cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11839581.v1
title: Vaccarin hastens wound healing by promoting angiogenesis via activation of MAPK/ERK and PI3K/AKT signaling pathways in vivo

description: Abstract Purpose To explore the potential role and unclear molecular mechanisms of vaccarin in wound healing. Methods Rats’ skin excision model to study the effects of vaccarin on wound healing in vivo . Hematoxylin and eosin staining was performed to evaluate Histopathologic characteristics. Immunohistochemistry was employed to assess the effects of vaccarin in accelerating angiogenesis. Western blot was used to evaluate relative protein expressed levels. Results Vaccarin could significantly promote wound healing and endothelial cells and fibroblasts proliferation in the wound site. Immunohistochemistry and Western blot studies showed that the nodal proteins and receptor (bFGFR) related to angiogenesis signaling pathway were activated, and the microvascular density in the wound site was markedly higher than that in the control group. Conclusions The present study was the first to demonstrate that vaccarin is able to induce angiogenesis and accelerate wound healing in vivo by increasing expressions of p-Akt, p-Erk and p-bFGFR. This process is mediated by MAPK/ERK and PI3K/AKT signaling pathways.
DOI: 10.6084/m9.figshare.11839614.v1
title: Dynamic changes of periostin and collagen I in the sclera during progressive myopia in guinea pigs

description: ABSTRACT Purpose: To investigate periostin and collagen I expression during a scleral remodeling in myopic eyes and to determine their role in collagen remodeling of the myopic sclera. Methods: Fifty one-week-old guinea pigs were divided into the control and form-deprivation myopia (FDM) groups. The eyes of animals in the form-deprivation myopia group were covered for 2, 4, and 8 weeks, or were covered for 4 weeks and then uncovered for 2 weeks. The diopters and axial lengths in the eyes in each group of guinea pigs were measured. Immunohistochemistry and reverse transcription polymerase chain reaction were used to detect the relative protein and mRNA expressions of periostin and collagen I in the scleral tissues of guinea pig. Results: Before masking, guinea pigs in the control and form-deprivation myopia groups were hypermetropic and did not differ significantly (p&gt;0.05). Hypermetropic refraction in the control group gradually decreased. In guinea pigs from the form-deprivation myopia group, the refractive power gradually changed from +2.14 ± 0.33 D to -7.22 ± 0.51 D, and the axial length gradually changed from 5.92 ± 0.37 mm to 8.05 ± 0.34 mm from before until the end of masking. Before covering, no significant difference was observed in the relative collagen I and periostin mRNA and protein expression levels in the sclera of the guinea pig control and form-deprivation myopia groups (p&gt;0.05). The relative collagen I and periostin protein and mRNA expression levels in the sclera of guinea pigs in the form-deprivation myopia group at 2, 4, and 8 weeks, and after covering the eyes for 4 weeks followed by uncovering for 2 weeks, were significantly lower than those in the control group (p&lt;0.05). The collagen I and periostin mRNA expression levels were positively correlated with protein expression levels in the sclera of guinea pigs (protein: r=0.936, p&lt;0.05; mRNA: r=0.909, p&lt;0.05). Conclusions: Periostin was expressed in the myopic sclera of guinea pigs, and changes in periostin and collagen I expression were highly consistent. Periostin and collagen I may be involved in the regulation of scleral remodeling in myopia.
DOI: 10.6084/m9.figshare.18131137.v1
title: The role of Populus <i>MYB94</i> transcription factor in seed germination requires the expression of ABA-responsive genes

description: Plant seed germination is easily influenced by endogenous gene expression, hormones and environmental conditions. Here, we investigated a Populus R2R3-MYB transcription factor (referred to as <i>MYB94</i>) that plays a role in seed germination in close relation to the hormone abscisic acid (ABA). Two independent Arabidopsis transgenic lines overexpressing <i>MYB94</i> (Oe-lines) and wild-type (Wt) were no clear differences in the seed germination rates under normal conditions, but the germination rates of the two Oe-lines were both significantly delayed under ABA treatment. This delay in germination is most likely associated with the endogenous hormone abscisic acid (ABA). We find that the transcript levels of several representative genes in relation to ABA synthesis or signaling in the <i>MYB94 </i> Oe-lines showed significantly increased compared with those of the Wt plants. Taken together, our results here reveal the role of the Populus R2R3-MYB transcription factor <i>MYB94</i> in regulating the ABA-responsive genes in plant seed germination.
DOI: 10.6084/m9.figshare.21276706
title: Independent prognostic value of left ventricular mass index in patients with light-chain amyloidosis

