cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17919093
title: Vitamin D<sub>3</sub> and carbamazepine protect against <i>Clostridioides difficile</i> infection in mice by restoring macrophage lysosome acidification

description: <i>Clostridioides difficile</i> infection (CDI) is a common cause of nosocomial diarrhea. TcdB is a major <i>C. difficile</i> exotoxin that activates macrophages to promote inflammation and epithelial damage. Lysosome impairment is a known trigger for inflammation. Herein, we hypothesize that TcdB could impair macrophage lysosomal function to mediate inflammation during CDI. Effects of TcdB on lysosomal function and the downstream pro-inflammatory SQSTM1/p62-NFKB (nuclear factor kappa B) signaling were assessed in cultured macrophages and in a murine CDI model. Protective effects of two lysosome activators (i.e., vitamin D<sub>3</sub> and carbamazepine) were assessed. Results showed that TcdB inhibited CTNNB1/β-catenin activity to downregulate MITF (melanocyte inducing transcription factor) and its direct target genes encoding components of lysosomal membrane vacuolar-type ATPase, thereby suppressing lysosome acidification in macrophages. The resulting lysosomal dysfunction then impaired autophagic flux and activated SQSTM1-NFKB signaling to drive the expression of IL1B/IL-1β (interleukin 1 beta), IL8 and CXCL2 (chemokine (C-X-C motif) ligand 2). Restoring MITF function by enforced MITF expression or restoring lysosome acidification with 1α,25-dihydroxyvitamin D<sub>3</sub> or carbamazepine suppressed pro-inflammatory cytokine expression <i>in vitro</i>. In mice, gavage with TcdB-hyperproducing <i>C. difficile</i> or injection of TcdB into ligated colon segments caused prominent MITF downregulation in macrophages. Vitamin D<sub>3</sub> and carbamazepine lessened TcdB-induced lysosomal dysfunction, inflammation and histological damage. In conclusion, TcdB inhibits the CTNNB1-MITF axis to suppress lysosome acidification and activates the downstream SQSTM1-NFKB signaling in macrophages during CDI. Vitamin D<sub>3</sub> and carbamazepine protect against CDI by restoring MITF expression and lysosomal function in mice. <b>Abbreviations:</b> ATP6V0B: ATPase H+ transporting V0 subunit b; ATP6V0C: ATPase H+ transporting V0 subunit c; ATP6V0E1: ATPase H+ transporting V0 subunit e1; ATP6V1H: ATPase H+ transporting V1 subunit H; CBZ: carbamazepine; CDI: <i>C. difficile</i> infection; CXCL: chemokine C-X-X motif ligand; IL: interleukin; LAMP1: lysosomal-associated membrane protein 1; LC3: microtubule-associated protein 1 light chain 3; LEF: lymphoid enhancer binding factor 1; MITF: melanocyte inducing transcription factor; NFKB: nuclear factor kappa B; PMA: phorbol 12-myristate 13-acetate; TcdA: Clostridial toxin A; TcdB: Clostridial toxin B; TFE3: transcription factor E3; TFEB: transcription factor EB.
DOI: 10.6084/m9.figshare.5335855.v4
title: Quality assessment of positron emission tomography scans: recommendations for future multicentre trials

description: <b>Background:</b> Standardization protocols and guidelines for positron emission tomography (PET) in multicenter trials are available, despite a large variability in image acquisition and reconstruction parameters exist. In this study, we investigated the compliance of PET scans to the guidelines of the European Association of Nuclear Medicine (EANM). From these results, we provide recommendations for future multicenter studies using PET. <b>Material and methods:</b> Patients included in a multicenter randomized phase II study had repeated PET scans for early response assessment. Relevant acquisition and reconstruction parameters were extracted from the digital imaging and communications in medicine (DICOM) header of the images. The PET image parameters were compared to the guidelines of the EANM for tumor imaging version 1.0 recommended parameters. <b>Results:</b> From the 223 included patients, 167 baseline scans and 118 response scans were available from 15 hospitals. Scans of 19% of the patients had an uptake time that fulfilled the Uniform Protocols for Imaging in Clinical Trials response assessment criteria. The average quality score over all hospitals was 69%. Scans with a non-compliant uptake time had a larger standard deviation of the mean standardized uptake value (SUVmean) of the liver than scans with compliant uptake times. <b>Conclusions:</b> Although a standardization protocol was agreed on, there was a large variability in imaging parameters. For future, multicenter studies including PET imaging a prospective central quality review during patient inclusion is needed to improve compliance with image standardization protocols as defined by EANM.
DOI: 10.6084/m9.figshare.17919092.v1
title: Synthesis, <i>in vitro</i> biological screening and docking study of benzo[<i>d</i>]oxazole <i>bis</i> Schiff base derivatives as a potent anti-Alzheimer agent

