cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24277276.v1
title: The activation of SIRT1 by resveratrol reduces breast cancer metastasis to lung through inhibiting neutrophil extracellular traps

description: Neutrophil extracellular traps (NETs) play a crucial role in breast cancer metastasis. However, the therapeutic target of NETs in breast cancer metastasis is still unknown. Using a natural metabolite library and single-cell sequencing data analysis, we identified resveratrol (RES), a polyphenolic natural phytoalexin, and agonist of silent information regulator-1 (SIRT1) that suppressed NETs formation after cathepsin C (CTSC) treatment. <i>In vivo</i>, RES significantly hindered breast cancer metastasis in a murine orthotopic 4T1 breast cancer model. Serum levels of myeloperoxidase-DNA and neutrophil elastase-DNA in mouse breast cancer model were significantly lower after RES treatment. Correspondingly, the tumour infiltrated CD8<sup>+</sup>T cells in the lungs increased after the treatment. Mechanistically, RES targets SIRT1 in neutrophils and significantly inhibits the citrullination of histones H3, which is essential for chromatin decondensation and NETs formation. Furthermore, we identified that the NETs were suppressed by RES in bone marrow neutrophils after CTSC treatment, while specific deficiency of SIRT1 in neutrophils promoted NETs formation and breast cancer to lung metastasis. Thus, our results revealed that RES could be potentially identified as a viable therapeutic drug to prevent neutrophil cell death and breast cancer metastasis.
DOI: 10.6084/m9.figshare.22177989
title: Characterization of the mitochondrial genome of the lawn cutworm <i>Spodoptera depravata</i> (Lepidoptera: Noctuidae)

description: The lawn cutworm, <i>Spodoptera depravata</i>, is one of the most important pests that causes economic damage to grass crops. This study reports the complete mitochondrial genome of an <i>S. depravata</i> sample collected in China. The genome is a circular molecule 15,460 bp in length with an overall A + T content of 81.6%. It contains 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The gene content and organization of the mitogenome of <i>S. depravata</i> are identical to those of other <i>Spodoptera</i> species. Maximum-likelihood phylogenetic analysis based on mitogenomes showed a close evolutionary relationship between <i>S. depravata</i> and <i>S. exempta</i>. This study provides new molecular data for the identification and further phylogenetic analyses of <i>Spodoptera</i> species.
DOI: 10.6084/m9.figshare.16413246
title: Apatinib inhibits cell proliferation and migration of osteosarcoma via activating LINC00261/miR-620/PTEN axis

description: Apatinib has been recently identified as a potential treatment option for osteosarcoma (OS). Nonetheless, the molecular mechanism of Apatinib in regulating OS progression remains unclear. To explore the downstream molecules that mediated the tumor-suppressive effect of Apatinib on OS. Expression levels of genes were detected by RT-qPCR and western blot assays. Functional assays including Transwell assay were applied to detect the proliferation, apoptosis and migration of OS cells. Molecular interactions were detected by luciferase reporter assay and RIP assay. Apatinib inhibited the proliferation and migration of OS cells. LINC00261 was down-regulated in OS cells but then up-regulated after the treatment by Apatinib. Silencing LINC00261 abrogated the suppressive effect of Apatinib on OS cell proliferation and migration. MicroRNA-620 (miR-620) could be sponged by LINC00261. Besides, miR-620 was up-regulated in OS cells and Apatinib treatment reduced miR-620 expression. Furthermore, LINC00261 acted as a competitive endogenous RNA (ceRNA) by sequestering miR-620 to up-regulate the expression of phosphatase and tensin homolog (PTEN). Moreover, Apatinib hindered <i>in vitro</i> cell proliferation and migration as well as the <i>in vivo</i> tumorigenesis of OS through LINC00261/miR-620/PTEN axis. Apatinib-enhanced LINC00261 restrained OS via miR-620/PTEN axis, indicating LINC00261 might promote the efficacy of Apatinib on OS.
DOI: 10.5281/zenodo.10642217
title: IODP Expedition 390C Alkalinity and pH

description: Alkalinity was determined by Gran titration with an autotitrator (Metrohm 794 basic Titrino) using 0.1 M HCl at 20 degrees C. Report includes alkalinity, correction factor (if applicable), and pH.
DOI: 10.5281/zenodo.10642218
title: IODP Expedition 390C Alkalinity and pH

