cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7491626
title: An Interactive Greedy Approach to Group Sparsity in High Dimensions

description: Sparsity learning with known grouping structure has received considerable attention due to wide modern applications in high-dimensional data analysis. Although advantages of using group information have been well-studied by shrinkage-based approaches, benefits of group sparsity have not been well-documented for greedy-type methods, which much limits our understanding and use of this important class of methods. In this paper, generalizing from a popular forward-backward greedy approach, we propose a new interactive greedy algorithm for group sparsity learning and prove that the proposed greedy-type algorithm attains the desired benefits of group sparsity under high dimensional settings. An estimation error bound refining other existing methods and a guarantee for group support recovery are also established simultaneously. In addition, we incorporate a general M-estimation framework and introduce an interactive feature to allow extra algorithm flexibility without compromise in theoretical properties. The promising use of our proposal is demonstrated through numerical evaluations including a real industrial application in human activity recognition at home. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7491626.v1
title: An Interactive Greedy Approach to Group Sparsity in High Dimensions

description: Sparsity learning with known grouping structure has received considerable attention due to wide modern applications in high-dimensional data analysis. Although advantages of using group information have been well-studied by shrinkage-based approaches, benefits of group sparsity have not been well-documented for greedy-type methods, which much limits our understanding and use of this important class of methods. In this paper, generalizing from a popular forward-backward greedy approach, we propose a new interactive greedy algorithm for group sparsity learning and prove that the proposed greedy-type algorithm attains the desired benefits of group sparsity under high dimensional settings. An estimation error bound refining other existing methods and a guarantee for group support recovery are also established simultaneously. In addition, we incorporate a general M-estimation framework and introduce an interactive feature to allow extra algorithm flexibility without compromise in theoretical properties. The promising use of our proposal is demonstrated through numerical evaluations including a real industrial application in human activity recognition at home. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8015969
title: A Sparse Random Projection-Based Test for Overall Qualitative Treatment Effects

description: In contrast to the classical “one-size-fits-all” approach, precision medicine proposes the customization of individualized treatment regimes to account for patients’ heterogeneity in response to treatments. Most of existing works in the literature focused on estimating optimal individualized treatment regimes. However, there has been less attention devoted to hypothesis testing regarding the existence of overall qualitative treatment effects, especially when there are a large number of prognostic covariates. When covariates do not have qualitative treatment effects, the optimal treatment regime will assign the same treatment to all patients regardless of their covariate values. In this article, we consider testing the overall qualitative treatment effects of patients’ prognostic covariates in a high-dimensional setting. We propose a sample splitting method to construct the test statistic, based on a nonparametric estimator of the contrast function. When the dimension of covariates is large, we construct the test based on sparse random projections of covariates into a low-dimensional space. We prove the consistency of our test statistic. In the regular cases, we show the asymptotic power function of our test statistic is asymptotically the same as the “oracle” test statistic which is constructed based on the “optimal” projection matrix. Simulation studies and real data applications validate our theoretical findings. Supplementary materials for this article are available online.
DOI: 10.5281/zenodo.10642534
title: MoCA evaluated and improved versions for all cases
DOI: 10.5281/zenodo.10642535
title: MoCA evaluated and improved versions for all cases
DOI: 10.6084/m9.figshare.12731415
title: Additional file 2 of Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

description: Additional file 2: Table S2. Binning results for CAMI-low datasets.
DOI: 10.6084/m9.figshare.12731424
title: Additional file 5 of Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

description: Additional file 5: Table S5. Evaluation results on CAMI datasets.
DOI: 10.17632/wfb26ndw57.1
title: Persistent and Transitory Components of Firm Characteristics 2

description: Part One of Dataset for replicating Persistent and Transitory Components of Firm Characteristics 1
DOI: 10.17632/j7sfr8w6ts.1
title: Persistent and Transitory Components of Firm Characteristics 4

description: Part 4 of Dataset for replicating Persistent and Transitory Components of Firm Characteristics
DOI: 10.6084/m9.figshare.20072219.v1
title: Exosomal circRNA FNDC3B promotes the progression of esophageal squamous cell carcinoma by sponging miR-490-5p and regulating thioredoxin reductase 1 expression