description: Echocardiographic-determined left ventricular mass index (LVMI) provides quantitative information on left-ventricular structure. However, its prognostic value on light-chain (AL) amyloidosis has not been clearly defined. We included 99 patients with newly diagnosed AL amyloidosis between July 2013 and March 2022. Clinical features and echocardiographic parameters were collected. LVMI ≥113.4 g/m<sup>2</sup> was predictive for overall survival (OS) and progression-free survival (PFS) with respective hazard ratios (HRs) of 2.87 (95% CI: 1.04–7.79) and 2.91 (95% CI: 1.25–6.68). Patients in the LVMI-high group had higher NT-proBNP, cTnT, and FLC-diff levels. They were more likely to be cardiac involved and have increased mean left ventricular wall thickness, decreased left ventricular ejection fraction, and higher proportion of patients with pericardial effusion. In subgroup analysis, LVMI-high group was associated with a reduced OS [HR: 4.74 (95% CI: 1.26–17.77)] and PFS [HR: 7.16 (95% CI: 2.10–24.40)] in patients with cardiac amyloidosis (CA). Besides, LVMI-high was associated with a reduced OS [HR: 3.58 (95% CI: 1.17–11.02)] and PFS [HR: 4.79 (95% CI: 1.77–12.94), <i>p</i> = 0.00] among patients staged of II or III (Mayo 2004), as well as reduced OS [HR: 22.65 (95% CI: 1.66–299.31)] and PFS [HR: 18.73 (95% CI: 2.36–148.35)] among patients staged of III or IV (Mayo 2012). LVMI is a reliable prognostic indicator of survival. A cut-off of LVMI (113.4 g/m<sup>2</sup>) was prognostic for OS and PFS. Importantly, LVMI was able to identify a subset of patients with poorer prognosis in the context of CA or in the late stages according to the biomarker staging systems.
DOI: 10.6084/m9.figshare.11839614
title: Dynamic changes of periostin and collagen I in the sclera during progressive myopia in guinea pigs

description: ABSTRACT Purpose: To investigate periostin and collagen I expression during a scleral remodeling in myopic eyes and to determine their role in collagen remodeling of the myopic sclera. Methods: Fifty one-week-old guinea pigs were divided into the control and form-deprivation myopia (FDM) groups. The eyes of animals in the form-deprivation myopia group were covered for 2, 4, and 8 weeks, or were covered for 4 weeks and then uncovered for 2 weeks. The diopters and axial lengths in the eyes in each group of guinea pigs were measured. Immunohistochemistry and reverse transcription polymerase chain reaction were used to detect the relative protein and mRNA expressions of periostin and collagen I in the scleral tissues of guinea pig. Results: Before masking, guinea pigs in the control and form-deprivation myopia groups were hypermetropic and did not differ significantly (p&gt;0.05). Hypermetropic refraction in the control group gradually decreased. In guinea pigs from the form-deprivation myopia group, the refractive power gradually changed from +2.14 ± 0.33 D to -7.22 ± 0.51 D, and the axial length gradually changed from 5.92 ± 0.37 mm to 8.05 ± 0.34 mm from before until the end of masking. Before covering, no significant difference was observed in the relative collagen I and periostin mRNA and protein expression levels in the sclera of the guinea pig control and form-deprivation myopia groups (p&gt;0.05). The relative collagen I and periostin protein and mRNA expression levels in the sclera of guinea pigs in the form-deprivation myopia group at 2, 4, and 8 weeks, and after covering the eyes for 4 weeks followed by uncovering for 2 weeks, were significantly lower than those in the control group (p&lt;0.05). The collagen I and periostin mRNA expression levels were positively correlated with protein expression levels in the sclera of guinea pigs (protein: r=0.936, p&lt;0.05; mRNA: r=0.909, p&lt;0.05). Conclusions: Periostin was expressed in the myopic sclera of guinea pigs, and changes in periostin and collagen I expression were highly consistent. Periostin and collagen I may be involved in the regulation of scleral remodeling in myopia.
DOI: 10.6084/m9.figshare.19703720
title: Additional file 2 of Rice (Oryza sativa L.) cytochrome P450 protein 716A subfamily CYP716A16 regulates disease resistance

