cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14325336.v1
title: A machine learning based approach for efficient safety evaluation of the high speed train and short span bridge system

description: Abstract The dynamic responses of the high-speed railway bridge under the train passage can greatly affect the safety of the entire high-speed train and bridge system. Traditionally, these responses are obtained using either field measurement or numerical analysis. Both tools have their own limitations. For instance, the coupling dynamic train-bridge analysis is generally complicated and time-consuming. This paper proposes a novel machine learning based approach for efficient safety evaluation of the high speed train and short span bridge system. Artificial neural networks are established to map the complicated train-bridge system and to attain the critical bridge displacements. The proposed approach incorporates a complete numerical train-bridge system model to produce reliable data for the neural network training, considering multiple significant random features in the train-bridge system. Various neural network architectures are investigated and compared to find optimal ones that have considerable potentials in realizing online response prediction and safety evaluation. Although the proposed approach focuses on the high-speed train and short span bridge, the methodology is general and can also be applied to other scenarios associated with the vehicle-bridge systems.
DOI: 10.6084/m9.figshare.6461165
title: Additional file 1 of Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

description: Table S1. A pairwise genome comparison matrix of SNP differences for E. coli ST131. (XLS 34 kb)
DOI: 10.6084/m9.figshare.14325236
title: Analytical solution of circular tunnel in elastic-viscoplastic rock mass

description: Abstract This paper deals with a deep circular tunnel excavated in infinite homogeneous and isotropic elasto-viscoplastic rock mass subjected to a hydrostatic initial stresses. The tunnel is divided into the initial plastic, viscoplastic, and elastic zones. By combining the generalized Bingham model with Mohr-Coulomb yield criteria, analytical solutions of the circular tunnel are derived with the consideration of non-associated flow rule and elasto-viscoplasticity. The initial plastic zone is defined as the instantaneous change of rock mass excavation. Based on the initial plastic zone, the stresses in viscoplastic zone are transferred to the deep surrounding rock with time due to the initial earth stresses. The results are compared with the elastic-brittle solution at static conditions, and the solutions of this paper are validated. Moreover, the presented results shows that the stress and displacement of the surrounding rock varies with time, and the solutions can be obtained at different instants of time.
DOI: 10.6084/m9.figshare.6461072
title: Additional file 11: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: Predicted TF targets from top 1 million edges in each tissue. “max _tissue” means which tissue has the highest number of interactions. “CV” is the coefficient of variance. (XLSX 76 kb)
DOI: 10.6084/m9.figshare.6985082.v1
title: photoluminescence from High-sensitive and fast response to 255 nm deep-UV light of CH<sub>3</sub>NH<sub>3</sub>PbX<sub>3</sub> (X = Cl, Br, I) bulk crystals

description: Original data of the photoluminescence spectra of the sample
DOI: 10.6084/m9.figshare.14325236.v1
title: Analytical solution of circular tunnel in elastic-viscoplastic rock mass

description: Abstract This paper deals with a deep circular tunnel excavated in infinite homogeneous and isotropic elasto-viscoplastic rock mass subjected to a hydrostatic initial stresses. The tunnel is divided into the initial plastic, viscoplastic, and elastic zones. By combining the generalized Bingham model with Mohr-Coulomb yield criteria, analytical solutions of the circular tunnel are derived with the consideration of non-associated flow rule and elasto-viscoplasticity. The initial plastic zone is defined as the instantaneous change of rock mass excavation. Based on the initial plastic zone, the stresses in viscoplastic zone are transferred to the deep surrounding rock with time due to the initial earth stresses. The results are compared with the elastic-brittle solution at static conditions, and the solutions of this paper are validated. Moreover, the presented results shows that the stress and displacement of the surrounding rock varies with time, and the solutions can be obtained at different instants of time.
DOI: 10.6084/m9.figshare.6461096
title: Additional file 13: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: Key TFs in four tissues. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6461189
title: Additional file 1: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: RNA-Seq libraries used in this analysis. (XLSX 71Â kb)
DOI: 10.6084/m9.figshare.14325254
title: Experimental study of the seismic behavior of an existing bridge abutment located on soft clay deposits

description: Abstract In this study, a dynamic centrifuge experiment is designed to investigate the seismic behavior of an existing bridge subjected to the earthquake-induced lateral movement of soft clay soil. The pile-supported bridge abutment at the movable bearing side is modeled at the 1/75 scale. The material and thickness of the soft clay layer are set as the experimental parameters. Under the effect of the lateral movement of the soft clay layer during base shaking, a collision between the bridge abutment wall and the girder occurs, and the bridge abutment wall is restrained at the top; however, the footing largely moves forward, resulting in the large backward inclination of the bridge abutment wall. In addition, it is confirmed that during base shaking, the pile bending moment largely increases due to the ground lateral movement and then remains nearly constant, even at the end of the base shaking phase. Furthermore, it is found that when the soft clay has a high shear strength, the ground lateral movement may cause a high pile earth pressure, resulting in the large corresponding internal bending moment on the pile sections; however, when the soft clay layer is very thick, the high pile earth pressure generally occurs locally, instead of along the whole pile length.
DOI: 10.6084/m9.figshare.14325254.v1
title: Experimental study of the seismic behavior of an existing bridge abutment located on soft clay deposits

