26
|
Sun X, Tang S, Hou B, Duan Z, Liu Z, Li Y, He S, Wang Q, Chang Q. Overexpression of P-glycoprotein, MRP2, and CYP3A4 impairs intestinal absorption of octreotide in rats with portal hypertension. BMC Gastroenterol 2021; 21:2. [PMID: 33407159 PMCID: PMC7789354 DOI: 10.1186/s12876-020-01532-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
Background Portal hypertension (PH) is the main cause of complications and death in liver cirrhosis. The effect of oral administration of octreotide (OCT), a drug that reduces PH by the constriction of mesenteric arteries, is limited by a remarkable intestinal first-pass elimination.
Methods The bile duct ligation (BDL) was used in rats to induce liver cirrhosis with PH to examine the kinetics and molecular factors such as P-glycoprotein (P-gp), multidrug resistance-associated protein 2 (MRP2) and cytochrome P450 3A4 (CYP3A4) influencing the intestinal OCT absorption via in situ and in vitro experiments on jejunal segments, transportation experiments on Caco-2 cells and experiments using intestinal microsomes and recombinant human CYP3A4. Moreover, RT-PCR, western blot, and immunohistochemistry were performed. Results Both in situ and in vitro experiments in jejunal segments showed that intestinal OCT absorption in both control and PH rats was largely controlled by P-gp and, to a lesser extent, by MRP2. OCT transport mediated by P-gp and MRP2 was demonstrated on Caco-2 cells. The results of RT-PCR, western blot, and immunohistochemistry suggested that impaired OCT absorption in PH was in part due to the jejunal upregulation of these two transporters. The use of intestinal microsomes and recombinant human CYP3A4 revealed that CYP3A4 metabolized OCT, and its upregulation in PH likely contributed to impaired drug absorption. Conclusions Inhibition of P-gp, MRP2, and CYP3A4 might represent a valid option for decreasing intestinal first-pass effects on orally administered OCT, thereby increasing its bioavailability to alleviate PH in patients with cirrhosis.
Collapse
|
27
|
Liu W, Duan Z, Zhang C, Hu XX, Cao JB, Liu LJ., Lin L. Experimental observations and density functional simulations on the structural transition behavior of a two-dimensional transition-metal dichalcogenide. Sci Rep 2020; 10:18255. [PMID: 33106537 PMCID: PMC7588463 DOI: 10.1038/s41598-020-75240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/15/2020] [Indexed: 11/29/2022] Open
Abstract
In this work, we show an obvious evidence of nondestructive Raman spectra for the structural transition, i.e., the existence of a charge density wave (CDW) in monolayer 2H-TaS2, which can exhibit a much higher transition temperature than bulk and results in additional vibrational modes, indicating strong interactions with light. Furthermore, we reveal that the degenerate breath and wiggle modes of 2H-TaS2 originated from the periodic lattice distortion can be probed using the optical methods. Since recently several light-tunable devices have been proposed based on the CDW phase transition of 1 T-TaS2, our study and in particular, the theoretical results will be very helpful for understanding and designing electronic devices based on the CDW of 2H-TaS2.
Collapse
|
28
|
Duan Z. [The exploration of Hujia Pasture wooden slip medicine prescription]. ZHONGHUA YI SHI ZA ZHI (BEIJING, CHINA : 1980) 2020; 50:307-310. [PMID: 33287499 DOI: 10.3760/cma.j.cn112155-20200804-00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Some features in the medical prescriptions of western Han dynasty on the wooden slips unearthed in Hujia Pasture were interpreted, and the words were annotated and translated. The study found that this recipe with male magpie excrement treatment epileptic disease is the first moxibustion combined with drugs to treat epilepsy. This is the earliest recorded treatment. The drug is still administered to lactate children by applying it to the mother's nipple and making the child to suck, and it is the earliest recorded of its kind.
