cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19664297
title: The potential mechanism of Fructus Ligustri Lucidi promoting osteogenetic differentiation of bone marrow mesenchymal stem cells based on network pharmacology, molecular docking and experimental identification

description: Recent studies have shown that the differentiation of bone marrow mesenchymal stem cells (BMSCs) into osteogenic lineages can promotes bone formation and maintains bone homeostasis, which has become a promising therapeutic strategy for skeletal diseases such as osteoporosis. Fructus Ligustri Lucidi (FLL) has been widely used for the treatment of osteoporosis and other orthopedic diseases for thousands of years. However, whether FLL plays an anti-osteoporosis role in promoting the osteogenic differentiation of BMSCs, as well as its active components, targets, and specific molecular mechanisms, has not been fully elucidated. First, we obtained 13 active ingredients of FLL from the Traditional Chinese Medicine Systems Pharmacology (TCSMP) database, and four active ingredients without any target were excluded. Subsequently, 102 common drug-disease targets were subjected to protein-protein interaction (PPI) analysis, Gene Oncology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The results of the three analyses were highly consistent, indicating that FLL promoted the osteogenic differentiation of BMSCs by activating the PI3K/AKT signaling pathway. Finally, we validated previous predictions using in vitro experiments, such as alkaline phosphatase (ALP) staining, alizarin red staining (ARS), and western blot analysis of osteogenic-related proteins. The organic combination of network pharmacological predictions with in vitro experimental validation comprehensively confirmed the reliability of FLL in promoting osteogenic differentiation of BMSCs. This study provides a strong theoretical support for the specific molecular mechanism and clinical application of FLL in the treatment of bone formation deficiency.
DOI: 10.6084/m9.figshare.19664297.v1
title: The potential mechanism of Fructus Ligustri Lucidi promoting osteogenetic differentiation of bone marrow mesenchymal stem cells based on network pharmacology, molecular docking and experimental identification

description: Recent studies have shown that the differentiation of bone marrow mesenchymal stem cells (BMSCs) into osteogenic lineages can promotes bone formation and maintains bone homeostasis, which has become a promising therapeutic strategy for skeletal diseases such as osteoporosis. Fructus Ligustri Lucidi (FLL) has been widely used for the treatment of osteoporosis and other orthopedic diseases for thousands of years. However, whether FLL plays an anti-osteoporosis role in promoting the osteogenic differentiation of BMSCs, as well as its active components, targets, and specific molecular mechanisms, has not been fully elucidated. First, we obtained 13 active ingredients of FLL from the Traditional Chinese Medicine Systems Pharmacology (TCSMP) database, and four active ingredients without any target were excluded. Subsequently, 102 common drug-disease targets were subjected to protein-protein interaction (PPI) analysis, Gene Oncology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The results of the three analyses were highly consistent, indicating that FLL promoted the osteogenic differentiation of BMSCs by activating the PI3K/AKT signaling pathway. Finally, we validated previous predictions using in vitro experiments, such as alkaline phosphatase (ALP) staining, alizarin red staining (ARS), and western blot analysis of osteogenic-related proteins. The organic combination of network pharmacological predictions with in vitro experimental validation comprehensively confirmed the reliability of FLL in promoting osteogenic differentiation of BMSCs. This study provides a strong theoretical support for the specific molecular mechanism and clinical application of FLL in the treatment of bone formation deficiency.
DOI: 10.5281/zenodo.10126795
title: The effect of climate change on forest fire danger and severity in the Canadian boreal forests for the period 1976-2100

description: There are 5 files uploaded.
 
(1) fwi26.txt.gz, RCP26
(2) fwi45.txt.gz, RCP45
(3) fwi85.txt.gz, RCP85
(4) msk20231028.txt
(5) Shape_Canadian_Boreal_Forests.7z
 
mask20231028.txt is an ascii file covering the Canadian Boreal Forests.
This file can be imported into GisMAP to generate a mask raster.
 