description: We have synthesized benzo[<i>d</i>]oxazole derivatives (<b>1–21</b>) through a multistep reaction. Alteration in the structure of derivatives was brought in the last step <i>via</i> using various substituted aromatic aldehydes. In search of an anti-Alzheimer agent, all derivatives were evaluated against acetylcholinesterase and butyrylcholinesterase enzyme under positive control of standard drug donepezil (IC<sub>50</sub> = 0.016 ± 0.12 and 4.5 ± 0.11 µM) respectively. In case of acetylcholinesterase enzyme inhibition, derivatives <b>8</b>, <b>9</b> and <b>18</b> (IC<sub>50</sub> = 0.50 ± 0.01, 0.90 ± 0.05 and 0.3 ± 0.05 µM) showed very promising inhibitory potentials. While in case of butyrylcholinesterase enzyme inhibition, most of the derivatives like <b>6, 8, 9, 13, 15, 18</b> and <b>19</b> (IC<sub>50</sub> = 2.70 ± 0.10, 2.60 ± 0.10, 2.20 ± 0.10, 4.25 ± 0.10, 3.30 ± 0.10, 0.96 ± 0.05 and 3.20 ± 0.10 µM) displayed better inhibitory potential than donepezil. Moreover, derivative <b>18</b> is the most potent one among the series in both inhibitions. The binding interaction of derivatives with the active gorge of the enzyme was confirmed <i>via</i> a docking study. Furthermore, the binding interaction between derivatives and the active site of enzymes was correlated through the SAR study. Structures of all derivatives were confirmed through spectroscopic techniques such as <sup>1</sup>H-NMR, <sup>13</sup>C-NMR and HREI-MS, respectively. Communicated by Ramaswamy H. Sarma
DOI: 10.5281/zenodo.10635757
title: kaempferia_rotunda_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10635758
title: kaempferia_rotunda_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.20016289.v1
title: SAMHD1, positively regulated by KLF4, suppresses the proliferation of gastric cancer cells through MAPK p38 signaling pathway

description: SAMHD1 was reported to be related with the development of tumors, while its function in gastric cancer (GC) has not been elucidated yet. Here, we investigated the role and mechanism of SAMHD1 in regulating the proliferation of GC, as well as the mechanism of its expression regulation. Our results revealed that SAMHD1 was downregulated in GC tissues and cell lines, which was correlated with tumor size, depth of invasion and TNM stage. Overexpression of SAMHD1 inhibited the proliferation, clone formation, DNA synthesis and cell cycle progression, while knockdown of SAMHD1 promoted the proliferation of GC cells in vitro and vivo. Meanwhile, SAMHD1 inhibited the activation of MAPK p38 signaling pathway. Moreover, SB203580, as a MAPK p38 inhibitor, could reverse the proliferation and activation of MAPK p38 signaling pathway caused by knockdown of SAMHD1 in GC cells. Additionally, transcription factor Krüppel-like factor 4 (KLF4) bound to the core promoter of SAMHD1, increasing its transcriptional expression in GC cells. In conclusion, SAMHD1 suppressed the proliferation of GC through negatively regulating the activation of MAPK p38 signaling pathway and was upregulated by KLF4 in GC cells.
DOI: 10.25549/usctheses-ouc11362352
title: The Effect of a Pontoon Transitional Design on the Performance of Seventh and Eighth Grade Students in a Non-public Secondary School
DOI: 10.6084/m9.figshare.16869876
title: Additional file 3 of Hsa_circ_0004296 inhibits metastasis of prostate cancer by interacting with EIF4A3 to prevent nuclear export of ETS1 mRNA

