cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14330795.v12
title: Dexamethasone modulates immature neutrophils and interferon programming in severe COVID-19

description: While critical for host defense, innate immune cells are also pathologic drivers of acute respiratory distress syndrome (ARDS). Innate immune dynamics during COVID-19 ARDS, compared to ARDS from other respiratory pathogens, is unclear. Moreover, mechanisms underlying beneficial effects of dexamethasone during severe COVID-19 remain elusive. Using scRNA-seq and plasma proteomics, we discovered that compared to bacterial ARDS, COVID-19 was associated with distinct neutrophil polarization characterized by interferon (IFN) and prostaglandin (PG) active states. Dexamethasone during severe COVID-19 depleted circulating neutrophils, altered IFN<sup>active</sup> neutrophils, downregulated interferon-stimulated gene, and activated IL1R2<sup>+ve</sup> neutrophils. Dexamethasone also expanded immature neutrophils expressing immunosuppressive molecules and remodeled cellular interactions by changing neutrophils from information receivers into information providers. Male patients had higher proportions of IFN<sup>active</sup> neutrophils, preferential steroid-induced immature neutrophil expansion, and possibly different effects on outcome. Our single-cell atlas (www.biernaskielab.ca/COVID_neutrophil) defines COVID-19-enriched neutrophil states and molecular mechanisms of dexamethasone action to develop targeted immunotherapies for severe COVID-19.<br>
DOI: 10.6084/m9.figshare.19738444.v2
title: Phytochemical Composition and Potential Bioactivities of the Essential Oil from the Peels of <i>Paramignya trimera</i> (Oliv.) Guillaum from Vietnam

description: <i>Paramignya trimera</i> (Oliv.) Guillaum <i>(Xao tam phan)</i>, found mostly in South Vietnam, is a herbal medicine traditionally used for liver protection ability and dermatologic diseases. Recent studies showed that different extracts, fractions and isolated compounds from <i>P. trimera</i> exhibited many interesting bioactivities such as antioxidant, anticancer, anti-inflammatory and alpha-glucosidase inhibitory activities. However, research on the chemical profile and bioactivities of essential oil from the peels of this species has been limited. Therefore, this study aims to determine the chemical composition of this product and examine its anticancer and antibacterial activities. Phytochemical profile of the essential oil was analyzed using gas chromatography coupled to mass spectrometry. Indeed, twenty-four constituents were characterized; of which sesquiterpenes dominated the profile, with three major compounds: β-caryophyllene (19.09%), α-humulene (24.81%), and trans-muurola-4(14),5-diene (24.84%). <i>P. trimera</i> peel essential oil also contained potent inhibitory effects against six clinical multidrug-resistant bacterial strains including both Gram-positive and Gram-negative bacteria. This extract showed the strongest activity against two <i>Pseudomonas aeruginosa</i> strains with minimum inhibitory concentration (MIC) of 256 µg/mL for both, followed by 2 strains of <i>Staphylococcus aureus</i> and 2 strains of <i>Salmonella sp.</i> with MIC values of 384, 480 and 512 µg/mL, respectively. In addition, <i>P. trimera</i> peel essential oil displayed strong cytotoxicity in a dose-dependent manner against liver HepG2 cancer cells, with the half maximal inhibitory concentration of 21 µg/mL. This preliminary result suggested the potential bioactivities of <i>P. trimera</i> peel essential oil and can be helpful for further investigation to develop an phytomedicine-based therapy for cancer and infectious diseases.
DOI: 10.6084/m9.figshare.19738444
title: Phytochemical Composition and Potential Bioactivities of the Essential Oil from the Peels of <i>Paramignya trimera</i> (Oliv.) Guillaum from Vietnam

