cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19682200
title: Suppression of lncRNA <i>Gm47283</i> attenuates myocardial infarction via <i>miR-706</i>/ <i>Ptgs2</i>/ferroptosis axis

description: Myocardial infarction (MI) is the leading cause of sudden death. Long non-doing RNAs (lncRNAs) were demonstrated to play crucial roles in multiple diseases, including cancer and cardiovascular diseases. Nevertheless, the molecular mechanism of lncNRAs in MI is unclear. In this study, we integrated bioinformatics and molecular biological experiments to identify the novel lncRNA transcripts and elucidated its regulatory mechanism in MI. First, we identified 10 dysregualted lncRNAs and found that lncRNA <i>Gm47283</i> was the top risk factor in MI. Bioinformatics analysis predicted that lncRNA <i>Gm47283</i> exerted function via targeting <i>miR-706</i> and <i>Ptgs2. Ptgs2</i> was also the known regulator of ferroptosis. Inhibition or overexpression of lncRNA <i>Gm47283</i> could regulate <i>Ptgs2</i> expression and downstream ferroptosis activity. Overexpression of <i>miR-706</i> could inhibit the expression of <i>Ptgs2</i> and the activity of ferroptosis, thereby attenuated cellular injury. Mechanically, co-transfection experiments showed that overexpression of <i>miR-706</i> could reverse the damage effect that was caused by lncRNA <i>Gm47283</i> overexpression, via inhibiting <i>Ptgs2</i> and ferroptosis. Additionally, inhibition of lncRNA <i>Gm47283</i> by stem cell membrane coated siRNA could attenuate MI in <i>vivo</i>. Our study elucidated a novel mechanism containing lncRNA <i>Gm47283</i>/<i>miR-706</i>/<i>Ptgs2</i>/ferroptosis in MI, which provided a potential therapeutic for MI. Graphical Abstract. Stem cell membrane coated siRNA of lncRNA <i>Gm47283</i> inhibits cardiomyocyte ferroptosis in myocardial infarction rat. Stem cell membrane-coated siRNA of lncRNA <i>Gm47283</i> increases <i>miR-706</i>, and then <i>miR-706</i> suppresses the <i>expression of Ptgs2</i> to reduce lipid peroxidation toxicity, and then inhibits cardiomyocyte ferroptosis. PUFA: polyunsaturated fatty acid.
DOI: 10.6084/m9.figshare.7624409
title: A New Process Control Chart for Monitoring Short-Range Serially Correlated Data

description: <b><i>Abstract–</i>Statistical process control (SPC) charts are critically important for quality control and management in manufacturing industries, environmental monitoring, disease surveillance, and many other applications. Conventional SPC charts are designed for cases when process observations are independent at different observation times. In practice, however, serial data correlation almost always exists in sequential data. It has been well demonstrated in the literature that control charts designed for independent data are unstable for monitoring serially correlated data. Thus, it is important to develop control charts specifically for monitoring serially correlated data. To this end, there is some existing discussion in the SPC literature. Most existing methods are based on parametric time series modeling and residual monitoring, where the data are often assumed to be normally distributed. In applications, however, the assumed parametric time series model with a given order and the normality assumption are often invalid, resulting in unstable process monitoring. Although there is some nice discussion on robust design of such residual monitoring control charts, the suggested designs can only handle certain special cases well. In this article, we try to make another effort by proposing a novel control chart that makes use of the restarting mechanism of a CUSUM chart and the related spring length concept. Our proposed chart uses observations within the spring length of the current time point and ignores all history data that are beyond the spring length. It does not require any parametric time series model and/or a parametric process distribution. It only requires the assumption that process observation at a given time point is associated with nearby observations and independent of observations that are far away in observation times, which should be reasonable for many applications. Numerical studies show that it performs well in different cases.</b>
DOI: 10.6084/m9.figshare.7624409.v1
title: A New Process Control Chart for Monitoring Short-Range Serially Correlated Data