description: Exosomal circular RNAs (circRNAs) have been reported to play critical roles in esophageal squamous cell carcinoma (ESCC). We aimed to investigate the function of exosomal circRNA FNDC3B (circFNDC3B). The RNA levels and protein levels were examined using RT-qPCR and western blot (WB) assays. Colony formation and EdU assays were used to assess cell proliferative ability. Cell migratory and invasive abilities were detected by wound healing and transwell assays. Cell apoptosis was measured by flow cytometry. Glycolysis was measured using commercial kits. Transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA) were applied to examine the morphology and size of exosomes. Dual-luciferase reporter, RIP and RNA pull-down assays assessed the interaction of miR-490-5p with circFNDC3B or thioredoxin reductase 1 (TXNRD1). Xenograft tumor model determined the role of exosomal circFNDC3B <i>in vivo</i>. We observed that circFNDC3B was upregulated in ESCC samples and cells, as well as ESCC-derived exosomes. CircFNDC3B could be delivered via exosomes in tumor cells, and the colony formation, proliferation, migration, invasion, glycolysis, and <i>in vivo</i> growth ability of recipient cells were weakened after co-incubation with exosomal circFNDC3B-knockdown donor cells. CircFNDC3B was a miR-490-5p sponge, and miR-490-5p inhibition reversed the role of exosomal circFNDC3B-downregulating in ESCC cells. TXNRD1 was a miR-490-5p target, and TXNRD1 elevation weakened the anti-cancer function of miR-490-5p upregulation in ESCC cells. CircFNDC3B mediated TXNRD1 expression by interacting with miR-490-5p. In conclusion, exosomal circFNDC3B drove ESCC progression via regulating the miR-490-5p/TXNRD1 axis. Abbreviations EC: esophageal cancer; ESCC: esophageal squamous cell carcinoma; circRNA: circular RNA; WB: western blot; TEM: transmission electron microscopy; NTA: nanoparticle tracking analysis; TXNRD1: thioredoxin reductase 1; IHC: immunohistochemistry; RT-qPCR: reverse transcription-polymerase quantitative chain reaction; GLUT1: glucose transport protein type 1; LDHA: lactate dehydrogenase A
DOI: 10.6084/m9.figshare.21644459.v1
title: An Approximated Collapsed Variational Bayes Approach to Variable Selection in Linear Regression

description: In this work, we propose a novel approximated collapsed variational Bayes approach to model selection in linear regression. The approximated collapsed variational Bayes algorithm offers improvements over mean field variational Bayes by marginalizing over a subset of parameters and using mean field variational Bayes over the remaining parameters in an analogous fashion to collapsed Gibbs sampling. We have shown that the proposed algorithm, under typical regularity assumptions, (a) includes variables in the true underlying model at an exponential rate in the sample size, or (b) excludes the variables at least at the first order rate in the sample size if the variables are not in the true model. Simulation studies show that the performance of the proposed method is close to that of a particular Markov chain Monte Carlo sampler and a path search based variational Bayes algorithm, but requires an order of magnitude less time. The proposed method is also highly competitive with penalized methods, expectation propagation, stepwise AIC/BIC, BMS, and EMVS under various settings. Supplementary materials for the article are available online.
DOI: 10.6084/m9.figshare.20064683
title: Additional file 14 of Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line

description: Additional file 14: Table S12. Comparison of lignocellulose degradation-related modules in the bins recovered in this work and corresponding public species genomes from the NCBI database.
DOI: 10.6084/m9.figshare.14304335
title: Burnout syndrome and engagement among critical care providers: a cross-sectional study