description: <i>Paramignya trimera</i> (Oliv.) Guillaum <i>(Xao tam phan)</i>, found mostly in South Vietnam, is a herbal medicine traditionally used for liver protection ability and dermatologic diseases. Recent studies showed that different extracts, fractions and isolated compounds from <i>P. trimera</i> exhibited many interesting bioactivities such as antioxidant, anticancer, anti-inflammatory and alpha-glucosidase inhibitory activities. However, research on the chemical profile and bioactivities of essential oil from the peels of this species has been limited. Therefore, this study aims to determine the chemical composition of this product and examine its anticancer and antibacterial activities. Phytochemical profile of the essential oil was analyzed using gas chromatography coupled to mass spectrometry. Indeed, twenty-four constituents were characterized; of which sesquiterpenes dominated the profile, with three major compounds: β-caryophyllene (19.09%), α-humulene (24.81%), and trans-muurola-4(14),5-diene (24.84%). <i>P. trimera</i> peel essential oil also contained potent inhibitory effects against six clinical multidrug-resistant bacterial strains including both Gram-positive and Gram-negative bacteria. This extract showed the strongest activity against two <i>Pseudomonas aeruginosa</i> strains with minimum inhibitory concentration (MIC) of 256 µg/mL for both, followed by 2 strains of <i>Staphylococcus aureus</i> and 2 strains of <i>Salmonella sp.</i> with MIC values of 384, 480 and 512 µg/mL, respectively. In addition, <i>P. trimera</i> peel essential oil displayed strong cytotoxicity in a dose-dependent manner against liver HepG2 cancer cells, with the half maximal inhibitory concentration of 21 µg/mL. This preliminary result suggested the potential bioactivities of <i>P. trimera</i> peel essential oil and can be helpful for further investigation to develop an phytomedicine-based therapy for cancer and infectious diseases.
DOI: 10.6084/m9.figshare.20057630
title: The new educational paradigm in Covid era: Can Blackboard replace physical teaching in EFL writing classrooms?

description: This study investigates the effectiveness of Blackboard in promoting EFL students’ writing performance in the Department of English Language and Translation at Qassim University. The data were collected for two periods: before (spring 2019) and after (spring 2020) the spread of COVID-19 virus. The study analyzed the students’ final grades in three different levels of writing courses. The results were collected and analyzed across the two different teaching approaches (face-to-face and Blackboard) to evaluate the two learning experiences and to highlight suggestions for enhancing students’ and teachers’ experience in online learning in the future. <br> This study enlisted two groups of undergraduate male and female Saudi students who had applied for English language courses at Qassim University. Ethical considerations were applied by obtaining permission from the deanship of scientific affairs to the head of the departments and the students. Students were also assured that their information would be only used for the study and that they were not required to disclose their identity in any way. The first group comprised students who took Writing 1, 2, and 3 prior to the pandemic, and the second group were those who took the same courses after the pandemic. The participants were assigned to take these three compulsory writing courses in the first three semesters after joining the program. The study sample thus included a total of 833 participants (287 males and 546 females). The students had prior experience with Blackboard as a learning tool. All freshman students, in traditional and pandemic times, are introduced to the most important features of Blackboard at the beginning of each semester. Additionally, three general courses were taught completely online during the first semester after students’ full enrolment in the program. <br>
DOI: 10.6084/m9.figshare.20057630.v1
title: The new educational paradigm in Covid era: Can Blackboard replace physical teaching in EFL writing classrooms?

description: This study investigates the effectiveness of Blackboard in promoting EFL students’ writing performance in the Department of English Language and Translation at Qassim University. The data were collected for two periods: before (spring 2019) and after (spring 2020) the spread of COVID-19 virus. The study analyzed the students’ final grades in three different levels of writing courses. The results were collected and analyzed across the two different teaching approaches (face-to-face and Blackboard) to evaluate the two learning experiences and to highlight suggestions for enhancing students’ and teachers’ experience in online learning in the future. <br> This study enlisted two groups of undergraduate male and female Saudi students who had applied for English language courses at Qassim University. Ethical considerations were applied by obtaining permission from the deanship of scientific affairs to the head of the departments and the students. Students were also assured that their information would be only used for the study and that they were not required to disclose their identity in any way. The first group comprised students who took Writing 1, 2, and 3 prior to the pandemic, and the second group were those who took the same courses after the pandemic. The participants were assigned to take these three compulsory writing courses in the first three semesters after joining the program. The study sample thus included a total of 833 participants (287 males and 546 females). The students had prior experience with Blackboard as a learning tool. All freshman students, in traditional and pandemic times, are introduced to the most important features of Blackboard at the beginning of each semester. Additionally, three general courses were taught completely online during the first semester after students’ full enrolment in the program. <br>
DOI: 10.5281/zenodo.6622072
title: Salmon SPLiT-seq tutorial data