Shape_Canadian_Boreal_Forests.7z is a compressed shape file cover the
Canadian Boreal Forests.
 
fwi26.txt.gz, fwi45.txt.gz, and fwi85.txt.gz are the zipped file of FFMC
and DSR daily surfaces. There are 6 fields in the files:
 
Field 1: row number in the mask file of mask20231028.txt.
Field 2: column number.
Field 3: Years; 1, 2, 3, ... 95 correspoind to 2006, 2007, 2008, ..., 2100.
Field 4: Days; 1, 2, 3, ..., 365 in a year.
Field 5: Daily FFMC values.
Field 6: Daily DSR values.
DOI: 10.6084/m9.figshare.13372855
title: Tris(2-thienyl)phosphine-substituted diiron propanedithiolate complexes: Synthesis, spectroscopy, crystal structures, electrochemistry, and fungicidal activity

description: In this article, we report two diiron propanedithiolate complexes with monosubstituted tris(2-thienyl)phosphine. Reaction of [Fe<sub>2</sub>(CO)<sub>6</sub>{<i>μ</i>-SCH<sub>2</sub>CH<sub>2</sub>CH<sub>2</sub>S}] (<b>1</b>) or [Fe<sub>2</sub>(CO)<sub>6</sub>{<i>μ</i>-SCH<sub>2</sub>CH(CH<sub>3</sub>)S}] (<b>2</b>) with one equivalent of tris(2-thienyl)phosphine and Me<sub>3</sub>NO·2H<sub>2</sub>O as the oxidative reagent yielded complexes [Fe<sub>2</sub>(CO)<sub>5</sub>P(2-C<sub>4</sub>H<sub>3</sub>S)<sub>3</sub>{<i>μ</i>-SCH<sub>2</sub>CH<sub>2</sub>CH<sub>2</sub>S}] (<b>3</b>) and [Fe<sub>2</sub>(CO)<sub>5</sub>P(2-C<sub>4</sub>H<sub>3</sub>S)<sub>3</sub>{<i>μ</i>-SCH<sub>2</sub>CH(CH<sub>3</sub>)S}] (<b>4</b>) in 75% and 91% yields, respectively. The new complexes <b>3</b> and <b>4</b> have been characterized by elemental analysis, IR, <sup>1</sup>H NMR, <sup>31</sup>P{<sup>1</sup>H} NMR, and single crystal X-ray diffraction analysis. Additionally, the electrochemistry of complexes <b>3</b> and <b>4</b> has been studied by cyclic voltammetry. Interestingly, the fungicidal activity has been studied.
DOI: 10.6084/m9.figshare.7138790
title: Additional file 9: of Identification, characterization and expression analysis of the VQ motif-containing gene family in tea plant (Camellia sinensis)

description: Table S8. The CsWRKY proteins maps to the WRKY proteins in Arabidopsis thaliana. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7138790.v1
title: Additional file 9: of Identification, characterization and expression analysis of the VQ motif-containing gene family in tea plant (Camellia sinensis)

description: Table S8. The CsWRKY proteins maps to the WRKY proteins in Arabidopsis thaliana. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.19664162.v1
title: The biological function of the long non-coding RNA endogenous born avirus-like nucleoprotein in lung adenocarcinoma is mediated through the microRNA-655-3p/B-cell lymphoma-2 axis

description: Lung adenocarcinoma (LUAD) is a subtype of lung cancer, and therapy remains a great challenge. A growing body of evidence shows that long-chain non-coding RNAs (lncRNAs) play an important role in the occurrence and development of LUAD. This study investigated the roles and mechanisms of action of EBLN3P in LUAD. The bioinformatics software starBase and TargetScan were used to predict the binding sites of the lncRNA endogenous born avirus-like nucleoprotein (EBLN3P) and microRNA (miR)-655-3p in LUAD. The regulatory role of EBLN3P and miR-655-3p in cell proliferation was verified through the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2 H-tetrazolium bromide (MTT) assay. The binding sites between EBLN3P, miR-655-3p, and B-cell lymphoma-2 (Bcl-2) were assessed using dual-luciferase reporter assay, western blotting, and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Flow cytometry (FCM) was performed to analyze the apoptotic rates of A549 cells after transfection. The results revealed that EBLN3P was upregulated, whereas miR-655-3p was downregulated in LUAD cell lines (A549 and NCI-H23). Bioinformatics analysis and dual-luciferase reporter assays indicated that EBLN3P interacted with miR-655-3p. Knockdown of EBLN3P notably inhibited the bioactivity and induced apoptosis in A549 cells by upregulating miR-655-3p. Mechanistically, miR-655-3p inhibits cell viability and induces apoptosis by inhibiting Bcl-2 expression. The high expression of Bcl-2 reversed the impact of miR-655-3p on the inhibition of cell bioactivity and induction of apoptosis in A549 cells. In conclusion, this study demonstrated that EBLN3P silencing inhibits bioactivity and induces apoptosis via the miR-655-3p/Bcl-2 axis, providing a potential therapeutic target for lung adenocarcinoma.
DOI: 10.6084/m9.figshare.22723432
title: Extended Data 1: Biodiversity RIs & Projects