description: Additional file 2: Supplementary Table S1. The sequence data for the transcriptome.
DOI: 10.6084/m9.figshare.19703720.v1
title: Additional file 2 of Rice (Oryza sativa L.) cytochrome P450 protein 716A subfamily CYP716A16 regulates disease resistance

description: Additional file 2: Supplementary Table S1. The sequence data for the transcriptome.
DOI: 10.6084/m9.figshare.20226860
title: Additional file 26 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 26: Table S25. Correlation between quercetin 3-O-glucoside contents and expression profiles of genes in Chr. 5: 0-5 Mb in peach fruits at different developmental stages.
DOI: 10.6084/m9.figshare.20226869
title: Additional file 29 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 29: Table S28. Metabolite content changes in peach fruits after cold treatment.
DOI: 10.6084/m9.figshare.20226890
title: Additional file 3 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 3: Table S2. Widely targeted metabolite analysis in peach fruits.
DOI: 10.6084/m9.figshare.19703726
title: Additional file 4 of Rice (Oryza sativa L.) cytochrome P450 protein 716A subfamily CYP716A16 regulates disease resistance

description: Additional file 4: Supplementary Table S3. Differentially expressed metabolites in the leaves of the WT and CYP716A16-OE lines.
DOI: 10.6084/m9.figshare.20226809.v1
title: Additional file 10 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 10: Table S9. Statistics of lead SNPs associated with each metabolite in the two seasons.
DOI: 10.6084/m9.figshare.20226872
title: Additional file 2 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 2: Table S1. List of 252 peach accessions used in this study.
DOI: 10.6084/m9.figshare.6600155
title: Additional file 3: of Clinical and genetic characteristics of Chinese patients with familial or sporadic pediatric cataract

description: Table S3. Target NGS analysis. (XLS 28Â kb)
DOI: 10.6084/m9.figshare.6600170.v1
title: Additional file 4: of Clinical and genetic characteristics of Chinese patients with familial or sporadic pediatric cataract

description: Table S4. Pediatric cataract families with uncertain significance variants. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.12364205
title: Additional file 4 of Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

description: Additional file 4: Table S3. Tandem and segmental duplication gene pairs identified in TaASRs.
DOI: 10.6084/m9.figshare.12364205.v1
title: Additional file 4 of Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

description: Additional file 4: Table S3. Tandem and segmental duplication gene pairs identified in TaASRs.
DOI: 10.6084/m9.figshare.12364208.v1
title: Additional file 5 of Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

description: Additional file 5: Table S4. Gene structure of TaASR genes.
DOI: 10.6084/m9.figshare.11839581
title: Vaccarin hastens wound healing by promoting angiogenesis via activation of MAPK/ERK and PI3K/AKT signaling pathways in vivo

description: Abstract Purpose To explore the potential role and unclear molecular mechanisms of vaccarin in wound healing. Methods Rats’ skin excision model to study the effects of vaccarin on wound healing in vivo . Hematoxylin and eosin staining was performed to evaluate Histopathologic characteristics. Immunohistochemistry was employed to assess the effects of vaccarin in accelerating angiogenesis. Western blot was used to evaluate relative protein expressed levels. Results Vaccarin could significantly promote wound healing and endothelial cells and fibroblasts proliferation in the wound site. Immunohistochemistry and Western blot studies showed that the nodal proteins and receptor (bFGFR) related to angiogenesis signaling pathway were activated, and the microvascular density in the wound site was markedly higher than that in the control group. Conclusions The present study was the first to demonstrate that vaccarin is able to induce angiogenesis and accelerate wound healing in vivo by increasing expressions of p-Akt, p-Erk and p-bFGFR. This process is mediated by MAPK/ERK and PI3K/AKT signaling pathways.
DOI: 10.6084/m9.figshare.25232438
title: Increased biotic homogenisation in a montane plant-pollinator network over nearly a half-century

description: Data from historical and contemporary plant-pollinator networks in Aotearoa New Zealand.
DOI: 10.6084/m9.figshare.25232438.v1
title: Increased biotic homogenisation in a montane plant-pollinator network over nearly a half-century

description: Data from historical and contemporary plant-pollinator networks in Aotearoa New Zealand.
DOI: 10.6084/m9.figshare.19703813
title: Additional file 7 of VHL Ser65 mutations enhance HIF2α signaling and promote epithelial-mesenchymal transition of renal cancer cells