description: This is the data required to run the salmon and alevin-fry tutorial on SPLiT-seq data.
description: This project is funded by the Chan-Zuckerberg Initiative.
DOI: 10.5281/zenodo.6011695
title: Salmon SPLiT-seq tutorial data

description: This is the data required to run the salmon and alevin-fry tutorial on SPLiT-seq data.
description: This project is funded by the Chan-Zuckerberg Initiative.
DOI: 10.6084/m9.figshare.20058836.v1
title: Supplementary Material for: Severe Inflammatory Colitis Related to Encorafenib and Binimetinib following Immune Checkpoint Inhibitor Therapy

description: Encorafenib, a BRAF kinase inhibitor, in combination with binimetinib, a selective MEK inhibitor have known gastrointestinal adverse events; however, adverse colitis events have not been well studied. We report a case series of 4 patients with melanoma who developed inflammatory colitis after BRAF and MEK inhibition with encorafenib and binimetinib, respectively. In the setting of immune checkpoint inhibitor use, BRAF and MEK inhibitors can cause significant inflammatory colitis with endoscopic patterns of predominant right colon ulcerations. It can lead to significant morbidity and frequent interruption of cancer treatment. Early recognition and prompt intervention are critical to improving patient outcomes.
DOI: 10.6084/m9.figshare.20058731
title: Source Data

description: source data for main figures in the paper " <strong>Mitochondria dysfunction in Charcot Marie Tooth 2B Peripheral Sensory Neuropathy</strong> "
DOI: 10.6084/m9.figshare.19948331
title: Sample dataset.rar

description: A sample dataset, which anyone can see how the anaysis were done utilizing Collect Earth.
DOI: 10.6084/m9.figshare.19948331.v5
title: Sample dataset.rar

description: A sample dataset, which anyone can see how the anaysis were done utilizing Collect Earth.
DOI: 10.6084/m9.figshare.19948331.v4
title: Sample dataset.rar

description: A sample dataset, which anyone can see how the anaysis were done utilizing Collect Earth.
DOI: 10.25934/pr00003489.0
title: Available IPD datapackage for study 'LUX Lung 2 A Phase II Single-arm Trial of BIBW 2992 in Non-small Cell Lung Cancer Patients With EGFR Activating Mutations'

description: The primary objective of this open-label, single arm Phase II trial is to explore the efficacy of BIBW 2992 defined by the objective response rate (CR, PR) as determined by RECIST criteria in patients with advanced NSCLC Stage IIIB or IV whose tumors harbor activating mutations within exon 18 to exon 21 of the EGFR receptor. Patients progressing or relapsing after one prior cytotoxic chemotherapy regimen as well as chemotherapy naïve patients (only in stage 2) will be allowed to enter into the trial.
DOI: 10.4228/zalf-c9xf-wh91
title: Logger based water table measurements in selected kettle holes in the Uckermark (NE Germany, Brandenburg) (Part 1 of data collection, table Kettle_holes_Uckermark_watertable)

description: Water-table and water-temperature measurements were conducted by Water Level Data Logger (AckermannKG) during 2019-2021 in hourly time steps of 17 kettle holes in the Uckermark region (Nordeast Germany, Land Brandenburg). The elevation data are related to DHHN2016 (Deutsches Haupthöhennetz 2016, German Hight Reference Frame 2016).

Related datasets are listed in the metadata element 'Related Identifier'.
Dataset version 1.0
DOI: 10.15151/esrf-es-822390813
title: Yttria-stabilised-zirconia with Xe implantation

description: Investigation of the effects of Xe implantation at different energies and depths on single crystal yttria-stabilised-zirconia.
DOI: 10.15151/esrf-es-800146527
title: Time-resolved SAXS and USAXS of the formation of lignin nanoparticles in a levitating droplet

description: Lignin is one the most abundant biopolymers and has due to its sustainability and accessibility generated interest in industrial as well as research communities. Lignin nanoparticles (LNPs) have emerged within the past few years as a promising type of colloidal materials for applications ranging from coatings and composites to biomedical adhesives.1 While ex situ data has given some insight in the growth mechanism of LNPs, in situ measurements have not been performed before. We thus aim on elucidating the growth mechanism of LNPs using time-resolved SAXS data. We intend to extract information on molecular arrangement, packing density, and porosity of LNPs.
DOI: 10.15151/esrf-es-808439902
title: In-situ Study of Quantum Dots Self-assembly at the air/liquid interface

