Publications by authors named "Yixin Cao"

17 Publications

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X-Ray Tomography Investigation of Cyclically Sheared Granular Materials.

Phys Rev Lett 2021 Jan;126(4):048002

School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.

We perform combined x-ray tomography and shear force measurements on a cyclically sheared granular system with highly transient behaviors, and obtain the evolution of microscopic structures and macroscopic shear force during the shear cycle. We explain the macroscopic behaviors of the system based on microscopic processes, including particle level structural rearrangement and frictional contact variation. Specifically, we show how contact friction can induce large structural fluctuations and cause significant shear dilatancy effect for granular materials, and we also construct an empirical constitutive relationship for the macroscopic shear force.
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http://dx.doi.org/10.1103/PhysRevLett.126.048002DOI Listing
January 2021

Upregulated lncRNA DLX6-AS1 underpins hepatocellular carcinoma progression via the miR-513c/Cul4A/ANXA10 axis.

Cancer Gene Ther 2021 May 4;28(5):486-501. Epub 2020 Dec 4.

Department of Oncology, The First Affiliated Hospital of Nanchang University, 330006, Nanchang, P.R. China.

Recent studies have illustrated the role of aberrant regulatory interactions in the mediation of malignant phenotypes of cancer cells, which could potentially provide novel therapeutic targets to limit the destructive recurrence and metastasis of hepatocellular carcinoma (HCC). Herein, we clarify the oncogenic role of the long noncoding RNA (lncRNA) distal-less homeobox 6 antisense 1 (DLX6-AS1) in HCC in vivo and in vitro. To this end, we knocked down lncRNA DLX6-AS1 and manipulated the expression of miR-513c to characterize their effects in HCC cell viability, migration, invasion, and apoptosis. Furthermore, we probed the interactions with miR-513c's target gene Cullin4A (Cul4A) and the degradation of Annexin A10 (ANXA10) protein. Our data show that lncRNA DLX6-AS1 and Cul4A were highly expressed, while miR-513c and ANXA10 were poorly expressed in HCC tissues and cells. Moreover, the silencing of lncRNA DLX6-AS1 impeded the viability, invasion, and migration of HCC cells, while stimulating cell apoptosis. Further data indicated that lncRNA DLX6-AS1 targeted and repressed miR-513c expression, where the tumor-inhibiting effects of lncRNA DLX6-AS1 silencing was achieved by elevating miR-513c expression. Importantly, the lncRNA DLX6-AS1 upregulated the expression of Cul4A through sponging of miR-513c. The silencing of Cul4A restricted the malignant phenotypes of HCC cells by repressing the ubiquitination-mediated degradation of ANXA10. In vivo experiments verified that lncRNA DLX6-AS1 promoted the progression of HCC through the miR-513c/Cul4A/ANXA10 axis. Thus, the silencing of lncRNA DLX6-AS1 impaired miR-513c-dependent Cul4A inhibition and subsequently elevated ubiquitination-mediated degradation of ANXA10, thereby preventing the occurrence and development of HCC.
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http://dx.doi.org/10.1038/s41417-020-00233-0DOI Listing
May 2021

Fluorescent sensing film decorated with ratiometric probe for visual and recyclable monitoring of Cu.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Mar 16;249:119217. Epub 2020 Nov 16.

Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Lab of Tissue Engineering, the College of Life Sciences, Faculty of Life Science & Medicine, Northwest University, Xi'an, Shaanxi Province 710069, China. Electronic address:

Specifically, visually, and quantitatively monitor copper ion (Cu) is critical in the area of biological and environmental detection. Herein, a ratiometric fluorescent probe with benzoxazole appended xanthenes skeleton was constructed and further employed to monitor Cu in Hela cells, real water samples, and test strips. An easily distinguishable colorimetric (colorless to red) and fluorescence (green to red) change could be observed by naked eye under the portable UV lamp (365 nm) and the changes could be recovered by adding S. Furthermore, electrospinning technique was employed to fabricate a probe composited fluorescent sensing film (PMMA) for realizing the visual and recyclable monitoring of Cu, indicating that the probe-composited fluorescent sensing film has great potential for on-site and naked-eye detection of Cu in practical.
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http://dx.doi.org/10.1016/j.saa.2020.119217DOI Listing
March 2021

Amelioration of nonalcoholic fatty liver disease by swertiamarin in fructose-fed mice.

