cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16570725.v1
title: Exploration of differentially-expressed exosomal mRNAs, lncRNAs and circRNAs from serum samples of gallbladder cancer and xantho-granulomatous cholecystitis patients

description: Gallbladder cancer (GBC) is the most common biliary tract malignancy worldwide. Although a growing number of studies have explored the mechanism of GBC, thus far, few molecules have been discovered that can be utilized as specific biomarkers for the early diagnosis and therapeutic treatment of GBC. Recent studies have shown that exosomes not only participate in the progression of tumors, but also carry specific information that can define multiple cancer types. The present study investigated the expression profiles of coding (or messenger) ribonucleic acids (mRNAs) and non-coding RNAs (ncRNAs, including long non-coding RNAs [lncRNAs] and circular RNAs [circRNAs]) in plasma-derived exosomes from GBC patients. Using high-throughput RNA sequencing and subsequent bioinformatic analysis, a number of differentially expressed (DE) mRNAs, lncRNAs, and circRNAs were identified in GBC exosomes, compared to their expressions in xantho-granulomatous cholecystitis (XGC) exosomes. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analyses were then conducted to investigate the potential functions of these DE RNAs. Furthermore, the interaction networks and competing endogenous RNA networks of these DE RNAs and their target genes were investigated, revealing a complex regulatory network among mRNAs and ncRNAs. In summary, this study demonstrates the diagnostic value of plasma-derived exosomes in GBC and provides a new perspective on the mechanism of GBC.
DOI: 10.6084/m9.figshare.16570726
title: A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

description: Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors was explored based on the datasets of gene expression omnibus and the cancer genome atlas. Differential expression of ACTB was found between cancer and adjacent normal tissues, and significant associations was found between ACTB expression and prognosis of tumor patients. In most cancers, ACTB expression was associated with immune cells infiltration, immune checkpoints and other immune modulators. Relevance between ACTB and metastasis and invasion was identified in various types of cancers by CancerSEA. Moreover, focal adhesion and actin regulation-associated pathways were included in the functional mechanisms of ACTB. The expression of ACTB was verified by quantitative real-time polymerase chain reaction. Knockdown of ACTB inhibited head and neck squamous carcinoma cell migration and invasion by NF-κB and Wnt/β-catenin pathways. Our first pan-cancer study of ACTB offers insight into the prognostic and immunological roles of ACTB across different tumors, indicating ACTB may be a potential biomarker for poor prognosis and immune infiltration in cancers, and the role of ACTB as a reference gene in cancers was challenged.
DOI: 10.6084/m9.figshare.16570726.v2
title: A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

description: Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors was explored based on the datasets of gene expression omnibus and the cancer genome atlas. Differential expression of ACTB was found between cancer and adjacent normal tissues, and significant associations was found between ACTB expression and prognosis of tumor patients. In most cancers, ACTB expression was associated with immune cells infiltration, immune checkpoints and other immune modulators. Relevance between ACTB and metastasis and invasion was identified in various types of cancers by CancerSEA. Moreover, focal adhesion and actin regulation-associated pathways were included in the functional mechanisms of ACTB. The expression of ACTB was verified by quantitative real-time polymerase chain reaction. Knockdown of ACTB inhibited head and neck squamous carcinoma cell migration and invasion by NF-κB and Wnt/β-catenin pathways. Our first pan-cancer study of ACTB offers insight into the prognostic and immunological roles of ACTB across different tumors, indicating ACTB may be a potential biomarker for poor prognosis and immune infiltration in cancers, and the role of ACTB as a reference gene in cancers was challenged.
DOI: 10.6084/m9.figshare.16570726.v1
title: A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

description: Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors was explored based on the datasets of gene expression omnibus and the cancer genome atlas. Differential expression of ACTB was found between cancer and adjacent normal tissues, and significant associations was found between ACTB expression and prognosis of tumor patients. In most cancers, ACTB expression was associated with immune cells infiltration, immune checkpoints and other immune modulators. Relevance between ACTB and metastasis and invasion was identified in various types of cancers by CancerSEA. Moreover, focal adhesion and actin regulation-associated pathways were included in the functional mechanisms of ACTB. The expression of ACTB was verified by quantitative real-time polymerase chain reaction. Knockdown of ACTB inhibited head and neck squamous carcinoma cell migration and invasion by NF-κB and Wnt/β-catenin pathways. Our first pan-cancer study of ACTB offers insight into the prognostic and immunological roles of ACTB across different tumors, indicating ACTB may be a potential biomarker for poor prognosis and immune infiltration in cancers, and the role of ACTB as a reference gene in cancers was challenged.
DOI: 10.6084/m9.figshare.12900766
title: Additional file 2 of AKT/FOXO1 axis links cross-talking of endothelial cell and pericyte in TIE2-mutated venous malformations