description: Abstract In this study, a dynamic centrifuge experiment is designed to investigate the seismic behavior of an existing bridge subjected to the earthquake-induced lateral movement of soft clay soil. The pile-supported bridge abutment at the movable bearing side is modeled at the 1/75 scale. The material and thickness of the soft clay layer are set as the experimental parameters. Under the effect of the lateral movement of the soft clay layer during base shaking, a collision between the bridge abutment wall and the girder occurs, and the bridge abutment wall is restrained at the top; however, the footing largely moves forward, resulting in the large backward inclination of the bridge abutment wall. In addition, it is confirmed that during base shaking, the pile bending moment largely increases due to the ground lateral movement and then remains nearly constant, even at the end of the base shaking phase. Furthermore, it is found that when the soft clay has a high shear strength, the ground lateral movement may cause a high pile earth pressure, resulting in the large corresponding internal bending moment on the pile sections; however, when the soft clay layer is very thick, the high pile earth pressure generally occurs locally, instead of along the whole pile length.
DOI: 10.6084/m9.figshare.12752288
title: Additional file 5 of Hypomethylation in HBV integration regions aids non-invasive surveillance to hepatocellular carcinoma by low-pass genome-wide bisulfite sequencing

description: Additional file 5:. Table S4. Clinical information of 54 individuals by low-pass WGBS.
DOI: 10.6084/m9.figshare.12752291
title: Additional file 6 of Hypomethylation in HBV integration regions aids non-invasive surveillance to hepatocellular carcinoma by low-pass genome-wide bisulfite sequencing

description: Additional file 6:. Table S5. The statistical information of 54 cfDNA samples by low-pass WGBS.
DOI: 10.6084/m9.figshare.14325270.v1
title: Free vibration analysis and optimal design of adhesively bonded double-strap joints by using artificial neural networks

description: Abstract This study investigates the free vibration characteristics of an adhesively bonded double-strap joint with viscoelastic adhesive layer. To simplify the spatial finite element mesh generation and efficiently model the adhesively bonded joint, a layerwise plate finite element was extended to accommodate to the modeling of the joint, where the joint structure is treated as a special sandwich laminate. The proposed method was validated by three-dimensional finite element analysis and then applied to generate sampling points for training artificial neural networks (ANNs). The effects of the adhesive material properties and joint geometrical parameters on the joint dynamic characteristics were investigated in detail using the trained ANNs. The optimum design problem is defined as a multi-objective optimization problem considering maximizing the first natural frequency and corresponding loss factor while minimizing the total structural weight. The nondominated sorting genetic algorithm combined with the ANNs were employed to tackle the problem. The proposed method provides a computationally efficient alternative for analyzing and optimizing the adhesive double-strap joints.
DOI: 10.6084/m9.figshare.14325297
title: Mechanical properties modeling of severely plastically deformed biodegradable ZK60 magnesium alloy for bone implants

description: Abstract The effectiveness of magnesium (Mg) alloys to improve the capability of bone tissue generation may be severely diminished if the required mechanical properties are not provided. Here, the effort is directed to model the mechanical performance of severely plastically deformed biodegradable ZK60 Mg alloy in bone regeneration protocols. For this purpose, the effects of parallel tubular channel angular pressing (PTCAP) on yield strength (σ YS ), ultimate tensile strength (σ UTS ), and elongation to failure (δ) were addressed. Given the multifaceted variables of the PTCAP with nonlinear interactions, a precise determination of the mechanical properties requires a large number of experiments. Therefore, gene expression programming (GEP) and genetic programming (GP) models were proposed to achieve appropriate combinations of mechanical properties for bone implant purposes based on a rational hypothesis that for correlation coefficient (|R|) higher than 0.8, a strong correlation is established between the predicted and measured values. The results verified that the highest mechanical performance was achieved at the second pass of PTCAP, thus has a great potential to be the most promising candidate for biodegradable implant material. Besides, the proposed models were capable of precisely predicting the mechanical performance of the SPD-processed biodegradable ZK60 Mg.
DOI: 10.6084/m9.figshare.14325342
title: Investigating the Relationship between the Brittleness Index and Crack Initiation Stress for the Granite under Triaxial Compression