Phytomedicine 2019 Jun 10;59:152782. Epub 2018 Dec 10.

Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an 710069, China; Biomedicine Key Laboratory of Shaanxi Province, College of Life Science, Northwest University, Xi'an 710069, China.

Background: Nonalcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver disease. Swertia bimaculata (Sieb. et Zucc.) Hook. Thoms.ex Clarke, a glabrous or procumbent perennial herb, is a traditional herb medicine. Swertiamarin, a secoiridoid glycoside, is a representative ingredient in this medical plant crude extract and shows antidiabetic and antihyperlipidaemic activities and protective effect against hepatic injury.

Purpose: The present study aimed to determine whether swertiamarin can attenuate NAFLD in fructose-fed mice.

Methods: Healthy male mice freely drank water containing 10% fructose for 12 consecutive weeks, whereas animals in those swertiamarin tested groups received different doses of swertiamarin (25, 50 and 100 mg/kg) by intragastric administration once a day from the ninth week to the twelfth week.

Results: At the end of the experiment, fructose-fed mice administrated with swertiamarin showed low levels of serum glucose, triglycerides, uric acid, alanine aminotransferase and aspartate transaminase. Histological examinations suggested the alleviation of hepatic ballooning degeneration and steatosis by swertiamarin treatment. Moreover, swertiamarin administration mitigated hepatic oxidative stress along with decreases of hepatic pro-inflammation cytokines, which was associated with decrease of hepatic xanthine oxidase (XO) activity and enhancements of anti-oxidant defense system enzymes, as well as activation of nuclear factor E2-related factor 2 (Nrf2) in fructose-fed mice. In addition, swertiamarin down-regulated expression of sterol-regulatory element-binding protein-1 (SREBP-1), fatty acid synthase (FAS) and acetyl-CoA carboxylase 1 (ACC1) in liver of fructose-fed mice.

Conclusion: The present study demonstrates that swertiamarin alleviates NAFLD and metabolic alterations in fructose-fed mice.
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http://dx.doi.org/10.1016/j.phymed.2018.12.005DOI Listing
June 2019

Aquaporins Alteration Profiles Revealed Different Actions of Senna, Sennosides, and Sennoside A in Diarrhea-Rats.

Int J Mol Sci 2018 Oct 17;19(10). Epub 2018 Oct 17.

Key Laboratory of Resource Biology and Modern Biotechnology in Western China, Ministry of Education, Northwest University, No. 229 TaiBai North Road, Xi'an 710069, China.

Senna and its main components sennosides are well-known effective laxative drugs and are used in the treatment of intestinal constipation in the world. Their potential side effects have attracted more attention in clinics but have little scientific justification. In this study, senna extract (SE), sennosides (SS), and sennoside A (SA) were prepared and used to generate diarrhea rats. The diarrhea rats were investigated with behaviors, clinical signs, organ index, pathological examination, and gene expression on multiple aquaporins () including , , , , , , , , , and . Using qRT-PCR, the expression profiles were constructed for six organs including colon, kidney, liver, spleen, lung, and stomach. The alteration profiles were characterized and was performed with Principle Component Analysis (PCA). The SE treatments on the rats resulted in a significant body weight loss ( < 0.001), significant increases ( < 0.001) on the kidney index (27.72%) and liver index (42.55%), and distinguished changes with up-regulation on expressions in the kidneys and livers. The SS treatments showed prominent laxative actions and down regulation on expression in the colons. The study results indicated that the SE had more influence/toxicity on the kidneys and livers. The SS showed more powerful actions on the colons. We suggest that the caution should be particularly exercised in the patients with kidney and liver diseases when chronic using senna-based products.
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http://dx.doi.org/10.3390/ijms19103210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6213963PMC
October 2018

Structural and topological nature of plasticity in sheared granular materials.