description: Additional file 1: Figure S1. SNP sequencing results of four other patients diagnosed with TIE2-L914 caused VMs. The red arrows indicate the mutation site. Figure S2. A representative HE stained section of a patient with venous malformation. The dotted line indicates a malformed vein. VM: venous malformation. Scale bar, 200 μm. Figure S3. (A) A representative picture of ECs morphology. (B) Immunofluorescence showed cells extracted from umbilical cord expressing vWF. Scale bar, 200 μm.
DOI: 10.6084/m9.figshare.12900766.v1
title: Additional file 2 of AKT/FOXO1 axis links cross-talking of endothelial cell and pericyte in TIE2-mutated venous malformations

description: Additional file 1: Figure S1. SNP sequencing results of four other patients diagnosed with TIE2-L914 caused VMs. The red arrows indicate the mutation site. Figure S2. A representative HE stained section of a patient with venous malformation. The dotted line indicates a malformed vein. VM: venous malformation. Scale bar, 200 μm. Figure S3. (A) A representative picture of ECs morphology. (B) Immunofluorescence showed cells extracted from umbilical cord expressing vWF. Scale bar, 200 μm.
DOI: 10.6084/m9.figshare.12900767
title: Additional file 1 of EIF3H promotes aggressiveness of esophageal squamous cell carcinoma by modulating Snail stability

description: Additional file 1 Table S1. LC-MS/MS results of co-immunoprecipitation assay.
DOI: 10.6084/m9.figshare.12900767.v1
title: Additional file 1 of EIF3H promotes aggressiveness of esophageal squamous cell carcinoma by modulating Snail stability

description: Additional file 1 Table S1. LC-MS/MS results of co-immunoprecipitation assay.
DOI: 10.6084/m9.figshare.12900844
title: Additional file 10 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 10. EAR motif in C2H2 ZFPs with one zinc finger. ‘N.A.’ indicated that this C2H2 ZFP did not contain the EAR motif.
DOI: 10.6084/m9.figshare.12900844.v1
title: Additional file 10 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 10. EAR motif in C2H2 ZFPs with one zinc finger. ‘N.A.’ indicated that this C2H2 ZFP did not contain the EAR motif.
DOI: 10.6084/m9.figshare.12900856
title: Additional file 13 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 13. The list of primers.
DOI: 10.6084/m9.figshare.12900856.v1
title: Additional file 13 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 13. The list of primers.
DOI: 10.6084/m9.figshare.12900859
title: Additional file 1 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 1. C2H2 ZFPs in Medicago truncatula. The list of gene ID, location, probeset, physicochemical property, splice variant, ortholog locus, motif, and protein sequence for each C2H2 ZFPs.
DOI: 10.6084/m9.figshare.12900859.v1
title: Additional file 1 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 1. C2H2 ZFPs in Medicago truncatula. The list of gene ID, location, probeset, physicochemical property, splice variant, ortholog locus, motif, and protein sequence for each C2H2 ZFPs.
DOI: 10.6084/m9.figshare.12900862
title: Additional file 2 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 2. The protein sequences of C2H2 ZFPs.
DOI: 10.6084/m9.figshare.12900862.v1
title: Additional file 2 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 2. The protein sequences of C2H2 ZFPs.
DOI: 10.6084/m9.figshare.12900865
title: Additional file 3 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 3. The C2H2 motif sequences of C2H2 ZFPs.
DOI: 10.6084/m9.figshare.12900865.v1
title: Additional file 3 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 3. The C2H2 motif sequences of C2H2 ZFPs.
DOI: 10.6084/m9.figshare.12900868
title: Additional file 4 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 4. Distribution of C2H2 ZFPs on chromosomes in M.truncatula.
DOI: 10.6084/m9.figshare.12900868.v1
title: Additional file 4 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 4. Distribution of C2H2 ZFPs on chromosomes in M.truncatula.
DOI: 10.6084/m9.figshare.12900871
title: Additional file 5 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 5. Local gene duplications of C2H2 ZFPs in M.truncatula.
DOI: 10.6084/m9.figshare.12900871.v1
title: Additional file 5 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 5. Local gene duplications of C2H2 ZFPs in M.truncatula.
DOI: 10.6084/m9.figshare.12900874
title: Additional file 6 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 6. C2H2 ZFP gene pairs originated from whole-genome duplication in M.truncatula.
DOI: 10.6084/m9.figshare.12900874.v1
title: Additional file 6 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 6. C2H2 ZFP gene pairs originated from whole-genome duplication in M.truncatula.
DOI: 10.6084/m9.figshare.12900877
title: Additional file 7 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 7. C2H2 ZFPs paired sequence similarity analysis.
DOI: 10.6084/m9.figshare.12900877.v1
title: Additional file 7 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 7. C2H2 ZFPs paired sequence similarity analysis.
DOI: 10.6084/m9.figshare.12900880
title: Additional file 8 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 8. Classification of C2H2 motif in M.truncatula.
DOI: 10.6084/m9.figshare.12900880.v1
title: Additional file 8 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 8. Classification of C2H2 motif in M.truncatula.
DOI: 10.6084/m9.figshare.12900883
title: Additional file 9 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 9. Classification of C2H2 ZFPs in M.truncatula.
DOI: 10.6084/m9.figshare.12900883.v1
title: Additional file 9 of Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