description: Alkalinity was determined by Gran titration with an autotitrator (Metrohm 794 basic Titrino) using 0.1 M HCl at 20 degrees C. Report includes alkalinity, correction factor (if applicable), and pH.
DOI: 10.6084/m9.figshare.22704757
title: Mapping high-resolution forest aboveground biomass of China using multisource remote sensing data

description: Forest aboveground biomass (AGB) estimation is crucial for carbon cycle studies and climate change mitigation actions. However, because of limitations in timely and reliable forestry surveys and high-resolution remote sensing data, producing a fine resolution and spatial continuous forest AGB map of China is challenging. Here, we combined 4789 ground-truth AGB measurements and multisource remote sensing data such as a recently released forest canopy-height product, optical spectral indexes, topographic data, climatological data, and soil properties to train a random forest regression model for forest AGB estimation of China at 30-m resolution. The accuracy of the estimated AGB can yield R<sup>2</sup> = 0.67 and RMSE = 70.71 Mg/ha. The nationwide estimates show that the average forest AGB and total forest carbon storage were 97.57 ± 23.85 Mg/ha and 11.06 Pg C for the year 2019, respectively. The value of AGB uncertainty ranges from 0.68 Mg/ha to 37.80 Mg/ha, and the average AGB uncertainty was 4.32 ± 1.75 Mg/ha. The forest AGB estimates of China in this study correspond reasonably well with the AGB estimates derived from the forestry and grassland statistical yearbook at the provincial level (R<sup>2</sup> = 0.61, RMSE = 30.15 Mg/ha). In addition, we found that previous AGB products generally underestimate the forest AGB compared with our estimated AGB at the pixel-level and ground-truth AGB measurements. The high-resolution forest AGB map provides an important alternative data source for forest carbon cycle studies and can be used as a baseline map for forest management and conservation practices.
DOI: 10.6084/m9.figshare.8549204
title: Data and material for the Carpinus fangiana genome

description: Data 1: Information for the repetitive elements in Carpinus fangiana genome.Data 2.txt: Information for the long treminal repeats (LTRs) in Carpinus fangiana genome.Data 3: Information for the predicted protein-coding gene models in Carpinus fangiana genome.Data 4: The CDS sequences of the predicted protein-coding gene models in Carpinus fangiana genome.Data 5: The protein sequences of the predicted protein-coding gene models in Carpinus fangiana genome.Data 6: Information for the predicted non-coding genes in Carpinus fangiana genome.Data 7.fasta: The sequences of the predicted non-coding genes in Carpinus fangiana genome.Data 8.txt: Information for the predicted tRNA in Carpinus fangiana genome.Data 9.fasta: The sequences of the prediceted tRNA in Carpinus fangiana genome.Material 1: Perl script for the quality contral of pair-end Illumina sequencing data.Material 2: Perl script for computing heterozygosity of the Carpinus genome based on variant calling results.
DOI: 10.6084/m9.figshare.11170838
title: Hair follicle miRNAs: a novel biomarker for primary blast Induced-Mild traumatic brain injury

description: <b>Context:</b> Due to the wide use of improvised explosive devices during modern warfare, primary blast-derived mild traumatic brain injury (mTBI) has become a major medical condition in the military. With minimal visually identifiable symptoms, an effective molecular biomarker system is desirable. <b>Objective:</b> We assessed the potential of mammalian hair follicle miRNAs as an mTBI biomarker. <b>Materials and methods:</b> Due to their well-established roles in mTBI molecular pathology, the expression level of miR-183, miR-26a, miR-181c, miR-29a, miR-34a and miR-27b was determined using qRT-PCR in whisker hair follicles from rats subject to head-only exposure to a single-pulse shock wave. Based on established transcriptomics profiles, sub-network enrichment analysis (SNEA) was also conducted. <b>Results:</b> The results revealed that molecular networks involving miR-183, miR-26a and miR-181c were enriched in multiple treatments, whereas sub-networks of miR-29a, miR-34a and miR-27b were unique to individual exposure groups. <b>Discussion:</b> Our study showed that all six miRNAs were reflective of the mTBI signature involved in cellular responses. Noteworthy was that the decrease in the transcript levels of miR-181c was correlated with shockwave exposure severity. <b>Conclusion:</b> This study demonstrates for the first time that mammalian hair follicles are capable of housing miRNA biomarkers for TBI.
DOI: 10.6084/m9.figshare.11170838.v1
title: Hair follicle miRNAs: a novel biomarker for primary blast Induced-Mild traumatic brain injury

