important clues as to how fibrils contribute to disease. The results of these studies will provide a preliminary assessment of whether or not different fibrillar polymorphs spread by a prion-like process during disease progression and provide insights into the mechanisms by which different strains are associated with different disease subtypes.
DOI: 10.15151/esrf-es-1221035271
title: Electronic-magnetic phase separation in an axion insulator candidate

description: We propose a scanning resonant x-ray diffraction microscopy (SXDM) study to characterize mesoscale phase-separation phenomena in Eu5In2Sb6. Our interest in this structural family is due to its two perpendicular glide symmetries. On the one hand, this non-symmorphicity may give rise to topological crystalline insulating states including wallpaper fermions or the elusive axion-insulator. On the other hand, we recently discovered that these symmetries enforce complex noncollinear magnetic order that separates into compensated antiferromagnetic and weakly Ising-ferrimagnetic regimes. Neutron and muon studies and (conventional) resonant x-ray scattering have provided us with strong evidence that this mesoscale magnetism must occur on a length scale between 90nm and 15um. The real-space observation using nanofocus-SXDM will open up a range of follow-up studies, with the ultimate goal to magnetically manipulate arrangements of topologically distinct insulating domains.
DOI: 10.15151/esrf-es-1221044548
title: High-Energy X-ray Diffraction to Understand Desalination Batteries

description: Improving water desalination required immediate attention. Desalination batteries (DB) provide a low-cost and energy-efficient method to (selectively) remove ions from water using faradaic electrodes. Because DBs are at their infancy, improved understanding is necessary towards their practical implementation. This proposal aims to further the understanding of ion intercalation and degradation phenomena observed in manganese oxide-based DB electrodes by utilizing operando high-energy X-ray diffraction mapping of flow-by reactors. We will investigate Li and Na manganese oxide ((Li/Na0.88)Mn2O4) as intercalation electrodes in both baseline ((Li/Na2SO4) and realistic (synthetic seawater) salt water environments. The results will provide novel information regarding the intercalation mechanism of ions into DB electrodes and their degradation both at the atomic and the full electrode scale towards rational improvements of DBs.
DOI: 10.15151/esrf-es-1220323500
title: Structural changes in a model photoreceptor protein: quaternary transitions in the milliseconds to seconds time scale

description: The CarH photoreceptor is a light-activated transcription regulator and it is a promising target for optogenetic applications. We have recently shown that structural changes in CarH after light absorption can be followed by time-resolved X-ray scattering (LS-2958). To disentangle tertiary and quaternary signals, we performed a second experiment ( LS-3091) on a mutant (H132A-CarH) and a homolog of CarH in which quaternary changes are prevented or modified, respectively. The previous experiments enabled us to follow the cascade of structural events occurring in CarH on a time scale from µs to hundreds of ms. A comparison with static data showed that the relevant time scale of the photoreaction in native CarH extends longer than hundreds of ms, most likely because of the presence of large scale slow quaternary changes leading to the photoproduct. Here we propose to complete our study by collecting time-resolved scattering data in native CarH on the time scale from ms to several s.
DOI: 10.15151/esrf-es-1220323710
title: Advancing grain growth models for transparent alumina ceramics

description: Understanding grain growth as a function of grain boundary energy through simulations informed by in-situ measurements is the motivation for this proposal. We will measure grain boundary velocity as a function of grain boundary character using scanning 3D X-ray diffraction (scanning 3DXRD) during in-situ sintering of undoped alumina. 3DXRD is necessary to spatially resolve the crystallographic orientations across the sample (to measure grain boundary character and positions as a function of time). Because the grains will be small (1−10 μm, slightly larger than is typically desirable for resolvability), we require scanning 3DXRD, which has a higher spatial resolution than conventional 3DXRD dictated by the beam cross-section (150−200 nm^2). The results will be integrated into a computational methodology using a Cauchy-Crofton/graph-based approach, and, more generally, develop a modern predictive understanding of grain growth that takes grain boundary energies into consideration.
DOI: 10.15151/esrf-es-1220324260
title: Alcohol-doping-controlled interfacial freezing of buried oil-water interfaces

description: Spherical-to-polyhedral shape transitions of liquid emulsion droplets have recently attracted a broad research interest, due to their importance for fundamental physics, bio-morphogenesis, and broad range of potential technological applications. Our recent microscopy studies demonstrate that doping the droplets by long-chain alcohols allows an unprecedented controllability of their transition temperatures, highly important for applications. Yet, the mechanism of this effect is currently unknown. Modelling the droplets’ interfaces by a planar alcohol-doped alkane:water interface we offer to study its structure by x-ray reflectivity, for several alcohol:alkane:surfactant combinations. The resolved structure should allow the role of alcohols in these systems to be elucidated, opening new routes towards technological applications, and shedding light onto the mechanisms of this intriguing droplet morphogenesis.
DOI: 10.15151/esrf-es-1220328556
title: Compounds of Fe and H under planetary pressures