Nat Commun 2018 07 25;9(1):2911. Epub 2018 Jul 25.

School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, 200240, China.

Upon mechanical loading, granular materials yield and undergo plastic deformation. The nature of plastic deformation is essential for the development of the macroscopic constitutive models and the understanding of shear band formation. However, we still do not fully understand the microscopic nature of plastic deformation in disordered granular materials. Here we used synchrotron X-ray tomography technique to track the structural evolutions of three-dimensional granular materials under shear. We establish that highly distorted coplanar tetrahedra are the structural defects responsible for microscopic plasticity in disordered granular packings. The elementary plastic events occur through flip events which correspond to a neighbor switching process among these coplanar tetrahedra (or equivalently as the rotation motion of 4-ring disclinations). These events are discrete in space and possess specific orientations with the principal stress direction.
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http://dx.doi.org/10.1038/s41467-018-05329-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060108PMC
July 2018

Translational and Rotational Dynamical Heterogeneities in Granular Systems.

Phys Rev Lett 2018 Jul;121(1):018002

School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.

We use x-ray tomography to investigate the translational and rotational dynamical heterogeneities of a three dimensional hard ellipsoid granular packing driven by oscillatory shear. We find that particles which translate quickly form clusters with a size distribution given by a power law with an exponent that is independent of the strain amplitude. Identical behavior is found for particles that are translating slowly, rotating quickly, or rotating slowly. The geometrical properties of these four different types of clusters are the same as those of random clusters. Different cluster types are considerably correlated or anticorrelated, indicating a significant coupling between translational and rotational degrees of freedom. Surprisingly, these clusters are formed already at time scales that are much shorter than the α-relaxation time, in stark contrast to the behavior found in glass-forming systems.
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http://dx.doi.org/10.1103/PhysRevLett.121.018002DOI Listing
July 2018

Granular materials flow like complex fluids.

Nature 2017 11 1;551(7680):360-363. Epub 2017 Nov 1.

School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.

Granular materials such as sand, powders and foams are ubiquitous in daily life and in industrial and geotechnical applications. These disordered systems form stable structures when unperturbed, but in the presence of external influences such as tapping or shear they 'relax', becoming fluid in nature. It is often assumed that the relaxation dynamics of granular systems is similar to that of thermal glass-forming systems. However, so far it has not been possible to determine experimentally the dynamic properties of three-dimensional granular systems at the particle level. This lack of experimental data, combined with the fact that the motion of granular particles involves friction (whereas the motion of particles in thermal glass-forming systems does not), means that an accurate description of the relaxation dynamics of granular materials is lacking. Here we use X-ray tomography to determine the microscale relaxation dynamics of hard granular ellipsoids subject to an oscillatory shear. We find that the distribution of the displacements of the ellipsoids is well described by a Gumbel law (which is similar to a Gaussian distribution for small displacements but has a heavier tail for larger displacements), with a shape parameter that is independent of the amplitude of the shear strain and of the time. Despite this universality, the mean squared displacement of an individual ellipsoid follows a power law as a function of time, with an exponent that does depend on the strain amplitude and time. We argue that these results are related to microscale relaxation mechanisms that involve friction and memory effects (whereby the motion of an ellipsoid at a given point in time depends on its previous motion). Our observations demonstrate that, at the particle level, the dynamic behaviour of granular systems is qualitatively different from that of thermal glass-forming systems, and is instead more similar to that of complex fluids. We conclude that granular materials can relax even when the driving strain is weak.
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http://dx.doi.org/10.1038/nature24062DOI Listing
November 2017

Origin of Noncubic Scaling Law in Disordered Granular Packing.

Phys Rev Lett 2017 Jun 9;118(23):238002. Epub 2017 Jun 9.

Department of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.

