cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16604508.v1
title: Identification and verification of vascular cell adhesion protein 1 as an immune-related hub gene associated with the tubulointerstitial injury in diabetic kidney disease

description: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD), but the pathogenesis is not completely understood. Tubulointerstitial injury plays critical roles in the development and progression of DKD. The present study aimed to investigate the profile of tubulointerstitial immune cell infiltration and reveal the underlying mechanisms between tubular cell injury and interstitial inflammation in DKD using bioinformatics strategies. First, xCell analysis identified immune cells displaying significant changes in the DKD tubulointerstitium, including upregulated CD4<sup>+</sup> T cells, Th2 cells, CD8<sup>+</sup> T cells, M1 macrophages, activated dendritic cells (DCs) and conventional DCs, as well as downregulated Tregs. Second, pyroptosis was identified as the main form of cell death compared with other forms of programmed cell death. Vascular cell adhesion protein 1 (VCAM1) was identified as the top ranked hub gene. The correlation analysis showed that VCAM1 was significantly positively correlated with pyroptosis and infiltrated immune cells in the tubulointerstitium. Upregulation of VCAM1 in the DKD tubulointerstitium was further verified in European Renal cDNA Bank cohort and was observed to negatively correlate with the glomerular filtration rate (GFR). Our <i>in vitro</i> study validated increased VCAM1 expression in HK-2 cells under diabetic conditions, and pyroptosis inhibition by disulfiram decreased VCAM1 expression, inflammatory cytokine release and fibrosis. In conclusion, our study identified upregulated VCAM1 expression in renal tubular cells, which might interact with infiltrated immune cells, thus promoting fibrosis. The FDA-approved drug disulfiram might improve fibrosis in DKD by targeting tubular pyroptosis and VCAM1 expression.
DOI: 10.6084/m9.figshare.16604508.v2
title: Identification and verification of vascular cell adhesion protein 1 as an immune-related hub gene associated with the tubulointerstitial injury in diabetic kidney disease

description: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD), but the pathogenesis is not completely understood. Tubulointerstitial injury plays critical roles in the development and progression of DKD. The present study aimed to investigate the profile of tubulointerstitial immune cell infiltration and reveal the underlying mechanisms between tubular cell injury and interstitial inflammation in DKD using bioinformatics strategies. First, xCell analysis identified immune cells displaying significant changes in the DKD tubulointerstitium, including upregulated CD4<sup>+</sup> T cells, Th2 cells, CD8<sup>+</sup> T cells, M1 macrophages, activated dendritic cells (DCs) and conventional DCs, as well as downregulated Tregs. Second, pyroptosis was identified as the main form of cell death compared with other forms of programmed cell death. Vascular cell adhesion protein 1 (VCAM1) was identified as the top ranked hub gene. The correlation analysis showed that VCAM1 was significantly positively correlated with pyroptosis and infiltrated immune cells in the tubulointerstitium. Upregulation of VCAM1 in the DKD tubulointerstitium was further verified in European Renal cDNA Bank cohort and was observed to negatively correlate with the glomerular filtration rate (GFR). Our <i>in vitro</i> study validated increased VCAM1 expression in HK-2 cells under diabetic conditions, and pyroptosis inhibition by disulfiram decreased VCAM1 expression, inflammatory cytokine release and fibrosis. In conclusion, our study identified upregulated VCAM1 expression in renal tubular cells, which might interact with infiltrated immune cells, thus promoting fibrosis. The FDA-approved drug disulfiram might improve fibrosis in DKD by targeting tubular pyroptosis and VCAM1 expression.
DOI: 10.6084/m9.figshare.12410438
title: Purification and characteristics of individual major royal jelly protein 1–3