Collapse
|
29
|
Kim HJ, Yardımcı GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS. Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. PLoS Comput Biol 2020; 16:e1008173. [PMID: 32946435 PMCID: PMC7526900 DOI: 10.1371/journal.pcbi.1008173] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 09/30/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023] Open
Abstract
Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate nine different single-cell combinatorial indexed Hi-C (sci-Hi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 19,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sci-Hi-C data in the form of “chromatin topics.” We further show enrichment of particular compartment structures associated with locus pairs in these topics. The genomes of higher organisms are intricately folded and organized in a dynamic manner that has strong implications for many biological processes. Each chromosome undergoes dramatic changes to their three dimensional conformation during the cell cycle, whereas the positioning of chromosomes within the nucleus plays an important role in controlling the activation of specific genes. Recently, it has become possible to investigate the 3D conformations of the genomes of individual cells using a high throughput sequencing assay called single cell Hi-C (scHi-C). However, data from these assays are sparse and noisy, making analysis and interpretation of scHi-C data challenging. In this work, we generated a scHi-C dataset of over 19,000 cells from five human cell lines and applied a natural language processing method called topic modeling to discover cell type-specific “chromatin” topics. We show that these topics can be used to distinguish between cells at different stages of the cell cycle and cells from different tissues based on the 3D conformation of their genomes, despite the sparsity of the data. We further show that the 3D conformations of single cells are linked to the expression of cell type-specific genes and to cell cycle-associated conformational patterns.
Collapse
|
30
|
Singh R, Demetci P, Bonora G, Ramani V, Lee C, Fang H, Duan Z, Deng X, Shendure J, Disteche C, Noble WS. Unsupervised manifold alignment for single-cell multi-omics data. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2020; 2020:1-10. [PMID: 33954299 PMCID: PMC8095090 DOI: 10.1145/3388440.3412410] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Integrating single-cell measurements that capture different properties of the genome is vital to extending our understanding of genome biology. This task is challenging due to the lack of a shared axis across datasets obtained from different types of single-cell experiments. For most such datasets, we lack corresponding information among the cells (samples) and the measurements (features). In this scenario, unsupervised algorithms that are capable of aligning single-cell experiments are critical to learning an in silico co-assay that can help draw correspondences among the cells. Maximum mean discrepancy-based manifold alignment (MMD-MA) is such an unsupervised algorithm. Without requiring correspondence information, it can align single-cell datasets from different modalities in a common shared latent space, showing promising results on simulations and a small-scale single-cell experiment with 61 cells. However, it is essential to explore the applicability of this method to larger single-cell experiments with thousands of cells so that it can be of practical interest to the community. In this paper, we apply MMD-MA to two recent datasets that measure transcriptome and chromatin accessibility in ~2000 single cells. To scale the runtime of MMD-MA to a more substantial number of cells, we extend the original implementation to run on GPUs. We also introduce a method to automatically select one of the user-defined parameters, thus reducing the hyperparameter search space. We demonstrate that the proposed extensions allow MMD-MA to accurately align state-of-the-art single-cell experiments.
Collapse
|
31
|
Yang H, Yang H, Wang L, Shi H, Liu B, Lin X, Chang Q, Chen JDZ, Duan Z. Transcutaneous Neuromodulation improved inflammation and sympathovagal ratio in patients with primary biliary ssscholangitis and inadequate response to Ursodeoxycholic acid: a pilot study. BMC Complement Med Ther 2020; 20:242. [PMID: 32738911 PMCID: PMC7395375 DOI: 10.1186/s12906-020-03036-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Background At present, ursodeoxycholic acid (UDCA) is internationally recognized as a therapeutic drug in clinic. However, about 40% Primary Biliary Cholangitis (PBC) patients are poor responders to UDCA. It has been demonstrated that Transcutaneous Neuromodulation (TN) can be involved in gut motility, metabolism of bile acids, immune inflammation, and autonomic nerve. Therefore, this study aimed to explore the effect of TN combined with UDCA on PBC and related mechanisms. Methods According to inclusion and exclusion criteria, 10 healthy volunteers and 15 PBC patients were recruited to control group and TN group, respectively. PBC patients were alternately but blindly assigned to group A (TN combined with UDCA) and group B (sham-TN combined with UDCA), and a crossover design was used. The TN treatment was performed via the posterior tibial nerve and acupoint ST36 (Zusanli) 1 h twice/day for 2 weeks. T test and nonparametric test were used to analyze the data. Results 1. TN combined with UDCA improved the liver function of PBC patients shown by a significant decrease of alkaline phosphatase and gamma-glutamyltransferase (γ-GT) (P < 0.05). 2. The treatment also decreased serum IL-6 levels (P < 0.05), but not the level of Tumor Necrosis Factor-α, IL-1β or IL-10. 3. TN combined with UDCA regulated autonomic function, enhanced vagal activity, and decreased the sympathovagal ratio assessed by the spectral analysis of heart rate variability (P < 0.05). 4. There was no change in 13 bile acids in serum or stool after TN or sham-TN. Conclusions TN cssombined with UDCA can significantly improve the liver function of PBC patients. It is possibly via the cholinergic anti-inflammatory pathway. TN might be a new non-drug therapy for PBC. Further studies are required. Trial registration The study protocol was registered in Chinese Clinical Trial Registry (number ChiCTR1800014633) on 25 January 2018.