Recent diffraction experiments on metallic glasses have unveiled an unexpected noncubic scaling law between density and average interatomic distance, which led to the speculation of the presence of fractal glass order. Using x-ray tomography we identify here a similar noncubic scaling law in disordered granular packing of spherical particles. We find that the scaling law is directly related to the contact neighbors within the first nearest neighbor shell, and, therefore, is closely connected to the phenomenon of jamming. The seemingly universal scaling exponent around 2.5 arises due to the isostatic condition with a contact number around 6, and we argue that the exponent should not be universal.
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http://dx.doi.org/10.1103/PhysRevLett.118.238002DOI Listing
June 2017

The structural origin of the hard-sphere glass transition in granular packing.

Nat Commun 2015 Sep 28;6:8409. Epub 2015 Sep 28.

Department of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.

Glass transition is accompanied by a rapid growth of the structural relaxation time and a concomitant decrease of configurational entropy. It remains unclear whether the transition has a thermodynamic origin, and whether the dynamic arrest is associated with the growth of a certain static order. Using granular packing as a model hard-sphere glass, we show the glass transition as a thermodynamic phase transition with a 'hidden' polytetrahedral order. This polytetrahedral order is spatially correlated with the slow dynamics. It is geometrically frustrated and has a peculiar fractal dimension. Additionally, as the packing fraction increases, its growth follows an entropy-driven nucleation process, similar to that of the random first-order transition theory. Our study essentially identifies a long-sought-after structural glass order in hard-sphere glasses.
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http://dx.doi.org/10.1038/ncomms9409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598628PMC
September 2015

In-line phase-contrast and grating-based phase-contrast synchrotron imaging study of brain micrometastasis of breast cancer.

Sci Rep 2015 Mar 30;5:9418. Epub 2015 Mar 30.

Department of Breast Surgery, Breast Cancer Institute, Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.

Current bio-medical imaging researches aim to detect brain micrometastasis in early stage for its increasing incidence and high mortality rates. Synchrotron phase-contrast imaging techniques, such as in-line phase-contrast (IPC) and grating-based phase-contrast (GPC) imaging, could provide a high spatial and density imaging study of biological specimens' 3D structures. In this study, we demonstrated the detection efficiencies of these two imaging tools on breast cancer micrometastasis in an ex vivo mouse brain. We found that both IPC and GPC can differentiate abnormal brain structures induced by micrometastasis from the surrounding normal tissues. We also found that GPC was more sensitive in detecting the small metastasis as compared to IPC.
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http://dx.doi.org/10.1038/srep09418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377630PMC
March 2015

Angularly anisotropic correlation in granular packings.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Dec 1;90(6):062201. Epub 2014 Dec 1.

Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA.

We present an x-ray microtomography study of the three-dimensional structural correlations in monodisperse granular packings. By measuring an orientation-dependent pair correlation function, we find that the local structure shows an angularly anisotropic orientation correlation. The correlation is strongest along the major axis of the local Minkowski tensor of the Voronoi cell. It turns out that this anisotropic correlation is consistent with the existence of some locally favored structures. The study suggests the importance of high-order structural correlations in random granular packings.
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http://dx.doi.org/10.1103/PhysRevE.90.062201DOI Listing
December 2014

Similarity of wet granular packing to gels.

Nat Commun 2014 Sep 23;5:5014. Epub 2014 Sep 23.

Department of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.

To date, there is still no general consensus on the fundamental principle that governs glass transition. Colloidal suspensions are ordinarily utilized as model systems to study the dynamical arrest mechanisms in glass or gels. Here, we tackle the problem using athermal granular particles. Slow dynamics and structural evolution of granular packing upon tapping are monitored by fast X-ray tomography. When the packing are wet and short-range attractive interactions exist, we find a large amount of locally favoured structures with fivefold symmetry, which bear great structural similarity to colloidal gels. In addition, these structures are almost absent in dry packing with similar packing fractions. The study leads strong support for the geometrical frustration mechanism for dynamic arrest in both thermal and athermal systems with attractive interactions. It also suggests nontrivial structural mechanism, if exists, for dynamic arrest in systems with purely repulsive interactions.
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http://dx.doi.org/10.1038/ncomms6014DOI Listing
September 2014

X-ray tomography study of the random packing structure of ellipsoids.