description: A non-exhaustive list of biodiversity research infrastructures, collected as part of the development of the ELIXIR Biodiversity Community white paper 2022-2023.
DOI: 10.17632/g3vxppc8k4.2
title: Outlier Detection

description: The algorithm you can consult is in https://github.com/sebalp1987/outlier_model. As it is a real dataset, the data is totally masked.
DOI: 10.6084/m9.figshare.25034558
title: Supplementary Material for: Identification of a new enhancer that promotes Sox9 expression by a comparative analysis of mouse and Sry-deficient Amami spiny rat

description: Introduction: Testis differentiation is initiated by the SRY gene on the Y chromosome in mammalian species. However, the Amami spiny rat, Tokudaia osimensis, lacks both the Y chromosome and the Sry gene, and acquired an unique Sox9 regulatory mechanism via a male-specific duplication upstream of Sox9, without Sry. In general mammalian species, the SRY protein binds to a testis-specific enhancer to promote SOX9 gene expression. Several enhancers located upstream of Sox9/SOX9 have been reported in mice and humans. In particular, the binding of SRY to the highly conserved enhancer Enh13 is thought to be a common mechanism underlying testis differentiation and sex determination in mammals. Methods: Sequences of T. osimensis homologues of three Sox9 enhancers that were previously reported in mice, Enh8, Enh14, and Enh13, were determined. We performed in vitro assays to confirm enhancer activity involved in Sox9 regulation in T. osimensis. Results: T. osimensis Enh13 showed enhancer activity when co-transfected with NR5A1 and SOX9. Mouse Enh13 was activated by NR5A1 and SRY; however, T. osimensis Enh13 did not respond to SRY, even though the binding sites of SRY and NR5A1 were conserved. To identify the key sequence that is present in mouse but absent from T. osimensis, we performed reporter gene assays using vectors in which partial sequences of T. osimensis Enh13 were replaced with mouse sequences. For T. osimensis Enh13 in which the second half (approximately 430 bp) was replaced with the corresponding mouse sequence, activity in response to NR5A1 and SRY was recovered. Further reporter assays revealed that multiple regions in the second half of the mouse Enh13 sequence are required for the response to NR5A1 and SRY. The latter 49 bp was particularly important and contained four binding sites for three transcription factors, POU2F1, HOXA3, and GATA1. Conclusion: We showed that there are unknown sequences responsible for the interaction between NR5A1 and SRY and mEnh13 based on comparative analyses of Sry-dependent and Sry-independent species. Our comparative analyses revealed new molecular mechanisms underlying mammalian sex determination.
DOI: 10.1285/i20398573v9n1p43
title: Executive Power and Accountability in Italy and the Government's Response to Covid-19

description: In this article, we add to the existing literature on the political consequences of Covid-19 by studying executive power in Italy during the 2020 – 22 emergency. Given the direct, inverse link between executive centrality and accountability intended as the formal and informal institutions that limit unilateral action, we examine the behavior and practices of Italian executives in the context of the government-parliament relationship, the dynamics between the central state and the regional authorities (horizontal accountability), and the media (diagonal accountability). We focus on the choices made by the government during the Covid crisis. We present descriptive evidence indicating that executive centrality and standards of accountability fluctuated with an intensity proportional to the threat levels of the various stages of the pandemic.
DOI: 10.6084/m9.figshare.9178430
title: MOESM5 of Comparative transcriptome analysis reveals the genetic basis underlying the biosynthesis of polysaccharides in Hericium erinaceus

description: Additional file 5:Â Dataset 4. The annotated of all transcripts in six H.erinaceus samples.
DOI: 10.6084/m9.figshare.14945414
title: Data mining and network analysis reveals C-X-C chemokine receptor type 5 is involved in the pathophysiology of age-related macular degeneration

description: Our previous studies found that the C-X-C motif chemokine receptor 5 (CXCR5) loss leads to retinal pigment epithelium (RPE) dysfunction and AMD pathogenesis. The current study aimed to characterize the G protein-coupled receptor (GPCR) structure of CXCR5 and analyze its interactions with AMD-related risk genes. The sequence alignments, homology model of CXCR5 and structural assessment analysis were performed. Data and text mining were then performed to identify AMD-related risk genes and their interaction with CXCR5 using statistical and mathematical algorithms. Sequence alignment and phylogenetic tree analysis revealed that human CXCR5 was highly similar (85.4839%) to the rabbit. The least similarity (33.871%) was found to be in zebrafish compared to the other species. The CXCR5 model structural assessment and secondary structure analysis exhibited an excellent model. Network analysis revealed that IL10, TNF, ICAM1, CXCL1, CXCL8, APP, TLR4, SELL, C3, IL17A and CCR2 were the most connected genes CXCR5. These findings suggest that CXCR5 signaling may regulate the biological function of RPE and modulate AMD pathophysiology via GPCR signaling and interacting with identified AMD risk genes. In summary, the data presented here provide novel and crucial insights into the molecular mechanisms of CXCR5 involvement in AMD. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9178430.v1
title: MOESM5 of Comparative transcriptome analysis reveals the genetic basis underlying the biosynthesis of polysaccharides in Hericium erinaceus

