cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21082241.v1
title: CircNFIX knockdown inhibited AML tumorigenicity by the miR-876-3p/TRIM31 axis

description: Acute myeloid leukemia (AML) is one of the most common malignant myeloid diseases in adults with a dismal prognosis. We aimed to explore the effects of circNFIX on the proliferation and apoptosis of AML cells. The expressions of circNFIX, miR-876-3p and tripartite motif (TRIM) 31 in the bone marrow specimens of AML patients and AML cell lines were detected by qRT-PCR or western blot. Cell proliferation was evaluated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and 5-ethynyl-29-deoxyuridine (EdU) assays. Cell cycle and apoptosis were analyzed by flow cytometry. Western blot was used to detect protein expression. The relationship between miR-876-3p and circNFIX or TRIM31 was identified by dual-luciferase reporter assay or RNA pull-down assay. The expression level of circNFIX was significantly increased in the bone marrow samples of AML patients and AML cells when compared with normal controls. CircNFIX silencing inhibited AML cell proliferation and promoted apoptosis. Inhibition of miR-876-3p reversed the effect of circNFIX knockdown on AML cell progression. In addition, circNFIX indirectly regulated TRIM31 through miR-876-3p. Further, TRIM31 overexpression counteracted the effect of circNFIX silencing on AML cell proliferation and apoptosis. CircNFIX knockdown could suppress the proliferation and induce the apoptosis of AML cells by targeting the miR-876-3p/TRIM31 axis.
DOI: 10.6084/m9.figshare.6401954
title: Additional file 5: of Transcriptomics reveals the molecular processes of light-induced rapid darkening of the non-obligate cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura) and their genetic basis of pigmentation strategy

description: Table S4. Summary of enrichment based on light-inducible genes (1662). (XLSX 46 kb)
DOI: 10.6084/m9.figshare.6401954.v1
title: Additional file 5: of Transcriptomics reveals the molecular processes of light-induced rapid darkening of the non-obligate cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura) and their genetic basis of pigmentation strategy

description: Table S4. Summary of enrichment based on light-inducible genes (1662). (XLSX 46 kb)
DOI: 10.6084/m9.figshare.24615369
title: Raw data file of 20th set within 20th subject

description: Raw data file of 20th subject
DOI: 10.6084/m9.figshare.24615369.v1
title: Raw data file of 20th set within 20th subject

description: Raw data file of 20th subject
DOI: 10.6084/m9.figshare.24615372
title: Raw data file of 3rd set within 3rd subject

description: Raw data file of 3rd subject
DOI: 10.6084/m9.figshare.23700648.v1
title: Additional file 1 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 1: Primer sequences of quantitative real-time.
DOI: 10.6084/m9.figshare.23700651
title: Additional file 2 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 2: Antibodies information of Western blotting.
DOI: 10.6084/m9.figshare.24615372.v1
title: Raw data file of 3rd set within 3rd subject

description: Raw data file of 3rd subject
DOI: 10.6084/m9.figshare.23700663
title: Additional file 6 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 6:(A) qRT-PCR verifies that the mRNA expression of FAP in OEFAP-HFFs is significantly higher than in NCFAP-HFFs and T24 cells. (B, C) WB indicates that the protein expression of FAP in OEFAP-HFFs is significantly higher than in NCFAP-HFFs and T24 cells. (D, E) WB show that HFF-CM (stimulated or not stimulated) has a pro-EMT effect, with downregulated E-cadherin and upregulated N-cadherin and Vimentin. The pro-EMT effects of HFF-CM were significantly amplified after TGF-β1 induction or overexpression FAP, while the TGF-β1 neutralizing antibody reverses the pro-EMT effects of TGF-β1 induction.
DOI: 10.6084/m9.figshare.22655274
title: Additional file 9 of Identification of a m6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma

description: Additional file 9: Supplementary Table 6-S2. The raw data used to generate Figure 6B-D.
DOI: 10.6084/m9.figshare.22655280
title: Additional file 11 of Identification of a m6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma

description: Additional file 11: Supplementary Table 8-S1. The raw data used to generate Figure 8A-C
DOI: 10.6084/m9.figshare.6401885
title: Additional file 1: of Transcriptomics reveals the molecular processes of light-induced rapid darkening of the non-obligate cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura) and their genetic basis of pigmentation strategy

description: Table S1. Summary of sequencing quality. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.22655280.v1
title: Additional file 11 of Identification of a m6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma

description: Additional file 11: Supplementary Table 8-S1. The raw data used to generate Figure 8A-C
DOI: 10.6084/m9.figshare.24615375
title: Raw data file of 5th set within 5th subject

description: Raw data file of 5th subject
DOI: 10.6084/m9.figshare.24615375.v1
title: Raw data file of 5th set within 5th subject

description: Raw data file of 5th subject
DOI: 10.6084/m9.figshare.22655268
title: Additional file 7 of Identification of a m6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma

description: Additional file 7: Supplementary Table 5. The raw data used to generate Figure 5A,C,E,G.
DOI: 10.6084/m9.figshare.22655277
title: Additional file 10 of Identification of a m6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma

description: Additional file 10: Supplementary Table 7-S3. The raw data used to generate Figure 7C-F.
DOI: 10.6084/m9.figshare.23700672.v1
title: Additional file 9 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 9: qRT-PCR (A, B), WB(C, D), and immunohistochemistry (E, F) showed that TGF-β1/FAP/VCAN axis regulates bladder cancer EMT in vivo. CAF has a stronger EMT-inducing effect than NF. Overexpression of FAP enhanced the EMT-inducing effects of stromal fibroblasts, while knockdown of FAP weakened those effects.
DOI: 10.6084/m9.figshare.24615378
title: Raw data file of 1st set within 1st subject

description: Raw data file of 1st subject
DOI: 10.6084/m9.figshare.24615378.v1
title: Raw data file of 1st set within 1st subject

description: Raw data file of 1st subject
DOI: 10.6084/m9.figshare.24615381
title: Raw data file of 4th set within 4th subject

description: Raw data file of 4th subject
DOI: 10.6084/m9.figshare.24615381.v1
title: Raw data file of 4th set within 4th subject

description: Raw data file of 4th subject
DOI: 10.6084/m9.figshare.22655277.v1
title: Additional file 10 of Identification of a m6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma

description: Additional file 10: Supplementary Table 7-S3. The raw data used to generate Figure 7C-F.
DOI: 10.6084/m9.figshare.24615384
title: Raw data file of 2nd set within 2nd subject

description: Raw data file of 2nd subject
DOI: 10.6084/m9.figshare.24615384.v1
title: Raw data file of 2nd set within 2nd subject

description: Raw data file of 2nd subject
DOI: 10.6084/m9.figshare.6401939.v1
title: Additional file 4: of Transcriptomics reveals the molecular processes of light-induced rapid darkening of the non-obligate cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura) and their genetic basis of pigmentation strategy

description: Table S3. Summary of FPKM. (XLSX 20703 kb)
DOI: 10.6084/m9.figshare.7975283.v1
title: Additional file 1: of Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem

description: Table S1. Molecular identification of epiphytic and endophytic fungi at a 97% sequence identity level in this study. (XLSX 113 kb)
DOI: 10.6084/m9.figshare.7975295
title: Additional file 3: of Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem

description: Table S2. Comparison of the relative abundance of abundant operational taxonomic units (OTUs, &gt;â 1000 reads) between epiphytic and endophytic fungi. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.22134351
title: Research on map emotional semantics using deep learning approach

