cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22778894
title: Prolonged Anaerobic Environment Weakens the Linkage Between Paddy Soil Organic Carbon (SOC) Sink and Climate Factors

description: We collected research articles regarding soil organic carbon (SOC) change following long-term fertilization in Chinese paddy soil. A keyword search was conducted via Web of Science, SCOPUS, and CNKI until April 2022, with search terms “long-term fertilization”, “fertilization”, “organic carbon”, “paddy”, and “rice” (and a combination of them). On aggregate, an initial of 1298 studies was obtained. The collected literature was further screened based on the following criteria. i) Only field experiments with durations longer than 3 years in China, and ii) design allowing pairwise comparison between fertilization treatments and controls (without fertilizers) were included, besides, iii) soil samples were collected during the rice season. iv) The means and the number of replicates of target variables were reported clearly. We also used WebPlotDigitizer (version 3.8) software to extract data only presented in the figures.. Based on these criteria, a total of 168 individual studies including 686 paired data of SOC were retrieved in our study.
DOI: 10.6084/m9.figshare.16613797
title: The microRNA-451a/chromosome segregation 1-like axis suppresses cell proliferation, migration, and invasion and induces apoptosis in nasopharyngeal carcinoma

description: MicroRNA-451a (miR-451a) has been implicated in the initiation and progression of multiple cancers. However, the regulatory mechanisms underlying its function in nasopharyngeal carcinoma (NPC) are poorly understood. Thus, we investigated in detail the role of the microRNA-451a/chromosome segregation 1-like (miR-45a/CSE1L) axis and its regulatory mechanism in NPC. We examined the levels of miR-451a and CSE1L in NPC, and assessed the effects of miR-451a and CSE1L on NPC by cell functional experiments. Furthermore, we elucidated the direct regulatory effect of miR-451a on <i>CSE1L</i> by the luciferase reporter assay, RNA pull-down assay, and RNA immunoprecipitation and validated our observations by calculating the Pearson’s correlation coefficient. We found that miR-451a was down-regulated in NPC cells, and its over-expression attenuated cell proliferation, migration, and invasion, and tumor growth in 5–8 F and SUNE-1 cells and promoted apoptosis. Moreover, <i>CSE1L</i> was the direct gene target of miR-451a, and its over-expression abrogated miR-451a-dependent inhibition of malignancy in 5–8 F and SUNE-1 cells. The Pearson’s correlation coefficient indicated a negative correlation between <i>CSE1L</i> and miR-451a. miR-451a serves as a tumor suppressor and targets <i>CSE1L</i>. miR-451a suppresses <i>CSE1L</i> expression, thereby reducing proliferation, invasion, and migration and increasing apoptosis of NPC cells.
DOI: 10.6084/m9.figshare.16613797.v1
title: The microRNA-451a/chromosome segregation 1-like axis suppresses cell proliferation, migration, and invasion and induces apoptosis in nasopharyngeal carcinoma

description: MicroRNA-451a (miR-451a) has been implicated in the initiation and progression of multiple cancers. However, the regulatory mechanisms underlying its function in nasopharyngeal carcinoma (NPC) are poorly understood. Thus, we investigated in detail the role of the microRNA-451a/chromosome segregation 1-like (miR-45a/CSE1L) axis and its regulatory mechanism in NPC. We examined the levels of miR-451a and CSE1L in NPC, and assessed the effects of miR-451a and CSE1L on NPC by cell functional experiments. Furthermore, we elucidated the direct regulatory effect of miR-451a on <i>CSE1L</i> by the luciferase reporter assay, RNA pull-down assay, and RNA immunoprecipitation and validated our observations by calculating the Pearson’s correlation coefficient. We found that miR-451a was down-regulated in NPC cells, and its over-expression attenuated cell proliferation, migration, and invasion, and tumor growth in 5–8 F and SUNE-1 cells and promoted apoptosis. Moreover, <i>CSE1L</i> was the direct gene target of miR-451a, and its over-expression abrogated miR-451a-dependent inhibition of malignancy in 5–8 F and SUNE-1 cells. The Pearson’s correlation coefficient indicated a negative correlation between <i>CSE1L</i> and miR-451a. miR-451a serves as a tumor suppressor and targets <i>CSE1L</i>. miR-451a suppresses <i>CSE1L</i> expression, thereby reducing proliferation, invasion, and migration and increasing apoptosis of NPC cells.
DOI: 10.6084/m9.figshare.21197987
title: A Bayesian Partially Observable Online Change Detection Approach with Thompson Sampling