description: Additional file 7: Table S2. Primers sequences.
DOI: 10.6084/m9.figshare.12888569.v1
title: Analysis of clinical features of COVID-19 in cancer patients

description: Analysis of clinical features of COVID-19 in cancer patients
DOI: 10.6084/m9.figshare.20227015.v1
title: Additional file 6 of Integrated transcriptome and hormonal analysis of naphthalene acetic acid-induced adventitious root formation of tea cuttings (Camellia sinensis)

description: Additional file 6: Table S2. KEGG enrichment analysis of DEGs in the red-stem cutting groups.
DOI: 10.6084/m9.figshare.11839821.v1
title: Deformation and Solidification Characteristics and Microstructure of Arc Sprayed Ni-Al Composition Coatings

description: Droplets deformation and solidification characteristics in twin-wire arc sprayed Ni-Al were explored in depth. Both theoretical method and numerical model were established for calculating the deformation process of the droplets impacting on the substrate and their solidification behavior in airflow, which based on two models of the volume of fluid (VOF) dual-phase flow and the standard k-ε. The morphology and the microstructure of the composite coatings were analyzed by XRD, SEM and TEM. The results of the experiment indicate the droplets cooling rate ranges from 3.0×107 to 7.5×107 K/s. The main components of Ni-5wt.% Al coating were Ni solid solution, and a small number of Ni3Al4, Al2O3 and NiO. The main phases of Ni-20wt.% Al coating are Ni3Al and NiAl. EDS and TEM analysis shows that there are a few amorphous and equiaxed crystals in the Ni-Al coating. The surface roughness increases with the decrease of spraying pressure and spraying distance.
DOI: 10.6084/m9.figshare.19704050.v1
title: SNF5 promotes cell proliferation and immune evasion in non-small cell lung cancer

description: Immune evasion is the process that tumor cells accelerate growth and metastasis by evading the recognition and attack of immune cells. SNF5 is one of the core subunits of SWI/SNF, which is involved in the development of a variety of malignancies. However, the functions of SNF5 in Non-Small Cell Lung Cancer (NSCLC) and the mechanism of SNF5 regulates immune evasion are still unclear. Based on this, we analyzed the expression of SNF5 and overall survival of lung cancer tissues through the cancer genome atlas (TCGA) database. Then we performed genetic gain and loss of function experiments with SNF5 using lentivirus infection and siRNA in NSCLC A549 and NCI-H1299 cells, respectively. We investigated the proliferation and immune evasion of these cells. We further explored the mechanism of SNF5 on NSCLC cells immune evasion. Our data showed that SNF5 was significantly increased in lung cancer tissues than that in normal lung tissues. Furthermore, SNF5 promoted NSCLC cells proliferation and the expressions of immune evasion-related genes. Meantime, overexpressed SNF5 reduced mortality of A549 cells when co-cultured with T cells. Moreover, SNF5 regulated the immune evasion by activating the signal transducer and activator of transcription (STAT3)/ phospho-STAT3 pathway in NSCLC cells. Together, our results validate SNF5 as a tumor oncogene and provide a new target for NSCLC treatment.
DOI: 10.6084/m9.figshare.21801293
title: Optimal Planning of Hybrid DER Penetration in Distribution Network under Actual Geographical Condition: A Case Study

description: Integration of distributed energy resources into optimum location and a suitable size is still one of the major issues faced by electric utilities. In this article, a model is proposed that highlights the key issues of hybrid penetration and integrates renewable resources. In this context, optimization has been done that suggests the optimal combination of renewable energy sources based on cost and carbon emissions for the implementation of an integrated assessment of available energy resources. The proposed model is compared with grid-connected and various hybrid energy models. In addition to renewable penetration, the study also focused on significant reductions in greenhouse gas emissions. For analysis of the proposed approach, a study has been carried out on a selected test feeder named Ramchandrapura feeder of Kota, Rajasthan, India. The results obtained from the simulations include the optimal combination of cost-effective distributed energy resources considering actual weather conditions such as solar radiation, temperature, and wind speed. The overall optimization is done with the help of Homer-Pro software. The major contribution of the article is the economic study of test feeders with real geographic data which also considers the environmental impact of DER integration.
DOI: 10.6084/m9.figshare.7121528
title: Different response to middle-Palaeozoic magmatism during intracontinental orogenic processes: evidence from southeastern South China Block