description: <b>Context:</b> Due to the wide use of improvised explosive devices during modern warfare, primary blast-derived mild traumatic brain injury (mTBI) has become a major medical condition in the military. With minimal visually identifiable symptoms, an effective molecular biomarker system is desirable. <b>Objective:</b> We assessed the potential of mammalian hair follicle miRNAs as an mTBI biomarker. <b>Materials and methods:</b> Due to their well-established roles in mTBI molecular pathology, the expression level of miR-183, miR-26a, miR-181c, miR-29a, miR-34a and miR-27b was determined using qRT-PCR in whisker hair follicles from rats subject to head-only exposure to a single-pulse shock wave. Based on established transcriptomics profiles, sub-network enrichment analysis (SNEA) was also conducted. <b>Results:</b> The results revealed that molecular networks involving miR-183, miR-26a and miR-181c were enriched in multiple treatments, whereas sub-networks of miR-29a, miR-34a and miR-27b were unique to individual exposure groups. <b>Discussion:</b> Our study showed that all six miRNAs were reflective of the mTBI signature involved in cellular responses. Noteworthy was that the decrease in the transcript levels of miR-181c was correlated with shockwave exposure severity. <b>Conclusion:</b> This study demonstrates for the first time that mammalian hair follicles are capable of housing miRNA biomarkers for TBI.
DOI: 10.6084/m9.figshare.24278092
title: Code

description: The vignette explaining and demonstrating the code.
DOI: 10.6084/m9.figshare.24278092.v1
title: Code

description: The vignette explaining and demonstrating the code.
DOI: 10.6084/m9.figshare.8025353.v1
title: A systematic review of the approaches to multi-level learning in the general practice context, using a realist synthesis approach: BEME Guide No. 55

description: <b>Background:</b> Recent global increases in medical student numbers and shifts in medical education from teaching hospitals to community settings call for effective strategies to meet the demand for general practice teaching placements. It has been proposed that “multi-level learning” (MLL), in which learning and teaching are shared across different levels of learners, may provide teaching efficiencies and valuable experiences for learners and teachers. <b>Aims:</b> To identify, evaluate and synthesize the evidence related to the types, benefits, challenges, and facilitators of MLL in community-based general practice, and the underlying mechanisms and associated contexts to explain the reported outcomes. <b>Method:</b> A realist synthesis approach guided the systematic review. <b>Results</b>: Fifteen papers were identified, providing primary evaluation data predominantly from interviews with or surveys of key stakeholders. Generally, all levels of learners reported overall satisfaction with their MLL experiences. Medical students appreciated learning from prevocational doctors and registrars due to social and cognitive congruence. Mechanisms and contexts that supported our hypotheses regarding successful MLL outcomes were identified, with “a strong teaching culture” being a major mechanism. <b>Conclusions:</b> The findings can help inform practices considering the implementation or enhancement of MLL initiatives in general practice. Further research should include measuring defined learning outcomes.
DOI: 10.6084/m9.figshare.5928256
title: Antitumor efficacy of liposome-encapsulated NVP-BEZ 235 in combination with irreversible electroporation

description: Irreversible electroporation (IRE) is an emerging minimally invasive tumor ablation technique that delivers short pulses of strong electric fields and kills cancer cells by disrupting their cell membranes with the electric pulses. However, clinical studies report that more than 10% of local tumor recurrences occur at the original ablated site. NVP BEZ-235 (BEZ) is a dual PI3K/mTOR inhibitor that has substantial anticancer effects. However, the clinical trials of BEZ was not satisfactory because of its low bioavailability and high toxicity, which stemmed from the use of oral administration of high doses over a long period of time. In this research, we prepared a liposomal formulation of BEZ (L-BEZ) for intratumoral injection and studied its antitumor efficacy alone and in combination with IRE. We hypothesized that IRE could release BEZ from the liposomes and that the combination could decrease tumor viability. Our results show that IRE released BEZ from its liposomal encapsulation. The combination of L-BEZ and IRE killed more Hep3B tumor cells <i>in vitro</i> than did L-BEZ or IRE alone and also inhibited cancer cell proliferation in nude mice bearing Hep3B xenografts. Combination of chemotherapeutic agent loaded nanoparticles could enhance the antitumor efficacy of IRE.
DOI: 10.6084/m9.figshare.5928256.v1
title: Antitumor efficacy of liposome-encapsulated NVP-BEZ 235 in combination with irreversible electroporation