description: Fe and H are two major constituents of planetary interiors. It was shown that pressure dramatically increases the H uptake in Fe. Many stoichiometric compounds have been synthesized in the Fe-H system under pressure, from interstitial hydrides, FeH and FeH2 to compounds, FeH3 and FeH5. Yet, the exploration have been limited to 130 GPa. We propose to explore by combined XAS/XRD experiment the Fe-H phase diagram up to Earth’s core conditions, in order to uncover and characterize novel high stoichiometry iron hydrides.
DOI: 10.15151/esrf-es-1220330871
title: Unraveling the effect of dimensionality on multi-magnons

description: We have recently discovered novel multi-magnon excitations in single crystals of Fe2O3 using 2p3d resonant inelastic x-ray scattering. These excitations correspond to triple-, quadruple- and quintuple-magnons that propagate these higher multiples of spin angular momentum beyond the conventional single- and double-magnons. The higher-rank magnetic quasiparticles have never been observed (or studied before) making 2p3d RIXS a unique method to investigate these original states. Our goal is to study the dimensionality effect on the novel higher-rank magnetic excitations by studying LaFeO3 grown on SrTiO3 in the limit of 1-, 3- and 25-unit cells.
DOI: 10.21227/9gbq-gz50
title: UMMC ER-IHC Breast Histopathology Whole Slide Image and Allred Score

description: This database contains 37 estrogen receptor immunohistochemistry (ER-IHC) whole slide images (WSIs) obtained from Universiti Malaya Medical Centre (UMMC), Malaysia. The WSI is scanned using 3DHistech Pannoramic DESK at 20x magnification with an approximate dimension of 80,000 pixels width and 200,000 pixels height per WSI. These 37 WSIs have Allred scoring by the collaborating pathologists with a breakdown of 17 ER-negative (4 score of 0; 13 score of 2), and 20 ER-positive (12 score of 3; 5 score of 7; 3 score of 8) with regions annotated by the pathologist to assist computational method in obtaining Allred scores. Image name with related score is listed in Table 5 of our paper, and the WSI annotations (referred as ROI-WSI) are included in this database using WKT format (POLYGON ((x1 y1, x2 y2, x3 y3, ..., xn yn, x1 y1))).
DOI: 10.17632/mp4nv3yccy.1
title: Function test of a 5 kW Generator using the Biodiesel obtained from the Neem oil as a biofuel

description: This video shows the function test of a 5 kW Generator using the Biodiesel obtained from the Neem oil as a biofuel.
DOI: 10.17632/6xg75kr8gb.1
title: Reasons for the superior annealing-induced hardening behavior of the Cr27.3Co33.3Ni33.3Mo6 and MP35N alloys compared to the equiatomic CrCoNi medium-entropy alloy

description: In this compilation of data, we unconver reasons for the superior annealing-induced hardening behavior of the Cr27.3Co33.3Ni33.3Mo6 (Mo-6) and MP35N alloys compared to the equiatomic CrCoNi (Mo-0) medium-entropy alloy. All the data are ORIGIN and EXCEL files (.opj and .xlsx). Here is a short description of the origin files, which are numbered according to their order of appearence in the corresponding research article and supplementary materials: 
Fig01+S1+S2: Vickers microhardness of Mo-6 after two-step hardening.
Fig02: Tensile responses of Mo-0 and Mo-6 MEAs. 
Fig06: 1D-composition profiles (crossing a GB and TBs) and frequency distribution of the elements extracted from APT experiments.
Fig07: The plot shows the temperature dependence of Vickers microhardness over the whole longitudinal-section of the Mo-0 and Mo-6 MEAs, from which the recrystallization temperature can be determined.
Fig08: Effect of plastic deformation and post-deformation condition (as-swaged and post-deformation annealed for 4 h at 773 or 923 K) on the yield stress and ultimate tensile strength (UTS) in Mo-0 and Mo-6 MEAs.
Fig10: Relative strengthening related to post-deformation annealing in the Mo-0 and Mo-6 MEAs.
Fig11: Ashby map showing the ultimate tensile strength as a function of elongation to fracture of CrCoNi-based MEAs and HEAs.
FigS8+S9: XRD patterns of Mo-6 and MP35N.