cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19664162
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.9178421.v1
title: MOESM4 of Comparative transcriptome analysis reveals the genetic basis underlying the biosynthesis of polysaccharides in Hericium erinaceus

description: Additional file 4: Dataset 3. 13-co-existed genes involved in polysaccharides biosynthesis and 5 genes involved in fructose and mannose metabolism.
DOI: 10.26050/wdcc/rcm_cmip6_ssp245-hr
title: CMIP6 ScenarioMIP DKRZ MPI-ESM1-2-HR ssp245 - RCM-forcing data

description: Project: RCM forcing data from MPI-ESM1-2 (ECHAM6/JSBACH/MPIOM/HAMOCC) CMIP6 experiments - This project provides variables from MPI-ESM1-2 CMIP6 experiments performed by DKRZ, MPI-M and DWD in the context of the BMBF funded CMIP6 DICAD project (FKZ 01LP1605A). The experiments are described at https://www.wcrp-climate.org/wgcm-cmip/wgcm-cmip6 . Essential variables for regional climate modelling (RCM) are available. They are stored in native GRIB-format (e.g. spectral). The CMIP6 experiments have been performed with various model versions of MPI-ESM1-2. The low-resolution version MPI-ESM1-2-LR has been run with T63L47 (192 x 96 gridpoints; 47 vertical layers) for ECHAM6/JSBACH and GR15 (ca. 1.5 deg) of MPIOM/HAMOCC. The high-resolution version MPI-ESM1-2-HR has been run with T127L95 (384 x 192 gridpoints; 95 vertical layers) for ECHAM6/JSBACH and TP04 (tripolar grid, ca. 0.4 deg) of MPIOM/HAMOCC. CMIP6 ensemble members are named 'rNiNpNfN': rN is the realisation, iN is the initialisation method, pN stands for the parametrisation or physics variant and fN stands for the forcing variant of the experiment. Different experiment realisations (rN) differ with respect to their restart files. For each experiment-member five datasets are provided: 1 .._rcm_c5 contains: divergence, vorticity, and air temperature 2 .._rcm_c5_133 contains: specific_humidity and surface pressure 3 .._rcm_etc contains: cloud water/ice; land/sea surface - and ice temperature; sea ice thickness/area fraction; soil moisture content; snow thickness on sea ice 4 .._rcm_land contains: temperature (5 soil levels) 5 .._rcm_fx contains: land/sea - and glacier mask, orographie (as geopotential) and soil moisture at field capacity . Abbreviatons in the dataset-acronyms: echam6: eh6 jsbach: jsb The variables of frequency 6hrPt on model levels are contained in the first and second dataset. However, ua and va have to be calculated from divergence and vorticity (e.g. with 'cdo dv2uv ...'). Spectral to gridpoint transformation can be done with 'cdo sp2gp ...'. Summary: RCM forcing data from 2 realisations (r*i1p1f1) of the CMIP6/ScenarioMIP experiment ssp245, conducted with the MPI-ESM1-2-HR on the Mistral supercomputer of the DKRZ. The experiment covers the years 2015 to 2100 and branches from realisations of the CMIP6/CMIP historical experiment. The file format is gzip-compressed GRIB (*.grb.gz). ScenarioMIP website: https://cmip.ucar.edu/scenario-mip ScenarioMIP paper: https://doi.org/10.5194/gmd-9-3461-2016 Experiment description ssp245: SSP-based RCP scenario with medium radiative forcing by the end of the century. Following approximately RCP4.5 global forcing pathway with SSP2 socioeconomic conditions. Radiative forcing reaches a level of 4.5 W/m2 in 2100. Concentration-driven.
DOI: 10.5286/isis.e.rb1768021
title: Inelastic Neutron scattering studies of CaMn7O12 based multiferroic compounds