description: Additional file 5:Â Dataset 4. The annotated of all transcripts in six H.erinaceus samples.
DOI: 10.6084/m9.figshare.14945414.v1
title: Data mining and network analysis reveals C-X-C chemokine receptor type 5 is involved in the pathophysiology of age-related macular degeneration

description: Our previous studies found that the C-X-C motif chemokine receptor 5 (CXCR5) loss leads to retinal pigment epithelium (RPE) dysfunction and AMD pathogenesis. The current study aimed to characterize the G protein-coupled receptor (GPCR) structure of CXCR5 and analyze its interactions with AMD-related risk genes. The sequence alignments, homology model of CXCR5 and structural assessment analysis were performed. Data and text mining were then performed to identify AMD-related risk genes and their interaction with CXCR5 using statistical and mathematical algorithms. Sequence alignment and phylogenetic tree analysis revealed that human CXCR5 was highly similar (85.4839%) to the rabbit. The least similarity (33.871%) was found to be in zebrafish compared to the other species. The CXCR5 model structural assessment and secondary structure analysis exhibited an excellent model. Network analysis revealed that IL10, TNF, ICAM1, CXCL1, CXCL8, APP, TLR4, SELL, C3, IL17A and CCR2 were the most connected genes CXCR5. These findings suggest that CXCR5 signaling may regulate the biological function of RPE and modulate AMD pathophysiology via GPCR signaling and interacting with identified AMD risk genes. In summary, the data presented here provide novel and crucial insights into the molecular mechanisms of CXCR5 involvement in AMD. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.19664246
title: Long non-coding RNA placenta‑specific protein 2 regulates the chemosensitivity of cancer cells to cisplatin in hepatocellular carcinoma (HCC) by sponging microRNA-96 to upregulate X-linked inhibitor of apoptosis protein

description: This study was conducted to investigate the roles of lncRNA PLAC2 and XiaP in hepatocellular carcinoma (HCC). HCC and paired non-tumor tissues were collected from 62 HCC patients who received cisplatin-based treatment. At 0, 2, and 4 months of post-cisplatin-based therapy, blood samples (5 ml) were collected from all patients and prepared plasma samples. LncRNA PLAC2 expression in tissue and plasma samples was determined by RT-qPCR. The interactions between lncRNA PLAC2 and XiaP in HCC cell lines were assessed by overexpression experiments. Cell viability and apoptosis under cisplatin treatment were analyzed by MTT assay and cell apoptosis assay, respectively. The direct interaction between lncRNA PLAC2 and miR-96, which can target XiaP, was analyzed by performing RNA–RNA pulldown assay. It was observed that lncRNA PLAC2 was upregulated in HCC tissues than in non-tumor tissues. LncRNA PLAC2 expression in HCC tissues was not affected by HBV and HCV but upregulated after cisplatin-based treatment. Similarly, cisplatin treatment of HCC cells increased PLAC2 expression. LncRNA PLAC2 and XiaP overexpression increased viability and decreased apoptosis of cisplatin-treated HCC cells, while lncRNA PLAC2 knockdown decreased viability and increased apoptosis of cisplatin-treated HCC cells. Western blot analysis showed that lncRNA PLAC2 increased XiaP protein accumulation, while lncRNA PLAC2 siRNA silencing decreased XiaP expression in HCC cells. LncRNA PLAC2 and miR-96 directly interacted with each other, while they failed to regulate the expression of each other. In conclusion, lncRNA PLAC2 negatively regulates the chemosensitivity of HCC cells to cisplatin, possibly by sponging miR-96 to upregulate miR-96.
DOI: 10.17188/1268761
title: Materials Data on Na2CaSiO4 by Materials Project

