cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21082241
title: CircNFIX knockdown inhibited AML tumorigenicity by the miR-876-3p/TRIM31 axis

description: Acute myeloid leukemia (AML) is one of the most common malignant myeloid diseases in adults with a dismal prognosis. We aimed to explore the effects of circNFIX on the proliferation and apoptosis of AML cells. The expressions of circNFIX, miR-876-3p and tripartite motif (TRIM) 31 in the bone marrow specimens of AML patients and AML cell lines were detected by qRT-PCR or western blot. Cell proliferation was evaluated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and 5-ethynyl-29-deoxyuridine (EdU) assays. Cell cycle and apoptosis were analyzed by flow cytometry. Western blot was used to detect protein expression. The relationship between miR-876-3p and circNFIX or TRIM31 was identified by dual-luciferase reporter assay or RNA pull-down assay. The expression level of circNFIX was significantly increased in the bone marrow samples of AML patients and AML cells when compared with normal controls. CircNFIX silencing inhibited AML cell proliferation and promoted apoptosis. Inhibition of miR-876-3p reversed the effect of circNFIX knockdown on AML cell progression. In addition, circNFIX indirectly regulated TRIM31 through miR-876-3p. Further, TRIM31 overexpression counteracted the effect of circNFIX silencing on AML cell proliferation and apoptosis. CircNFIX knockdown could suppress the proliferation and induce the apoptosis of AML cells by targeting the miR-876-3p/TRIM31 axis.
DOI: 10.6084/m9.figshare.21082247.v1
title: Modeling and Active Learning for Experiments with Quantitative-Sequence Factors

description: A new type of experiment that aims to determine the optimal quantities of a sequence of factors is eliciting considerable attention in medical science, bioengineering, and many other disciplines. Such studies require the simultaneous optimization of both quantities and sequence orders of several components which are called quantitative-sequence (QS) factors. Given the large and semi-discrete solution spaces in such experiments, efficiently identifying optimal or near-optimal solutions by using a small number of experimental trials is a nontrivial task. To address this challenge, we propose a novel active learning approach, called QS-learning, to enable effective modeling and efficient optimization for experiments with QS factors. QS-learning consists of three parts: a novel mapping-based additive Gaussian process (MaGP) model, an efficient global optimization scheme (QS-EGO), and a new class of optimal designs (QS-design). The theoretical properties of the proposed method are investigated, and optimization techniques using analytical gradients are developed. The performance of the proposed method is demonstrated via a real drug experiment on lymphoma treatment and several simulation studies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6401975
title: Additional file 8: of Transcriptomics reveals the molecular processes of light-induced rapid darkening of the non-obligate cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura) and their genetic basis of pigmentation strategy

description: Table S6. Information of unigenes used in analysis and figures. (XLSX 538 kb)
DOI: 10.6084/m9.figshare.23700533
title: Additional file 4 of Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

description: Supplementary File 4
DOI: 10.6084/m9.figshare.6401975.v1
title: Additional file 8: of Transcriptomics reveals the molecular processes of light-induced rapid darkening of the non-obligate cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura) and their genetic basis of pigmentation strategy

description: Table S6. Information of unigenes used in analysis and figures. (XLSX 538 kb)
DOI: 10.6084/m9.figshare.23700536
title: Additional file 5 of Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

description: Supplementary File 5
DOI: 10.6084/m9.figshare.23700539
title: Additional file 6 of Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

description: Supplementary File 6
DOI: 10.6084/m9.figshare.23700539.v1
title: Additional file 6 of Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

description: Supplementary File 6
DOI: 10.6084/m9.figshare.6402149.v1
title: Data Availability from How silanization influences aggregation and moisture sorption behaviours of silanized silica: analysis of porosity and multilayer moisture adsorption