description: The main purpose of the research on map emotional semantics is to describe and express the emotional responses caused by people observing images through computer technology. Nowadays, map application scenarios tend to be diversified, and the increasing demand for emotional information of map users bring new challenges for cartography. However, the lack of evaluation of emotions in the traditional map drawing process makes it difficult for the resulting maps to reach emotional resonance with map users. The core of solving this problem is to quantify the emotional semantics of maps, it can help mapmakers to better understand map emotions and improve user satisfaction. This paper aims to perform the quantification of map emotional semantics by applying transfer learning methods and the efficient computational power of convolutional neural networks (CNN) to establish the correspondence between visual features and emotions. The main contributions of this paper are as follows: (1) a Map Sentiment Dataset containing five discrete emotion categories; (2) three different CNNs (VGG16, VGG19, and InceptionV3) are applied for map sentiment classification task and evaluated by accuracy performance; (3) six different parameter combinations to conduct experiments that would determine the best combination of learning rate and batch size; and (4) the analysis of visual variables that affect the sentiment of a map according to the chart and visualization results. The experimental results reveal that the proposed method has good accuracy performance (around 88%) and that the emotional semantics of maps have some general rules. A Map Sentiment Dataset with five discrete emotions is constructedMap emotional semantics are classified by deep learning approachesVisual variables Influencing map sentiment are analyzed. A Map Sentiment Dataset with five discrete emotions is constructed Map emotional semantics are classified by deep learning approaches Visual variables Influencing map sentiment are analyzed.
DOI: 10.6084/m9.figshare.23700530.v1
title: Additional file 3 of Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

description: Supplementary File 3
DOI: 10.6084/m9.figshare.23700599
title: Additional file 1 of Duck plague virus tegument protein vp22 plays a key role in the secondary envelopment and cell-to-cell spread

description: Additional file 1. Sequences and primer pair characteristics.
DOI: 10.6084/m9.figshare.7975283
title: Additional file 1: of Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem

description: Table S1. Molecular identification of epiphytic and endophytic fungi at a 97% sequence identity level in this study. (XLSX 113 kb)
DOI: 10.6084/m9.figshare.23700530
title: Additional file 3 of Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

description: Supplementary File 3
DOI: 10.6084/m9.figshare.21085897
title: CM-Power near-real-time monitoring of global power generation on hourly to daily scales

description:   
We constructed a near-real-time global power generation dataset: CM-Power since January 1, 2016 at national levels with near-global coverage and hourly to daily time resolution. The data is frequently updated. The power generation data presented in this study are collected from 37 countries across all continents for eight power source groups, including three types of fossil sources (coal, natural gas, and oil), nuclear energy, and four groups of renewable energy sources (solar energy, wind energy, hydro energy and other renewable sources including biomass, geothermal, etc.). The global near-real-time power dataset shows the dynamics of the global power system, including its hourly, daily, weekly and seasonal patterns as influenced by daily periodical activities (i.e., working hours), weekends, seasonal cycles, as well as by regular and irregular events such as holidays (i.e., Thanksgiving Day) and extreme events such as the COVID-19 pandemic. The CM-Power dataset reveals that the COVID-19 pandemic has caused strong disruptions in some countries (i.e., China, India, and South Africa), even leading to a temporary or long-lasting shift to low carbon intensity, while it had only little impact in some other countries (i.e., Australia). This daily and hourly updated power dataset offer a large range of opportunities for power-related scientific research and policy-making.
DOI: 10.6084/m9.figshare.12173169
title: Revision of <i>Triplicatella</i> (Orthothecida, Hyolitha) with preserved digestive tracts from the early Cambrian Chengjiang Lagerstätte, South China

description: The cap-shaped shells of <i>Triplicatella</i> are known almost exclusively from small shelly fossil assemblages with articulated specimens showing unequivocally that they represent the operculum of a hyolith. Abundant specimens of <i>Triplicatella opimus</i> from the fine-grained shales of the Chengjiang Lagerstätte of South China with soft-part preservation are documented herein. The soft tissues, including the feeding apparatus and complex digestive system, in <i>T. opimus</i> strongly suggest that <i>Triplicatella</i> was a deposit feeder. The digestive tract of <i>T. opimus</i> consists of two limbs, a spiral loop folded into a chevron-like structure and a slightly recurved to straight anal tube, which are preserved as reddish-black traces enriched in iron. The new anatomical information obtained from <i>T. opimus</i> in the Chengjiang Biota suggests an intermediate stage in the development of the characteristic folded gut of orthothecid hyoliths. The new anatomical information reported here shows that <i>Triplicatella</i> is one of the best-preserved early members of the Orthothecida and promotes our understanding of the general anatomy and evolution of the Hyolitha.
DOI: 10.6084/m9.figshare.21082247
title: Modeling and Active Learning for Experiments with Quantitative-Sequence Factors

