26
|
Wang Y, Qiu X, Zhang H, Xie X. Data-Driven-Based Event-Triggered Control for Nonlinear CPSs Against Jamming Attacks. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022; 33:3171-3177. [PMID: 33417573 DOI: 10.1109/tnnls.2020.3047931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This brief considers the security control problem for nonlinear cyber-physical systems (CPSs) against jamming attacks. First, a novel event-based model-free adaptive control (MFAC) framework is established. Second, a multistep predictive compensation algorithm (PCA) is developed to make compensation for the lost data caused by jamming attacks, even consecutive attacks. Then, an event-triggering mechanism with the dead-zone operator is introduced in the adaptive controller, which can effectively save communication resources and reduce the calculation burden of the controller without affecting the control performance of systems. Moreover, the boundedness of the tracking error is ensured in the mean-square sense, and only the input/output (I/O) data are used in the whole design process. Finally, simulation comparisons are provided to show the effectiveness of our method.
Collapse
|
27
|
Zhao Y, Qiu X, Ma Z, Zhao C, Li Z, Zhai S. Fabrication of Pd/Sludge-biochar electrode with high electrochemical activity on reductive degradation of 4-chlorophenol in wastewater. ENVIRONMENTAL RESEARCH 2022; 209:112740. [PMID: 35085561 DOI: 10.1016/j.envres.2022.112740] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Effective treatment and utilization of sludge contribute to achieve conventional carbon emission reduction and resource recovery, which is of great significance to realize carbon neutralization of WWTPs. Sludge carbonization derived biochar has attracted more interest because of high potential as catalytic materials. Therein, sludge-derived electrode exhibits a promising potential in the case of sludge utilization for electrocatalysis, however, electrocatalytic performance of the already reported sludge-derived electrode is unsatisfactory due to insufficient active sites. In this study, an efficient Pd/sludge-biochar loaded foam nickel (Pd-SAC@Ni) was successfully fabricated using simple pyrolysis and solidification method, and exhibited remarkable electrocatalytic performance for 4-chlorophenol (4-CP) degradation. Furthermore, the morphology, element distribution and crystal composition were characterized by SEM, EDS, XPS and XRD. The Pd-SAC@Ni electrode exhibited superior electrocatalytic performance than Ni, SAC@Ni, Pd-Ni electrodes. The reduction rate of 98.9% was achieved at current density of 5 mA cm-2, 4-CP concentration of 0.8 mM and initial pH of 7.0. Also, Pd-SAC@Ni electrode showed desirable reusability and achieved 98% of 4-CP removal after multiple runs of experiments. Moreover, the active hydrogen species (H*) generation capacity of electrodes was determined using tert-butanol (TBA) as trapping agent. The mechanism analysis demonstrated that direct reduction process and indirect reduction process both involved in the 4-CP degradation process, and their contribution were 19.5% and 80.5%, respectively. Then, the intermediates formed in the electrochemical degradation of 4-CP were revealed by HPLC and the plausible degradation pathway was proposed. This study provides a cost-effective approach for preparing sludge biochar electrode, and explored a novel way to promote resourceful utilization of sludge for carbon neutrality.