description: Intracontinental orogens are major sites to better understand tectonic regime of plate interior. However, deep response to those processes remains poorly constrained due to the rare exposure of magmatic rocks. Middle-Palaeozoic magmatic rocks from the eastern Yangtze Block (EYB) and Cathaysia Block (CB) of the southeastern South China Block (SCB) have markedly unimodal age distribution with peaks at ~424 and ~438 Ma, respectively. The zircon saturation temperatures (T<sub>–Zr</sub>) range from 699 to 920°C, and increase in granitic rocks of younger age in the CB; however, most of the granitic T<sub>–Zr</sub> values in EYB are low and relatively uniform (643–855°C, most of them lower than 800°C). In CB, the Nd-Hf isotopic ratios of the granitic rocks (εNd(t) = – 13.2 to + 1.0; magmatic zircon εHf(t) = – 36 to + 12) are variable, nonetheless they clearly show the presence of a juvenile component. On the contrary, Nd isotopic ratios (εNd(t) = – 7.8 to + 1.6) of mafic rocks in EYB abruptly increase in rocks of younger age. Within the long-lived intracontinental orogenic processes of EYB and CB, consistent age peaks between metamorphism and magmatism and the abrupt increase in contributions of juvenile materials suggest that the thickened lithospheric roots were delaminated into asthenospheric mantle as many independent parts below the metamorphic domes in CB. The data suggest that the deep response to the intracontinental orogenic processes was strong non-uniform between EYB and CB in terms of magmatic period and contribution of mantle derived material to granitic magmas (related to the crustal reworking). We deduced that the combined influence of far-field stress transmission (derived from the convergence of Australia and the SCB), local delamination event in CB and different degree of reworking of the crustal sources, is the main reason to the different responses between EYB and CB.
DOI: 10.6084/m9.figshare.12364178.v1
title: Additional file 1 of Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

description: Additional file 1: Table S1. Sequences and ID loci information of ASRs in wheat and other species.
DOI: 10.6084/m9.figshare.12364187
title: Additional file 2 of Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

description: Additional file 2: Table S2. Primers used for qRT-PCR.
DOI: 10.5281/zenodo.10043460
title: Deep learning segmentation projects of FIB-SEM dataset of U2-OS cell

description: This submission includes ground truth datasets that were used to segment the nuclear envelope (NE), mitochondria, endoplasmic reticulum (ER) and Golgi from a human bone osteosarcoma epithelial cell (U2-OS) imaged using focused-ion beam scanning electron microscopy (FIB-SEM).
The full FIB-SEM dataset is deposited to EMPIAR (https://www.ebi.ac.uk/empiar, EMPIAR-11746). 
description: Training of convolutional neural network models and prediction of datasets were done in DeepMIB tool of Microscopy Image Browser (https://mib.helsinki.fi/)
description: For the full description see:

"Datasets and DeepMIB projects for segmentation of organelles of U2OS cell.pdf" document attached to this deposition
Explanation video on youtube.com (https://youtu.be/-IXB4Da9VMw)
DOI: 10.5281/zenodo.10043461
title: Deep learning segmentation projects of FIB-SEM dataset of U2-OS cell

description: This submission includes ground truth datasets that were used to segment the nuclear envelope (NE), mitochondria, endoplasmic reticulum (ER) and Golgi from a human bone osteosarcoma epithelial cell (U2-OS) imaged using focused-ion beam scanning electron microscopy (FIB-SEM).
The full FIB-SEM dataset is deposited to EMPIAR (https://www.ebi.ac.uk/empiar, EMPIAR-11746). 
description: Training of convolutional neural network models and prediction of datasets were done in DeepMIB tool of Microscopy Image Browser (https://mib.helsinki.fi/)
description: For the full description see:

"Datasets and DeepMIB projects for segmentation of organelles of U2OS cell.pdf" document attached to this deposition
Explanation video on youtube.com (https://youtu.be/-IXB4Da9VMw)
DOI: 10.6084/m9.figshare.12364208
title: Additional file 5 of Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

description: Additional file 5: Table S4. Gene structure of TaASR genes.
DOI: 10.6084/m9.figshare.12364220.v1
title: Additional file 8 of Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

description: Additional file 8: Table S7. Analysis of TF binding sites in the TaASR promoters.