description: CaMn7O12 is an interesting multiferroic material showing colossal electric polarization below the magnetic transition despite its helical magnetic structure with screw axis. Recently, we have studied the sample by doping trivalent La at the Ca site and a large change in polarization is observed. The multiferroicity in CaMn7O12 is still a matter of debate and at least two possible mechanisms are mooted in the literature. We propose here to perform inelastic neutron scattering experiment on the polycrystalline samples to investigate the spin wave excitations in the parent CaMn7O12 compound and its La derivatives to resolve the issue. The experiment will probe several other novel properties such as spin-gap, crystal field anomalies and will help us to provide a microscopic picture of magnetic interactions pathways and their natture relative strength.
DOI: 10.6084/m9.figshare.8129558.v1
title: Additional file 6: of Biological and RNA regulatory function of MOV10 in mammalian germ cells

description: Table S7. Sequences of oligonucleotides used in this study. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7081901
title: Additional file 9: of Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing

description: Table S7. CircRNAs with protein-coding potential. (XLSX 42 kb)
DOI: 10.25345/c5ns0m80c
title: MassIVE MSV000093021 - GNPS - Exploring Oxylipin Diversity with NEO-MSMS
title: Paper title: From MS/MS Library Implementation to Molecular Networks: Exploring Oxylipin Diversity with NEO-MSMS Author List: Anis Elloumi, Lindsay Mas-Normand, Jamie Bride, Guillaume Reversat, Valerie Bultel-Ponce, Alexandre Guy, Camille Oger, Marie Demion, Jean-Yves Le Guennec, Thierry Durand, Claire Vigor, Angel Sanchez-Illana, Jean-Marie Galano Brief description of the data submitted: This dataset encompasses MS/MS data derived from pure non-enzymatic oxygenated metabolites of PUFAs (NEO-PUFA) and LC-MS/MS data dependent acquisition-based analysis (DDA) of in vitro free radical-induced oxidations encompassing diverse PUFAs and oxylipins. Additionally, it includes four serum samples and three microalgae samples as a proof of concept for the experimental methodology applied to real samples.
DOI: 10.6084/m9.figshare.12848435
title: Disability and Job Constraint in Post Civil War Cambodia

description: Using an augmented random utility model, we incorporate capability-associated constraints on the set of job choices to identify and estimate the reduced number of jobs due to disabilities – to show that capability disadvantages can be converted to a form of income through the compensation variation denoted as capability-equivalent income. We deliberately chose Cambodia for the empirical analysis, because the civil war and genocide that occurred in the 1970s in the country can be considered a ‘natural shock’. Based on the utility function and the estimated parameters, we simulate the amount of capability-equivalent income of individuals after being compensated for their capability disadvantage by taxing the top earners. We show that after the transfer, the inequality in terms of both income and welfare decreases, and the overall welfare increases.
DOI: 10.6084/m9.figshare.19664246.v1
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: 10.6084/m9.figshare.8129558
title: Additional file 6: of Biological and RNA regulatory function of MOV10 in mammalian germ cells

description: Table S7. Sequences of oligonucleotides used in this study. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.19663904
title: Expression of ATP-binding cassette subfamily B member 1 gene in peripheral blood of patients with acute myocardial infarction

description: This study aimed to determine the amount of expression of the <i>ATP-binding cassette subfamily B member 1 (ABCB1)</i> gene chip as a prospective diagnostic marker for acute myocardial infarction (AMI) in a wide population . In the AMI and control groups, 113 patients with AMI and 83 persons with non-coronary artery disease were selected for peripheral venous leukocyte collection. Western blot and real-time polymerase chain reaction (RT-PCR) were employed to detect relative <i>ABCB1</i> expression in both groups. The results showed that the <i>ABCB1</i> transcription and protein levels in the AMI group were higher than in the control. The relative mRNA expression of <i>ABCB1</i> was 0.26 (0.03–0.79) in the AMI group and 0.13 (0.01–0.52) in the control group (P &lt; 0.05). The expression of the <i>ABCB1</i> gene at the protein level in the AMI group was 1.65 times that in the control (P &lt; 0.05). Further, the subjects in the AMI group were older (P &lt; 0.001), had lower levels of high-density lipoprotein cholesterol (P = 0.038), and had higher incidence of type II diabetes mellitus (P = 0.003) compared with the control. Logistic regression analysis showed that the expression of <i>ABCB1</i> in peripheral blood was correlated with the occurrence of AMI (P = 0.003). High <i>ABCB1</i> expression, type II diabetes, and advanced age were found to serve as potential independent risk factors for AMI, with a 4.88-fold, 2.99-fold, and 2.63-fold increased risk of AMI. Overall, the high expression of <i>ABCB1</i> in peripheral blood might be related to the occurrence of AMI.
DOI: 10.6084/m9.figshare.7138748.v1
title: Additional file 6: of Identification, characterization and expression analysis of the VQ motif-containing gene family in tea plant (Camellia sinensis)