Collapse
|
28
|
Shi XY, Zhang XL, Shi QY, Qiu X, Wu XB, Zheng BL, Jiang HX, Qin SY. IFN-γ affects pancreatic cancer properties by MACC1-AS1/MACC1 axis via AKT/mTOR signaling pathway. Clin Transl Oncol 2022; 24:1073-1085. [PMID: 35037236 DOI: 10.1007/s12094-021-02748-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/01/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Metastasis-related in colon cancer 1 (MACC1) is highly expressed in a variety of solid tumours, but its role in pancreatic cancer (PC) remains unknown. Interferon gamma (IFN-γ) affecting MACC1 expression was explored as the potential mechanism following its intervention. METHODS Expressions of MACC1 treated with IFN-γ gradient were confirmed by quantitative real-time PCR (qRT-PCR) and western blot (WB). Proliferation, migration, and invasion abilities of PC cells treated with IFN-γ were analysed by CCK8, EDU, colony formation, Transwell (with or without matrix gel) and wound-healing assays. Expression of antisense long non-coding RNA of MACC1, MACC1-AS1, and proteins of AKT/mTOR pathway, (pho-)AKT, and (pho-)mTOR was also assessed by qRT-PCR and WB. SiRNA kit and lentiviral fluid were conducted for transient expression of MACC1 and stable expression of MACC1-AS1, respectively. Rescue assays of cells overexpressing MACC1-AS1 and of cells silencing MACC1 were performed and cellular properties and proteins were assessed by the above-mentioned assays as well. RESULTS IFN-γ inhibited MACC1 expression in a time- and dose-dependent manner; 100 ng/mL IFN-γ generally caused downregulation of most significant (p ≤ 0.05). In vitro experiments revealed that IFN-γ decreased cellular proliferation, migration, and invasion abilities and downregulated the expression of pho-AKT and pho-mTOR (p ≤ 0.05). Conversely, overexpression of MACC1-AS1 upregulated pho-AKT and pho-mTOR proteins, and reversed cellular properties (p ≤ 0.05). Rescue assays alleviated the above changes of pho-AKT/ mTOR and cellular properties. CONCLUSION IFN-γ affected PC properties by MACC1-AS1/MACC1 axis via AKT/mTOR signaling pathway, which provides novel insight for candidate targets for treating PC.
Collapse
|
29
|
Yang D, Jones MG, Naranjo S, Rideout WM, Min KHJ, Ho R, Wu W, Replogle JM, Page JL, Quinn JJ, Horns F, Qiu X, Chen MZ, Freed-Pastor WA, McGinnis CS, Patterson DM, Gartner ZJ, Chow ED, Bivona TG, Chan MM, Yosef N, Jacks T, Weissman JS. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell 2022; 185:1905-1923.e25. [PMID: 35523183 DOI: 10.1016/j.cell.2022.04.015] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 12/19/2022]
Abstract
Tumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth and expansion to neighboring and distal tissues. The study of phylogenetic relationships between cancer cells provides key insights into these processes. Here, we introduced an evolving lineage-tracing system with a single-cell RNA-seq readout into a mouse model of Kras;Trp53(KP)-driven lung adenocarcinoma and tracked tumor evolution from single-transformed cells to metastatic tumors at unprecedented resolution. We found that the loss of the initial, stable alveolar-type2-like state was accompanied by a transient increase in plasticity. This was followed by the adoption of distinct transcriptional programs that enable rapid expansion and, ultimately, clonal sweep of stable subclones capable of metastasizing. Finally, tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates progression by creating novel trajectories. Our study elucidates the hierarchical nature of tumor evolution and, more broadly, enables in-depth studies of tumor progression.
Collapse
|
30
|
Chen A, Liao S, Cheng M, Ma K, Wu L, Lai Y, Qiu X, Yang J, Xu J, Hao S, Wang X, Lu H, Chen X, Liu X, Huang X, Li Z, Hong Y, Jiang Y, Peng J, Liu S, Shen M, Liu C, Li Q, Yuan Y, Wei X, Zheng H, Feng W, Wang Z, Liu Y, Wang Z, Yang Y, Xiang H, Han L, Qin B, Guo P, Lai G, Muñoz-Cánoves P, Maxwell PH, Thiery JP, Wu QF, Zhao F, Chen B, Li M, Dai X, Wang S, Kuang H, Hui J, Wang L, Fei JF, Wang O, Wei X, Lu H, Wang B, Liu S, Gu Y, Ni M, Zhang W, Mu F, Yin Y, Yang H, Lisby M, Cornall RJ, Mulder J, Uhlén M, Esteban MA, Li Y, Liu L, Xu X, Wang J. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 2022; 185:1777-1792.e21. [PMID: 35512705 DOI: 10.1016/j.cell.2022.04.003] [Citation(s) in RCA: 353] [Impact Index Per Article: 176.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/24/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022]
Abstract
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.