description: Additional file 3: Table S2. The specific RBPs interacted with circ_0004296.
DOI: 10.6084/m9.figshare.16870664.v1
title: Pathogenic Mechanisms of Preeclampsia with Severe Features Implied by the Plasma Exosomal miRNA Profile

description: Preeclampsia is a complication of pregnancy characterised by high blood pressure and organ damage after 20 gestational weeks. It is associated with high maternal and fetal morbidity and mortality; however, at present, there is no effective prevention or treatment for this condition. Previous studies have revealed that plasma exosomal miRNAs from pregnant women with preeclampsia could serve as biomarkers of pathogenic factors. However, the roles of plasma exosomal miRNAs in preeclampsia with severe features (sPE), which is associated with poorer pregnancy outcomes, remain unknown. Thus, the aims of this study were to characterise plasma exosomal miRNAs in sPE and explore the related pathogenic mechanisms using bioinformatic analysis. Plasma exosomes were isolated using a mirVana RNA isolation kit. The exosomal miRNAs were detected using high-throughput sequencing and the miRNAs related to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene ontology (GO) terms were analysed using the clusterProfiler package of R. Fifteen miRNAs exhibited increased expression and fourteen miRNAs exhibited reduced expression in plasma exosomes from women with sPE as compared to normal pregnant women. Further, gene set enrichment analysis revealed that the differentially expressed plasma exosomal miRNAs were related to the stress response and cell junction regulation, among others. In summary, this study is the first to identify the differentially expressed plasma exosomal miRNAs in sPE. These findings highlight promising pathogenesis mechanisms underlying preeclampsia.
DOI: 10.6084/m9.figshare.16870664.v2
title: Pathogenic mechanisms of preeclampsia with severe features implied by the plasma exosomal mirna profile

description: Preeclampsia is a complication of pregnancy characterized by high blood pressure and organ damage after 20 gestational weeks. It is associated with high maternal and fetal morbidity and mortality. However, at present, there is no effective prevention or treatment for this condition. Previous studies have revealed that plasma exosomal mirnas from pregnant women with preeclampsia could serve as biomarkers of pathogenic factors. However, the roles of plasma exosomal mirnas in preeclampsia with severe features (sPE), which is associated with poorer pregnancy outcomes, remain unknown. Thus, the aims of this study were to characterize plasma exosomal miRNAs in sPE and explore the related pathogenic mechanisms using bioinformatic analysis. Plasma exosomes were isolated using a mirVana RNA isolation kit. the exosomal miRNAs were detected using high-throughput sequencing and the mirnas related to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene ontology (GO) terms were analyzed using the clusterprofiler package of R. Fifteen miRNAs exhibited increased expression and fourteen miRNAs exhibited reduced expression in plasma exosomes from women with sPE as compared to normal pregnant women. Further, gene set enrichment analysis revealed that the differentially expressed plasma exosomal miRNAs were related to the stress response and cell junction regulation, among others. In summary, this study is the first to identify the differentially expressed plasma exosomal miRNAs in sPE. These findings highlight promising pathogenesis mechanisms underlying preeclampsia.
DOI: 10.6084/m9.figshare.16869874
title: Additional file 2 of Hsa_circ_0004296 inhibits metastasis of prostate cancer by interacting with EIF4A3 to prevent nuclear export of ETS1 mRNA

description: Additional file 2: Table S1. Primers, siRNAs, probes, and plasmid used in the present study.
DOI: 10.6084/m9.figshare.16869874.v1
title: Additional file 2 of Hsa_circ_0004296 inhibits metastasis of prostate cancer by interacting with EIF4A3 to prevent nuclear export of ETS1 mRNA

description: Additional file 2: Table S1. Primers, siRNAs, probes, and plasmid used in the present study.
DOI: 10.6084/m9.figshare.16869876.v1
title: Additional file 3 of Hsa_circ_0004296 inhibits metastasis of prostate cancer by interacting with EIF4A3 to prevent nuclear export of ETS1 mRNA

description: Additional file 3: Table S2. The specific RBPs interacted with circ_0004296.
DOI: 10.6084/m9.figshare.16869884.v1
title: Additional file 7 of Hsa_circ_0004296 inhibits metastasis of prostate cancer by interacting with EIF4A3 to prevent nuclear export of ETS1 mRNA

