cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23499738.v1
title: Supplementary Material for: Serum IGFBP7 deriving from spleen and lung could be used for early recognition of cardiac surgery-associated acute kidney injury

description: Introduction: The utility of arithmetic product of urinary tissue metalloproteinase inhibitor 2 (TIMP2) and insulin-like growth factor-binding protein 7 (IGFBP7) concentrations has been widely accepted on early diagnosis of acute kidney injury (AKI). However, which organ is the main source of those two factors and how the concentration of IGFBP7 and TIMP2 changed in serum during AKI still remain to be defined. Methods: In mice, gene transcription and protein levels of IGFBP7/TIMP2 in the heart, liver, spleen, lung, and kidney were measured in both ischaemia-reperfusion injury (IRI)- and cisplatin-induced AKI models. Serum IGFBP7 and TIMP2 levels were measured and compared in patients before cardiac surgery, and at inclusion (0 h), 2 h, 6 h and 12 h after Intensive Care Unit (ICU) admission, and compared with serum creatinine, blood urea nitrogen (BUN), estimated glomerular filtration rate (eGFR) and serum uric acid (UA). Results: In mouse IRI-AKI model, compared with the sham group, the expression levels of IGFBP7 and TIMP2 did not change in the kidney, but significantly upregulated in the spleen and lung. Compared with patients who did not develop AKI, the concentration of serum IGFBP7 at as early as 2 h after ICU admission (s[IGFBP7]-2 h) was significantly higher in patients who developed AKI. The relationships between s[IGFBP7]-2 h in AKI patients and log2(SCr), log2(BUN), log2(eGFR), and log2(UA) were statistically significant. The diagnostic performance of s[IGFBP7]-2 h measured by the macro-averaged area under the receiver operating characteristic curve (AUC) was 0.948 ([95% CI], 0.853 to 1.000; P&lt;0.001). Discussion/Conclusion: The spleen and lung might be the main source of serum IGFBP7 and TIMP2 during AKI. The serum IGFBP7 value demonstrated good predictive accuracy for AKI following cardiac surgery within 2 h after ICU admission.
DOI: 10.6084/m9.figshare.23499750
title: Supplementary Material for: Serum IGFBP7 deriving from spleen and lung could be used for early recognition of cardiac surgery-associated acute kidney injury

description: Introduction: The utility of arithmetic product of urinary tissue metalloproteinase inhibitor 2 (TIMP2) and insulin-like growth factor-binding protein 7 (IGFBP7) concentrations has been widely accepted on early diagnosis of acute kidney injury (AKI). However, which organ is the main source of those two factors and how the concentration of IGFBP7 and TIMP2 changed in serum during AKI still remain to be defined. Methods: In mice, gene transcription and protein levels of IGFBP7/TIMP2 in the heart, liver, spleen, lung, and kidney were measured in both ischaemia-reperfusion injury (IRI)- and cisplatin-induced AKI models. Serum IGFBP7 and TIMP2 levels were measured and compared in patients before cardiac surgery, and at inclusion (0 h), 2 h, 6 h and 12 h after Intensive Care Unit (ICU) admission, and compared with serum creatinine, blood urea nitrogen (BUN), estimated glomerular filtration rate (eGFR) and serum uric acid (UA). Results: In mouse IRI-AKI model, compared with the sham group, the expression levels of IGFBP7 and TIMP2 did not change in the kidney, but significantly upregulated in the spleen and lung. Compared with patients who did not develop AKI, the concentration of serum IGFBP7 at as early as 2 h after ICU admission (s[IGFBP7]-2 h) was significantly higher in patients who developed AKI. The relationships between s[IGFBP7]-2 h in AKI patients and log2(SCr), log2(BUN), log2(eGFR), and log2(UA) were statistically significant. The diagnostic performance of s[IGFBP7]-2 h measured by the macro-averaged area under the receiver operating characteristic curve (AUC) was 0.948 ([95% CI], 0.853 to 1.000; P&lt;0.001). Discussion/Conclusion: The spleen and lung might be the main source of serum IGFBP7 and TIMP2 during AKI. The serum IGFBP7 value demonstrated good predictive accuracy for AKI following cardiac surgery within 2 h after ICU admission.
DOI: 10.6084/m9.figshare.23499750.v1
title: Supplementary Material for: Serum IGFBP7 deriving from spleen and lung could be used for early recognition of cardiac surgery-associated acute kidney injury