description: This article proposes a Bayesian learning framework for online change detection of high-dimensional data streams where only a subset of variables can be observed at each time point due to limited sensing capacities. On the one hand, we need to build a change detection scheme based on partial observations. On the other, the scheme should be able to adaptively and actively select the most critical sensing variables to observe to maximize the detection power. To address these two points, in this article, first, a novel Bayesian Spike-Slab Composite Decomposition (BSSCD) is proposed to decompose the high-dimensional signals onto normal and abnormal bases, where the projection coefficients are efficiently estimated via variational Bayesian inference. Built upon it, the posterior Bayes factor is constructed as the detection statistic. Second, by further formulating the detection statistic as the reward function of combinatorial multi-armed bandit (CMAB), a Thompson sampling strategy is proposed for selecting the potential changed variables with the balance of exploration and exploitation. The efficacy and applicability of our method are demonstrated in practice with numerical studies and a real case study.
DOI: 10.6084/m9.figshare.20673428.v1
title: Additional file 1 of Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma

description: Additional file 1. Result of H3K9me3 Peaks.
DOI: 10.6084/m9.figshare.20673434.v1
title: Additional file 3 of Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma

description: Additional file 3. Differentlly expressed genes in ICC.
DOI: 10.6084/m9.figshare.20673434
title: Additional file 3 of Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma

description: Additional file 3. Differentlly expressed genes in ICC.
DOI: 10.6084/m9.figshare.21197986
title: A subsampling method for regression problems based on minimum energy criterion

description: The extraordinary amounts of data generated nowadays pose heavy demands on computational resources and time, which hinders the implementation of various statistical methods. An efficient and popular strategy of downsizing data volumes and thus alleviating these challenges is subsampling. However, the existing methods either rely on specific assumptions for the underlying models or acquire partial information from the available data. For regression problems, we propose a novel approach, termed adaptive subsampling with the minimum energy criterion (ASMEC). The proposed method requires no explicit model assumptions and “smartly” incorporates information on covariates and responses. ASMEC subsamples possess two desirable properties: space-fillingness and spatial adaptiveness. We investigate the limiting distribution of ASMEC subsamples and their theoretical properties under the smoothing spline regression model. The effectiveness and robustness of the ASMEC approach are also supported by a variety of synthetic examples and two real-life examples.
DOI: 10.6084/m9.figshare.21197986.v1
title: A subsampling method for regression problems based on minimum energy criterion

description: The extraordinary amounts of data generated nowadays pose heavy demands on computational resources and time, which hinders the implementation of various statistical methods. An efficient and popular strategy of downsizing data volumes and thus alleviating these challenges is subsampling. However, the existing methods either rely on specific assumptions for the underlying models or acquire partial information from the available data. For regression problems, we propose a novel approach, termed adaptive subsampling with the minimum energy criterion (ASMEC). The proposed method requires no explicit model assumptions and “smartly” incorporates information on covariates and responses. ASMEC subsamples possess two desirable properties: space-fillingness and spatial adaptiveness. We investigate the limiting distribution of ASMEC subsamples and their theoretical properties under the smoothing spline regression model. The effectiveness and robustness of the ASMEC approach are also supported by a variety of synthetic examples and two real-life examples.
DOI: 10.6084/m9.figshare.12293324
title: The Rs12569232 SNP Association with Vogt-Koyanagi-Harada Disease and Behcet’s Disease is Probably Mediated by Regulation of Linc00467 Expression

description: <b>Purpose</b>: To investigate whether the rs12569232 SNP association with Vogt-Koyanagi-Harada disease and Behcet’s disease is mediated by regulation of Linc00467 expression. <b>Methods</b>: The expression of linc00467 was detected by real-time PCR. Adenovirus carrying the linc00467 was transduced into CD4<sup>+</sup>T cells and the effect on cell viability was measured by the CCK-8 test. Human proteome microarray and starBase 2.0 were used to identify the binding proteins of linc00467 and RNA Immunoprecipitation (RIP) was used to confirm the identity of bound proteins. <b>Results</b>: The rs12569232 was associated with the expression of linc00467. The expression of linc00467 was up-regulated in PBMCs and CD4<sup>+</sup>T cells from VKH disease and BD patients. Over-expression of linc00467 increased cell viability of CD4<sup>+</sup>T cells. HUR was the common binding protein identified by the two methods and confirmed by RIP. <b>Conclusions</b>: The rs12569232 association with VKH disease and BD may be mediated via regulating the expression of linc00467.
DOI: 10.6084/m9.figshare.3380461
title: Robust Treatment Comparison Based on Utilities of Semi-Competing Risks in Non-Small-Cell Lung Cancer