description: Additional file 7.
DOI: 10.6084/m9.figshare.16869818
title: Additional file 1 of Identification and response analysis of xyloglucan endotransglycosylase/hydrolases (XTH) family to fluoride and aluminum treatment in Camellia sinensis

description: Additional file 1: The CDS of CsXTHs. The coding sequences (CDS) of 14 XTH genes from Camellia sinensis.
DOI: 10.6084/m9.figshare.16869816.v1
title: Additional file 1 of CircCD44 plays oncogenic roles in triple-negative breast cancer by modulating the miR-502–5p/KRAS and IGF2BP2/Myc axes

description: Additional file 1.
DOI: 10.6084/m9.figshare.10058351
title: Collaborative task scheduling with new task arrival in cloud manufacturing using improved multi-population biogeography-based optimization

description: This is the experimental data of the manuscript entitled "Collaborative task scheduling with new task arrival in cloud manufacturing using improved multi-population biogeography-based optimization". All data are generated through computer simulation and saved in the file with txt format. The data are consistent with the real-world case. The “illustrative case data.txt” is used in Section 5.2 as illustrative examples corresponding to table 1 and table 2, respectively. Other data are used in Section 5.3 and 5.4.
DOI: 10.6084/m9.figshare.22117004
title: Model Trained by Children’s Dental Panoramic Radiographs Dataset

description: Model Trained by Children’s Dental Panoramic Radiographs Dataset
DOI: 10.5525/gla.researchdata.1596
title: Wi-Fi and Radar Fusion for Head Movement Sensing Through Walls Leveraging Deep Learning

description: The dataset pertains to head movements, preserved in a manner that respects privacy. Specifically, radio frequency (RF) sensing technology was employed to capture the unique channel variations caused by head movements. The USRP x300, equipped with a VERT2450 omnidirectional antenna for transmission and a HyperLOG 7040 X for reception, was utilized. Additionally, the experiment was replicated using a Xethru UWB radar to capture Doppler frequency shifts resulting from lip movements. Six classes of lip movements were identified: Head Up, Head Down, Right 90, Left 90, Right 45, and Left 45. These classes were recorded in scenarios both with and without a wall, using Wi-Fi and radar signals. We succeeded in detecting head movements even when obstructed by a wall. Four subjects—two males and two females—participated in the experiments.
DOI: 10.6084/m9.figshare.14248535.v1
title: Super Resolution for Multi-Sources Image Stream Data using Smooth and Sparse Tensor Completion and its Applications in Data Acquisition of Additive Manufacturing

description: Recent developments of advanced imaging systems spur their applications in many areas, ranging from satellite remote sensing for geographic information to thermal imaging analysis for manufacturing process monitoring and control. Due to different specifications of imaging systems, the resulting image stream data (videos) have different spatial and temporal resolutions. This proposed work is based on the image stream data captured by multiple imaging systems for the same object with different but complementary spatial and temporal resolutions. For example, one system has high spatial but low temporal resolutions while the other one has opposite resolutions. The goal of this paper is to develop a new super resolution method that integrates these different types of image stream data to improve both spatial and temporal resolutions, which is critical to obtaining more insightful information for more effective quality control of targeted processes or systems. To fulfill this goal, a new tensor completion model is developed by considering both smooth and sparse features simultaneously and is thus termed smooth and sparse tensor completion (SSTC). The results of the extensive case studies illustrate the superiority of our method over the elaborately selected benchmark methods.
DOI: 10.6084/m9.figshare.14248536.v1
title: High-dimensional Cost-constrained Regression via Non-convex Optimization

description: Budget constraints become an important consideration in modern predictive modeling due to the high cost of collecting certain predictors. This motivates us to develop cost-constrained predictive modeling methods. In this paper, we study a new high-dimensional cost-constrained linear regression problem, that is, we aim to find the cost-constrained regression model with the smallest expected prediction error among all models satisfying a budget constraint. The non-convex budget constraint makes this problem NP-hard. In order to estimate the regression coefficient vector of the cost-constrained regression model, we propose a new discrete first-order continuous optimization method. In particular, our method delivers a series of estimates of the regression coefficient vector by solving a sequence of 0-1 knapsack problems. Theoretically, we prove that the series of the estimates generated by our iterative algorithm converge to a first-order stationary point, which can be a globally optimal solution under some conditions. Furthermore, we study some extensions of our method that can be used for general statistical learning problems and problems with groups of variables. Numerical studies using simulated datasets and a real dataset from a diabetes study indicate that our proposed method can solve problems of fairly high dimensions with promising performance. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.13724939
title: Additional file 5 of Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