description: Based on the results of nitrogen adsorption and dynamic vapour sorption as well as analysis by the Hailwood–Horrobin (H-H) model, the effects of γ-methacryloxypropyltrimethoxysilane (MPTS) on the agglomeration and moisture sorption properties of fumed silica particles were investigated. After adding various concentrations (2%, 4%, 6% and 8%) of MPTS, different degrees of silanization were obtained by showing various ─OH group contents on the silica surface, which resulted in silica agglomerates with different porous structures. The bigger mesopores in the unmodified silica agglomerates became smaller and finally disappeared after MPTS modification and the Bruanuer–Emmett–Teller surface area decreased more gradually with an increase in MPTS concentration. The H-H model fitted the sorption isotherms very well, and both hydrated water and dissolved water showed decreasing trends with the increase in MPTS concentration, showing reduced hygroscopicity. Up to 6% MPTS, the ─OH groups decreased with increasing MPTS concentration, as indicated by reduced <i>K</i><sub>h</sub> and <i>W</i> parameters, while at 8% MPTS an extensive self-condensation of MPTS occurred. Adsorption hysteresis appeared for moisture sorption on silanized silica, especially at low relative humidity values and at low MPTS concentrations, which could be explained by a synergistic effect of the surface ─OH group content and pore characteristics. These results could aid our understanding of the applications of silane-modified silica particles.
DOI: 10.6084/m9.figshare.21082235
title: Crop Yield Prediction Using Bayesian Spatially Varying Coefficient Models with Functional Predictors

description: Reliable prediction for crop yield is crucial for economic planning, food security monitoring, and agricultural risk management. This study aims to develop a crop yield forecasting model at large spatial scales using meteorological variables closely related to crop growth. The influence of climate patterns on agricultural productivity can be spatially inhomogeneous due to local soil and environmental conditions. We propose a Bayesian spatially varying functional model (BSVFM) to predict county-level corn yield for five Midwestern states, based on annual precipitation and daily maximum and minimum temperature trajectories modeled as multivariate functional predictors. The proposed model accommodates spatial correlation and measurement errors of functional predictors, and respects the spatially heterogeneous relationship between the response and associated predictors by allowing the functional coefficients to vary over space. The model also incorporates a Bayesian variable selection device to further expand its capacity to accommodate spatial heterogeneity. The proposed method is demonstrated to outperform other highly competitive methods in corn yield prediction, owing to the flexibility of allowing spatial heterogeneity with spatially varying coefficients in our model. Our study provides further insights into understanding the impact of climate change on crop yield. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.25195547
title: gene_vector_averages_3b.pt

description: These are 3B ESM embeddings grouped by gene symbol and averaged out.
DOI: 10.6084/m9.figshare.25195547.v1
title: gene_vector_averages_3b.pt

description: These are 3B ESM embeddings grouped by gene symbol and averaged out.
DOI: 10.20372/aau_rdm/qflrjo
title: Mycobacterium tuberculosis

description: The data was Mycobacterium tuberculosis (M. tuberculosis) isolated from homeless individuals in Addis Ababa, Ethiopia. The Spoligotyping and 24-loci Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing were used for genotyping of the 59 isolates.
DOI: 10.6084/m9.figshare.21082253
title: Bayesian Spatial Blind Source Separation via the Thresholded Gaussian Process

description: Blind source separation (BSS) aims to separate latent source signals from their mixtures. For spatially dependent signals in high-dimensional and large-scale data, such as neuroimaging, most existing BSS methods do not take into account the spatial dependence and the sparsity of the latent source signals. To address these major limitations, we propose a Bayesian spatial blind source separation (BSP-BSS) approach for neuroimaging data analysis. We assume the expectation of the observed images as a linear mixture of multiple sparse and piece-wise smooth latent source signals, for which we construct a new class of Bayesian nonparametric prior models by thresholding Gaussian processes. We assign the vMF priors to mixing coefficients in the model. Under some regularity conditions, we show that the proposed method has several desirable theoretical properties including the large support for the priors, the consistency of joint posterior distribution of the latent source intensity functions and the mixing coefficients, and the selection consistency on the number of latent sources. We use extensive simulation studies and an analysis of the resting-state fMRI data in the Autism Brain Imaging Data Exchange (ABIDE) study to demonstrate that BSP-BSS outperforms the existing method for separating latent brain networks and detecting activated brain activation in the latent sources. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21082253.v1
title: Bayesian Spatial Blind Source Separation via the Thresholded Gaussian Process