description: Irreversible electroporation (IRE) is an emerging minimally invasive tumor ablation technique that delivers short pulses of strong electric fields and kills cancer cells by disrupting their cell membranes with the electric pulses. However, clinical studies report that more than 10% of local tumor recurrences occur at the original ablated site. NVP BEZ-235 (BEZ) is a dual PI3K/mTOR inhibitor that has substantial anticancer effects. However, the clinical trials of BEZ was not satisfactory because of its low bioavailability and high toxicity, which stemmed from the use of oral administration of high doses over a long period of time. In this research, we prepared a liposomal formulation of BEZ (L-BEZ) for intratumoral injection and studied its antitumor efficacy alone and in combination with IRE. We hypothesized that IRE could release BEZ from the liposomes and that the combination could decrease tumor viability. Our results show that IRE released BEZ from its liposomal encapsulation. The combination of L-BEZ and IRE killed more Hep3B tumor cells <i>in vitro</i> than did L-BEZ or IRE alone and also inhibited cancer cell proliferation in nude mice bearing Hep3B xenografts. Combination of chemotherapeutic agent loaded nanoparticles could enhance the antitumor efficacy of IRE.
DOI: 10.6084/m9.figshare.24278338
title: <b>S-9-PAHSA regulates glycolipid metabolism by enhancing autophagy and upregulating PI3K/AKT pathway</b>

description: The disorders of glucolipid metabolism are prevalent in patients with type 2 diabetes mellitus (T2DM). Since the effects of Palmitic-Acid-Hydroxy-Stearic Acid (PAHSA) on T2DM were not fully understood, the study aimed to investigate the role of S-9-PAHSA in diabetes and the possible mechanisms. Male C57BL6 mice were fed with a high-fat diet (HFD) and injected with streptozotocin (STZ) to establish the diabetic mice model, and then administered with low- or high-dose S-9-PAHSA. Insulin, glycosylated serum protein (GSP), glucagon-like peptide-1 (GLP-1), and oxidized low-density lipoprotein (ox-LDL) were assessed by ELISA. SH-SY 5Y cells were incubated in a diabetic environment and treated with S-9-PAHSA, R-9-PAHSA, or 9-PAHSA. Cell viability, cell proliferation, apoptosis, lactate dehydrogenase (LDH), and reactive oxygen species (ROS) were measured by corresponding kits. Protein expressions were determined by western blot. The results showed high-does S-9-PAHSA improved insulin resistance and lowered ox-LDL. Compared with the control group, the significantly up-regulated expression of p62 and down-regulated expression of beclin 1 were found in diabetic mice and could be reversed by S-9-PAHSA. In vitro, S-9-PAHSA increased cell viability and proliferation while reducing LDH and ROS. S-9-PAHSA could reduce the expression of cleaved caspase-3 and TUNEL-positive cells, and increase the ratio of LC3II/I after high glucose and fatty acid stimulation in vitro. Downward trends were observed in PI3K and the phosphorylation of AKT in diabetic environments, which could be slightly restored by S-9-PAHSA. In conclusion, S-9-PAHSA could regulate glycolipid metabolism both in vivo and in vitro, indicating the vital role of S-9-PAHSA in T2DM.
DOI: 10.6084/m9.figshare.11171330
title: Inflammatory signature in lung tissues in patients with combined pulmonary fibrosis and emphysema

description: <b>Background:</b> The aetiology and inflammatory profile of combined pulmonary fibrosis and emphysema (CPFE) remain uncertain currently. <b>Objective:</b> We aimed to examine the levels of inflammatory proteins in lung tissue in a cohort of patients with emphysema, interstitial pulmonary fibrosis (IPF), and CPFE. <b>Materials and methods:</b> Explanted lungs were obtained from subjects with emphysema, IPF, CPFE, (or normal subjects), and tissue extracts were prepared. Thirty-four inflammatory proteins were measured in each tissue section. <b>Results:</b> The levels of all 34 proteins were virtually indistinguishable in IPF compared with CPFE tissues, and collectively, the inflammatory profile in the emphysematous tissues were distinct from IPF and CPFE. Moreover, inflammatory protein levels were independent of the severity of the level of diseased tissue. <b>Conclusions:</b> We find that emphysematous lung tissues have a distinct inflammatory profile compared with either IPF or CPFE. However, the inflammatory profile in CPFE lungs is essentially identical to lungs from patients with IPF. These data suggest that distinct inflammatory processes collectively contribute to the disease processes in patients with emphysema, when compared to IPF and CPFE.
DOI: 10.6084/m9.figshare.11171330.v1
title: Inflammatory signature in lung tissues in patients with combined pulmonary fibrosis and emphysema

