cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11703033.v1
title: Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy

description: Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (<i>Atg5</i> or <i>Ulk1/Ulk2</i>) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of <i>CALCOCO1</i> disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway. <b>Abbreviations:</b> ATG: autophagy-related; CALCOCO1: calcium binding and coiled-coil domain protein 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain protein 2; CLIR: MAP1LC3C-interacting region; CQ: chloroquine; KO: knockout; LIR: MAP1LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MLN: MLN0128 ATP-competitive MTOR kinase inhibitor; MTOR: mechanistic target of rapamycin kinase; reticulophagy: selective autophagy of the endoplasmic reticulum; TAX1BP1/CALCOCO3: TAX1 binding protein 1; ULK: unc 51-like autophagy activating kinase; WT: wild-type.
DOI: 10.6084/m9.figshare.14318159.v1
title: Nigella sativa ameliorates oxidative stress induced adverse effects in rodent modeling studies: Indices of serum chemistry and hematology

description: Abstract In this era, various traditional medicinal herbs were researched for their toxicological and safety aspects. The present study focused on using Nigella sativa fixed (NSFO) and essential oil (NSEO) to mitigate the adverse consequences of oxidative stress. For the purpose, oxidative stress was induced in Sprague Dawley rats using potassium bromate injection. The effect of NSFO and NSEO on indices of serum chemistry and hematology were studied. The results indicated that potassium bromate imparted drastic changes in serum chemistry and hematology e.g. it increased the blood cholesterol and blood glucose along with decreasing the insulin secretion. Oxidative stress also influenced the hematological attributes negatively but experimental diets were slightly successful in normalizing the values. The experimental diets especially essential oil that contains significant quantities of thymoquinone modulated the adverse consequences of oxidative stress with special reference to hematology and serological attributes. In the nutshell, NSFO and NSEO hold potential to mitigate the oxidative stress, and improved various serological and hematological attributes.
DOI: 10.6084/m9.figshare.20085520.v1
title: Rank-based Greedy Model Averaging for High-Dimensional Survival Data

description: Model averaging is an effective way to enhance prediction accuracy. However, most previous works focus on low-dimensional settings with completely observed responses. To attain an accurate prediction for the risk effect of survival data with high-dimensional predictors, we propose a novel method: <b>r</b>ank-based <b>g</b>reedy (RG) model averaging. Specifically, adopting the transformation model with splitting predictors as working models, we doubly utilize the smooth concordance index function to derive the candidate predictions and optimal model weights. The final prediction is achieved by weighted averaging all the candidates. Our approach is flexible, computationally efficient, and robust against model misspecification, as it neither requires the correctness of a joint model nor involves the estimation of the transformation function. We further adopt the greedy algorithm for high dimensions. Theoretically, we derive an asymptotic error bound for the optimal weights under some mild conditions. In addition, the summation of weights assigned to the correct candidate submodels is proven to approach one in probability when there are correct models included among the candidate submodels. Extensive numerical studies are carried out using both simulated and real datasets to show the proposed approach’s robust performance compared to the existing regularization approaches.
DOI: 10.6084/m9.figshare.6978368
title: Additional file 2: of Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

description: Minimum, maximum and mean values of phenotypic traits measured in the parents (Carrera and CDC Striker) and the PR-07 population. (XLS 19 kb)
DOI: 10.6084/m9.figshare.6978395
title: Additional file 4: of Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

description: Combined correlation eoefficients between phenotypes measured in PR-02 RIL population in six trials. (XLS 7 kb)
DOI: 10.6084/m9.figshare.6978368.v1
title: Additional file 2: of Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

description: Minimum, maximum and mean values of phenotypic traits measured in the parents (Carrera and CDC Striker) and the PR-07 population. (XLS 19 kb)
DOI: 10.6084/m9.figshare.16935698.v1
title: Additional file 5 of Model constructions of chemosensitivity and prognosis of high grade serous ovarian cancer based on evaluation of immune microenvironment and immune response

description: Additional file 5: Table S5. Primer Sequences in RT-qPCR.
DOI: 10.6084/m9.figshare.6978191
title: Additional file 7: of Aberrantly expressed messengerÂ RNAs and long noncoding RNAs in degenerative nucleus pulposus cells co-cultured with adipose-derived mesenchymal stem cells

description: Full list of differentially expressed mRNAs and lncRNAs. (XLSX 1394 kb)
DOI: 10.6084/m9.figshare.6978353.v1
title: Additional file 1: of Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

description: Minimum, maximum and mean values of phenotypic traits measured in the parents (Orb and CDC Striker) and the PR-02 population. (XLS 14 kb)
DOI: 10.6084/m9.figshare.13269855.v1
title: Additional file 4 of Correction to: ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing

description: Additional file 4: Dataset S1.
DOI: 10.6084/m9.figshare.6978395.v1
title: Additional file 4: of Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