Collapse
|
32
|
Zhang X, Nan D, Zha C, He G, Zhang W, Duan Z. Long-term intervention of taurocholic acid over-expressing in cholestatic liver disease inhibits the growth of hepatoma cells. Cell Mol Biol (Noisy-le-grand) 2020. [DOI: 10.14715/cmb/2020.66.2.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Bile acids usually build up in patients with cholestatic liver disease. It was found that the concentration of taurocholic acid (TCA), one of the taurine conjugates of primary bile acids in serum, was elevated the most. While the role played by TCA in the disease is unclear, there is concern whether TCA contributes to the development of hepatocarcinoma from cholestasis. In the present study, the cell viability, flow cytometry, real-time polymerase chain reaction, intracellular ROS measurement, and intracellular Ca2+ measurement were used to investigate the effects of TCA on THLE-2 and HepG2 cells. The results showed that TCA is capable of inhibiting HepG2 cell growth whereas it has relatively little or no impact on that of THLE-2 cells until later stages of 16-day treatment. The growth inhibition is a result of cell apoptosis induced by the increase of Ca2+ and ROS level, and also associated with the increased expression of c-Myc, CEBPα, TNF-α, ICAM-1, VCAM-1, CXCL-2, Egr-1. HepG2 growth inhibition could contribute to the research on the treatment methods of patients already with hepatocarcinoma.
Collapse
|
33
|
Zhang X, Nan D, Zha C, He G, Zhang W, Duan Z. Long-term intervention of taurocholic acid over-expressing in cholestatic liver disease inhibits the growth of hepatoma cells. Cell Mol Biol (Noisy-le-grand) 2020; 66:65-70. [PMID: 32415929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/03/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Bile acids usually build up in patients with cholestatic liver disease. It was found that the concentration of taurocholic acid (TCA), one of the taurine conjugates of primary bile acids in serum, was elevated the most. While the role played by TCA in the disease is unclear, there is concern whether TCA contributes to the development of hepatocarcinoma from cholestasis. In the present study, the cell viability, flow cytometry, real-time polymerase chain reaction, intracellular ROS measurement, and intracellular Ca2+ measurement were used to investigate the effects of TCA on THLE-2 and HepG2 cells. The results showed that TCA is capable of inhibiting HepG2 cell growth whereas it has relatively little or no impact on that of THLE-2 cells until later stages of 16-day treatment. The growth inhibition is a result of cell apoptosis induced by the increase of Ca2+ and ROS level, and also associated with the increased expression of c-Myc, CEBPα, TNF-α, ICAM-1, VCAM-1, CXCL-2, Egr-1. HepG2 growth inhibition could contribute to the research on the treatment methods of patients already with hepatocarcinoma.
Collapse
|
34
|
Duan Z, Yuan Y, Lu JC, Wang JL, Li Y, Svanberg S, Zhao GY. Underwater spatially, spectrally, and temporally resolved optical monitoring of aquatic fauna. OPTICS EXPRESS 2020; 28:2600-2610. [PMID: 32121945 DOI: 10.1364/oe.383061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
A continuous-wave (CW) Scheimpflug underwater multi-spectral lidar system was constructed to monitor aquatic fauna with spatial, spectral, and temporal resolution. Utilizing a 1 W 414 nm diode laser and a detection set-up with a reflective grating, measurements of shrimp pleopod movements at fixed range, and the swimming of small fish trapped in a clear tube were performed in a 5 m ×0.6 m ×0.6 m water tank. The spatial resolution is about 5 mm, the spectral resolution is 10 nm (from 400 nm to 700 nm), and with proper binning of the CCD, a read-out repetition rate up to 150 Hz can be reached. The experimental results demonstrate that the underwater Scheimpflug lidar system has great potential for detailed monitoring of the small aquatic fauna in oceanic environments.