description: <b><i>Abstract–</i>Statistical process control (SPC) charts are critically important for quality control and management in manufacturing industries, environmental monitoring, disease surveillance, and many other applications. Conventional SPC charts are designed for cases when process observations are independent at different observation times. In practice, however, serial data correlation almost always exists in sequential data. It has been well demonstrated in the literature that control charts designed for independent data are unstable for monitoring serially correlated data. Thus, it is important to develop control charts specifically for monitoring serially correlated data. To this end, there is some existing discussion in the SPC literature. Most existing methods are based on parametric time series modeling and residual monitoring, where the data are often assumed to be normally distributed. In applications, however, the assumed parametric time series model with a given order and the normality assumption are often invalid, resulting in unstable process monitoring. Although there is some nice discussion on robust design of such residual monitoring control charts, the suggested designs can only handle certain special cases well. In this article, we try to make another effort by proposing a novel control chart that makes use of the restarting mechanism of a CUSUM chart and the related spring length concept. Our proposed chart uses observations within the spring length of the current time point and ignores all history data that are beyond the spring length. It does not require any parametric time series model and/or a parametric process distribution. It only requires the assumption that process observation at a given time point is associated with nearby observations and independent of observations that are far away in observation times, which should be reasonable for many applications. Numerical studies show that it performs well in different cases.</b>
DOI: 10.6084/m9.figshare.24925971
title: <b>Flexible Calorimetric Flow Sensor with Unprecedented Sensitivity and Directional Resolution for Multiple Flight Parameter Detection</b>

description: These datasets are used for training and testing MLP-Net.
DOI: 10.25378/janelia.22304002
title: Entire C. elegans dauer transmission electron microscopy acquisition (e1370) - nuclei segmentations

description: TEM acquistion of an entire C. elegans in dauer stage (e1370) using 70nm slices. Acquired using the Leginon software, reconstructed with TrakEM2, all nuclei segmented using a custom active contours and machine learning approach.
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DOI: 10.6084/m9.figshare.22826802
title: Additional file 1 of Single-cell RNA sequencing reveals the vascular smooth muscle cell phenotypic landscape in aortic aneurysm

description: Additional file 1.
DOI: 10.6084/m9.figshare.24082641
title: share.zip

description: The file contains the training data for the ensemble deep learning model, and a python code to training the model. I applied mask to secure the privacy
DOI: 10.6084/m9.figshare.24082641.v1
title: share.zip

description: The file contains the training data for the ensemble deep learning model, and a python code to training the model
DOI: 10.5281/zenodo.10666651
title: software fault data
DOI: 10.5281/zenodo.10666652
title: software fault data
DOI: 10.6084/m9.figshare.22826802.v1
title: Additional file 1 of Single-cell RNA sequencing reveals the vascular smooth muscle cell phenotypic landscape in aortic aneurysm

description: Additional file 1.
DOI: 10.6084/m9.figshare.20206271
title: Optimization of the vancomycin administration regimen by clinical pharmacists based on a population pharmacokinetics model: a prospective interventional study

description: In vancomycin treatment, the rates of correct blood sampling and initial trough concentrations within the target range are very low. Studies of interventions by clinical pharmacists based on population pharmacokinetics (PPK) models are limited. This study aimed to evaluate the intervention effect of clinical pharmacist-mediated optimization of the vancomycin administration regimen based on a PPK model. Retrospectively enrolled patients constituted the control group, and prospectively enrolled patients constituted the intervention group. The vancomycin administration regimen, trough concentration, pharmacokinetic parameters, and clinical outcomes of the two groups were compared. The control and intervention groups comprised 236 and 138 patients, respectively. Compared with those in the control group, the therapeutic drug monitoring (TDM) and correct TDM sampling time rates in the intervention group were significantly higher (76.92% vs. 43.59%; 63.9% vs. 39.0%, both <i>p &lt;</i> 0.001). The rates of an initial trough concentration within 10–20 mg/L and an adjusted regimen were also significantly higher in the intervention group (55.80% vs. 30.51%, 71.95% vs. 39.18%, both <i>p &lt;</i> 0.001). The rate of an area under the curve (AUC) within 400–650 mg·h/L was higher in the intervention group than in the control group (52.7% vs. 36.6%, <i>p &lt;</i> 0.001). The eradication rates of Gram-positive bacteria were 91.4% in the intervention group and 81.3% in the control group (<i>p</i> = 0.049). Eight patients developed acute kidney injury (AKI) in the control group; however, no AKI occurred in the intervention group (<i>p</i> = 0.029). Intervention by clinical pharmacists can increase the rate of correct sampling time. Using the PPK model combined with Bayesian estimation, clinical pharmacists can greatly increase the trough concentration and AUCs within the target range, especially for adjusted regimens. Higher PK/PD target rates resulted in better Gram-positive bacterial eradication and reduced renal toxicity of vancomycin.
DOI: 10.6084/m9.figshare.8148251
title: Additional file 2: of Development of a transcriptomic database for 14 species of scleractinian corals