description: ABSTRACT Objective: To evaluate the frequency of severe burnout syndrome among critical care providers and to correlate it with work engagement. Methods: A self-administered survey including the Maslach Burnout Inventory, Depression Anxiety and Stress Scales, and Gallup questionnaire was distributed. All analyses were stratified by setting (intensive care unit or step-down unit) and by professional group (nurses versus physicians versus physiotherapists). Results: Between February 2017 and June 2017, 206 out of 325 invited professionals (63.4%) answered the questionnaires. Of these, 55 were physicians (26.7%), 88 were physiotherapists (42.7%) and 63 were nurses (30.6%). The frequency of severe burnout was 34.3% (27.9 - 41.4%), and no difference was found between professional groups or settings. The frequency of severe or very severe cases of depression, anxiety or stress was 12.9%, 11.4% and 10.5%, respectively. The median (interquartile range) score observed on the Gallup questionnaire was 41 (34 - 48), and no differences were found between professional groups or settings. There was a negative correlation between burnout and work engagement (r = -0.148; p = 0.035). Conclusion: There is a high frequency of severe burnout among critical care providers working in the intensive care unit and step-down unit. There was a negative correlation between burnout and work engagement.
DOI: 10.6084/m9.figshare.14304335.v1
title: Burnout syndrome and engagement among critical care providers: a cross-sectional study

description: ABSTRACT Objective: To evaluate the frequency of severe burnout syndrome among critical care providers and to correlate it with work engagement. Methods: A self-administered survey including the Maslach Burnout Inventory, Depression Anxiety and Stress Scales, and Gallup questionnaire was distributed. All analyses were stratified by setting (intensive care unit or step-down unit) and by professional group (nurses versus physicians versus physiotherapists). Results: Between February 2017 and June 2017, 206 out of 325 invited professionals (63.4%) answered the questionnaires. Of these, 55 were physicians (26.7%), 88 were physiotherapists (42.7%) and 63 were nurses (30.6%). The frequency of severe burnout was 34.3% (27.9 - 41.4%), and no difference was found between professional groups or settings. The frequency of severe or very severe cases of depression, anxiety or stress was 12.9%, 11.4% and 10.5%, respectively. The median (interquartile range) score observed on the Gallup questionnaire was 41 (34 - 48), and no differences were found between professional groups or settings. There was a negative correlation between burnout and work engagement (r = -0.148; p = 0.035). Conclusion: There is a high frequency of severe burnout among critical care providers working in the intensive care unit and step-down unit. There was a negative correlation between burnout and work engagement.
DOI: 10.6084/m9.figshare.20064677
title: Additional file 12 of Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line

description: Additional file 12: Table S10. Organic carbon analysis of intestinal contents in the PBL midgut and hindgut.
DOI: 10.6084/m9.figshare.12731491.v1
title: Additional file 10 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 10: Dataset S4. The objects stats of cells in a vertical Arabidopsis root section using SR-Tesseler software.
DOI: 10.6084/m9.figshare.5394859
title: Recovering hidden sub-layers of repainted automotive paint by 3D optical coherence tomography

description: In violent vehicular crimes, the damaged area of a vehicle is usually repainted artificially in order to conceal the evidence. Detecting and recovering the hidden sub-layer morphology of repainted automotive paint is highly valuable for providing trace evidence in hit-and-run cases. Optical coherence tomography (OCT) is a novel forensic imaging technique for repainted automotive paint analysis with the advantages of non-destructive, noncontact, high-resolution and cross-sectional imaging. In this study, we applied a custom-built spectral-domain OCT configuration with ~6 μm axial and lateral resolution to obtain three-dimensional (3D) images of an artificially prepared, internally-damaged, repainted automotive paint surface. Two-dimensional (2D) cross-sectional images were produced to locate the damaged area and 3D-OCT reconstruction was performed to directly visualize the sub-layers beneath the repainted paint surface. The results demonstrate that 3D-OCT technology manages to recover high-resolution sub-layer images of the repainted automotive paint through volumetric imaging, and thus provides more valuable information for forensic purposes.
DOI: 10.17632/mwh4njxr4y.1
title: Persistent and Transitory Components of Firm Characteristics 3