description: Major royal jelly proteins (MRJPs) are deemed to the most characteristic and abundant constituents in royal jelly. The present paper establishes a sequential process to purify the natural MRJP 1–3 by three different chromatographic procedures. Five individual proteins were obtained, including MRJP 1 oligomer 1, MRJP 1 oligomer 2, MRJP 1 monomer, MRJP 2 and MRJP 3s (contain three MRJP 3 variants) with a purity of 89.88%, 67.79%, 99.92%, 99.41%, and 99.97%, respectively. This is the first report that MRJP 1 mainly possesses three oligomers: a 228 kDa MRJP 1 oligomer 1, a 408 kDa MRJP 1 oligomer 2 and a 639 kDa MRJP 1 oligomer 3. We infer that MRJP 1 oligomer 3 (639 kDa) may be assembled by MRJP 1 oligomer 1 (228 kDa) and MRJP 1 oligomer 2 (408 kDa). The secondary structure of the purified MRJP 1–3 consisted predominantly of β-sheets and random coil in the native conformation. Our results will contribute to the physiological and physicochemical function of the purified individual MRJPs.
DOI: 10.6084/m9.figshare.12410438.v1
title: Purification and characteristics of individual major royal jelly protein 1–3

description: Major royal jelly proteins (MRJPs) are deemed to the most characteristic and abundant constituents in royal jelly. The present paper establishes a sequential process to purify the natural MRJP 1–3 by three different chromatographic procedures. Five individual proteins were obtained, including MRJP 1 oligomer 1, MRJP 1 oligomer 2, MRJP 1 monomer, MRJP 2 and MRJP 3s (contain three MRJP 3 variants) with a purity of 89.88%, 67.79%, 99.92%, 99.41%, and 99.97%, respectively. This is the first report that MRJP 1 mainly possesses three oligomers: a 228 kDa MRJP 1 oligomer 1, a 408 kDa MRJP 1 oligomer 2 and a 639 kDa MRJP 1 oligomer 3. We infer that MRJP 1 oligomer 3 (639 kDa) may be assembled by MRJP 1 oligomer 1 (228 kDa) and MRJP 1 oligomer 2 (408 kDa). The secondary structure of the purified MRJP 1–3 consisted predominantly of β-sheets and random coil in the native conformation. Our results will contribute to the physiological and physicochemical function of the purified individual MRJPs.
DOI: 10.5281/zenodo.10670912
title: Understanding the Impact of Symmetrical Substitution on the Photodynamics of Sinapate Esters Using Gas-Phase Ultrafast Spectroscopy

description: Data set for J. Phys. Chem. Lett. 2023, 14, 39, 8771–8779.
description: Two model biomimetic systems, ethyl sinapate (ES) and its symmetrical analogue, diethyl 2-(4-hydroxy-3,5-dimethoxybenzylidene)malonate (or diethyl sinapate, DES), are stripped to their core fundamentals through gas-phase spectroscopy to understand the underlying photophysics of photothermal materials. Following photoexcitation to the optically bright S1(ππ*) state, DES is found to repopulate the electronic ground state over 3 orders of magnitude quicker than its nonsymmetrical counterpart, ES. Our XMS-CASPT2 calculations shed light on the experimental results, revealing crucial differences in the potential energy surfaces and conical intersection topography between ES and DES. From this work, a peaked conical intersection, seen for DES, shows vital importance for the nonradiative ground-state recovery of photothermal materials. This fundamental comparative study highlights the potential impact that symmetrical substitution can have on the photodynamics of sinapate esters, providing a blueprint for future advancement in photothermal technology.
DOI: 10.5281/zenodo.10670913
title: Understanding the Impact of Symmetrical Substitution on the Photodynamics of Sinapate Esters Using Gas-Phase Ultrafast Spectroscopy

description: Data set for J. Phys. Chem. Lett. 2023, 14, 39, 8771–8779.
description: Two model biomimetic systems, ethyl sinapate (ES) and its symmetrical analogue, diethyl 2-(4-hydroxy-3,5-dimethoxybenzylidene)malonate (or diethyl sinapate, DES), are stripped to their core fundamentals through gas-phase spectroscopy to understand the underlying photophysics of photothermal materials. Following photoexcitation to the optically bright S1(ππ*) state, DES is found to repopulate the electronic ground state over 3 orders of magnitude quicker than its nonsymmetrical counterpart, ES. Our XMS-CASPT2 calculations shed light on the experimental results, revealing crucial differences in the potential energy surfaces and conical intersection topography between ES and DES. From this work, a peaked conical intersection, seen for DES, shows vital importance for the nonradiative ground-state recovery of photothermal materials. This fundamental comparative study highlights the potential impact that symmetrical substitution can have on the photodynamics of sinapate esters, providing a blueprint for future advancement in photothermal technology.
DOI: 10.6084/m9.figshare.17129266
title: LncRNA DDX11 antisense RNA 1 promotes EMT process of esophageal squamous cell carcinoma by sponging miR-30d-5p to regulate SNAI1/ZEB2 expression and Wnt/β-catenin pathway