description: Table S5. List of predicted microRNAs targeting CsVQ genes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9178508.v1
title: Additional file 3: of FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation

description: SBR to FoxH1 peaks. (XLSX 76 kb)
DOI: 10.6084/m9.figshare.9178205
title: Additional file 3: of Improved the expression level of active transglutaminase by directional increasing copy of mtg gene in Pichia pastoris

description: Figures S2, S3. Secondary structure diagram of mRNA of mtg and pro. Figure S2. The secondary structure diagram of mRNA of mtg-WT and mtg-Opt. Figure S3. The secondary structure diagram of mRNA of pro-WT and pro-Opt. (ZIP 93 kb)
DOI: 10.6084/m9.figshare.9178205.v1
title: Additional file 3: of Improved the expression level of active transglutaminase by directional increasing copy of mtg gene in Pichia pastoris

description: Figures S2, S3. Secondary structure diagram of mRNA of mtg and pro. Figure S2. The secondary structure diagram of mRNA of mtg-WT and mtg-Opt. Figure S3. The secondary structure diagram of mRNA of pro-WT and pro-Opt. (ZIP 93 kb)
DOI: 10.6084/m9.figshare.11276222
title: The plant-type phospho<i>enol</i>pyruvate carboxylase Gmppc2 is developmentally induced in immature soy seeds at the late maturation stage: a potential protein biomarker for seed chemical composition

description: Phospho<i>enol</i>pyruvate carboxylase (PEPC) is a carbon-fixing enzyme with critical roles in seed development. Previously we observed a positive correlation between PEPC activity and protein content in mature seeds among soybean cultivars and varietal differences of PEPC activity in immature seeds, which is concordant with seed protein accumulation. Here, we report a PEPC isoform (Gmppc2) which is preferentially expressed in immature soybean seeds at the late maturation stage. <i>Gmppc2</i> was co-expressed with enzyme genes involved in starch degradation: <i>α-amylase, hexokinase</i>, and <i>α-glucan phosphorylase. Gmppc2</i> was developmentally induced in the external seed coats, internal seed coats, hypocotyls, and cotyledons at the late maturation stage. The expression of Gmppc2 protein was negatively regulated by the application of a nitrogen fertilizer, which suppressed nodule formation. These results imply that Gmppc2 is involved in the metabolism of nitrogen originated from nodules into seeds, and Gmppc2 might be applicable as a biomarker of seed protein content. <b>Abbreviations:</b> PEP: phospho<i>enol</i>pyruvate; PEPC: phospho<i>enol</i>pyruvate carboxylase; RNA-Seq: RNA sequencing; PCA: principal component analysis; SE: standard error A hypothetical model which represents the metabolism in Immature soybean seeds at the late maturation stage. In this model, PEPC (Gmppc2) acts on provision of oxaloacetate for biosynthesis of amino acids that were coordinately originated from vegetative organs.
DOI: 10.6084/m9.figshare.11276222.v1
title: The plant-type phospho<i>enol</i>pyruvate carboxylase Gmppc2 is developmentally induced in immature soy seeds at the late maturation stage: a potential protein biomarker for seed chemical composition