description: Alignment. The alignment of one-to-one homologous genes of 18 stony coral species. (FASTA 3031 kb)
DOI: 10.6084/m9.figshare.8148251.v1
title: Additional file 2: of Development of a transcriptomic database for 14 species of scleractinian corals

description: Alignment. The alignment of one-to-one homologous genes of 18 stony coral species. (FASTA 3031 kb)
DOI: 10.5281/zenodo.10666598
title: Datasety Venkoobchod TL05000558
DOI: 10.5281/zenodo.10666599
title: Datasety Venkoobchod TL05000558
DOI: 10.6084/m9.figshare.14963444.v1
title: The role of CCR2 in prognosis of patients with endometrial cancer and tumor microenvironment remodeling

description: Tumor microenvironment (TME) plays a core role in the genesis and progress of endometrial carcinoma (EC). The immune system, a crucial element of TME, functions in various immune cells. In this paper, we have tried to evaluate the prognosis in EC patients by the status of TME. The ESTIMATE algorithm was implemented to computer the number of immune and stromal components in EC tissues from the Cancer Genome Atlas dataset. The CIBERSORT algorithm was employed to assess the proportion of tumor-infiltrating immune cells in EC tissues, which were quantified as Stromal score and Immune score. After the construction of protein–protein interaction network, cell–cell chemokine receptor 2 (CCR2) was identified as a potential predictive element for EC. Further analysis indicated that a higher expression of CCR2 in EC patients was correlated with a better prognosis and a prolonged disease-free survival. According to the transcript level of CCR2, samples were separated into low- and high-expression groups. Gene Set Enrichment Analysis unveiled that metabolism-related pathways were mostly abundant in groups with high-expression, the other one was primarily correlated to immune-related activities. We figured out that some immune cells were positively related to CCR2, suggesting that CCR2 might serve as the immune-dominant status of TME, which was verified by qRT-PCR and HPA analysis in transcriptome and protein level, respectively. Also, CCR2 showed high correlation with immune modulators and chemokine signaling pathway. Thus, the level of CCR2 might have a prognostic value for EC patients, which provides a novel insight for therapeutic strategies of EC.
DOI: 10.6084/m9.figshare.19682051.v1
title: Additional file 6 of Systematic evaluation of colorectal cancer organoid system by single-cell RNA-Seq analysis

description: Additional file 6: Table S4.
DOI: 10.6084/m9.figshare.21780527
title: Chromosome-level genome assembly of Zoroaster sp.

description:    
<strong>Zoroaster.cds:</strong> Genome annotation
<strong>Zoroaster.pep:</strong> Genome annotation
<strong>Zoroaster.gff:</strong> Genome annotation
<strong>expansion.gene:</strong> Expansion genes
<strong>Zoroaster.InterProscan.gff3:</strong> InterProScan annotations for predicted genes
<strong>total.repeat.gff:</strong> Repeat annotation
<strong>Zoroaster.Nr.gene:</strong> NR annotations for predicted genes
<strong>Zoroaster.SwissProt.submit.gene:</strong> Swissprot annotations for predicted genes
<strong>Zoroaster.pfam.results:</strong> Pfam annotations for predicted genes
<strong>expansion.GO.submit.xlsx:</strong> Expansion gene GO enrichment
DOI: 10.6084/m9.figshare.19682659
title: Increased homocysteine regulated by androgen activates autophagy by suppressing the mammalian target of rapamycin pathway in the granulosa cells of polycystic ovary syndrome mice