description: Abstract The brittle failure of rock is closely related to the rock crack initiation, propagation, coalescences and nucleation. Although many brittleness indexes have been proposed to describe the brittle behavior of rocks, the relationship between the brittleness index and crack initiation stress under triaxial compressive states has not been fully understood. This paper introduced the current main brittleness indexes and discussed their applicabilities for triaxial compressive tests. Granite specimens from a gold mine are prepared for experimental tests. The triaxial compressive tests are carried out on stiff testing machine and the confining pressures are 5 to 110 MPa. Experimental results on the stress-strain curves show that the post-peak behaviors of the granite under confining pressures are in Class I and Class II types. The brittleness indexes, crack initiation stress, compressive strength, elastic moduls and Poisson’s ratio of the granite are obtained and discussed. It has been found that, the crack initiation stress linearly increases with the increasing of confining pressure. Moreover, a power function can describe the relationship between the brittleness index and crack initiation stress for Class I rock behavior while an exponential function can describe the relationship between the brittleness index and crack initiation stress for Class II rock behavior.
DOI: 10.6084/m9.figshare.6461027.v1
title: Additional file 1: of Chromosome painting and its applications in cultivated and wild rice

description: The chromosome 9-specific oligo sequence data. (BED 1827 kb)
DOI: 10.6084/m9.figshare.20086052.v1
title: Additional file 1 of The study of direct and indirect effects of radiofrequency ablation on tumor microenvironment in liver tumor animal model

description: Additional file 1.
DOI: 10.6084/m9.figshare.6461153.v1
title: Additional file 16: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: GO enrichment analysis for the largest module in leaf detected by MCL. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6461171
title: Additional file 17: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: A short tutorial on visualize mGRN data in Cytoscape and R. (HTML 3228 kb)
DOI: 10.6084/m9.figshare.6461027
title: Additional file 1: of Chromosome painting and its applications in cultivated and wild rice

description: The chromosome 9-specific oligo sequence data. (BED 1827 kb)
DOI: 10.6084/m9.figshare.6461096.v1
title: Additional file 13: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: Key TFs in four tissues. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6461165.v2
title: Additional file 1 of Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

description: Table S1. A pairwise genome comparison matrix of SNP differences for E. coli ST131. (XLS 34 kb)
DOI: 10.6084/m9.figshare.6461183
title: Additional file 2 of Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

description: Table S2. A pairwise genome comparison matrix of SNP differences for E. coli ST10 clonal complex. (XLS 29 kb)
DOI: 10.6084/m9.figshare.6461189.v1
title: Additional file 1: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: RNA-Seq libraries used in this analysis. (XLSX 71Â kb)
DOI: 10.6084/m9.figshare.6461171.v1
title: Additional file 17: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: A short tutorial on visualize mGRN data in Cytoscape and R. (HTML 3228 kb)
DOI: 10.6084/m9.figshare.8033720.v1
title: Fibroblasts rescue oral squamous cancer cell from metformin-induced apoptosis via alleviating metabolic disbalance and inhibiting AMPK pathway

description: Metformin is an antidiabetic drug widely used for the treatment of type 2 diabetes. Growing evidence suggests that it may exert antitumor effects <i>in vivo</i> and <i>in vitro</i>. However, even with the promising potency on defeating cancer cells, the pre-clinical and epidemiological studies of metformin on various kinds of cancers are not satisfactory, and the reasons and underlying mechanisms remain unknown. Since cancer is a complex system, dependent on a promoting microenvironment, we hypothesize that the interactions between cancer cells and their neighborhood fibroblasts are essential for metformin resistance. To test this, we used a cell co-culture model closely mimicking the <i>in vivo</i> interactions and metabolic exchanges between normal stromal cells (NOFs) and oral squamous cancer cells (OSCC). Here we show that while metformin can significantly inhibit cell growth and induce apoptosis of OSCC cultured alone in a dose-dependent manner through activating p-AMPK<sup>T172</sup> and modulating Bcl-2, Bax, and cleaved PARP. However, when OSCC are co-cultured with NOFs the metformin effects on OSCC cells are annihilated. NOFs are rescuing OSCC from metformin – induced apoptosis, at least partially, through inhibiting the activity of AMPK and PARP, maintaining mitochondrial membrane potential and increasing the oxidative stress. Our results indicate that metformin effects on oral cancer cells are modulated by the microenvironment and that this has to be taken into consideration in the context of developing a new combination of drugs for oral cancer treatment.
DOI: 10.6084/m9.figshare.14325355.v1
title: Fragmentation Characteristics and Damage Capacity of Radial Layered PELE