Soft Matter 2014 Feb;10(7):990-6

We present an X-ray tomography study for the random packing of ellipsoids. The local structure displays short-range correlations. In addition to the contact number Z, we introduce ρshell, the average contact radius of curvature for contacting neighbors, as an additional parameter to characterize the local orientational geometry. In general, the local free volume w is affected by both Z and ρshell. We believe that the particle asphericity induces a polydispersity effect to influence the packing properties. A model is introduced which explicitly maps the ellipsoid packing onto a polydispersed sphere one, and it reproduces most of the experimental observations.
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http://dx.doi.org/10.1039/c3sm52841cDOI Listing
February 2014

A dynamic synchrotron X-ray imaging study of effective temperature in a vibrated granular medium.

Soft Matter 2014 Aug 16;10(29):5398-404. Epub 2014 Jun 16.

Department of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China.

We present a dynamic synchrotron X-ray imaging study of the effective temperature Teff in a vibrated granular medium. By tracking the directed motion and the fluctuation dynamics of the tracers inside, we obtained Teff of the system using the Einstein relationship. We found that as the system unjams with increasing vibration intensities Γ, the structural relaxation time τ increases substantially which can be fitted by an Arrhenius law using Teff. And the characteristic energy scale of structural relaxation yielded by the Arrhenius fitting is E = 0.20 ± 0.02pd(3), where p is the pressure and d is the background particle diameter, which is consistent with those from hard sphere simulations in which the structural relaxation happens via the opening up of free volume against pressure.
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http://dx.doi.org/10.1039/c4sm00602jDOI Listing
August 2014

Identifying overlapping communities as well as hubs and outliers via nonnegative matrix factorization.

Sci Rep 2013 Oct 21;3:2993. Epub 2013 Oct 21.

1] School of Computer Science and Technology, Tianjin University, Tianjin 300072, China [2] State Key Laboratory of Information Security, Institute of Information Engineering, Chinese Academy of Sciences, Beijing 100093, China.

Community detection is important for understanding networks. Previous studies observed that communities are not necessarily disjoint and might overlap. It is also agreed that some outlier vertices participate in no community, and some hubs in a community might take more important roles than others. Each of these facts has been independently addressed in previous work. But there is no algorithm, to our knowledge, that can identify these three structures altogether. To overcome this limitation, we propose a novel model where vertices are measured by their centrality in communities, and define the identification of overlapping communities, hubs, and outliers as an optimization problem, calculated by nonnegative matrix factorization. We test this method on various real networks, and compare it with several competing algorithms. The experimental results not only demonstrate its ability of identifying overlapping communities, hubs, and outliers, but also validate its superior performance in terms of clustering quality.
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http://dx.doi.org/10.1038/srep02993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797436PMC
October 2013

X-ray microtomography study of the compaction process of rods under tapping.

Phys Rev E Stat Nonlin Soft Matter Phys 2012 May 30;85(5 Pt 1):051311. Epub 2012 May 30.

Department of Physics, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.

We present an x-ray microtomography study of the compaction process of cylindrical rods under tapping. The process is monitored by measuring the evolution of the orientational order parameter, local, and overall packing densities as a function of the tapping number for different tapping intensities. The slow relaxation dynamics of the orientational order parameter can be well fitted with a stretched-exponential law with stretching exponents ranging from 0.9 to 1.6. The corresponding relaxation time versus tapping intensity follows an Arrhenius behavior which is reminiscent of the slow dynamics in thermal glassy systems. We also investigated the boundary effect on the ordering process and found that boundary rods order faster than interior ones. In searching for the underlying mechanism of the slow dynamics, we estimated the initial random velocities of the rods under tapping and found that the ordering process is compatible with a diffusion mechanism. The average coordination number as a function of the tapping number at different tapping intensities has also been measured, which spans a range from 6 to 8.
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http://dx.doi.org/10.1103/PhysRevE.85.051311DOI Listing
May 2012