Collapse
|
31
|
Chen N, Qiu X, Wang D, Cui BQ, Chang XD. [Establishment and stress analysis of a finite element model of a marathon runner's hip joint based on material properties given by CT gray value]. ZHONGHUA YI XUE ZA ZHI 2022; 102:679-682. [PMID: 35249314 DOI: 10.3760/cma.j.cn112137-20210817-01854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this study, a finite element model of the hip joint of a marathon runner was established based on the method of assigning material properties by CT gray value, and the biomechanics of the hip joint were analyzed when standing on one foot. The results of the study demonstrated that the stress was concentrated in the arcuate line, the greater sciatic notch, the pubic comb, and the acetabular region in the pelvis model; in the femoral model, the stress was concentrated in the femoral head, medial side of femoral neck and femoral shaft. The stress is transmitted from the sacroiliac joint to the acetabular dome through the arcuate line, on one side of the femoral head, from the medial side of the femoral neck to the lower side of the lesser trochanter to the medial side of the femoral shaft, and on the other side from the upper side of the femoral neck to the lateral side of the femoral shaft. The maximum principal stress was distributed in the posterior superior of the acetabular roof (7.22 MPa) and the posterior superior of the femoral head (6.68 MPa). The displacement of the model was about 1 to 3 mm at the upper edge of the ilium, and gradually decreased along the femoral axis, and the displacement at the hip joint was about 0.1 to 0.3 mm.
Collapse
|
32
|
Qiu X, Zhang Y, Martin-Rufino JD, Weng C, Hosseinzadeh S, Yang D, Pogson AN, Hein MY, Hoi Joseph Min K, Wang L, Grody EI, Shurtleff MJ, Yuan R, Xu S, Ma Y, Replogle JM, Lander ES, Darmanis S, Bahar I, Sankaran VG, Xing J, Weissman JS. Mapping transcriptomic vector fields of single cells. Cell 2022; 185:690-711.e45. [PMID: 35108499 PMCID: PMC9332140 DOI: 10.1016/j.cell.2021.12.045] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 10/08/2021] [Accepted: 12/28/2021] [Indexed: 01/03/2023]
Abstract
Single-cell (sc)-RNA-seq, together with RNA-velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. Here, we introduce an analytical framework dynamo, that infers absolute RNA velocity, reconstructs continuous vector-field functions that predict cell fates, employs differential geometry to extract underlying regulations, and ultimately predicts optimal reprogramming paths and perturbation outcomes. We highlight dynamo’s power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically-labeled human hematopoiesis scRNA-seq dataset. Furthermore, differential geometry analyses reveal mechanisms driving early megakaryocyte appearance and elucidate asymmetrical regulation within the PU.1–GATA1 circuit. Leveraging the Least-Action-Path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. Finally, in silico perturbations predict cell-fate diversions induced by gene perturbations. Dynamo thus represents an important step in advancing quantitative and predictive theories of cell-state transitions.
Collapse
|
33
|
Zhao Y, Zhao C, Yang Y, Li Z, Qiu X, Gao J, Ji M. Adsorption of sulfamethoxazole on polypyrrole decorated volcanics over a wide pH range: Mechanisms and site energy distribution consideration. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2021.120165] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
34
|
Qiu X, Wang Y, Zhang H, Xie X. Resilient Model Free Adaptive Distributed LFC for Multi-Area Power Systems Against Jamming Attacks. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2021; PP:1-10. [PMID: 34739384 DOI: 10.1109/tnnls.2021.3123235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This article is concerned with distributed resilient load frequency control (LFC) for multi-area power interconnection systems against jamming attacks. First, considering uncertainties and high dimension nonlinearity, the model-free adaptive control (MFAC) model is adopted for the power system, in which only input and output (I/O) data are used. Second, jamming attacks are modeled in a stochastic process, and a multistep predictive compensation algorithm is developed to mitigate the impact of jamming attacks. Then, the distributed MFAC protocol with predictive compensation algorithm is designed such that the frequency tracking errors under the predictive compensation algorithm of multi-area power interconnection systems converge consensually into a small neighborhood of origin in the mean square sense. Simulation results show the effectiveness of the approach.