description: Combined correlation eoefficients between phenotypes measured in PR-02 RIL population in six trials. (XLS 7 kb)
DOI: 10.6084/m9.figshare.13269855
title: Additional file 4 of Correction to: ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing

description: Additional file 4: Dataset S1.
DOI: 10.6084/m9.figshare.14318497.v1
title: Cooking fuel and the risk of pregnancy-induced hypertension in Lanzhou, China: A birth cohort study

description: Abstract Background The relationship between the solid fuels and the occurrence of pregnancy-induced hypertension (PIH) is inconclusive. Methods A birth cohort study of 10,452 pregnant women without chronic hypertension was conducted from 2010 to 2012 at the Gansu Provincial Maternity and Child Care Hospital in Lanzhou, China. Multivariable logistic regression models were used to assess the relationship. Results Compared to pregnant women using gas as cooking fuel, pregnant women using coal (OR=2.55, 95% CI: 1.85-3.51)and biomass (OR=3.58, 95% CI: 2.29-5.60) were associated with an increased risk of PIH, gestational hypertension (biomass: OR=3.38, 95% CI: 1.68-6.80), and preeclampsia (coal: OR=2.89, 95% CI: 1.98-4.21; biomass: OR=3.38, 95% CI: 1.95-5.84).The relationship between cooking fuel and PIH is modified by maternal age(p&lt;0.0001), pre-pregnancy BMI (p&lt;0.0001), gestational weigh gain(p&lt;0.0001), parity(p&lt;0.0001), and multiple birth (p&lt;0.0001). Conclusions During pregnancy, exposure to coal or biomass was associated with an increased risk of PIH and preeclampsia.
DOI: 10.6084/m9.figshare.21129973
title: Additional file 2 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

description: Additional file 2.
DOI: 10.6084/m9.figshare.7508870.v1
title: Parametric Model Method and Deployment Simulation of Inflatable Antenna Structures

description: ABSTRACT: In this paper, we develop a parametric model method and simulate the deployment mechanism of inflatable antenna structures. Different folded methods are developed for the primary members of inflatable antenna structures, which include inflatable tubes, an inflatable torus, a reflector etc. The unstressed configuration and the folded configuration of these members are modeled parametrically using the developed folded methods. A simulation software is developed for the deployment mechanism of inflatable structures by the improved spring-mass system. The driving forces in the deployment process, i.e. the gas pressure and the moment of the fold hinges, are analyzed for each member. During the development process, self-contact or collision with the membrane occurs. A rule for identifying self-contact elements is applied, and a penalty function method is developed to solve this challenging problem. Finally, the equation of motion is solved using finite difference method. The developed simulation software is validated by simulating a cylindrical inflatable tube that is folded in half, and the simulation agrees well with the experiment. The deployment mechanism of the antenna model similar to that for the Inflatable Antenna Experiment (IAE) is modeled, analyzed and estimated. The deployed configurations and the dynamic parameters of each node are obtained. The numerical simulation results show that the simulation software for the deployment mechanism can correctly predict the deployment process of inflatable antenna structures.
DOI: 10.6084/m9.figshare.21129975.v1
title: Additional file 4 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

description: Additional file 4.
DOI: 10.6084/m9.figshare.7502765
title: Additional file 2: of Multiple transcription factors contribute to inter-chromosomal interaction in yeast

description: Table is for Bootstrap result of 105 TFs from multivariate method. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.7502801.v1
title: Additional file 6: of Multiple transcription factors contribute to inter-chromosomal interaction in yeast

description: Table is for the result of 105 TFs conducted by â Test For Trend In Proportionsâ (prop.trend.test function in R). (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6978401
title: Additional file 5: of Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

description: Combined correlation eoefficients between phenotypes measured in PR-07 RIL population. (XLS 15 kb)
DOI: 10.6084/m9.figshare.6978401.v1
title: Additional file 5: of Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

description: Combined correlation eoefficients between phenotypes measured in PR-07 RIL population. (XLS 15 kb)
DOI: 10.6084/m9.figshare.16935725
title: Additional file 1 of Physiological and proteomic analyses revealed the response mechanisms of two different drought-resistant maize varieties

description: Additional file 1: Table S1. Drought-responsive maize seedling leaf proteins observed specifically in tolerant variety SD609 and sensitive variety SD902, respectively; Differentially expressed proteins shared by two varieties under drought stress. Table S2. Corresponding genes of drought-stress responsive maize leaf identified proteins specific primers sequence.
DOI: 10.6084/m9.figshare.7502807
title: Additional file 7: of Multiple transcription factors contribute to inter-chromosomal interaction in yeast

description: Table contains the comparison between the top results of three approaches. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.13265694
title: Additional file 11 of Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