description: Ordered quantum dots (QD) superlattices (SL) are promising systems for many new technological applications. Understanding their formation process from solution is fundamental to obtain systems with improved properties. In this proposal we aim to understand the formation mechanism of 3D superlattices of PbSe colloidal QDs occurring at the liquid interface by using in-situ GISAXS under controlled solvent evaporation rate. The goal is to explore the optimum conditions to achieve maximum order prior transfer to solid substrates. This proposal is the first step of a large project where we aim to form ordered 3D SLs of merged QDs for opto-electronic applications with superior lateral ordering.
DOI: 10.15151/esrf-es-799260963
title: Monitoring the conservation of chiral memory during the solid-state cyclization reaction of linear dipeptides

description: We aim to investigate the fundamental mechanism of the conservation of chiral memory during the cyclization reaction of linear dipeptides. Our preliminary results showed that the chirality of the product (cyclic peptides) after thermal reaction depended on the absolute configuration (AC) of the residues of the reactant (linear dipeptides). After the cyclization reaction, the products spontaneously crystallized. This allows i) to refine the AC by single-crystal X-ray diffraction and to it compare with the configuration of reactants and ii) to investigate in situ the role of the AC of the residue in the morphological changes during the cyclization reaction using X-ray powder diffraction and Raman spectroscopy.
DOI: 10.15151/esrf-es-799269463
title: In situ study of recovery and recrystallization of Zr-2.5Nb alloy

description: Zirconium alloys are widely used in the nuclear industry due to their low neutron capture section and good resistance to corrosion, irradiation and creep. The microstructure of the Zr nuclear rector components evolves all along the manufacturing route and depending on process parameters it can impact the subsequent processes or the final component properties. It is therefore necessary to understand and master the structural evolution to increase the quality of the material. It is experimental evidence that recrystallization of the Zr-2.5Nb alloy containing metastable beta-Zr phase is very difficult if the material was not highly deformed. For finding the optimum processing route a comprehensive understanding of the phenomenon is necessary. The aim of the present proposal is performing an in situ analysis of the recovery and recrystallization for understanding the role of the stored energy and of the beta-Zr to beta-Nb transformation on the recrystallization process.
DOI: 10.15151/esrf-es-799083151
title: Unraveling the site density effect of single-atom Zn1/Al2O3-x catalysts as a potential candidate for the hydrogenation of CO2 to methanol an

description: In the transition to a more circular economy, better catalysts are urgently needed for the hydrogenation of CO2 to methanol and dimethyl ether. Herein we aim to reveal the synergetic interaction between neighbouring Zn atoms on a defective alumina support (Al2O3-x), which greatly enhanced the CO2 to DME catalytic activity and reduced the activation energy relative to isolated atoms. Employing operando XAS, we propose to study how Zn atom density on the support influences the Zn coordination environments and electronic properties at different reaction temperatures and pressures, and to verify the synergistic activation pathways of CO2 over neighbouring Zn single atoms, as anticipated from our previous kinetic studies. Combining experimental results and theoretical calculations, we expect to reveal the fundamental influence of the spatial distribution of metal atoms on the reaction pathways and activation energies, to guide rational design of practical and efficient industrial catalysts.
DOI: 10.15151/esrf-es-799085385
title: Coupling of plastic deformation and magnetism in Heusler alloys: an in situ microLaue experiment during compression of micropillars

description: Magnetic interactions strongly depend on local order and interatomic distances. Hence mechanical deformation can lead to interesting modifications of magnetic ordering. Recently the group at University of California at Santa Barbara has observed a decrease in net magnetization after plastic deformation of compressed ingots or ground powders of the Heusler alloys MnAu2Al. These experiments have clearly evidenced the role of plastic deformation on magnetic properties in this intermetallic alloy; the converse could also be a potent effect wherein long-range magnetic order could influence the energy landscape for dislocations and their mobility. This raises the interesting question of the impact of long-range magnetic order on plastic properties and dislocation dynamics. This proposal aims at a thorough investigation of the initial stages of plastic deformation in Heusler micropillars using a combination of microcompression and microLaue diffraction.
DOI: 10.15151/esrf-es-799087423
title: High-Energy Synchrotron Studies on Asteroid Samples Provided by Return Missions