description: Phospho<i>enol</i>pyruvate carboxylase (PEPC) is a carbon-fixing enzyme with critical roles in seed development. Previously we observed a positive correlation between PEPC activity and protein content in mature seeds among soybean cultivars and varietal differences of PEPC activity in immature seeds, which is concordant with seed protein accumulation. Here, we report a PEPC isoform (Gmppc2) which is preferentially expressed in immature soybean seeds at the late maturation stage. <i>Gmppc2</i> was co-expressed with enzyme genes involved in starch degradation: <i>α-amylase, hexokinase</i>, and <i>α-glucan phosphorylase. Gmppc2</i> was developmentally induced in the external seed coats, internal seed coats, hypocotyls, and cotyledons at the late maturation stage. The expression of Gmppc2 protein was negatively regulated by the application of a nitrogen fertilizer, which suppressed nodule formation. These results imply that Gmppc2 is involved in the metabolism of nitrogen originated from nodules into seeds, and Gmppc2 might be applicable as a biomarker of seed protein content. <b>Abbreviations:</b> PEP: phospho<i>enol</i>pyruvate; PEPC: phospho<i>enol</i>pyruvate carboxylase; RNA-Seq: RNA sequencing; PCA: principal component analysis; SE: standard error A hypothetical model which represents the metabolism in Immature soybean seeds at the late maturation stage. In this model, PEPC (Gmppc2) acts on provision of oxaloacetate for biosynthesis of amino acids that were coordinately originated from vegetative organs.
DOI: 10.6084/m9.figshare.25143731
title: Supplementary Material for: Severe aldosterone synthase deficiency in a nine-day old Lebanese boy: the importance of functional studies to establish pathogenicity of seemingly benign variants in CYP11B2

description: Introduction
Aldosterone synthase deficiency is a rare autosomal recessive disease characterized by vomiting, dehydration, salt wasting, life-threatening hyperkalemia in infancy, followed by failure to thrive. It results from pathogenic variants in CYP11B2. 
Case Presentation
A boy, born in Montreal to Lebanese parents who are first cousins, was referred at nine days of life for severe dehydration. A diagnosis of primary adrenal insufficiency was made, and treatment was started with fludrocortisone and hydrocortisone. Exome sequencing revealed a homozygous variant p.(Asn201Asp)(N201D). In silico, this variant was considered benign, but in vitro functional expression studies established it caused the severe aldosterone deficiency. It ended the diagnostic odyssey and allowed to safely stop hydrocortisone replacement.
Conclusion
If a gene variant co-segregates with a phenotype, in vitro functional studies are required even if in silico studies are negative
DOI: 10.6084/m9.figshare.8129660.v1
title: Additional file 4: of A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

description: The results of GO and KEGG enrichment analysis in prostate cancer. (XLSX 112 kb)
DOI: 10.6084/m9.figshare.19663820.v1
title: Additional file 8 of The Bursaphelenchus xylophilus effector BxML1 targets the cyclophilin protein (CyP) to promote parasitism and virulence in pine

description: Additional file 8.
DOI: 10.6084/m9.figshare.8129648.v1
title: Additional file 2: of A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

description: The results of GO and KEGG enrichment analysis in lung cancer. (XLSX 114 kb)
DOI: 10.26050/wdcc/rcm_cmip6_ssp585-hr_r1i1p1f1
title: CMIP6 ScenarioMIP DKRZ MPI-ESM1-2-HR ssp585_r1i1p1f1 - RCM-forcing data