description: Introduction: The utility of arithmetic product of urinary tissue metalloproteinase inhibitor 2 (TIMP2) and insulin-like growth factor-binding protein 7 (IGFBP7) concentrations has been widely accepted on early diagnosis of acute kidney injury (AKI). However, which organ is the main source of those two factors and how the concentration of IGFBP7 and TIMP2 changed in serum during AKI still remain to be defined. Methods: In mice, gene transcription and protein levels of IGFBP7/TIMP2 in the heart, liver, spleen, lung, and kidney were measured in both ischaemia-reperfusion injury (IRI)- and cisplatin-induced AKI models. Serum IGFBP7 and TIMP2 levels were measured and compared in patients before cardiac surgery, and at inclusion (0 h), 2 h, 6 h and 12 h after Intensive Care Unit (ICU) admission, and compared with serum creatinine, blood urea nitrogen (BUN), estimated glomerular filtration rate (eGFR) and serum uric acid (UA). Results: In mouse IRI-AKI model, compared with the sham group, the expression levels of IGFBP7 and TIMP2 did not change in the kidney, but significantly upregulated in the spleen and lung. Compared with patients who did not develop AKI, the concentration of serum IGFBP7 at as early as 2 h after ICU admission (s[IGFBP7]-2 h) was significantly higher in patients who developed AKI. The relationships between s[IGFBP7]-2 h in AKI patients and log2(SCr), log2(BUN), log2(eGFR), and log2(UA) were statistically significant. The diagnostic performance of s[IGFBP7]-2 h measured by the macro-averaged area under the receiver operating characteristic curve (AUC) was 0.948 ([95% CI], 0.853 to 1.000; P&lt;0.001). Discussion/Conclusion: The spleen and lung might be the main source of serum IGFBP7 and TIMP2 during AKI. The serum IGFBP7 value demonstrated good predictive accuracy for AKI following cardiac surgery within 2 h after ICU admission.
DOI: 10.25901/a1xy-qg22
title: Wirilda-Eucalyptus-Allocasuarina Open Grassy Woodland, SA. Ver. 1. VAST-2: Tracking the Transformation of Australia's Vegetated Landscapes
DOI: 10.5281/zenodo.8025839
title: TMT-MS Raw data

description: The raw MS data for TMT-quantitative MS
DOI: 10.5281/zenodo.8025838
title: TMT-MS Raw data

description: The raw MS data for TMT-quantitative MS
DOI: 10.6084/m9.figshare.22758421.v2
title: Chemical Composition, Synergistic Antimicrobial and Antioxidant Potential of <i>Hibiscus rosa-sinensis</i> L. Leaves Essential Oil and Its Major Compound

description: This study aimed to investigate the chemical composition, antioxidant and synergistic antimicrobial potential of <i>Hibiscus rosa-sinensis</i> L. (China rose) leaves essential oil and its major compound, Dioctyl phthalate (DOP). The essential oil was extracted from leaves by hydro-distillation using the Clevenger apparatus. The essential oil was characterized by Gas Chromatography-Mass Spectrometry (GC/MS) analysis which revealed the presence of DOP as a major compound. The essential oil and DOP were tested for antibacterial activity against <i>Klebsiella</i> sp. and <i>Pseudomonas aeruginosa</i> using the disc plate method, antifungal activity against <i>Fusarium oxysporum</i> by agar well diffusion method, and antioxidant activity by 2,2-diphenyl-1-picrylhydrazyl (DPPH), nitric oxide (NO) and 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) free radical scavenging assays. The synergistic antimicrobial interaction of essential oil and DOP was also tested against standard antimicrobials: tetracycline, chloramphenicol, fluconazole, and clotrimazole. The maximum antimicrobial potential was exhibited by China rose leaves essential oil with minimum inhibitory concentrations (MIC) of 18.5, 11.5, and 23.0 μg/mL against <i>Klebsiella</i> sp.<i>, P. aeruginosa</i>, and <i>F</i>. <i>oxysporum</i> respectively. Moreover, the essential oil exhibited synergistic interaction with standard antimicrobials with a 3.75 to 10 times decrease in their MIC values. The essential oil also exhibited median inhibitory concentration (IC<sub>50</sub>) values of 780, 800, and 860 μg/mL in DPPH, NO, and ABTS free radical scavenging assays respectively. Hence it can be concluded that China rose leaves essential oil has a huge significance in pharmaceutical industries as an alternative to synthetic antioxidants and antimicrobials in near future.
DOI: 10.6084/m9.figshare.22758421
title: Chemical Composition, Synergistic Antimicrobial and Antioxidant Potential of <i>Hibiscus rosa-sinensis</i> L. Leaves Essential Oil and Its Major Compound