description: LncRNA DDX11 antisense RNA 1 (DDX11-AS1) is recognized as having an imperative oncogenic role in different types of human cancer. Nevertheless, the functions, as well as the basic mechanisms of DDX11-AS1 in the EMT process of esophageal squamous cell carcinoma (ESCC), are yet to be clarified. In this research, high DDX11-AS1 expression was detected in ESCC cells as well as tissues and was linked to the poor prognosis of patients with ESCC. DDX11-AS1 promoted cell proliferation, migration, invasion ability and epithelial mesenchymal transition (EMT) process in vitro. Mechanistic analysis depicted that DDX11-AS1 may function as a ceRNA through sponging miR-30d-5p to upregulate the expression of SNAI1 and ZEB2. Meanwhile, overexpression of DDX11-AS1 might cause the activation of the Wnt/β-catenin signaling pathway via targeting miR-30d-5p. On the whole, the findings of this research illustrate that DDX11-AS1 may act as an EMT-related lncRNA to advance ESCC progression through sponging miR-30d-5p to regulate SNAI1/ZEB2 expression and activate the Wnt/β-catenin pathway, which indicates that it might serve as a probable therapeutic target for ESCC.
DOI: 10.6084/m9.figshare.17129266.v1
title: LncRNA DDX11 antisense RNA 1 promotes EMT process of esophageal squamous cell carcinoma by sponging miR-30d-5p to regulate SNAI1/ZEB2 expression and Wnt/β-catenin pathway

description: LncRNA DDX11 antisense RNA 1 (DDX11-AS1) is recognized as having an imperative oncogenic role in different types of human cancer. Nevertheless, the functions, as well as the basic mechanisms of DDX11-AS1 in the EMT process of esophageal squamous cell carcinoma (ESCC), are yet to be clarified. In this research, high DDX11-AS1 expression was detected in ESCC cells as well as tissues and was linked to the poor prognosis of patients with ESCC. DDX11-AS1 promoted cell proliferation, migration, invasion ability and epithelial mesenchymal transition (EMT) process in vitro. Mechanistic analysis depicted that DDX11-AS1 may function as a ceRNA through sponging miR-30d-5p to upregulate the expression of SNAI1 and ZEB2. Meanwhile, overexpression of DDX11-AS1 might cause the activation of the Wnt/β-catenin signaling pathway via targeting miR-30d-5p. On the whole, the findings of this research illustrate that DDX11-AS1 may act as an EMT-related lncRNA to advance ESCC progression through sponging miR-30d-5p to regulate SNAI1/ZEB2 expression and activate the Wnt/β-catenin pathway, which indicates that it might serve as a probable therapeutic target for ESCC.
DOI: 10.6084/m9.figshare.25112339.v4
title: ChirakkalEtAl_supplementaryinformation

description: See supplementary information which contains schematic sketch of the stratigraphy of each study sites with sampling points and sample names, complete <i>n</i>-alkanes and PAHs distribution and concentration data.<br>Authors: Aljasil Chirakkal, Calin Constantin Stiendal, Jago Jonathan Birk, Redzhep Kurbanov, David K Wright
DOI: 10.5281/zenodo.8314666
title: Data from UK2deport: Dataset 2

description: UK legal acts and guidances for UK Home Office caseworkers regulating immigration from the European Union.

Anonymised data of research participants.

The results of the analysis of the data has been published here: https://doi.org/10.1111/imig.13126

This research was funded in whole the National Science Centre under the grant number 2020/39/D/HS5/02319. For the purpose of Open Access, the author has applied a CC-BY public copyright licence to datasets linked to any Author Accepted Manuscript (AAM) version arising from this submission.
DOI: 10.5281/zenodo.8314667
title: Data from UK2deport: Dataset 2

description: UK legal acts and guidances for UK Home Office caseworkers regulating immigration from the European Union.

Anonymised data of research participants.