Collapse
|
35
|
Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Methods 2020; 170:61-68. [PMID: 31536770 PMCID: PMC6949367 DOI: 10.1016/j.ymeth.2019.09.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/13/2019] [Indexed: 12/31/2022] Open
Abstract
The highly dynamic nature of chromosome conformation and three-dimensional (3D) genome organization leads to cell-to-cell variability in chromatin interactions within a cell population, even if the cells of the population appear to be functionally homogeneous. Hence, although Hi-C is a powerful tool for mapping 3D genome organization, this heterogeneity of chromosome higher order structure among individual cells limits the interpretive power of population based bulk Hi-C assays. Moreover, single-cell studies have the potential to enable the identification and characterization of rare cell populations or cell subtypes in a heterogeneous population. However, it may require surveying relatively large numbers of single cells to achieve statistically meaningful observations in single-cell studies. By applying combinatorial cellular indexing to chromosome conformation capture, we developed single-cell combinatorial indexed Hi-C (sci-Hi-C), a high throughput method that enables mapping chromatin interactomes in large number of single cells. We demonstrated the use of sci-Hi-C data to separate cells by karytoypic and cell-cycle state differences and to identify cellular variability in mammalian chromosomal conformation. Here, we provide a detailed description of method design and step-by-step working protocols for sci-Hi-C.
Collapse
|
36
|
He Y, Li C, Xu H, Duan Z, Liu Y, Zeng R, Li M, Wang B. AKT‐dependent hyperproliferation of keratinocytes in familial hidradenitis suppurativa with a
NCSTN
mutation: a potential role of defective miR‐100‐5p. Br J Dermatol 2019; 182:500-502. [DOI: 10.1111/bjd.18460] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
37
|
Sarin SK, Choudhury A, Sharma MK, Maiwall R, Al Mahtab M, Rahman S, Saigal S, Saraf N, Soin AS, Devarbhavi H, Kim DJ, Dhiman RK, Duseja A, Taneja S, Eapen CE, Goel A, Ning Q, Chen T, Ma K, Duan Z, Yu C, Treeprasertsuk S, Hamid SS, Butt AS, Jafri W, Shukla A, Saraswat V, Tan SS, Sood A, Midha V, Goyal O, Ghazinyan H, Arora A, Hu J, Sahu M, Rao PN, Lee GH, Lim SG, Lesmana LA, Lesmana CR, Shah S, Prasad VGM, Payawal DA, Abbas Z, Dokmeci AK, Sollano JD, Carpio G, Shresta A, Lau GK, Fazal Karim M, Shiha G, Gani R, Kalista KF, Yuen MF, Alam S, Khanna R, Sood V, Lal BB, Pamecha V, Jindal A, Rajan V, Arora V, Yokosuka O, Niriella MA, Li H, Qi X, Tanaka A, Mochida S, Chaudhuri DR, Gane E, Win KM, Chen WT, Rela M, Kapoor D, Rastogi A, Kale P, Rastogi A, Sharma CB, Bajpai M, Singh V, Premkumar M, Maharashi S, Olithselvan A, Philips CA, Srivastava A, Yachha SK, Wani ZA, Thapa BR, Saraya A, Kumar A, Wadhawan M, Gupta S, Madan K, Sakhuja P, Vij V, Sharma BC, Garg H, Garg V, Kalal C, Anand L, Vyas T, Mathur RP, Kumar G, Jain P, Pasupuleti SSR, Chawla YK, Chowdhury A, Alam S, Song DS, Yang JM, Yoon EL. Correction to: Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update. Hepatol Int 2019; 13:826-828. [PMID: 31595462 PMCID: PMC6861344 DOI: 10.1007/s12072-019-09980-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022]
Abstract
The article Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update, written by [Shiv Sarin], was originally published electronically on the publisher's internet portal (currently SpringerLink) on June 06, 2019 without open access.
Collapse
|
38
|
Xiao J, Singh AD, Duan Z, Pan Y, Qin J. Overview of recycled concrete research through development years (2004-2018). ACTA ACUST UNITED AC 2019. [DOI: 10.1088/1755-1315/323/1/012134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abstract
Along with the urbanization process, large amount of construction and demolition (C&D) waste during the construction, reconstruction, expansion or demolition of buildings is generated. Meanwhile, the impact on environment due to natural aggregate mining has become increasingly significant. These factors have driven the building industry to look for environmentally friendly materials and focusing on sustainable construction. Through nearly a decade of research, recycled concrete (RC) made with recycled aggregates manufactured from construction and demolition (C&D) waste has shown a competitive performance compared to natural materials and has already achieved industrial application. Researches on sustainably recycled concrete have become an essential part of sustainable development and continue to play a vital role for future research.