description: Our project is embedded within the two sample return missions from near-Earth C-type asteroids ever undertaken so far in international space science, Hayabusa2 (JAXA) and OSIRIS-REx (NASA). The proposers of this Long Term Project are members of the Initial Analysis Team associated with JAXA’s Hayabusa2 mission and the goal of this proposal is to 1) establish the necessary experimental and data-analysis protocols for high-energy quantitative scanning 2D/3D X-ray fluorescence (XRF) and X-ray diffraction (XRD) micro-/nano-analysis of unique extra-terrestrial samples, and 2) to apply these methods to analyze unique sample materials originating from both carbonaceous asteroids which are remnants from the early Solar System, preserving primitive materials since their formation approximately 4.6 billion years ago.
DOI: 10.15151/esrf-es-799088076
title: X-ray induced amorphous-amorphous transition in vitreous silica

description: We propose an x-ray diffraction experiment to investigate the structural evolution of v-SiO2 under x-ray irradiation. Recent x-ray photon correlation experiments have revealed that the x-ray beam simultaneously pumps and probes the dynamics of oxide glasses at temperatures where the spontaneous structural relaxation is frozen. The observed dynamics is accompanied by a progressive rearrangement of the glass structure, which evolves towards a different amorphous configuration. This behaviour suggests the existence of a x-ray induced amorphous-amorphous transition. A detailed structural investigation is thus pivotal to elucidate the microscopic nature of the x-ray induced dynamics in glasses.
DOI: 10.15151/esrf-es-799087597
title: Correlative imaging for additive manufacturing of metallic alloys

description: Additive manufacturing of metallic alloys is an innovative process but several scientific issues need to be overcome for a strong development in industry. In this field, relevant scales are ranging from several centimenters down to submicron requiring the development of a multi-scale correlative imaging approach. We propose a dual strategy on ID16B and BM18 to extent their application domains: (i) an experimental approach linking in situ tests at several scales with dedicated sample environment and technical developments; (ii) a numerical approach based on artificial intelligence algorithms to reduce data acquisition (low number of projections, automatic segmentation) and increase quality (enhanced resolution, noise and rings removal). The multi-scale correlative imaging strategy will benefit to other imaging beamlines (BM05, ID19), will be transferable to other materials science fields leading to more industry participation at ESRF, thanks to an associated long life learning project.
DOI: 10.15151/esrf-es-799089889
title: Oxygen reduction reaction on FeNC catalysts- Identifying the contribution of iron environments to the direct and indirect reaction pathway

description: FeNC catalysts are promising catalysts for the oxygen reduction reaction (ORR) in fuel cells while their stability need to be improved. Due to their heterogeneous composition, it is difficult to discriminate the contribution of the various iron sites to the activity and degradation. During the ORR, oxygen is either reduced to water or to hydrogen peroxide (H2O2). It is suggested that H2O2 formation is one of the main reasons for the instability. It’s relevance for degradation might decrease, when the catalyst is capable of the further reduction of hydrogen peroxide. In this beam time, we will explore the potential induced changes of iron sites at different conditions to identify which iron sites contribute to which step(s) of the ORR mechanism. Complementary to XAS and XES, the samples will be probed at the same conditions by in situ Mössbauer spectroscopy. Data interpretation is assisted by theoretical calculations.
DOI: 10.15151/esrf-es-799094577
title: Imaging the magnetisation vector field by Fourier Transform Holography

description: Fourier Transform Holography (FTH) is an established microscopy technique with nanoscale resolution providing images of one projection of the magnetic moments in a thin sample. We propose to extend the scope of the technique to the full vectorial determination of the magnetic moments in 3D samples. This improvement is highly desirable for the study of materials with complex magnetic textures such as skyrmions, chiral domain walls, Bloch points, etc… Our previous beamtime yielded encouraging results, but severe issues with the detector prevented us from taking a full data set of suffient quality. We wish to complete our study.