description: Blind source separation (BSS) aims to separate latent source signals from their mixtures. For spatially dependent signals in high-dimensional and large-scale data, such as neuroimaging, most existing BSS methods do not take into account the spatial dependence and the sparsity of the latent source signals. To address these major limitations, we propose a Bayesian spatial blind source separation (BSP-BSS) approach for neuroimaging data analysis. We assume the expectation of the observed images as a linear mixture of multiple sparse and piece-wise smooth latent source signals, for which we construct a new class of Bayesian nonparametric prior models by thresholding Gaussian processes. We assign the vMF priors to mixing coefficients in the model. Under some regularity conditions, we show that the proposed method has several desirable theoretical properties including the large support for the priors, the consistency of joint posterior distribution of the latent source intensity functions and the mixing coefficients, and the selection consistency on the number of latent sources. We use extensive simulation studies and an analysis of the resting-state fMRI data in the Autism Brain Imaging Data Exchange (ABIDE) study to demonstrate that BSP-BSS outperforms the existing method for separating latent brain networks and detecting activated brain activation in the latent sources. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6402149
title: Data Availability from How silanization influences aggregation and moisture sorption behaviours of silanized silica: analysis of porosity and multilayer moisture adsorption

description: Based on the results of nitrogen adsorption and dynamic vapour sorption as well as analysis by the Hailwood–Horrobin (H-H) model, the effects of γ-methacryloxypropyltrimethoxysilane (MPTS) on the agglomeration and moisture sorption properties of fumed silica particles were investigated. After adding various concentrations (2%, 4%, 6% and 8%) of MPTS, different degrees of silanization were obtained by showing various ─OH group contents on the silica surface, which resulted in silica agglomerates with different porous structures. The bigger mesopores in the unmodified silica agglomerates became smaller and finally disappeared after MPTS modification and the Bruanuer–Emmett–Teller surface area decreased more gradually with an increase in MPTS concentration. The H-H model fitted the sorption isotherms very well, and both hydrated water and dissolved water showed decreasing trends with the increase in MPTS concentration, showing reduced hygroscopicity. Up to 6% MPTS, the ─OH groups decreased with increasing MPTS concentration, as indicated by reduced <i>K</i><sub>h</sub> and <i>W</i> parameters, while at 8% MPTS an extensive self-condensation of MPTS occurred. Adsorption hysteresis appeared for moisture sorption on silanized silica, especially at low relative humidity values and at low MPTS concentrations, which could be explained by a synergistic effect of the surface ─OH group content and pore characteristics. These results could aid our understanding of the applications of silane-modified silica particles.
DOI: 10.6084/m9.figshare.7975055
title: Anisotropic Strength of Granular Material Considering Fabric Evolution

description: Abstract The effect of fabric anisotropy on strength has not been considered in most strength criterions for granular material. Some criterions can describe the variation of material strength with stress-induced anisotropy, but micro-mechanism and physical meanings are undefined. Some criterions consider the effect of fabric anisotropy, but the evolution of fabric is ignored during loading by assuming a constant fabric tensor. Based on strength mechanical characteristics of granular material, in this paper, the relationship between macro stress and micro contact force of granular material is derived by micromechanics. Then, the concept of true stress tensor is proposed. An anisotropic strength criterion of granular material considering fabric evolution is established and its applicability is validated by comparing with test results for different granular materials. The analysis results indicate that the proposed anisotropic criterion can be utilized to describe the strength feature of anisotropic granular materials, which gives a way for the cause analysis of the strength of granular materials from the perspective of Microscopic mechanism.
DOI: 10.6084/m9.figshare.24615318
title: Raw data file of 15th set within 15th subject

description: Raw data file of 15th subject
DOI: 10.6084/m9.figshare.24615318.v1
title: Raw data file of 15th set within 15th subject

description: Raw data file of 15th subject
DOI: 10.6084/m9.figshare.24615321
title: Raw data file of 21-23 sets in 2nd scenario