description: Additional file 5: Supplementary Table S1. 3654 species used in probe design. Supplementary Table S2. The table of 568 representative species ID. Supplementary Table S3. Evaluation of designed probe. Supplementary Table S4. The bamboo species in this study. Supplementary Table S5. The table of bamboo plastid sequences from NCBI. Supplementary Table S6. The species used for species tree construction. Supplementary Table S7. Coverage and depth analysis of pan-CpGenome. Supplementary Table S8. Align the probes to 468 complete chloroplast genomes, which did not contain the sequences used to design the probes. Supplementary Table S9. The statistics of assembled plastid sequences after redundancy removing. Supplementary Table S10. Evaluation for target enrichment and assemblies.
DOI: 10.6084/m9.figshare.13724948.v1
title: Additional file 8 of Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

description: Additional file 8: Table X. The genes used in species tree construction.
DOI: 10.6084/m9.figshare.13724939.v1
title: Additional file 5 of Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

description: Additional file 5: Supplementary Table S1. 3654 species used in probe design. Supplementary Table S2. The table of 568 representative species ID. Supplementary Table S3. Evaluation of designed probe. Supplementary Table S4. The bamboo species in this study. Supplementary Table S5. The table of bamboo plastid sequences from NCBI. Supplementary Table S6. The species used for species tree construction. Supplementary Table S7. Coverage and depth analysis of pan-CpGenome. Supplementary Table S8. Align the probes to 468 complete chloroplast genomes, which did not contain the sequences used to design the probes. Supplementary Table S9. The statistics of assembled plastid sequences after redundancy removing. Supplementary Table S10. Evaluation for target enrichment and assemblies.
DOI: 10.6084/m9.figshare.13724942
title: Additional file 6 of Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

description: Additional file 6: Supplementary File F1. Pan-genome file. The file can be opened as txt file.
DOI: 10.6084/m9.figshare.13724945
title: Additional file 7 of Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

description: Additional file 7: Supplementary File F2. Probe sequences file. The file can be opened as txt file.
DOI: 10.6084/m9.figshare.13724945.v1
title: Additional file 7 of Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

description: Additional file 7: Supplementary File F2. Probe sequences file. The file can be opened as txt file.
DOI: 10.5281/zenodo.8370117
title: Data describing the life cycle and material flows of neodymium contained in products

description: Assumptions used to calculate flows of neodymium (Nd) in Europe. For various products (consumer products and industrial goods), the dataset describes the following properties: lifespan, product weight, neodymium content, end-of-life (EoL) fate, component weight, market share of Nd-containing components The classification of products is based on UNU Keys.
DOI: 10.5281/zenodo.8370118
title: Data describing the life cycle and material flows of neodymium contained in products

description: Assumptions used to calculate flows of neodymium (Nd) in Europe. For various products (consumer products and industrial goods), the dataset describes the following properties: lifespan, product weight, neodymium content, end-of-life (EoL) fate, component weight, market share of Nd-containing components The classification of products is based on UNU Keys.
DOI: 10.6084/m9.figshare.24257866
title: The role of osteoporosis in the association between hormone replacement therapy and hearing loss: a mediation analysis in NHANES

description: Supplemental Material<b> </b>for<i> </i><i>The role of osteoporosis in the association between hormone replacement therapy and hearing loss: a mediation analysis in NHANES</i>
DOI: 10.6084/m9.figshare.24257866.v3
title: The role of osteoporosis in the association between hormone replacement therapy and hearing loss: a mediation analysis in NHANES

description: Supplemental Material<b> </b>for<i> </i><i>The role of osteoporosis in the association between hormone replacement therapy and hearing loss: a mediation analysis in NHANES</i>
DOI: 10.34740/kaggle/ds/1562973
title:  Potato Disease Leaf Dataset(PLD)