This paper engages in the discussion and the overview of research done by the Research Group for Recycled Concrete Structures and Construction at Tongji University, Shanghai. The first part discusses the necessary mechanical and durability properties of recycled concrete with recycled aggregate as well as recycled powder focusing on workability, strength, Poisson’s ratio, stress-strain behaviour along with carbonation, chloride penetration shrinkage and creep. The second part throws light on the elements and structures made with recycled aggregate concrete (RAC), discussing the behaviours of RAC components and structures.
Collapse
|
39
|
Xue Y, Zhang J, Bai Y, Jing C, Zhang Z, Sun X, Yang D, Duan Z. Establishment and validation of a prognostic model for hepatocellular carcinoma after radical liver resection. JOURNAL OF B.U.ON. : OFFICIAL JOURNAL OF THE BALKAN UNION OF ONCOLOGY 2019; 24:1420-1428. [PMID: 31646786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
PURPOSE The prognostic factors related to survival of primary hepatocellular carcinoma (HCC) after radical resection were analyzed in order to establish a new prognostic model for HCC patients and to shed light on personalized treatments. METHODS 141 patients pathologically diagnosed with HCC were enrolled. The independent prognostic factors affecting overall survival were identified, and a prognostic mathematical model was established. Independent samples of 21 cases were used to validate the model's ability to predict prognosis of HCC patients. RESULTS The median survival time was 34 months, and the 1-, 3-, and 5-year overall survival rates were 93.2%, 80%, and 68.9%, respectively. Univariate analysis showed that alpha fetoprotein (AFP) serum level, tumor size, tumor capsule, liver cirrhosis, neutrophil-to-lymphocyte ratio (NLR), and total bilirubin (TBIL) were significantly correlated with overall survival (p<0.05). Cox multivariate analysis indicated that the independent prognostic factors were AFP serum level, liver cirrhosis, tumor size, tumor capsule, and NLR. The prognostic mathematical model was: Prognostic Index (PI)=1.725 * liver cirrhosis + 0.783 * NLR + 1.046 * AFP + 0.595 * tumor size - 0.811 * tumor capsule. Based on the PI quartiles, 3.933 (25%), 4.716 (50%), and 5.195 (75%), the patients were divided into 4 groups: low risk (PI﹤3.933), moderate-risk (3.933 ≤ PI < 4.716), high-risk (4.761 ≤ PI < 5.195), and very high-risk (PI ≥ 5.195) group. The median survival times were 60, 34, 32, and 20 months, respectively. The 1-, 2-, 3-, and 5-year cumulative survival rates were 100%, 96%, 96%, 86%; 89%, 75%, 68%, 68%; 77%, 68%, 57%, 44%; 50%, 34%, 29%, 29%, separately. The predictions of the prognostic model demonstrated good consistency with the actual results. The total accuracy rate was 80.9%, and the Kappa consistency coefficient was 0.571 (p=0.009). CONCLUSIONS The higher the PI, the lower the postoperative cumulative survival rate and the worse the prognosis. This model can be used as an effective method to assess the prognosis of HCC patients after resection.