description: Part 3 of Dataset for replicating Persistent and Transitory Components of Firm Characteristics
DOI: 10.6084/m9.figshare.12731503
title: Additional file 14 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 14: Dataset S8. Parameter identification of toluidine blue-labeled cells in a transverse section of a Populus trichocarpa stem by ImageJ software.
DOI: 10.6084/m9.figshare.12731509.v1
title: Additional file 16 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 16: Dataset S10. The objects stats of cells in a transverse section of a Populus trichocarpa stem by SR-Tesseler software.
DOI: 10.6084/m9.figshare.12731698.v1
title: Additional file 3 of The critical role of dysregulated Hh-FOXM1-TPX2 signaling in human hepatocellular carcinoma cell proliferation

description: Additional file 3: Table S5. Function clustering of DEGs.
DOI: 10.6084/m9.figshare.24269240
title: Additional file 1 of CmNAC25 targets CmMYB6 to positively regulate anthocyanin biosynthesis during the post-flowering stage in chrysanthemum

description: Additional file 1: Table S1. Summary of transcriptome sequencing data for ‘Arctic Queen’ petals at three flowering stages.
DOI: 10.6084/m9.figshare.20072219
title: Exosomal circRNA FNDC3B promotes the progression of esophageal squamous cell carcinoma by sponging miR-490-5p and regulating thioredoxin reductase 1 expression

description: Exosomal circular RNAs (circRNAs) have been reported to play critical roles in esophageal squamous cell carcinoma (ESCC). We aimed to investigate the function of exosomal circRNA FNDC3B (circFNDC3B). The RNA levels and protein levels were examined using RT-qPCR and western blot (WB) assays. Colony formation and EdU assays were used to assess cell proliferative ability. Cell migratory and invasive abilities were detected by wound healing and transwell assays. Cell apoptosis was measured by flow cytometry. Glycolysis was measured using commercial kits. Transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA) were applied to examine the morphology and size of exosomes. Dual-luciferase reporter, RIP and RNA pull-down assays assessed the interaction of miR-490-5p with circFNDC3B or thioredoxin reductase 1 (TXNRD1). Xenograft tumor model determined the role of exosomal circFNDC3B <i>in vivo</i>. We observed that circFNDC3B was upregulated in ESCC samples and cells, as well as ESCC-derived exosomes. CircFNDC3B could be delivered via exosomes in tumor cells, and the colony formation, proliferation, migration, invasion, glycolysis, and <i>in vivo</i> growth ability of recipient cells were weakened after co-incubation with exosomal circFNDC3B-knockdown donor cells. CircFNDC3B was a miR-490-5p sponge, and miR-490-5p inhibition reversed the role of exosomal circFNDC3B-downregulating in ESCC cells. TXNRD1 was a miR-490-5p target, and TXNRD1 elevation weakened the anti-cancer function of miR-490-5p upregulation in ESCC cells. CircFNDC3B mediated TXNRD1 expression by interacting with miR-490-5p. In conclusion, exosomal circFNDC3B drove ESCC progression via regulating the miR-490-5p/TXNRD1 axis. Abbreviations EC: esophageal cancer; ESCC: esophageal squamous cell carcinoma; circRNA: circular RNA; WB: western blot; TEM: transmission electron microscopy; NTA: nanoparticle tracking analysis; TXNRD1: thioredoxin reductase 1; IHC: immunohistochemistry; RT-qPCR: reverse transcription-polymerase quantitative chain reaction; GLUT1: glucose transport protein type 1; LDHA: lactate dehydrogenase A
DOI: 10.6084/m9.figshare.24269240.v1
title: Additional file 1 of CmNAC25 targets CmMYB6 to positively regulate anthocyanin biosynthesis during the post-flowering stage in chrysanthemum

description: Additional file 1: Table S1. Summary of transcriptome sequencing data for ‘Arctic Queen’ petals at three flowering stages.
DOI: 10.6084/m9.figshare.12731509
title: Additional file 16 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 16: Dataset S10. The objects stats of cells in a transverse section of a Populus trichocarpa stem by SR-Tesseler software.
DOI: 10.6084/m9.figshare.24269243
title: Additional file 2 of CmNAC25 targets CmMYB6 to positively regulate anthocyanin biosynthesis during the post-flowering stage in chrysanthemum