description: The purpose of this study was to explore the potential molecular mechanisms of excess homocysteine in relation to autophagic activity in the ovarian tissue of polycystic ovarian syndrome (PCOS) with hyperandrogenism.A PCOS model was constructed using ICR mice. ELISA was used to detect the Hcy levels in the serum and ovarian tissues of PCOS model. The expression level of key enzymes (Methionine synthase and Betaine-homocysteine methyltransferase, MTR and BHMT) in homocysteine metabolism and autophagy-related proteins were detected in ovarian tissues and mouse granulosa cells (mGCs) that were treated with homocysteine, androgen, autophagy inhibitors or BHMT-expressing plasmid by western blot and immunohistochemistry. Electron microscope experiments were used to evaluate autophagosomes in Hcy-treated mGCs. The prenatally androgenized (PNA) PCOS mouse model showed hyperhomocysteinemia and hyperandrogenism. Homocysteine levels displayed a significant increase, while its metabolic enzymes levels were significantly decreased in ovarian tissues of PCOS mice and dihydrotestosterone (DHT)-stimulated mGCs. The LC3II and Beclin1 expression levels were increased and the P62 and p-mTOR levels were decreased in vivo in ovarian tissue from the PCOS mice. The in vitro data were similarly with the in vivo by stimulation of mGCs with DHT or homocysteine. These effects could be diminished by the autophagy inhibitor (MHY1485), androgen receptor antagonists (ARN509) or BHMT-expressing plasmid. Androgen increases homocysteine concentration by downregulating the key enzymes in homocysteine metabolism. And then Hcy promotes GCs autophagy via the mTOR signal pathway.
DOI: 10.6084/m9.figshare.19682659.v1
title: Increased homocysteine regulated by androgen activates autophagy by suppressing the mammalian target of rapamycin pathway in the granulosa cells of polycystic ovary syndrome mice

description: The purpose of this study was to explore the potential molecular mechanisms of excess homocysteine in relation to autophagic activity in the ovarian tissue of polycystic ovarian syndrome (PCOS) with hyperandrogenism.A PCOS model was constructed using ICR mice. ELISA was used to detect the Hcy levels in the serum and ovarian tissues of PCOS model. The expression level of key enzymes (Methionine synthase and Betaine-homocysteine methyltransferase, MTR and BHMT) in homocysteine metabolism and autophagy-related proteins were detected in ovarian tissues and mouse granulosa cells (mGCs) that were treated with homocysteine, androgen, autophagy inhibitors or BHMT-expressing plasmid by western blot and immunohistochemistry. Electron microscope experiments were used to evaluate autophagosomes in Hcy-treated mGCs. The prenatally androgenized (PNA) PCOS mouse model showed hyperhomocysteinemia and hyperandrogenism. Homocysteine levels displayed a significant increase, while its metabolic enzymes levels were significantly decreased in ovarian tissues of PCOS mice and dihydrotestosterone (DHT)-stimulated mGCs. The LC3II and Beclin1 expression levels were increased and the P62 and p-mTOR levels were decreased in vivo in ovarian tissue from the PCOS mice. The in vitro data were similarly with the in vivo by stimulation of mGCs with DHT or homocysteine. These effects could be diminished by the autophagy inhibitor (MHY1485), androgen receptor antagonists (ARN509) or BHMT-expressing plasmid. Androgen increases homocysteine concentration by downregulating the key enzymes in homocysteine metabolism. And then Hcy promotes GCs autophagy via the mTOR signal pathway.
DOI: 10.6084/m9.figshare.22829108
title: Supplemental data for the manuscript: Fusion Oncogenes associated Nodal Metastasis are Age Dependent in Young Adult Patients with Thyroid Cancers

description:  Supplemental data for the manuscript: Fusion Oncogenes associated Nodal Metastasis are Age Dependent in Young Adult Patients with Thyroid Cancers
DOI: 10.6084/m9.figshare.22304824
title: Fatty Acid Binding Protein 5 Regulates Docetaxel Sensitivity in Taxane-Resistant Prostate Cancer Cells

description:   
Prostate cancer is a leading cause of cancer-related deaths in men in the United States. Although treatable when detected early, prostate cancer commonly transitions to an aggressive castration-resistant metastatic state. While taxane chemotherapeutics such as docetaxel are mainstay treatment options for prostate cancer, taxane resistance often develops. Fatty acid binding protein 5 (FABP5) is an intracellular lipid chaperone that is upregulated in advanced prostate cancer and is implicated as a key driver of its progression. The recent demonstration that FABP5 inhibitors produce synergistic inhibition of tumor growth when combined with taxane chemotherapeutics highlights the possibility that FABP5 may regulate other features of taxane function, including resistance. Employing taxane-resistant DU145-TXR cells and a combination of cytotoxicity, apoptosis, and cell cycle assays, our findings demonstrate that FABP5 knockdown sensitizes the cells to docetaxel. In contrast, docetaxel potency was unaffected by FABP5 knockdown in taxane-sensitive DU145 cells. Taxane-resistance in DU145-TXR cells stems from upregulation of the P-glycoprotein ATP binding cassette subfamily B member 1 (ABCB1). Expression analyses and functional assays confirmed that FABP5 knockdown in DU145-TXR cells markedly reduced ABCB1 expression and activity, respectively. Our study demonstrates a potential new function for FABP5 in regulating taxane sensitivity and the expression of a major P-glycoprotein efflux pump in prostate cancer cells.
DOI: 10.6084/m9.figshare.7624865
title: New antlions (Insecta: Neuroptera: Myrmeleontidae) from the mid-Cretaceous of Myanmar and their phylogenetic implications