Collapse
|
40
|
Sarin SK, Choudhury A, Sharma MK, Maiwall R, Al Mahtab M, Rahman S, Saigal S, Saraf N, Soin AS, Devarbhavi H, Kim DJ, Dhiman RK, Duseja A, Taneja S, Eapen CE, Goel A, Ning Q, Chen T, Ma K, Duan Z, Yu C, Treeprasertsuk S, Hamid SS, Butt AS, Jafri W, Shukla A, Saraswat V, Tan SS, Sood A, Midha V, Goyal O, Ghazinyan H, Arora A, Hu J, Sahu M, Rao PN, Lee GH, Lim SG, Lesmana LA, Lesmana CR, Shah S, Prasad VGM, Payawal DA, Abbas Z, Dokmeci AK, Sollano JD, Carpio G, Shresta A, Lau GK, Fazal Karim M, Shiha G, Gani R, Kalista KF, Yuen MF, Alam S, Khanna R, Sood V, Lal BB, Pamecha V, Jindal A, Rajan V, Arora V, Yokosuka O, Niriella MA, Li H, Qi X, Tanaka A, Mochida S, Chaudhuri DR, Gane E, Win KM, Chen WT, Rela M, Kapoor D, Rastogi A, Kale P, Rastogi A, Sharma CB, Bajpai M, Singh V, Premkumar M, Maharashi S, Olithselvan A, Philips CA, Srivastava A, Yachha SK, Wani ZA, Thapa BR, Saraya A, Shalimar, Kumar A, Wadhawan M, Gupta S, Madan K, Sakhuja P, Vij V, Sharma BC, Garg H, Garg V, Kalal C, Anand L, Vyas T, Mathur RP, Kumar G, Jain P, Pasupuleti SSR, Chawla YK, Chowdhury A, Alam S, Song DS, Yang JM, Yoon EL. Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update. Hepatol Int 2019; 13:353-390. [PMID: 31172417 PMCID: PMC6728300 DOI: 10.1007/s12072-019-09946-3] [Citation(s) in RCA: 423] [Impact Index Per Article: 84.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
The first consensus report of the working party of the Asian Pacific Association for the Study of the Liver (APASL) set up in 2004 on acute-on-chronic liver failure (ACLF) was published in 2009. With international groups volunteering to join, the "APASL ACLF Research Consortium (AARC)" was formed in 2012, which continued to collect prospective ACLF patient data. Based on the prospective data analysis of nearly 1400 patients, the AARC consensus was published in 2014. In the past nearly four-and-a-half years, the AARC database has been enriched to about 5200 cases by major hepatology centers across Asia. The data published during the interim period were carefully analyzed and areas of contention and new developments in the field of ACLF were prioritized in a systematic manner. The AARC database was also approached for answering some of the issues where published data were limited, such as liver failure grading, its impact on the 'Golden Therapeutic Window', extrahepatic organ dysfunction and failure, development of sepsis, distinctive features of acute decompensation from ACLF and pediatric ACLF and the issues were analyzed. These initiatives concluded in a two-day meeting in October 2018 at New Delhi with finalization of the new AARC consensus. Only those statements, which were based on evidence using the Grade System and were unanimously recommended, were accepted. Finalized statements were again circulated to all the experts and subsequently presented at the AARC investigators meeting at the AASLD in November 2018. The suggestions from the experts were used to revise and finalize the consensus. After detailed deliberations and data analysis, the original definition of ACLF was found to withstand the test of time and be able to identify a homogenous group of patients presenting with liver failure. New management options including the algorithms for the management of coagulation disorders, renal replacement therapy, sepsis, variceal bleed, antivirals and criteria for liver transplantation for ACLF patients were proposed. The final consensus statements along with the relevant background information and areas requiring future studies are presented here.
Collapse
|
41
|
Timoshenko J, Duan Z, Henkelman G, Crooks RM, Frenkel AI. Solving the Structure and Dynamics of Metal Nanoparticles by Combining X-Ray Absorption Fine Structure Spectroscopy and Atomistic Structure Simulations. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:501-522. [PMID: 30699037 DOI: 10.1146/annurev-anchem-061318-114929] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Extended X-ray absorption fine structure (EXAFS) spectroscopy is a premiere method for analysis of the structure and structural transformation of nanoparticles. Extraction of analytical information about the three-dimensional structure and dynamics of metal-metal bonds from EXAFS spectra requires special care due to their markedly non-bulk-like character. In recent decades, significant progress has been made in the first-principles modeling of structure and properties of nanoparticles. In this review, we summarize new approaches for EXAFS data analysis that incorporate particle structure modeling into the process of structural refinement.
Collapse
|
42
|
Krumm A, Duan Z. Understanding the 3D genome: Emerging impacts on human disease. Semin Cell Dev Biol 2019; 90:62-77. [PMID: 29990539 PMCID: PMC6329682 DOI: 10.1016/j.semcdb.2018.07.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/03/2018] [Indexed: 12/13/2022]
Abstract
Recent burst of new technologies that allow for quantitatively delineating chromatin structure has greatly expanded our understanding of how the genome is organized in the three-dimensional (3D) space of the nucleus. It is now clear that the hierarchical organization of the eukaryotic genome critically impacts nuclear activities such as transcription, replication, as well as cellular and developmental events such as cell cycle, cell fate decision and embryonic development. In this review, we discuss new insights into how the structural features of the 3D genome hierarchy are established and maintained, how this hierarchy undergoes dynamic rearrangement during normal development and how its perturbation will lead to human disease, highlighting the accumulating evidence that links the diverse 3D genome architecture components to a multitude of human diseases and the emerging mechanisms by which 3D genome derangement causes disease phenotypes.