description: Project: RCM forcing data from MPI-ESM1-2 (ECHAM6/JSBACH/MPIOM/HAMOCC) CMIP6 experiments - This project provides variables from MPI-ESM1-2 CMIP6 experiments performed by DKRZ, MPI-M and DWD in the context of the BMBF funded CMIP6 DICAD project (FKZ 01LP1605A). The experiments are described at https://www.wcrp-climate.org/wgcm-cmip/wgcm-cmip6 . Essential variables for regional climate modelling (RCM) are available. They are stored in native GRIB-format (e.g. spectral). The CMIP6 experiments have been performed with various model versions of MPI-ESM1-2. The low-resolution version MPI-ESM1-2-LR has been run with T63L47 (192 x 96 gridpoints; 47 vertical layers) for ECHAM6/JSBACH and GR15 (ca. 1.5 deg) of MPIOM/HAMOCC. The high-resolution version MPI-ESM1-2-HR has been run with T127L95 (384 x 192 gridpoints; 95 vertical layers) for ECHAM6/JSBACH and TP04 (tripolar grid, ca. 0.4 deg) of MPIOM/HAMOCC. CMIP6 ensemble members are named 'rNiNpNfN': rN is the realisation, iN is the initialisation method, pN stands for the parametrisation or physics variant and fN stands for the forcing variant of the experiment. Different experiment realisations (rN) differ with respect to their restart files. For each experiment-member five datasets are provided: 1 .._rcm_c5 contains: divergence, vorticity, and air temperature 2 .._rcm_c5_133 contains: specific_humidity and surface pressure 3 .._rcm_etc contains: cloud water/ice; land/sea surface - and ice temperature; sea ice thickness/area fraction; soil moisture content; snow thickness on sea ice 4 .._rcm_land contains: temperature (5 soil levels) 5 .._rcm_fx contains: land/sea - and glacier mask, orographie (as geopotential) and soil moisture at field capacity . Abbreviatons in the dataset-acronyms: echam6: eh6 jsbach: jsb The variables of frequency 6hrPt on model levels are contained in the first and second dataset. However, ua and va have to be calculated from divergence and vorticity (e.g. with 'cdo dv2uv ...'). Spectral to gridpoint transformation can be done with 'cdo sp2gp ...'. Summary: RCM forcing data from the 1st realisation (r1i1p1f1) of the CMIP6/ScenarioMIP experiment ssp585, conducted with the MPI-ESM1-2-HR on the Mistral supercomputer of the DKRZ. The experiment covers the years 2015 to 2100 and branches from realisations of the CMIP6/CMIP historical experiment. The file format is gzip-compressed GRIB (*.grb.gz). ScenarioMIP website: https://cmip.ucar.edu/scenario-mip ScenarioMIP paper: https://doi.org/10.5194/gmd-9-3461-2016 Experiment description ssp585: SSP-based RCP scenario with high radiative forcing by the end of the century. Following approximately RCP8.5 global forcing pathway with SSP5 socioeconomic conditions. Radiative forcing reaches a level of 8.5 W/m2 in 2100. Concentration-driven.
DOI: 10.6084/m9.figshare.9178517.v1
title: Additional file 4: of FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation

description: Microarray vs. ChIP. (XLSX 778 kb)
DOI: 10.5281/zenodo.8145252
title: Quantifying the linkage between SMAP soil moisture and fully-integrated hydrologic simulations

description: This dataset contains soil moisture (SM) (over multiple layers between 0‒100 cm depth) and groundwater (GW) storage simulated by a high resolution fully-integrated surface water - groundwater model HydroGeoSphere (HGS) over the South Nation Watershed (SNW) in eastern Canada. The dataset also provides the near-surface soil moisture (SSM) and Soil Water Index (SWI) derived from the Soil Moisture Active and Passive (SMAP) enhanced L3 radiometer 9 km EASE-grid SM (SPL3SMP_E) version 5 product. The temporal coverage for all data is from March 31, 2015 to December 31, 2017.
DOI: 10.6084/m9.figshare.8129654.v1
title: Additional file 3: of A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

description: The results of GO and KEGG enrichment analysis in breast cancer. (XLSX 147 kb)
DOI: 10.17043/zinke-2023-baltic-emissions-1
title: Comparison of aerosol eddy covariance fluxes and chamber-simulated sea spray emissions from the Baltic Sea