description: Abstract PELE (the Penetrator with Enhanced Lateral Effect) produces a large number of fragments after penetrating metal target plate, which can damage the high-value targets behind the shield plate in a large area. However, when facing the multi-layer spaced metal shield plates, it is difficult to penetrate them and damage the targets behind them due to the limited penetration ability of the fragments. Radial layered PELE was designed for damaging multi-layer spaced metal plates. The experiment and numerical simulation were carried out to study the deformation and fragmentation of the penetrator after penetrating 2A12 aluminum alloy or Q235 steel target plate at different velocities, as well as the damage to the witness plates after penetrating the main target plates. The results show that the fragmentation of PELE increases with the increase of impact velocity. At the same impact velocity and the same thickness of metal target plate, compared with penetrating the 2A12 aluminum alloy target plate, radial layered PELE is deformed and broken to a greater extent, resulting in heavier damage to the witness plates when penetrating the Q235 steel target plate. In the process of penetrating multi-layer metal target plates, the outer jacket of radial layered PELE is gradually broken to form a large number of flying fragments, but the inner jacket is difficult to deform and break, resulting in the strong penetration ability of the penetrator. Therefore, radial layered PELE has better penetration and damage capacity than non layered PELE.
DOI: 10.6084/m9.figshare.6461153
title: Additional file 16: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: GO enrichment analysis for the largest module in leaf detected by MCL. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.14325355
title: Fragmentation Characteristics and Damage Capacity of Radial Layered PELE

description: Abstract PELE (the Penetrator with Enhanced Lateral Effect) produces a large number of fragments after penetrating metal target plate, which can damage the high-value targets behind the shield plate in a large area. However, when facing the multi-layer spaced metal shield plates, it is difficult to penetrate them and damage the targets behind them due to the limited penetration ability of the fragments. Radial layered PELE was designed for damaging multi-layer spaced metal plates. The experiment and numerical simulation were carried out to study the deformation and fragmentation of the penetrator after penetrating 2A12 aluminum alloy or Q235 steel target plate at different velocities, as well as the damage to the witness plates after penetrating the main target plates. The results show that the fragmentation of PELE increases with the increase of impact velocity. At the same impact velocity and the same thickness of metal target plate, compared with penetrating the 2A12 aluminum alloy target plate, radial layered PELE is deformed and broken to a greater extent, resulting in heavier damage to the witness plates when penetrating the Q235 steel target plate. In the process of penetrating multi-layer metal target plates, the outer jacket of radial layered PELE is gradually broken to form a large number of flying fragments, but the inner jacket is difficult to deform and break, resulting in the strong penetration ability of the penetrator. Therefore, radial layered PELE has better penetration and damage capacity than non layered PELE.
DOI: 10.6084/m9.figshare.6461183.v2
title: Additional file 2 of Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

description: Table S2. A pairwise genome comparison matrix of SNP differences for E. coli ST10 clonal complex. (XLS 29 kb)
DOI: 10.6084/m9.figshare.6461201
title: Additional file 2: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: GO enrichment analysis for tissue-specific genes in four tissue GRNs. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.6461201.v1
title: Additional file 2: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

description: GO enrichment analysis for tissue-specific genes in four tissue GRNs. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.14843175
title: Additional file 2 of The dynamics of N6-methyladenine RNA modification in interactions between rice and plant viruses

description: Additional file 2: Table S1. Primers used for RSV and RBSDV detections in this study. Table S2. Sequenced and rice genome mapped reads in m6A-IP-seq, input RNA-seq rice samples. Table S3. Nucleotide localization and enrichment of the top 10 m6A peaks identified in Mock-, RSV-, and RBSDV-infected rice transcripts by m6A-IP-Seq. Table S4. The category of the differential m6A peaks upon two viruses' infection in rice. Table S5. Nucleotide localization and enrichment of the m6A peaks identified in RSV and RBSDV genomics by m6A-IP-Seq. Table S6. Gene ID and their fpkm analyses. Table S7. Different peaks statistic. Table S8. The m6A peaks appeared in different treatments. Table S9. The most abundant consensus motif in Mock, RSV-, and RBSDV-infected rice plant using suite of DREME and MEME. Table S10. Analyses of the m6A peaks that containing most four common consensus appeared in other species. Table S11. Detail information of ListHits Gene and m6A methylated genes under rice viruses’ infection derived from Additional file 2: Table S16. Table S12. Integrated analyses of the m6A methylation related genes with m6A modifications and expression profiles. Table S13. Integrated analyses of the anti-viral RNA silencing pathway related genes with m6A modification and expression profile. Table S14. Integrated analyses of the plant hormone metabolic genes with m6A modifications and expression profiles. Table S15. Integrated analyses of the relationship betwwen relative expression and m6A positions. Table S16. Summary of the m6A RNA methylation level in enriched top 5 KEGG pathways related genes from RNA-seq under rice viruses’ infection. Table S17. Detail information of the common m6A methylated genes appeared in enriched top 5 KEGG pathways under rice viruses' infection. Table S18. Primers used for qRT-PCR validation of the methylation of OsAGO18 and OsSLRL1 genes. Table S19. Primers used in qRT-PCR qualification of the candidate genes.