description: Na2CaSiO4 crystallizes in the cubic P2_13 space group. The structure is three-dimensional. there are two inequivalent Na1+ sites. In the first Na1+ site, Na1+ is bonded in a distorted trigonal planar geometry to six equivalent O2- atoms. There are three shorter (2.39 Å) and three longer (2.89 Å) Na–O bond lengths. In the second Na1+ site, Na1+ is bonded in a 3-coordinate geometry to three equivalent O2- atoms. All Na–O bond lengths are 2.31 Å. Ca2+ is bonded in a 7-coordinate geometry to seven O2- atoms. There are a spread of Ca–O bond distances ranging from 2.24–2.63 Å. Si4+ is bonded in a tetrahedral geometry to four O2- atoms. There is one shorter (1.63 Å) and three longer (1.66 Å) Si–O bond length. There are two inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted linear geometry to one Ca2+ and one Si4+ atom. In the second O2- site, O2- is bonded in a 1-coordinate geometry to three Na1+, two equivalent Ca2+, and one Si4+ atom.
DOI: 10.34808/j3t1-qg11
title: IKE1-IKE3 (C-1305 derivatives) inhibitory effect of the Yeast Topoisomerase II relaxation activity

description: Inhibition of Yeast Topoisomerase II were analyzed according to relaxation assay kit  from Inspiralis. Briefly, 250 ng of supercoiled pBR322 DNA, 1 mM ATP, 1-200 μM of analyzed compound were mixed with reaction buffer (1 mM Tris-HCl (pH 7.9), 10 mM KCl, 0.5 mM MgCl 2, 0.2 % (v/v) glycerol). The reaction was initiated by the addition of an enzyme, allowed to proceed at 30°C for 30 min and terminated by addition of 40% (w/v) sucrose, 100 mM Tris-HCl pH 8, 10 mM EDTA, 0.5 mg mL -1 Bromophenol Blue. Two step extraction with chloroform:isoamyl alcohol (24:1) and butanol water were made and mixtures were analyzed on the 1% agarose gel in 1x TAE buffer, 3h, 4.5 V cm -1. Gel was  stained in GelRed 3x staining solution for 30 min and photographed with Gel Doc XR+Gel Documentation System.
DOI: 10.6084/m9.figshare.7138787
title: Additional file 6: of Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs

description: Table S6. Eight hundred eighty plant orthologous groups composed of Cd-responsive orthologs in maize and rice. (XLSX 78Â kb)
DOI: 10.17632/bt6j9gyz5t.1
title: Neural data accompanying Crowe et al. 'A prefrontal network operating near steady and oscillatory states links spike desynchronization and synaptic deficits in schizophrenia'

description: The files contain neural data recorded from macaque prefrontal cortex during the performance of the DPX cognitive control task. Each trial includes a vector of the times of action potentials generated by a single neuron during a single trial of the task.
DOI: 10.6084/m9.figshare.19664167
title: Chronic Sigma 1 receptor activation alleviates right ventricular dysfunction secondary to pulmonary arterial hypertension

description: Sigma 1 receptor (S1R) has shown a preferable protective effect on left ventricular function, but whether it protects right ventricular (RV) function is still elusive.This study aimed to determine the effects of S1R on RV dysfunction secondary to pulmonary arterial hypertension.Sixty wild-type male Sprague–Dawley rats were randomly divided into the control group, the fluvoxamine group, the pulmonary arterial hypertension group and the pulmonary arterial hypertension combined with fluvoxamine group. Monocrotaline (60 mg/kg) was administered to induce pulmonary arterial hypertension, and fluvoxamine was given for 21 consecutive days to activate S1R after one week of monocrotaline administration. Echocardiographic, serologic, and histologic parameters, qRT-PCR, and western blotting were conducted after 4 weeks of monocrotaline administration.The expression of S1R was decreased in the right ventricle in pulmonary arterial hypertension. TAPSE, and the FAC of the right ventricle were significantly decreased, and RV EDP and the plasma concentration of N-terminal pro-B-type natriuretic peptide was increased in the pulmonary arterial hypertension group, but fluvoxamine partly restored those abnormalities (all P &lt; 0.05). Moreover, pulmonary arteriole remodeling, and fibrosis and hypertrophy in the RV were shown in the pulmonary arterial hypertension group; interestingly, fluvoxamine recovered RV structural remodeling (all P &lt; 0.05) but neither alleviated pulmonary arteriole remodeling nor reduced pulmonary artery pressure. Furthermore, S1R activation protects RV function by upgrading the NRF 2/HO 1-mediated antioxidant stress pathway. In conclusion, chronic S1R activation ameliorates structural remodeling and RV dysfunction secondary to pulmonary arterial hypertension without altering pulmonary artery pressure.