Collapse
|
43
|
Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T. Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. J Biol Chem 2019; 294:8760-8772. [PMID: 31010829 PMCID: PMC6552432 DOI: 10.1074/jbc.ra119.007832] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/18/2019] [Indexed: 12/23/2022] Open
Abstract
The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.
Collapse
|
44
|
|
45
|
Lang J, Lan M, Feng M, Xu P, Fu B, Duan Z, Zhang S, Qin Y, Peng X, Liu J, Li F, Lu S. Validation of the 8th Edition of the UICC/AJCC Staging System for Nasopharyngeal Carcinoma From non-Endemic Areas in the Era of Intensity-Modulated Radiation Therapy. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
46
|
Giordano S, Duan Z, Zhao H, Hwang J, Chavez MacGregor M. Hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV) screening prior to chemotherapy initiation among patients with solid tumors. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy300.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
47
|
Yang H, Duan Z. The Local Defender and Functional Mediator: Gut Microbiome. Digestion 2018; 97:137-145. [PMID: 29310114 DOI: 10.1159/000484687] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/31/2017] [Indexed: 02/04/2023]
Abstract
BACKGROUND The gut microbiome has been developing and making adaption all the time, which is consistent with their host from the initial colonization at birth or earlier. Emerging evidence is showing that dysbiosis is involved in various diseases associated with immune, metabolism, infection, nervous system, social behaviors, and psychopathology, etc., maybe via modulating gut barrier, microbiome-gut-brain axis, or some metabolites like short-chain fatty acids (SCFAs). SUMMARY In the review, we will conclude the recent researches related to the influence of microbiome on local structure, function, regulation, metabolism of gut, and systematic modulation to the host, as well as some affective factors such as diet or antibiotics. Key Messages: It is a reasonable hypothesis that the balance of bioactive factors or cells and the opposites such as the regulatory T/helper T17 balance and interleukin (IL)-10/IL-17 balance plays a vital role in homeostasis of immunity system. Meanwhile, the link between gut microbiome and immune system via microbiota-derived metabolite SCFAs involved in multi-function of the host locally and systematically has been revealed. We hope to contribute to the microbiome-targeted treatment and prevention of some diseases.
Collapse
|
48
|
Liu Z, Zhang Z, Huang M, Sun X, Liu B, Guo Q, Chang Q, Duan Z. Taurocholic acid is an active promoting factor, not just a biomarker of progression of liver cirrhosis: evidence from a human metabolomic study and in vitro experiments. BMC Gastroenterol 2018; 18:112. [PMID: 29996772 PMCID: PMC6042259 DOI: 10.1186/s12876-018-0842-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/02/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Previous studies have indicated that bile acid is associated with progression of liver cirrhosis. However, the particular role of specific bile acid in the development of liver cirrhosis is not definite. The present study aims to identify the specific bile acid and explore its possible mechanisms in promoting liver cirrhosis. METHODS Thirty two cirrhotic patients and 27 healthy volunteers were enrolled. Age, gender, Child-Pugh classification and serum of patients and volunteers were collected. Liquid chromatography tandem mass spectrometry (LC-MS) was utilized to determine concentrations of 12 bile acids in serum. Principal component analysis, fold change analysis and heatmap analysis were used to identify the most changed bile acid. And pathway analysis was used to identify the most affected pathway in bile acid metabolism. Spearman rank correlation analysis was employed to assess correlation between concentrations of bile acids and Child-Pugh classification. Hepatic stellate cells (LX-2) were cultured in DMEM. LX-2 cells were also co-cultured with HepG2 cells in the transwell chambers. LX-2 cells were treated with Na+/taurocholate in different concentrations. Western blot was used to evaluate the expression of alpha smooth muscle actin (α-SMA), type I collagen, and Toll-like receptor 4 (TLR4) in LX-2 cells. RESULTS Concentrations of 12 bile acids in serum of patients and healthy volunteers were determined with LC-MS successively. Principal component analysis, fold change analysis and heatmap analysis identified taurocholic acid (TCA) to be the most changed bile acid. Pathway analysis showed that TCA biosynthesis increased significantly. Spearman rank correlation analysis showed that concentration of TCA in serum of cirrhotic patients was positively associated with Child-Pugh classification. TCA increased the expression of α-SMA, type I collagen, and TLR4 in LX-2 cells. Moreover, the above effect was strengthened when LX-2 cells were co-cultured with HepG2 cells. CONCLUSIONS Increased TCA concentration in serum of liver cirrhotic patients is mainly due to increased bile acid biosynthesis. TCA is an active promoter of the progression of liver cirrhosis. TCA promoting liver cirrhosis is likely through activating hepatic stellate cells via upregulating TLR4 expression. TCA is a potential therapeutic target for the prevention and treatment of liver cirrhosis.