description: A new type of experiment that aims to determine the optimal quantities of a sequence of factors is eliciting considerable attention in medical science, bioengineering, and many other disciplines. Such studies require the simultaneous optimization of both quantities and sequence orders of several components which are called quantitative-sequence (QS) factors. Given the large and semi-discrete solution spaces in such experiments, efficiently identifying optimal or near-optimal solutions by using a small number of experimental trials is a nontrivial task. To address this challenge, we propose a novel active learning approach, called QS-learning, to enable effective modeling and efficient optimization for experiments with QS factors. QS-learning consists of three parts: a novel mapping-based additive Gaussian process (MaGP) model, an efficient global optimization scheme (QS-EGO), and a new class of optimal designs (QS-design). The theoretical properties of the proposed method are investigated, and optimization techniques using analytical gradients are developed. The performance of the proposed method is demonstrated via a real drug experiment on lymphoma treatment and several simulation studies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21995069.v3
title: Files for Main Figure 4

description: 6 Cell lines TE matrices quantified by long-read, Telescope(short-read), lasTEq(short-read). Used for main figure 4
<br>
1. SG-Nex_A549: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using A549 cell line in SG-NEx study
2. SG-Nex_HepG2: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using HepG2 cell line in SG-NEx study
3. SG-Nex_HCT116: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using HCT116 cell line in SG-NEx study
4. SG-Nex_K562: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using K562 cell line in SG-NEx study
5. SG-Nex_MCF-7: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using MCF-7 cell line in SG-NEx study
6. Inhouse_HCT116: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using HCT116 sample generated by our lab
DOI: 10.6084/m9.figshare.5353759.v3
title: Modeling <i>in vivo</i> relative biological effectiveness in particle therapy for clinically relevant endpoints

description: <b>Background:</b> The relative biological effectiveness (RBE) of particle therapy compared to photon radiotherapy is known to be variable but the exact dependencies are still subject to debate. <i>In vitro</i> data suggested that RBE is to a large extend independent of ion type if parametrized by the beam quality Q. This study analyzed the RBE dependence of pre-clinical data on late toxicity with an emphasis on the beam quality. <b>Material and methods:</b> Published pre-clinical RBE dose-response data of the spinal cord following one and two fractions of photon and carbon ion irradiation were compiled. The beam quality for each treatment condition was obtained from Monte Carlo simulations. The <i>α<sub>p</sub></i> and <i>β<sub>p</sub></i> parameters of the linear-quadratic (LQ) model for particle irradiation were determined from the pre-clinical data and was provided as a function of <i>Q</i>. An introduced model proposed <i>α<sub>p</sub></i> to increase linearly with <i>Q</i> and <i>β<sub>p</sub></i> to remain constant. RBE values predicted by the model were compared to the published data. <b>Results:</b> The α<sub>p</sub> parameter was highly correlated with <i>Q (R<sup>2</sup></i> = 0.96) with a linear slope of 0.019 Gy<sup>−1</sup>. No significant variation of <i>β<sub>p</sub></i> with <i>Q</i> was found. RBE and <i>Q</i> were also highly correlated (<i>R</i><sup>2</sup> = 0.98) for one and two fractions. The (extrapolated) RBE at <i>Q</i> = 0 (theoretical photon limit) for one and two fractions was 1.22 and significantly larger than 1 (<i>p</i> = .004). The model reproduced the dependence of RBE on fractionation well. <b>Conclusions</b>: Fraction dose and beam quality <i>Q</i> were sufficient to describe the RBE variability for a late toxicity model within a carbon ion treatment field. Assuming the independence of the identified RBE parameters on the ion type might suggest the translation of variable (pre-) clinical RBE data from carbon ion to proton therapy.
DOI: 10.6084/m9.figshare.7975328.v1
title: MOESM4 of Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass

description: Additional file 4. Enzyme activity abbreviations and transcriptome dataset tables. Table with enzyme activity, their abbreviations and their predicted target substrate used in this study. The same color scheme for target substrates was used in the main text. A gene to be assigned as expressed more on a substrate (CS or SBH) requires a foldchange &gt; 2.5, p ≤ 0.05 and at least 18 FPKM of expression in at least one condition. Genes with expression &lt; 18 FPKM in each condition were excluded from subsequent analysis, because they were considered to be too poorly expressed.
DOI: 10.6084/m9.figshare.7975331
title: Additional file 2: of The effects of a home-based exercise intervention on elderly patients with knee osteoarthritis: a quasi-experimental study

description: Information on the patients enrolled in the study. This file includes the demographic characteristics and all outcomes of the patients enrolled in the study. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.7975331.v1
title: Additional file 2: of The effects of a home-based exercise intervention on elderly patients with knee osteoarthritis: a quasi-experimental study

description: Information on the patients enrolled in the study. This file includes the demographic characteristics and all outcomes of the patients enrolled in the study. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.7975328
title: MOESM4 of Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass

description: Additional file 4. Enzyme activity abbreviations and transcriptome dataset tables. Table with enzyme activity, their abbreviations and their predicted target substrate used in this study. The same color scheme for target substrates was used in the main text. A gene to be assigned as expressed more on a substrate (CS or SBH) requires a foldchange &gt; 2.5, p ≤ 0.05 and at least 18 FPKM of expression in at least one condition. Genes with expression &lt; 18 FPKM in each condition were excluded from subsequent analysis, because they were considered to be too poorly expressed.
DOI: 10.6084/m9.figshare.22655259.v1
title: Additional file 4 of Identification of a m6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma

description: Additional file 4: Supplementary Table 4-S3. The raw data used to generate Figure 4G-H.
DOI: 10.6084/m9.figshare.14794947
title: Supplementary Table 4. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

description: <b>All results of the GO enrichment analysis.</b> See results.
DOI: 10.6084/m9.figshare.14794950
title: Supplementary Table 3. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

description: <b>Annotation of all genes in any of the intersections between duplication, positive selection and/or mitochondrial retargeting.</b> See <b>Figure 2.</b>
DOI: 10.6084/m9.figshare.14794953
title: Supplementary Dataset 1. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

description: <b>Schematic visualization of the evolutionary changes on KEGG pathways analyzed in this work.</b> Each file corresponds to one pathway, where the symbols are equivalent to those listed in <b>Supplementary Figure 4.</b> The scores of each enzyme are represented by the size of the dot (see legend), and they can be interactively added/removed. Each symbol represents a gene which, upon hover with the cursor, displays an informative box. This provides many lines of evolutionary information: 1) Gene name, one of the kegg orthologs (KOs) and name of the enzyme, KO for which the mapping was established. 2) Evolutionary processes found in this gene, including duplication (duplicated_in_any), positive selection (possel), mitochondrial retargeting (mito_retargeting), loss (lost_in_any), co-loss (co-lost_in_, meaning that this gene is lost together with orthologs of the other CI loss events), orphan and the intersections between all these categories. For orphan genes, the top 5 <i>blastp</i> hits to the latest version of the <i>trembl</i> database are shown, which should help to understand if they are true orphans. 3) The codon adaptation index (CAI) of the gene and the one of the orthologs of the sister CI+ species (CI+ orthologs). 4) The results of subcellular localization prediction (performed using <i>deeploc</i>) where, for each location with a p &gt; 0.1, the probability of localization (pLoc) of the gene and the CI+ orthologs are shown. 5) The interproscan annotations of the genes, where each gene is one annotation. 6) The InterProScan annotation of all CI+ orthologs, where each line corresponds to one ortholog, and the annotations are delimited by “|”.