description: Additional file 2: Table S2. The predicted upstream regulators of the CmMYB6 promoter identified using Y1H screening. The FPKM values represent the means of three biological replicates.
DOI: 10.6084/m9.figshare.12731536
title: Additional file 8 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 8: Dataset S2. Parameter identification of mCherry-labeled cells in a vertical Arabidopsis root section by ImageJ software.
DOI: 10.6084/m9.figshare.14305242
title: Sugarcane stem nodes based on the maximum value points of the vertical projection function

description: ABSTRACT: In order to solve the problem that the stem nodes are difficult to identify in the process of sugarcane seed automatic cutting, a method of identifying the stem nodes of sugarcane based on the extreme points of vertical projection function is proposed in this paper. Firstly, in order to reduce the influence of light on image processing, the RGB color image is converted to HSI color image, and the S component image of the HSI color space is extracted as a research object. Then, the S component image is binarized by the Otsu method, the hole of the binary image is filled by morphology closing algorithm, and the sugarcane and the background are initially separated by the horizontal projection map of the binary image. Finally, the position of sugarcane stem is preliminarily determined by continuously taking the derivative of the vertical projection function of the binary image, and the sum of the local pixel value of the suspicious pixel column is compared to further determine the sugarcane stem node. The experimental results showed that the recognition rate of single stem node is 100%, and the standard deviation is less than 1.1 mm. The accuracy of simultaneous identification of double stem nodes is 98%, and the standard deviation is less than 1.7 mm. The accuracy of simultaneous identification of the three stem nodes is 95%, and the standard deviation is less than 2.2 mm. Compared with the other methods introduced in this paper, the proposed method has higher recognition and accuracy.
DOI: 10.6084/m9.figshare.24269243.v1
title: Additional file 2 of CmNAC25 targets CmMYB6 to positively regulate anthocyanin biosynthesis during the post-flowering stage in chrysanthemum

description: Additional file 2: Table S2. The predicted upstream regulators of the CmMYB6 promoter identified using Y1H screening. The FPKM values represent the means of three biological replicates.
DOI: 10.6084/m9.figshare.12731494.v1
title: Additional file 11 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 11: Dataset S5. Parameter identification of cells in an Arabidopsis seed section by ImageJ software.
DOI: 10.6084/m9.figshare.12731533
title: Additional file 7 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 7: Dataset S1. Parameter identification of Populus trichocarpa embryo cells by ImageJ and Imaris software.
DOI: 10.6084/m9.figshare.6967742
title: The effects of inhaled NO on plasma vasoactive factor and CTnI level in rabbits with acute massive pulmonary embolism

description: Abstract Purpose: To investigate changes in the plasma concentrations of cardiac troponin I (CTnI), thromboxane A2 (TXA2), prostaglandin I2 (PGI2) and endothelin-1 (ET-1) in rabbits with massive pulmonary embolism (AMPE) and the impact of nitric oxide inhalation (NOI) on these indices. Methods: A total of 30 Japanese rabbits were used to construct an MPE model and were divided into 3 groups equally (n=10), including an EXP group (undergoing modeling alone), an NOI group (receiving NOI 2 h post-modeling) and a CON group (receiving intravenous physiological saline). Results: In the model group, plasma concentration of CTnI peaked at 16 h following modeling (0.46±0.10 µg/ml) and significantly decreased following NOI. Plasma levels of TXB2, PGI2 and ET-1 peaked at 12, 16 and 8 h following modeling, respectively, and significantly decreased at different time points (0, 2, 4, 8, 12, 16, 20 and 24 h) following NOI. A significant correlation was observed between the peak plasma CTnI concentration and peak TXB2, 6-keto prostaglandin F1α and ET-1 concentrations in the model and NOI groups. Conclusion: Increases in plasma TXA2, PGI2 and ET-1 levels causes myocardial damage in a rabbit model of AMPE; however, NOI effectively down regulates the plasma concentration of these molecules to produce a myocardial-protective effect.
DOI: 10.6084/m9.figshare.12731497
title: Additional file 12 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 12: Dataset S6. Modification of centroid coordinates of cells in an Arabidopsis seed section for analysis with SR-Tesseler software.