Collapse
|
49
|
Li X, Yang H, Duan Z, Chang Q, Wei X, Li C, Ba Y, Du J. A case series study of hypopituitarism in older patients with and without gastrointestinal symptoms. Postgrad Med 2018; 130:501-506. [PMID: 29863435 DOI: 10.1080/00325481.2018.1479612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/18/2018] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Some older individuals who present with gastrointestinal symptoms as their chief complaint were ultimately diagnosed with hypopituitarism instead of gastrointestinal diseases. The aim of this study was to find the characteristics of biochemical indicators in these patients so as to reduce early misdiagnosis. METHODS We conducted a retrospective review of 45 patients with hypopituitarism who were at least 60 years of age. Two groups were included: group of hypopituitarism patients with gastrointestinal symptoms (Group G) included 23 patients with gastrointestinal symptoms and group of hypopituitarism patients without gastrointestinal symptoms (Group N) included 22 patients without these symptoms. In Group G, we investigated the prevalence of different gastrointestinal symptoms, the response of these symptoms to treatment, the occurrence of electrolyte disorders, and target gland dysfunction. Then, we compared the electrolyte and target gland function indices between the two groups. RESULTS Nausea and vomiting were the most common complaints, accounting for 69.57% of the gastrointestinal symptoms in Group G. Hyponatremia was the most common electrolyte disorder, occurring in 72.86% (n = 18) of patients in Group G. Hypoadrenalism and hypothyroidism were reported by 69.57% and 60.78% of patients, respectively, in Group G. None of the gastrointestinal symptoms were relieved by 4 weeks of treatment with antacid and motility drugs. As mentioned, 18 patients also experienced refractory hyponatremia during early treatment including regular sodium supplements; however, their gastrointestinal symptoms and hyponatremia improved after only a week of treatment for hypopituitarism. Regarding the biochemical indicators, only serum sodium and cortisol in Group G were statistically lower compared with those in Group N (P < .05). CONCLUSION Nausea and vomiting were the most common gastrointestinal symptoms in older patients with hypopituitarism, which were associated with lower serum sodium and cortisol. In addition, we hope to share the research to our gastroenterologists that serum sodium and cortisol should be tested when meeting elder patients with unexplained gastrointestinal symptoms.
Collapse
|
50
|
Zhang H, Chang Z, Mehmood K, Yang MK, Liu Z, Duan Z, Yuan F, Ali MM, Adnan M, Qasim MU, Shaheen S, Abbas RZ, Tian Y, Guo R. Tetramethylpyrazine inhibited hypoxia-induced expression of calcium-sensing receptors in pulmonary artery smooth muscle cells in chickens. J BIOL REG HOMEOS AG 2018; 32:489-495. [PMID: 29921373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tetramethylpyrazine (TMP) is a biologically active ingredient, which is isolated from a popularChinese medicinal plant. It has been used effectively to treat ischemic heart problems, cerebrovascular and thrombotic vascular diseases. This study was designed to evaluate the effect of TMP on calciumsensing receptors in pulmonary artery smooth muscle in chickens. For this purpose forty day-old chicks were distributed into five groups: the control group, the hypoxia group (kept under low Oxygen treatment), and TMP groups (kept under low Oxygen treatment along with treatment of different concentrations of TMP). The pulmonary artery smooth muscle cells were also cultured on 6-well plates in high glucose culture medium and divided into the same five groups. We used in vivo and in vitro study models by applying immunohistochemistry, RT-qPCR assay and Western blotting analysis. Our results showed that pre-incubation with hypoxia markedly stimulated the activation of calcium-sensing receptor (CaSR) in pulmonary artery smooth muscle cells (PASMCs). The TMP decreased the mRNA and protein levels of CaSR. Treatment with TMP clearly inhibited the activation of all CaSR in a dose-dependent manner. Our data demonstrated that TMP can down-regulate the expression of CaSR. Therefore, these findings provide a new target to treat pulmonary arterial hypertension (PAH) under hypoxic conditions.
Collapse
|