description: This study aimed to investigate the chemical composition, antioxidant and synergistic antimicrobial potential of <i>Hibiscus rosa-sinensis</i> L. (China rose) leaves essential oil and its major compound, Dioctyl phthalate (DOP). The essential oil was extracted from leaves by hydro-distillation using the Clevenger apparatus. The essential oil was characterized by Gas Chromatography-Mass Spectrometry (GC/MS) analysis which revealed the presence of DOP as a major compound. The essential oil and DOP were tested for antibacterial activity against <i>Klebsiella</i> sp. and <i>Pseudomonas aeruginosa</i> using the disc plate method, antifungal activity against <i>Fusarium oxysporum</i> by agar well diffusion method, and antioxidant activity by 2,2-diphenyl-1-picrylhydrazyl (DPPH), nitric oxide (NO) and 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) free radical scavenging assays. The synergistic antimicrobial interaction of essential oil and DOP was also tested against standard antimicrobials: tetracycline, chloramphenicol, fluconazole, and clotrimazole. The maximum antimicrobial potential was exhibited by China rose leaves essential oil with minimum inhibitory concentrations (MIC) of 18.5, 11.5, and 23.0 μg/mL against <i>Klebsiella</i> sp.<i>, P. aeruginosa</i>, and <i>F</i>. <i>oxysporum</i> respectively. Moreover, the essential oil exhibited synergistic interaction with standard antimicrobials with a 3.75 to 10 times decrease in their MIC values. The essential oil also exhibited median inhibitory concentration (IC<sub>50</sub>) values of 780, 800, and 860 μg/mL in DPPH, NO, and ABTS free radical scavenging assays respectively. Hence it can be concluded that China rose leaves essential oil has a huge significance in pharmaceutical industries as an alternative to synthetic antioxidants and antimicrobials in near future.
DOI: 10.25901/ekgv-m036
title: Whroo Dry Eucalypt Site, Five Photopoint Image Collection
DOI: 10.34740/kaggle/dsv/5905370
title: Dota 2 Pro League Matches 2023
DOI: 10.6084/m9.figshare.23499378
title: G20E_Benign

description: A total of 213 PTEN missense variants comprising of 147 VUS, 54 ClinVar Pathogenic and 12 Benign variants were slected for classification utilizing the MD simulations study.
DOI: 10.6084/m9.figshare.23499378.v1
title: G20E_Benign

description: A total of 213 PTEN missense variants comprising of 147 VUS, 54 ClinVar Pathogenic and 12 Benign variants were slected for classification utilizing the MD simulations study.
DOI: 10.5281/zenodo.7870831
title: Light damage induces inflammatory factors in mouse retina and vitreous humor

description: Supplemental Files
DOI: 10.5281/zenodo.7870830
title: Light damage induces inflammatory factors in mouse retina and vitreous humor

description: Supplemental Files
DOI: 10.6084/m9.figshare.23272184.v1
title: Supplementary tables from Evidence of cospeciation between termites and their gut bacteria on a geological time scale

description: Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one <i>Cryptocercus</i> cockroach, we show that bacteria endemic to termite guts are mostly acquired by vertical transfers. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for fifteen mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.
DOI: 10.6084/m9.figshare.23461391.v2
title: Lindel data 557 class in annAdata

description: LINDEL data in anndata format
DOI: 10.6084/m9.figshare.23461391
title: Lindel data 557 class in annAdata