description: Myrmeleontidae (antlions) is the most species-rich family of the holometabolous order Neuroptera. Evolutionary history of this diverse lacewing family remains largely unexplored. Here we report on three new genera and four new species of antlions from the mid-Cretaceous amber of Myanmar, namely <i>Allopteroneura burmana</i> Lu, Zhang & Liu gen. et sp. nov., <i>Phylloleon elegans</i> Lu, Wang & Liu gen. et sp. nov., <i>Phylloleon stangei</i> Lu, Ohl & Liu gen. et sp. nov. and <i>Nanoleon wangae</i> Hu, Lu & Liu gen. et sp. nov. A phylogenetic analysis of the Burmese amber antlions is performed based on morphological characters. The result shows that the antlion species presently described belong to different major clades across the phylogenetic tree, suggesting a diverse palaeofauna of this family from the mid-Cretaceous of Myanmar. The phylogenetic status of the extinct subfamily Araripeneurinae is also discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:90D26B8B-1A59-465B-A530-0C0662D85E72
DOI: 10.6084/m9.figshare.7624865.v1
title: New antlions (Insecta: Neuroptera: Myrmeleontidae) from the mid-Cretaceous of Myanmar and their phylogenetic implications

description: Myrmeleontidae (antlions) is the most species-rich family of the holometabolous order Neuroptera. Evolutionary history of this diverse lacewing family remains largely unexplored. Here we report on three new genera and four new species of antlions from the mid-Cretaceous amber of Myanmar, namely <i>Allopteroneura burmana</i> Lu, Zhang & Liu gen. et sp. nov., <i>Phylloleon elegans</i> Lu, Wang & Liu gen. et sp. nov., <i>Phylloleon stangei</i> Lu, Ohl & Liu gen. et sp. nov. and <i>Nanoleon wangae</i> Hu, Lu & Liu gen. et sp. nov. A phylogenetic analysis of the Burmese amber antlions is performed based on morphological characters. The result shows that the antlion species presently described belong to different major clades across the phylogenetic tree, suggesting a diverse palaeofauna of this family from the mid-Cretaceous of Myanmar. The phylogenetic status of the extinct subfamily Araripeneurinae is also discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:90D26B8B-1A59-465B-A530-0C0662D85E72
DOI: 10.6084/m9.figshare.22829218
title: Morphometrical analyses revealed high diversity of the eastern honey bee (<i>Apis cerana</i>) in mountains and islands in China

description: The eastern honey bee (<i>Apis cerana</i>) is of great importance for ecosystems and agriculture in Asia, whose diversity has yet to be explored. Previous studies have found a high diversity of <i>A. cerana</i> in mountainous areas or islands. To better understand the morphological diversity of <i>A. cerana</i>, we focused on the eastern Qinghai-Tibet Plateau (QTP), a region with high mountains, Weizhou Island, Yongxing Island and Hainan Island, much of which lacks systematic investigation of honey bee diversity. Five sampling sites in the plain were also selected as references. A total of 140 colonies of <i>A. cerana</i> were collected from 9 localities in QTP, 3 localities in islands, and 5 localities in plain. We used standard morphometry and geometric morphometrics to assess the level of diversity, in which principal component analysis and discriminant analysis were conducted. The results revealed the <i>A. cerana</i> populations from QTP and islands were differentiated from the plain populations. Moreover, two populations from QTP and one from Yongxing Island showed significant divergence. Our study provided insights into the <i>A. cerana</i> diversity and provides information for the effective conservation of <i>A. cerana</i> genetic resources in China.