The results of the analysis of the data has been published here: https://doi.org/10.1111/imig.13126

This research was funded in whole the National Science Centre under the grant number 2020/39/D/HS5/02319. For the purpose of Open Access, the author has applied a CC-BY public copyright licence to datasets linked to any Author Accepted Manuscript (AAM) version arising from this submission.
DOI: 10.6084/m9.figshare.19750760
title: Additional file 1 of A selected population study reveals the biochemical mechanism of intramuscular fat deposition in chicken meat

description: Additional file 1: Table S1. P-value of correlation coefficient between IMF and its main components.
DOI: 10.6084/m9.figshare.19750760.v1
title: Additional file 1 of A selected population study reveals the biochemical mechanism of intramuscular fat deposition in chicken meat

description: Additional file 1: Table S1. P-value of correlation coefficient between IMF and its main components.
DOI: 10.6084/m9.figshare.19750763
title: Additional file 2 of A selected population study reveals the biochemical mechanism of intramuscular fat deposition in chicken meat

description: Additional file 2: Table S2. P-value of correlation coefficient between IMF/TG and fatty acids.
DOI: 10.6084/m9.figshare.19750763.v1
title: Additional file 2 of A selected population study reveals the biochemical mechanism of intramuscular fat deposition in chicken meat

description: Additional file 2: Table S2. P-value of correlation coefficient between IMF/TG and fatty acids.
DOI: 10.6084/m9.figshare.19750766
title: Additional file 3 of A selected population study reveals the biochemical mechanism of intramuscular fat deposition in chicken meat

description: Additional file 3: Table S3. The correlation analysis between gene expression level and the content IMF, TG and FAs.
DOI: 10.6084/m9.figshare.19750766.v1
title: Additional file 3 of A selected population study reveals the biochemical mechanism of intramuscular fat deposition in chicken meat

description: Additional file 3: Table S3. The correlation analysis between gene expression level and the content IMF, TG and FAs.
DOI: 10.5281/zenodo.10640032
title: Data from UK2deport: Dataset 1

description: The results of the analysis of the data has been published here: 



Agnieszka Radziwinowiczówna & Benjamin Morgan. (2022). London’s deportation apparatus: The ‘administrative removal’ of rough sleeping European Union citizens, 2010-17. Population, Space and Place. https://doi.org/10.1002/psp.2633

 

This research was funded in whole the National Science Centre under the grant number 2020/39/D/HS5/02319. For the purpose of Open Access, the author has applied a CC-BY public copyright licence to datasets linked to any Author Accepted Manuscript (AAM) version arising from this submission.
DOI: 10.5281/zenodo.10640033
title: Data from UK2deport: Dataset 1

description: The results of the analysis of the data has been published here: 



Agnieszka Radziwinowiczówna & Benjamin Morgan. (2022). London’s deportation apparatus: The ‘administrative removal’ of rough sleeping European Union citizens, 2010-17. Population, Space and Place. https://doi.org/10.1002/psp.2633

 

This research was funded in whole the National Science Centre under the grant number 2020/39/D/HS5/02319. For the purpose of Open Access, the author has applied a CC-BY public copyright licence to datasets linked to any Author Accepted Manuscript (AAM) version arising from this submission.
DOI: 10.6084/m9.figshare.24993672
title: Additional file 1 of Effect of transcutaneous electrical acupoint stimulation on remifentanil dosage during craniotomy aneurysm clipping: a prospective, randomized controlled study

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.24993672.v1
title: Additional file 1 of Effect of transcutaneous electrical acupoint stimulation on remifentanil dosage during craniotomy aneurysm clipping: a prospective, randomized controlled study

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.17129366
title: Cepharanthine loaded nanoparticles coated with macrophage membranes for lung inflammation therapy