description: A design is presented for a randomized clinical trial comparing two second-line treatments, chemotherapy versus chemotherapy plus reirradiation, for treatment of recurrent non-small-cell lung cancer. The central research question is whether the potential efficacy benefit that adding reirradiation to chemotherapy may provide justifies its potential for increasing the risk of toxicity. The design uses two co-primary outcomes: time to disease progression or death, and time to severe toxicity. Because patients may be given an active third-line treatment at disease progression that confounds second-line treatment effects on toxicity and survival following disease progression, for the purpose of this comparative study follow-up ends at disease progression or death. In contrast, follow-up for disease progression or death continues after severe toxicity, so these are semi-competing risks. A conditionally conjugate Bayesian model that is robust to misspecification is formulated using piecewise exponential distributions. A numerical utility function is elicited from the physicians that characterizes desirabilities of the possible co-primary outcome realizations. A comparative test based on posterior mean utilities is proposed. A simulation study is presented to evaluate test performance for a variety of treatment differences, and a sensitivity assessment to the elicited utility function is performed. General guidelines are given for constructing a design in similar settings, and a computer program for simulation and trial conduct is provided. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.23295276
title: The safety and efficacy of immunotherapy and palliative radiotherapy in patients with metastatic non-small cell lung cancer: a systematic review and meta-analysis of 13 prospective studies

description: Whether palliative RT (pRT) can influence the prognosis of mNSCLC patients who are treated with immune checkpoint inhibitors (ICIs) is still under debate. Therefore, we performed a systematic review and meta-analysis to evaluate the efficacy and safety of pRT plus ICIs in mNSCLC patients. PubMed, Cochrane, and Embase databases were searched, and only prospective studies and randomized controlled trials (RCTs) were included. All data were analyzed with Stata 14.0 and Review Manager Version 5.4 software. A total of 13 studies were included. The combined ORRs for the ICIs group, cRT plus ICIs group, and SBRT plus ICIs group were 0.22 (95% CI: 1.27, 4.04), 0.26 (95% CI: 0.04, 0.49), and 0.29 (95% CI: 0.17, 0.40), respectively. And PFS were 2.21 (95% CI: 1.71, 2.70), 4.63 (95% CI: 2.16, 7.09), and 7.38 (95% CI: 2.16, 12.60) months, respectively. OS was 5.96 (95% CI: 3.85, 8.07), 9.04 (95% CI: 6.49, 11.59), and 7.96 (95% CI: 4.02, 11.91) months for the above groups, respectively. For safety terms, patients receiving ICIs plus SBRT had an incidence of 5% (95% CI: 2%, 9%) for pneumonia. Patients with mNSCLC may benefit from the combination of ICIs and pRT therapy, but these findings need further validation.
DOI: 10.6084/m9.figshare.21192118
title: Additional file 1 of Comparative profiling of single-cell transcriptome reveals heterogeneity of tumor microenvironment between solid and acinar lung adenocarcinoma

description: Additional file 1: Table S1. Characteristics of the LUAD samples included in this study.
DOI: 10.6084/m9.figshare.21192121
title: Additional file 2 of Comparative profiling of single-cell transcriptome reveals heterogeneity of tumor microenvironment between solid and acinar lung adenocarcinoma

description: Additional file 2: Table S2. Data of epithelial cells analysis. (1) Differential expression genes between epithelial cells from solid and acinar samples; (2) Differentially enriched HALLMARK signatures in epithelial cells from solid and acinar samples; (3) Differentially enriched KEGG pathways in epithelial cells from solid and acinar samples; (4) Gene list of signatures for ssGSEA in bulk RNA-seq dataset of the TCGA LUAD cohort.
DOI: 10.6084/m9.figshare.11769177
title: Additional file 1 of Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream

description: Additional file 1. Annotation for phylogenetic trees of full and abbreviated NCBI 2015 listeriosis outbreak cluster linked to ice cream.
DOI: 10.6084/m9.figshare.11769177.v1
title: Additional file 1 of Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream

description: Additional file 1. Annotation for phylogenetic trees of full and abbreviated NCBI 2015 listeriosis outbreak cluster linked to ice cream.
DOI: 10.6084/m9.figshare.21192138.v1
title: Additional file 7 of Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) family genes in tea plant