description: Raw data file of 21-23 sets in 2nd scenario
DOI: 10.6084/m9.figshare.24615321.v1
title: Raw data file of 21-23 sets in 2nd scenario

description: Raw data file of 21-23 sets in 2nd scenario
DOI: 10.6084/m9.figshare.10075358
title: Zircon U-Pb-Hf isotopes and geochemistry of Jurassic igneous rocks from the southern Zhangguangcai Range, NE China: constraints on magmatism, petrogenesis and tectonic implications

description: In this study, we present new zircon U-Pb and Hf isotope data and geochemical analyses for Jurassic igneous rocks from the southern Zhangguangcai Range, NE China. In the context of our new U/Pb data together with other published data (n = 165), we recognize three major magmatic pulses in the eastern Songnen Block during the Jurassic: earliest Jurassic (200–195 Ma), late Early Jurassic (183–175 Ma) and early Late Jurassic (ca. 163 Ma). According to the petrological classification scheme, rocks are divided into two categories of andesite and I-type granitoids. Generally, Early Jurassic monzogranites have more evolved compositions with SiO<sub>2</sub>, Al<sub>2</sub>O<sub>3</sub>, and K<sub>2</sub>O+Na<sub>2</sub>O concentrations of 67–74 wt.%, 13.28–17.04 wt.% and 7.25–9.31 wt.%, respectively than Late Jurassic granodiorite. Early Jurassic andesite has SiO<sub>2</sub>, Al<sub>2</sub>O<sub>3</sub>, Na<sub>2</sub>O+K<sub>2</sub>O contents of 54.64–56 wt.%, 17.27–17.44 wt.% and 3.47–4.06 wt.%, respectively with low Mg# values of 0.18–0.26. In addition, all samples show enrichment in light rare earth elements (LREEs) and large-ion lithophile elements (LILEs) but depletion in high strength field elements (HSFEs, such as Nb, Ta, P and Ti) and low Sr/Y and (La/Yb)<sub>N</sub> ratios, all of which are characteristic of arc-type magmatic signatures. In view of the Hf isotope signatures, these rocks show high initial <sup>176</sup>Hf/<sup>177</sup>Hf ratios (0.282711–0.283069) corresponding to positive ε<sub>Hf</sub>(t) values (+0.39 to +13.66) and Neoproterozoic two-stage model ages (1154–550 Ma). In summary, the geochemical results suggest that the primary magmas of Jurassic granitoids were derived from variable degrees of partial melting of juvenile lower crust, whereas Early Jurassic andesite was derived from the partial melting of mantle wedge peridotite metasomatized by hydrous melts from subducting sediments and/or oceanic crust. The Jurassic arc-type magmatism in the eastern Songnen Block indicates that the Mudanjiang oceanic plate was still subducting in the Jurassic.
DOI: 10.6084/m9.figshare.7975055.v1
title: Anisotropic Strength of Granular Material Considering Fabric Evolution

description: Abstract The effect of fabric anisotropy on strength has not been considered in most strength criterions for granular material. Some criterions can describe the variation of material strength with stress-induced anisotropy, but micro-mechanism and physical meanings are undefined. Some criterions consider the effect of fabric anisotropy, but the evolution of fabric is ignored during loading by assuming a constant fabric tensor. Based on strength mechanical characteristics of granular material, in this paper, the relationship between macro stress and micro contact force of granular material is derived by micromechanics. Then, the concept of true stress tensor is proposed. An anisotropic strength criterion of granular material considering fabric evolution is established and its applicability is validated by comparing with test results for different granular materials. The analysis results indicate that the proposed anisotropic criterion can be utilized to describe the strength feature of anisotropic granular materials, which gives a way for the cause analysis of the strength of granular materials from the perspective of Microscopic mechanism.
DOI: 10.6084/m9.figshare.10075358.v1
title: Zircon U-Pb-Hf isotopes and geochemistry of Jurassic igneous rocks from the southern Zhangguangcai Range, NE China: constraints on magmatism, petrogenesis and tectonic implications