description: Additional file 11. Genes with Ka/Ks ratio &gt; 1 in Asian and European cultivated and wild pear groups.
DOI: 10.6084/m9.figshare.16415714
title: Up-regulation of miR-663a inhibits the cancer stem cell-like properties of glioma via repressing the KDM2A-mediated TGF-β/SMAD signaling pathway

description: Emerging reports have shown that microRNAs (miRNAs) function as vital regulators in tumor development via modulating gene expression at the posttranscriptional level. Here, we explored the role and underlying mechanism of miR-663a in the proliferation, migration, invasion, and cancer stem cell-like (CSC) properties of glioma cells. Quantitative reverse transcription PCR (qRT‐PCR) was implemented to detect miR-663a expression in glioblastoma tissues and the adjacent normal tissues. Additionally, gain- and loss-of-function assays of miR-633a were performed on U-251 MG cells or human primary glioblastoma cancer cells (pGBMC1). Cell proliferation, migration, invasion, CSC properties, and profiles of stem cell markers (including CD133, CD44) were examined by the MTT assay, Transwell assay, tumorsphere experiment, and Western blotting, respectively. The dual-luciferase reporter gene assay was performed to testify the targeted relationship between miR-663a and lysine demethylase 2A (KDM2A). The results showed that miR-663a was down-regulated in glioblastoma tissues and cells. Overexpressing miR-663a repressed the proliferation, migration, invasion, CSC properties of U-251 MG cells and pGBMC1, while miR-663a knockdown had the opposite effects. The <i>in-vivo</i> experiment confirmed that miR-663a repressed the growth of U-251 MG cells in nude mice. When cocultured with THP1 cells, U-251 MG cells gained enhanced proliferation, migration, invasion, and CSC properties. MiR-633a overexpression reversed THP1-mediated effects on U-251 MG cells, and reduced the “M2” polarization of THP1 cells. What’s more, Mechanistically, KDM2A was targeted by miR-663a. KDM2A knockdown suppressed the progression and CSC properties of U-251 MG cells <i>in vitro</i>, and dampened TGF-β. Overall, those data revealed that up-regulating miR-663a reduced glioma progression by inhibiting the KDM2A-mediated TGF-β/Smad pathway.
DOI: 10.6084/m9.figshare.13265694.v1
title: Additional file 11 of Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

description: Additional file 11. Genes with Ka/Ks ratio &gt; 1 in Asian and European cultivated and wild pear groups.
DOI: 10.6084/m9.figshare.13265703
title: Additional file 14 of Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

description: Additional file 14. NBS-encoding genes in a sorted physical genome order. Genomic and coding sequences of 338 genes genomic were combined into a long sequence with the sorted order, respectively.
DOI: 10.6084/m9.figshare.13265703.v1
title: Additional file 14 of Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

description: Additional file 14. NBS-encoding genes in a sorted physical genome order. Genomic and coding sequences of 338 genes genomic were combined into a long sequence with the sorted order, respectively.
DOI: 10.6084/m9.figshare.13269948
title: A new fungus-mediated RNAi method established and used to study the fatty acid and retinol binding protein function of the plant-parasitic nematode <i>Aphelenchoides besseyi</i>

description: RNA interference (RNAi) is a powerful tool for gene functional analysis of plant-parasitic nematodes (PPNs). RNAi involving soaking in a dsRNA solution and <i>in planta</i> methods is commonly applied in the study of gene function in PPNs. However, certain problems restrict the application of these methods. Therefore, more convenient and effective RNAi methods need to be established for different PPNs according to their biological characteristics. In this study, the fatty acid and retinoid binding protein genes (<i>Ab-far-1, Ab-far-4</i>, and combinatorial <i>Ab-far-1</i> and <i>Ab-far-4</i>) of the rice white tip nematode (RWTN), <i>Aphelenchoides besseyi</i>, were used as target genes to construct a fungal RNAi vector, and the <i>Ab-far-n</i> dsRNA transgenic <i>Botrytis cinerea</i> (ARTB<i>n</i>) were generated using <i>Agrobacterium</i>-mediated transformation technology. After RWTN feeding on ARTB<i>n</i>, the expression of <i>Ab-far-1</i> and <i>Ab-far-4</i> in the nematodes was efficiently silenced, and the reproduction and pathogenicity of the nematodes were clearly inhibited. The <i>Ab-far-1</i> and <i>Ab-far-4</i> co-RNAi effects were better than the effects when each gene was individually targeted with RNAi. Additionally, the RNAi induced when RWTNs fed on ARTB<i>1</i> were persistent and heritable. Thus, a new method of fungus-mediated RNAi was established for fungivorous PPNs and was verified as effective and applicable to the study of nematode gene function. This technique will remove the technological bottlenecks and provide a new method to studying the multiple genes with polygene co-RNAi in fungivorous PPNs. This study also provides a theoretical basis and new thought for further study of the gene function in PPNs. <b>Abbreviations:</b> FAR(Fatty acid and retinol-binding proteins); RWTN (The rice white tip nematode, <i>Aphelenchoides besseyi); Ab-far-n</i> (Fatty acid and retinol binding protein gene of <i>A. besseyi)</i>; ARTB<i>1</i> (<i>Ab-far-1</i> hpRNA transgenic <i>Botrytis cinerea</i>); ARTB<i>4</i> (<i>Ab-far-4</i> hpRNA transgenic <i>Botrytis cinerea</i>); ARTB<i>1</i>/<i>4</i> (combinatorial <i>Ab-far-1</i> and <i>Ab-far-4</i> hpRNA transgenic <i>B. cinerea</i>); EVTB (Empty vector transgenic <i>B. cinerea</i>); GRTB (eGFP hpRNA transgenic <i>B. cinerea</i>); WTB (Wild-type <i>B. cinerea</i>).
DOI: 10.6084/m9.figshare.7502738.v1
title: Additional file 2: of The miRNAome of ramie (Boehmeria nivea L.): identification, expression, and potential roles of novel microRNAs in regulation of cadmium stress response