description: Acute lung injury (ALI) is a disease associated with suffering and high lethality, but to date without any effective pharmacological management in the clinic. In the pathological mechanisms of ALI, a strong inflammatory response plays an important role. Herein, based on macrophage ‘homing’ into inflammation sites and cell membrane coating nanotechnology, we developed a biomimetic anti-inflammation nanosystem (MM-CEP/NLCs) for the treatment of ALI. MM-CEP/NLCs were made with nanostructured lipid carriers (NLCs) coated with natural macrophage membranes (MMs) to achieve effective accumulation of cepharanthine (CEP) in lung inflammation to achieve the effect of treating ALI. With the advantage of suitable physicochemical properties of NLCs and unique biological functions of the macrophage membrane, MM-CEP/NLCs were stabilized and enabled sustained drug release, providing improved biocompatibility and long-term circulation. <i>In vivo</i>, the macrophage membranes enabled NLCs to be targeted and accumulated in the inflammation sites. Further, MM-CEP/NLCs significantly attenuated the severity of ALI, including lung water content, histopathology, bronchioalveolar lavage cellularity, protein concentration, and inflammation cytokines. Our results provide a bionic strategy via the biological properties of macrophages, which may have greater value and application prospects in the treatment of inflammation.
DOI: 10.6084/m9.figshare.17129366.v1
title: Cepharanthine loaded nanoparticles coated with macrophage membranes for lung inflammation therapy

description: Acute lung injury (ALI) is a disease associated with suffering and high lethality, but to date without any effective pharmacological management in the clinic. In the pathological mechanisms of ALI, a strong inflammatory response plays an important role. Herein, based on macrophage ‘homing’ into inflammation sites and cell membrane coating nanotechnology, we developed a biomimetic anti-inflammation nanosystem (MM-CEP/NLCs) for the treatment of ALI. MM-CEP/NLCs were made with nanostructured lipid carriers (NLCs) coated with natural macrophage membranes (MMs) to achieve effective accumulation of cepharanthine (CEP) in lung inflammation to achieve the effect of treating ALI. With the advantage of suitable physicochemical properties of NLCs and unique biological functions of the macrophage membrane, MM-CEP/NLCs were stabilized and enabled sustained drug release, providing improved biocompatibility and long-term circulation. <i>In vivo</i>, the macrophage membranes enabled NLCs to be targeted and accumulated in the inflammation sites. Further, MM-CEP/NLCs significantly attenuated the severity of ALI, including lung water content, histopathology, bronchioalveolar lavage cellularity, protein concentration, and inflammation cytokines. Our results provide a bionic strategy via the biological properties of macrophages, which may have greater value and application prospects in the treatment of inflammation.
DOI: 10.6084/m9.figshare.17129509
title: Adaptor SH3BGRL drives autophagy-mediated chemoresistance through promoting PIK3C3 translation and ATG12 stability in breast cancers

description: Acquired chemotherapy resistance is one of the main culprits in the relapse of breast cancer. But the underlying mechanism of chemotherapy resistance remains elusive. Here, we demonstrate that a small adaptor protein, SH3BGRL, is not only elevated in the majority of breast cancer patients but also has relevance with the relapse and poor prognosis of breast cancer patients. Functionally, SH3BGRL upregulation enhances the chemoresistance of breast cancer cells to the first-line doxorubicin treatment through macroautophagic/autophagic protection. Mechanistically, SH3BGRL can unexpectedly bind to ribosomal subunits to enhance PIK3C3 translation efficiency and sustain ATG12 stability. Therefore, inhibition of autophagy or silence of PIK3C3 or ATG12 can effectively block the driving effect of SH3BGRL on doxorubicin resistance of breast cancer cells in vitro and in vivo. We also validate that SH3BGRL expression is positively correlated with that of PIK3C3 or ATG12, as well as the constitutive occurrence of autophagy in clinical breast cancer tissues. Taken together, our data reveal that SH3BGRL upregulation would be a key driver to the acquired chemotherapy resistance through autophagy enhancement in breast cancer while targeting SH3BGRL could be a potential therapeutic strategy against breast cancer. <b>Abbreviations:</b> ABCs: ATP-binding cassette transporters; Act D: actinomycin D; ACTB/β-actin: actin beta; ATG: autophagy-related; Baf A<sub>1</sub>: bafilomycin A<sub>1</sub>; CASP3: caspase 3; CHX: cycloheximide; CQ: chloroquine; Dox: doxorubicin; FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GEO: gene expression omnibus; GFP: green fluorescent protein; G6PD: glucose-6-phosphate dehydrogenase; GSEA: gene set enrichment analysis; IHC: immunochemistry; KEGG: Kyoto Encyclopedia of Genes and Genomes; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; 3-MA: 3-methyladenine; mRNA: messenger RNA; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; SH3BGRL: SH3 domain binding glutamate-rich protein-like; SQSTM1/p62: sequestosome 1; ULK1: unc-51 like autophagy activating kinase 1