description: In this study, we present new zircon U-Pb and Hf isotope data and geochemical analyses for Jurassic igneous rocks from the southern Zhangguangcai Range, NE China. In the context of our new U/Pb data together with other published data (n = 165), we recognize three major magmatic pulses in the eastern Songnen Block during the Jurassic: earliest Jurassic (200–195 Ma), late Early Jurassic (183–175 Ma) and early Late Jurassic (ca. 163 Ma). According to the petrological classification scheme, rocks are divided into two categories of andesite and I-type granitoids. Generally, Early Jurassic monzogranites have more evolved compositions with SiO<sub>2</sub>, Al<sub>2</sub>O<sub>3</sub>, and K<sub>2</sub>O+Na<sub>2</sub>O concentrations of 67–74 wt.%, 13.28–17.04 wt.% and 7.25–9.31 wt.%, respectively than Late Jurassic granodiorite. Early Jurassic andesite has SiO<sub>2</sub>, Al<sub>2</sub>O<sub>3</sub>, Na<sub>2</sub>O+K<sub>2</sub>O contents of 54.64–56 wt.%, 17.27–17.44 wt.% and 3.47–4.06 wt.%, respectively with low Mg# values of 0.18–0.26. In addition, all samples show enrichment in light rare earth elements (LREEs) and large-ion lithophile elements (LILEs) but depletion in high strength field elements (HSFEs, such as Nb, Ta, P and Ti) and low Sr/Y and (La/Yb)<sub>N</sub> ratios, all of which are characteristic of arc-type magmatic signatures. In view of the Hf isotope signatures, these rocks show high initial <sup>176</sup>Hf/<sup>177</sup>Hf ratios (0.282711–0.283069) corresponding to positive ε<sub>Hf</sub>(t) values (+0.39 to +13.66) and Neoproterozoic two-stage model ages (1154–550 Ma). In summary, the geochemical results suggest that the primary magmas of Jurassic granitoids were derived from variable degrees of partial melting of juvenile lower crust, whereas Early Jurassic andesite was derived from the partial melting of mantle wedge peridotite metasomatized by hydrous melts from subducting sediments and/or oceanic crust. The Jurassic arc-type magmatism in the eastern Songnen Block indicates that the Mudanjiang oceanic plate was still subducting in the Jurassic.
DOI: 10.6084/m9.figshare.24615327
title: Raw data file of 9th set within 9th subject

description: Raw data file of 9th subject
DOI: 10.6084/m9.figshare.24615327.v1
title: Raw data file of 9th set within 9th subject

description: Raw data file of 9th subject
DOI: 10.6084/m9.figshare.24615330
title: Raw data file of 11th set within 11th subject

description: Raw data file of 11th subject
DOI: 10.6084/m9.figshare.24615330.v1
title: Raw data file of 11th set within 11th subject

description: Raw data file of 11th subject
DOI: 10.34808/dmq0-dj47
title: Photocatalytic ethylene decomposition with the use of fluidized bed photoreactor

description: Data contain exported raw data recorded during decomposition of ethylene during utilization of fluidized bed photoreactor equipped with either UV-LEDs or fluorescent UV lamps as well as in either humid or dry conditions. In separate folder, the photographs of the photocatalytic system were included. As photocatalytic material, polystyrene spheres coated with SiO2 and/or TiO2 layer were used. The detailed dataset list was described in measurement info.txt file. Chromatograms were recorded using SRI 8610C Gas Chromatograph equipped with FID detector. Sampling was realised via the dosing sample loop.
DOI: 10.6084/m9.figshare.24615336
title: Raw data file of 14th set within 14th subject

description: Raw data file of 14th subject
DOI: 10.6084/m9.figshare.24615336.v1
title: Raw data file of 14th set within 14th subject

description: Raw data file of 14th subject
DOI: 10.6084/m9.figshare.6401918.v1
title: Additional file 3: of Transcriptomics reveals the molecular processes of light-induced rapid darkening of the non-obligate cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura) and their genetic basis of pigmentation strategy

description: Table S2. Unigene annotation details. (XLSX 49576 kb)