description: Additional file 7: Table S5. The Ka-Ks ratios of CsCAMTAs.
DOI: 10.6084/m9.figshare.21192138
title: Additional file 7 of Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) family genes in tea plant

description: Additional file 7: Table S5. The Ka-Ks ratios of CsCAMTAs.
DOI: 10.22002/s3e0x-nn738
title: MEF stably expressing IRE1α-GFP

description: Cryo-CLEM
description: <strong>Tilt Series Date:</strong> 2016-05-06</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> Mouse Embryonic Fibroblasts</p>
<strong>Strain:</strong> IRE1α-GFP stable expression</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Peter Walter, Han Tran</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cultured in high glucose DMEM media supplemented with 10% tetracycline-free fetal bovine serum (FBS; Takara Bio), 6 mM L-glutamine, and 100 U/ml penicillin/streptomycin.</p>
<strong>Sample Preparation:</strong> Prior to cell plating, gold Quantifoil London finder grids (EMS R2/2 LF-Au-NH2) were UV treated to sterilize and coated with cell adhesion matrix. For MEFs-IRE1-mNG cell line, grids were coated in droplets of 500 ug/mL Fibronectins (Sigma-Aldrich S5171-.5MG) for 5 minutes on each side, washed in PBS, blotted and air-dried. For U2OS-IRE1-mNG cell line, grids were coated with ~4 mg/mL undiluted Collagen type I (Corning 354236) droplets for 20 minutes, washed in PBS, blotted and air-dried. Cells were seeded at 15% confluence and allowed to adhere for 8 hours and induced with Doxycycline (500 nM) for 6 or 18 hours for MEFs and U-2 OS cell lines, respectively. ER stress was then induced by treatment with 1.5 ug/mL of Tunicamycin for 2 hours.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-06-8/rawdata/</p>tomo2.mrc,  Tilt Series (Pixel Size 6.167 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-06-8/rawdata/tomo2.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomo2.rec,  Reconstruction (Pixel Size 24.668 nm), 890.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-06-8/3dimage_102595/tomo2.rec"
        > <i class="download icon"></i> Download </a></p>

        tomography2new_full.rec,  Reconstruction (Pixel Size 0.0 nm), 666.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-06-8/3dimage_118603/tomography2new_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/x6amp-ydk34
title: WT tomogram data

description: Raw data files of WT tomogram data
description: <strong>Tilt Series Date:</strong> 2020-12-28</p>
<strong>Data Taken By:</strong> Rachel Rosenzweig</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Collaborators and Roles:</strong> Patrick Viollier</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Inoculated a single colony from a 2% M2G agar plate in 5mL M2G at 30C, 220rpm for 24hr. Diluted each 5mL culture in 15mL M2G at 30C, 220rpm for 3hrs to OD600 0.7. Transferred to a conical centrifuge tube. Centrifuged at 6,400xg at 4C for 10min. (Media and tubes now on ice). Aspirated supernatant, resuspended with 1mL cold 1X M2. Transferred to a new 2mL microcentrifuge tube. Centrifuged at 15,000xg at 4C for 3min. Aspirated supernatant, resuspended with 900uL cold 1X M2. Added and mixed 900uL cold Percoll® [Sigma-Aldrich #P4937]. Centrifuged at 15,000xg at 4C for 20min. Aspirated top stalked cells band, collected bottom swarmer band. Transferred to a new 1.5mL microcentrifuge tube. Washed cells by adding 1mL cold 1X M2. Centrifuged at 15,000xg at 4C for 3min. (**Repeated wash 3x). Aspirated supernatant to leave 20uL cell solution resuspended.</p>
<strong>Sample Preparation:</strong> Mixed 1mL 10nm Au with 250uL 5% BSA. Vortexed. Centrifuged at 18,000xg for 30min. Aspirated supernatant to leave 20uL Au solution resuspended. Mixed 1:1 ratio of Au:Cells. Vitrobot 3uL of solution @ RT with 100% humidity. Blot force: 2. Blot time: 4s. Quantifoil R3.5/1 200 Mesh grids</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rrb2020-12-28-244/rawdata/</p>Caulobacter257_movies.mrc,  Tilt Series (Pixel Size 0.33 nm), 2.8 GB  
        
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        Caulobacter257_movies_full.rec,  Reconstruction (Pixel Size 1.32 nm), 737.3 MB  
        
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        Caulobacter257.mrc.mdoc,  42.7 kB  
        
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