description: LINDEL data in anndata format <br> How to use? <br> 1. Copy the download link first 2. Then in terminal, type `wget --no-check-certificate LINK` 3. `mv xxx Lindel_557class.h5ad`
DOI: 10.6084/m9.figshare.23461391.v3
title: Lindel data 557 class in annAdata How to use? Copy the download link first Then in terminal, type `wget --no-check-certificate LINK` `mv xxx Lindel_557class.h5ad`

description: LINDEL data in anndata format
DOI: 10.6084/m9.figshare.23461391.v4
title: Lindel data 557 class in annAdata

description: LINDEL data in anndata format <br> How to use? <br> 1. Copy the download link first 2. Then in terminal, type `wget --no-check-certificate LINK` 3. `mv xxx Lindel_557class.h5ad`
DOI: 10.26036/cnp0004406
title: Unlocking the potentials of cyanobacterial photosynthesis for directly converting carbon dioxide into glucose

description: Glucose is the most abundant monosaccharide, serving as an essential energy source for cells in all domains of life and as an important feedstock for biorefinery industry. The current glucose supply is dominated by a plant-biomass-sugar route, while direct conversion of carbon dioxide into glucose through photosynthesis has not been well studied. Here, we demonstrated that the potential of Synechococcus elongatus PCC 7942 for photosynthetic glucose production can be unlocked by preventing native glucokinase activity. Knocking out two glucokinase genes caused a specific genomic mutation, leading to effective secretion of glucose from the previously underestimated sucrose metabolism pathway. Without heterologous catalysis or transportation genes, glucokinase deficiency and spontaneous genomic mutation enabled a glucose secretion of 1.5 g/L, which was further increased to 5 g/L through metabolic and cultivation engineering. Our study underliness the cyanobacterial metabolism plasticities and lays the foundation for the industrial applications of this novel glucose production technology.
DOI: 10.26036/cnp0004437
title: SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics

description: The basic analysis steps of spatial transcriptomics involves obtaining gene expression information from both space and cells. This process requires a set of tools to be completed, and existing tools face performance issues when dealing with large data sets. These issues include computationally intensive spatial localization, RNA genome alignment, and excessive memory usage in large chip scenarios. These problems affect the applicability and efficiency of the process. To address these issues, a high-performance and accurate spatial transcriptomics data analysis workflow called Stereo-Seq Analysis Workflow (SAW) has been developed for the Stereo-Seq technology developed by BGI. This workflow includes mRNA spatial position reconstruction, genome alignment, gene expression matrix generation and clustering, and generate results files in a universal format for subsequent personalized analysis. The excutation time for the entire analysis process is ~148 minutes on 1G reads 1*1 cm chip test data, 1.8 times faster than unoptimized workflow.
DOI: 10.5281/zenodo.8025015
title: 67989 1 PCR amplication

description: 1 step of PCR amplification of 67989 plasmids
DOI: 10.5281/zenodo.8025014
title: 67989 1 PCR amplication

description: 1 step of PCR amplification of 67989 plasmids
DOI: 10.15151/esrf-es-1117954013
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-1234094353
title: test of mini battery cell for solid state electrolytes

description: test of mini battery cell for solid state electrolytes
DOI: 10.15151/esrf-es-1180529478
title: Effect of chirality on the structural and topological features of quantum dot doped blue phase liquid crystal

description: The proposal aims to investigate the effect of chirality on the structure and topology of 3D soft photonic crystals based on blue phase liquid crystal. The blue phase (BP) is thermally stabilized by the inclusion of quantum dots (QD) and a gelator. Low chirality drives cubic molecular arrangement (BPI /BPII), with a lattice spacing of 100-400 nm, leading to soft photonic crystals operating in the visible regime, and high chirality induces amorphous BP (BPIII). Thermal and electric field-dependent X-ray scattering studies in the ultra-small and wide-angle regimes (USAXS / WAXS) are expected to elucidate the nano and sub-micron structures formed due to the interactions between the gelator and QD, whereas the X-ray Photon Correlation Spectroscopy (XPCS), the structural dynamics. Additionally, the lattice arrangement with a tunable photonic band gap in BPI/BPII, and the structural aspects governing BPIII for optimum electro-optic parameters would be discerned.
DOI: 10.15151/esrf-es-1180531710
title: Zinc mobility and chemical stability in the biogenic tooth nanocomposite of dentine