description: <b>Background:</b> The aetiology and inflammatory profile of combined pulmonary fibrosis and emphysema (CPFE) remain uncertain currently. <b>Objective:</b> We aimed to examine the levels of inflammatory proteins in lung tissue in a cohort of patients with emphysema, interstitial pulmonary fibrosis (IPF), and CPFE. <b>Materials and methods:</b> Explanted lungs were obtained from subjects with emphysema, IPF, CPFE, (or normal subjects), and tissue extracts were prepared. Thirty-four inflammatory proteins were measured in each tissue section. <b>Results:</b> The levels of all 34 proteins were virtually indistinguishable in IPF compared with CPFE tissues, and collectively, the inflammatory profile in the emphysematous tissues were distinct from IPF and CPFE. Moreover, inflammatory protein levels were independent of the severity of the level of diseased tissue. <b>Conclusions:</b> We find that emphysematous lung tissues have a distinct inflammatory profile compared with either IPF or CPFE. However, the inflammatory profile in CPFE lungs is essentially identical to lungs from patients with IPF. These data suggest that distinct inflammatory processes collectively contribute to the disease processes in patients with emphysema, when compared to IPF and CPFE.
DOI: 10.6084/m9.figshare.22682869
title: Data from paper: "Land-use change in the past 40 years explains shifts in arthropod community traits"

description: Community weighted means and community means of four important traits of carabid and spider arthropods in Switzerland. These datasets were analyzed to support the findings in the paper "Land-use change in the past 40 years explains shifts in arthropod community traits". Please, read the ReadMe file and the Materials and Methods in the paper for more details about the variables used.
DOI: 10.5519/qd.2dmlqaqz
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (347 records)
DOI: 10.6084/m9.figshare.13787746.v1
title: Additional file 2 of Targeting dopamine receptor D2 as a novel therapeutic strategy in endometrial cancer

description: Additional file 2.
DOI: 10.5281/zenodo.10642320
title: IODP Expedition 390C X-ray diffraction (XRD)

description: X-ray diffraction (XRD) is used to identify minerals and their proportions in sediment or hard rock sample powders on a Bruker AXS D4 Endeavor X-ray diffractometer. Results are returned as diffractograms in a viewable format (either PDF or PNG).
DOI: 10.5281/zenodo.10642321
title: IODP Expedition 390C X-ray diffraction (XRD)

description: X-ray diffraction (XRD) is used to identify minerals and their proportions in sediment or hard rock sample powders on a Bruker AXS D4 Endeavor X-ray diffractometer. Results are returned as diffractograms in a viewable format (either PDF or PNG).
DOI: 10.6084/m9.figshare.17982074
title: Additional file 1 of Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales

description: Additional file 1: Table S1. All sequences that were used for understanding the phylogenetic analysis within Sapindales, including their corresponding CDS information and GenBank accession numbers.
DOI: 10.6084/m9.figshare.20080953.v1
title: Additional file 1 of The use of a surgical boot camp combining anatomical education and surgical simulation for internship preparedness among senior medical students

description: Additional file 1.
DOI: 10.5281/zenodo.10650723
title: 3D Electron Diffraction data of GSF form I

description: 3D electron diffraction (3D ED) data of griseofulvin (GSF) form I collected automatically using software EPU-D at 100 K on a ThermoFisher Titan Krios (300 kV) equipped with a CETA-D detector.

A total of 231 datasets were collected from a sample containing multiple phases of GSF in 2 days. Crystal identification and selection were performed by an operator while 3D ED data collection was carried out fully automatically. Data was processed automatically by software package edtools (https://doi.org/10.5281/zenodo.6953489) using XDS (https://doi.org/10.1107/S0907444909047337). A hierarchical clustering analysis (HCA) algorithm implemented in edtools was used to cluster the datasets belonging to the same phase through the Euclidean distance between the unit cell parameters. Out of the 231 datasets collected, 31 datasets were idneitified as GSF form I.