description: Additional file 9. Classification of C2H2 ZFPs in M.truncatula.
DOI: 10.6084/m9.figshare.21813795
title: Global soil nitrogen cycle pattern and nitrogen enrichment effects: tropical versus subtropical forests

description: Global soil nitrogen cycle pattern and nitrogen enrichment effects: tropical versus subtropical forests
DOI: 10.6084/m9.figshare.25234021
title: Sequences of 1.600 viral contigs and 62 de-replicated metagenome-assembled genomes

description: Globally novel and locally diverse viruses inhabiting deep-sea seamount sedimentsviral contigs and MAGs<br><br>
DOI: 10.5281/zenodo.10670550
title: Empirical approach to advance the generalisation of multi-scale maps

description: This dataset is described in the article Empirical approach to advance the generalisation of multi-scale maps; summarized below: 

Since the advent of the web revolution, maps have undergone profound changes in their usage and design. Pan-scalar map design, in particular, emphasises interaction, enabling users to navigate diverse representations seamlessly across different scales.This study addresses gaps in understanding pan-scalar map specificity. Through empirical experimentation, a multi-scale map exemplar is constructed, focusing on map generalisation quality to reduce disorientation and facilitate information retrieval during exploration. Utilising a combination of generalisation strategies, including automatic and semi-automatic processes, this map serves as a foundational step in formalising new rules of map generalisation in a pan-scalar mapping context. Then, we initiate discussions on the lessons learnt from this exemplar construction. In particular, we discuss what constitutes good generalisation for pan-scalar maps and outline potential approaches for achieving it. 

It is composed of four folder :



All_Data contains all the data before generalisation. 

MS_Hydro contains the shapefile of generalised hydrographic element for each zoom level.

MS_Road contains the shapefile of generalised urban road elements for each zoom level.

Styles contains the style file to apply to create our map.
DOI: 10.5281/zenodo.10670551
title: Empirical approach to advance the generalisation of multi-scale maps

description: This dataset is described in the article Empirical approach to advance the generalisation of multi-scale maps; summarized below: 

Since the advent of the web revolution, maps have undergone profound changes in their usage and design. Pan-scalar map design, in particular, emphasises interaction, enabling users to navigate diverse representations seamlessly across different scales.This study addresses gaps in understanding pan-scalar map specificity. Through empirical experimentation, a multi-scale map exemplar is constructed, focusing on map generalisation quality to reduce disorientation and facilitate information retrieval during exploration. Utilising a combination of generalisation strategies, including automatic and semi-automatic processes, this map serves as a foundational step in formalising new rules of map generalisation in a pan-scalar mapping context. Then, we initiate discussions on the lessons learnt from this exemplar construction. In particular, we discuss what constitutes good generalisation for pan-scalar maps and outline potential approaches for achieving it. 

It is composed of four folder :



All_Data contains all the data before generalisation. 

MS_Hydro contains the shapefile of generalised hydrographic element for each zoom level.

MS_Road contains the shapefile of generalised urban road elements for each zoom level.

Styles contains the style file to apply to create our map.
DOI: 10.6084/m9.figshare.12901013
title: Light_field_endoscope.zmx

description: The Zemax lens design file of the main lens of a light field endoscope
DOI: 10.6084/m9.figshare.9962831
title: MOESM2 of Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

description: Additional file 2: Supplementary Data 1. Fasta file containing 40,583â G. japonicum transcript sequences. (FASTA 45632 kb)
DOI: 10.6084/m9.figshare.9962831.v1
title: MOESM2 of Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

description: Additional file 2: Supplementary Data 1. Fasta file containing 40,583â G. japonicum transcript sequences. (FASTA 45632 kb)
DOI: 10.6084/m9.figshare.12376787
title: Knockdown of SNHG1 inhibits cervical cancer growth through sponging miR-194 to regulate HCCR