description: Zinc is a natural trace-element in the natural biocomposite dentine that makes up the bony part of teeth. It can additionally diffuse out of artificially placed filling materials, as occasionally reported for clinically-used Zn containing biomaterials (e.g. root canal gutta-percha). Diffusion is extensive with high concentrations that can percolate many hundreds of µm across the bulk of the tooth, as we recently showed. This diffusion causes changes in the micro-structure and chemistry of dentine which have to be understood to determine benefits or possible slow degradation to healthy dentine. Filling materials typically contain ZnO while natural Zn can either be incorporated in the apatite crystals or reside in MMPs in the organic component, which we investigate by XANES. We propose to map the chemical state of Zn to elucidate relationships between resident and diffusion species in healthy dentine near filling material.
DOI: 10.15151/esrf-es-1180545215
title: Observing the Ni ion migration in rechargeable battery using high energy X-ray scattering

description: LiNiO2 (LNO) and other isostructural high-Ni compounds are promising cathode materials for Li-ion batteries. Many works have been reported to reduce particle cracking and improve surface chemistry for better electrochemical performance. However, the understanding of local structural change, such as the Ni migration, is still lacking. Here, we propose an experiment to observe the Ni migration during cycling by pair distribution function (PDF) with high-energy X-ray, which will guide us to develop methods to improve the reversibility of Ni migration to achieve better structural stability. It could provide essential knowledge of the mainstream cathode research for Li-lion batteries.
DOI: 10.15151/esrf-es-1108056003
title: Magnetic Coherent Diffraction Imaging with hard X

description: The purpose of the proposal is to develop a set of new techniques for magnetic imaging at the nanoscale. The techniques rely on the combination of Coherent Diffraction Imaging techniques (3D-CDI, Bragg CDI, ptychography) with magnetic scattering. While this has been done in the soft X-ray range at 3rd generation synchrotron sources to study 2D ferromagnetic materials, only the EBS provides sufficient brilliance to implement similar methods in the hard X-ray range. Using hard X-rays will allow extending the scientific scope to bulk ferromagnetic materials and to thin and bulk antiferromagnetic materials. The imaging techniques should be fully vectorial and have a resolution of ~50 nm and a field of view of a few microns. The project requires instrumental, methodological and numerical developments, which will be beneficial to the ESRF user community. The project is funded until June 2024 by the French research agency (ANR) and the CNRS, including 3 postdoc grants.
DOI: 10.15151/esrf-es-1179517828
title: Mapping interfacial strain during mechanical loading of 316L-Ni bimetallic structure fabricated by directed energy deposition additive manuf

description: Bimetallic structures, a combination of two different metals, have gained broad attention in recent years because of their multifunctional properties integrated in a single structure component. The 316L-Ni bimetallic structure we produced via directed energy deposition (DED) inherits excellent corrosion resistance and biocompatibility from AISI 316L stainless steel, and high electrical and thermal conductivities from pure nickel. However, there is a sharp microstructural transition region: the grain structure is distinguished at the interface due to the sudden change in the composition. Such discontinuity brings about the fracture weakness due to the interfacial residual strain. We seek to investigate the interfacial strain field during mechanical loading of this bimetallic structure by using in situ transmission X-ray powder diffraction. Various DED parameters will be assessed, hence providing guidance to optimise the manufacturing routine for industrial and scientific community.
DOI: 10.15151/esrf-es-1179517982
title: In situ monitoring of the early-stage microstructural development of MgO-hydromagnesite blend using synchrotron nanotomography

description: There is great potential for developing carbon-reactive cement using the massive magnesium resources, but we understand little about their hydration and carbonation kinetics to control their macro-level properties. The main objective of this project is to create high-resolution 3D models of early-stage microstructure development (including the sequence of MgO dissolution, precipitation, and nucleation, as well as the changes in pore structures) of MgO-hydromagnesite blend. We will perform a correlative study complementing the NanoCT data with rheology, XRD, and NMR characterization resulting in a descriptive model for the reaction kinetics.