description: Sheet 1. Sequence and ID of the 73 novel miRNAs identified in the present study. CL, Cd-free leaf (control); TL, Cd-treated leaf; CR, Cd-free root (control); TR, Cd-treated root. Sheet 2. Families matched by seven of the 73 novel miRNAs. Sheet 3. Differentially expressed novel miRNAs. The green color denotes differentially expressed miRNAs in the leaf and root samples. The yellow and red color denote unique miRNAs expressed in the leaf and root samples, respectively. Sheet 4. Predicted genes targeted by the novel miRNAs from the leaf library. Sheet 5. Predicted genes targeted by the novel miRNAs from the root library. (XLSX 5524â kb)
DOI: 10.6084/m9.figshare.7502897
title: Additional file 2: of High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

description: Table S2. The sequencing depth of 2b-RAD. (XLSX 31427 kb)
DOI: 10.34740/kaggle/dsv/7613281
title: Global Game Jam Dataset
DOI: 10.6084/m9.figshare.16935696.v1
title: Additional file 10 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height

description: Additional file 10: Table S9. Statistics of annotated non-coding RNAs.
DOI: 10.6084/m9.figshare.7502945
title: Additional file 7: of High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

description: Table S8. The position information of SNP markers in the linkage group. (XLSX 170 kb)
DOI: 10.6084/m9.figshare.7502753.v1
title: Additional file 1: of Multiple transcription factors contribute to inter-chromosomal interaction in yeast

description: Table is for the result of 105 TFs from Chi-square approach. (XLSX 34Â kb)
DOI: 10.6084/m9.figshare.7502765.v1
title: Additional file 2: of Multiple transcription factors contribute to inter-chromosomal interaction in yeast

description: Table is for Bootstrap result of 105 TFs from multivariate method. (XLSX 13Â kb)
DOI: 10.5281/zenodo.5768828
title: How to Build an Image Processing Pipeline for Automating Multiparameter Histocytometry Analysis

description: Image files for evaluation of an upcoming Current Protocols submission, as well as associated reference files.
DOI: 10.5281/zenodo.5781785
title: Non-intrusive semi-analytical uncertainty quantification using Bayesian quadrature with application to CFD simulations

description: The data contained in the uploaded '.zip' file is for some of the plots in the paper ‘Duan Y*, Eaton MD, Bluck MJ, 2021, Non-intrusive semi-analytical uncertainty quantification using Bayesian quadrature with application to CFD simulations, International Journal of Heat and Fluid Flow.’ (accepted)
DOI: 10.5281/zenodo.5781784
title: Non-intrusive semi-analytical uncertainty quantification using Bayesian quadrature with application to CFD simulations

description: The data contained in the uploaded '.zip' file is for some of the plots in the paper ‘Duan Y*, Eaton MD, Bluck MJ, 2021, Non-intrusive semi-analytical uncertainty quantification using Bayesian quadrature with application to CFD simulations, International Journal of Heat and Fluid Flow.’ (accepted)
DOI: 10.5517/ccdc.csd.cc28pkm5
title: CCDC 2106097: Experimental Crystal Structure Determination

description: Related Article: Jian-Quan Liu|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc28py53
title: CCDC 2106455: Experimental Crystal Structure Determination

description: Related Article: Lin Yang, Bruce M. Foxman|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc28py64
title: CCDC 2106456: Experimental Crystal Structure Determination

description: Related Article: Lin Yang, Bruce M. Foxman|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc28py86
title: CCDC 2106458: Experimental Crystal Structure Determination

description: Related Article: Lin Yang, Bruce M. Foxman|2021|CSD Communication|||