description: To investigate the mechanism of small nucleolar RNA host gene 1 (SNHG1) in cervical cancer (CC). <b>Methods:</b> The expression of SNHG1, miR-194 and human cervical cancer oncogene (HCCR) in CC tissues and cells was detected using qRT-PCR and western blot. The interaction among the three molecules was measured using dual-luciferase reporter assay and RNA immunoprecipitation assay. The function of SNHG1 in CC cells was detected by CKK-8 assay and flow cytometry analysis. <b>Results:</b> SNHG1 was highly expressed in CC tissues and CC cell lines. Knockdown of SNHG1 inhibited CC cell proliferation and enhanced the ability of cell apoptosis. Mechanism investigation revealed that SNHG1 modulated HCCR expression <i>via</i> acting as a competing endogenous RNA of miR-194. Moreover, miR-194 inhibitor changed the effects of si-SNHG1 on CC cells growth. <i>In vivo</i> experiment, silencing of SNHG1 suppressed CC tumor growth by modulating miR-194/HCCR axis. <b>Conclusion:</b> Knockdown of SNHG1 inhibited CC progression by targeting HCCR <i>via</i> sponging with miR-194.
DOI: 10.6084/m9.figshare.12376787.v1
title: Knockdown of SNHG1 inhibits cervical cancer growth through sponging miR-194 to regulate HCCR

description: To investigate the mechanism of small nucleolar RNA host gene 1 (SNHG1) in cervical cancer (CC). <b>Methods:</b> The expression of SNHG1, miR-194 and human cervical cancer oncogene (HCCR) in CC tissues and cells was detected using qRT-PCR and western blot. The interaction among the three molecules was measured using dual-luciferase reporter assay and RNA immunoprecipitation assay. The function of SNHG1 in CC cells was detected by CKK-8 assay and flow cytometry analysis. <b>Results:</b> SNHG1 was highly expressed in CC tissues and CC cell lines. Knockdown of SNHG1 inhibited CC cell proliferation and enhanced the ability of cell apoptosis. Mechanism investigation revealed that SNHG1 modulated HCCR expression <i>via</i> acting as a competing endogenous RNA of miR-194. Moreover, miR-194 inhibitor changed the effects of si-SNHG1 on CC cells growth. <i>In vivo</i> experiment, silencing of SNHG1 suppressed CC tumor growth by modulating miR-194/HCCR axis. <b>Conclusion:</b> Knockdown of SNHG1 inhibited CC progression by targeting HCCR <i>via</i> sponging with miR-194.
DOI: 10.6084/m9.figshare.9962843
title: MOESM3 of Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

description: Additional file 3: Supplementary Data 2. Fasta file containing 30,243â G. japonicum unigene sequences. (FASTA 24636 kb)
DOI: 10.6084/m9.figshare.9962843.v1
title: MOESM3 of Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

description: Additional file 3: Supplementary Data 2. Fasta file containing 30,243â G. japonicum unigene sequences. (FASTA 24636 kb)
DOI: 10.6084/m9.figshare.7658345
title: day_tp100.nc

description: These are model simulation data used in "mechanisms of northward propagation of boreal summer intraseasonal oscillation revealed by climate model experiment" by Yang et al. 2019. Due to limited space, only two year daily data are avaialble

<br>
DOI: 10.6084/m9.figshare.16571247
title: Brachyericines (Erinaceidae, Eulipotyphla) from the early Miocene of central Nei Mongol, China

description: Brachyericinae is a subfamily of Erinaceidae (hedgehogs and moonrats) with a very short history and limited distribution. Fossil records of brachyericines, with rare materials, were confined to the Oligocene and early Miocene in Central Asia and to the Miocene in North America. Here, we report three forms of short-faced hedgehogs: <i>Synexallerix junggarensis</i>, Brachyericinae gen. et sp. indet. 1 and Brachyericinae gen. et sp. indet. 2 from Aoerban and Gashunyin Adege, localities of the early Miocene in Central Nei Mongol. <i>S. junggarensis</i> is the first discovery outside the Suosuoquan Formation in Xinjiang and detailed description of the new materials, including a nearly complete skull, clarifies its taxonomic position within the Brachyericinae. The new Nei Mongol material is important not only because they include a nearly complete skull of <i>S. junggarensis</i> (previously known by a rostral part of the skull) but also because of the presence of three taxa of the brachyericines from the same general area. The similarity of its morphological characteristics with the North American genera also further confirms the close affinities of brachyericines from the two continents during the early Miocene.