Collapse
|
35
|
Qiu X, Chen H, Feng D, Dong W. [G-protein coupled receptor Smo positively regulates proliferation and migration of adult neural stem cells in vitro]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1588-1592. [PMID: 34755677 DOI: 10.12122/j.issn.1673-4254.2021.10.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the role of G-protein coupled receptor Smoothened (Smo) in regulating proliferation and migration of adult neural stem cells (ANSCs) and explore the underlying mechanism. METHODS Cultured ANSCs were treated with purmorphamine (PM, an agonist of Smo) or cyclopamine (CPM, an inhibitor of Smo), and the changes in cell proliferation migration abilities were assessed using cell counting kit-8 (CCK8) assay and wound healing assay, respectively. The mRNA expressions of membrane receptor Patched 1 (Ptch1), Smo, glioma-associated oncogene homolog 1 (Gli1), axon guidance cue slit1 (Slit1) and brain-derived neurotrophic factor (BDNF) in the treated cells were detected using real-time quantitative PCR (RT-PCR). RESULTS PM significantly promoted the proliferation (P < 0.01) and migration of ANSCs (P < 0.01), and up-regulated the mRNA expressions of Ptch1, Smo, Gli1, Slit1 and BDNF. Treatment with CPM significantly inhibited the proliferation and migration of ANSCs. CONCLUSION Modulating Smo activity can positively regulate the proliferation and migration of ANSCs possibly by regulating the expressions of BDNF and Slit1.
Collapse
|
36
|
Lu S, Huang D, Chen X, Wang B, Xue J, Wang J, Bao Y, Liang L, Qiu X, Zhang L. 1290P RATIONALE 304: Tislelizumab (TIS) plus chemotherapy (chemo) vs chemo alone as first-line (1L) treatment for non-squamous (non-sq) non-small cell lung cancer (NSCLC) in patients (pts) who are smokers vs non-smokers. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
37
|
Yin H, Chen M, Qiu X, Qiu X, Guo H. Can 68Ga-PSMA-11 PET/CT predict pathological upgrading of prostate cancer from MRI-targeted biopsy to radical prostatectomy? Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
38
|
Zhang T, Li W, Qiu X, Liu B, Li G, Feng C, Liao J, Lin K. [CRISPR/Cas9-mediated TEAD1 knockout induces phenotypic modulation of corpus cavernosum smooth muscle cells in diabetic rats with erectile dysfunction]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:567-573. [PMID: 33963717 DOI: 10.12122/j.issn.1673-4254.2021.04.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To construct a corpus cavemosum smooth muscle cell (CCSMCs) line with TEAD1 knockout from diabetic rats with erectile dysfunction (ED) using CRISPR/Cas9 technology and explore the role of TEAD1 in phenotypic modulation of CCSMCs in diabetic rats with ED. OBJECTIVE Models of diabetic ED were established in male Sprague-Dawley rats by intraperitoneal injection of streptozotocin. CCSMCs from the rat models were primarily cultured and identified with immunofluorescence assay. Three sgRNAs (sgRNA-1, sgRNA-2 and sgRNA-3) were transfected via lentiviral vectors into 293T cells to prepare the sgRNA-Cas9 lentivirus. CCSMCs from diabetic rats with ED were infected by the lentivirus, and the cellular expression of TEAD1 protein was detected using Western blotting. In CCSMCs infected with the sgRNA-Cas9 lentivirus (CCSMCs-sgRNA-2), or the empty lentiviral vector (CCSMCs-sgRNA-NC) and the blank control cells (CCSMCs-CK), the expressions of cellular phenotypic markers SMMHC, calponin and PCNA at the mRNA and protein levels were detected using real-time fluorescence quantitative RT-PCR (qRT-PCR) and Western blotting, respectively. OBJECTIVE The primarily cultured CCSMCs from diabetic rats with ED showed a high α-SMA-positive rate of over 95%. The recombinant lentivirus of TEAD1-sgRNA was successfully packaged, and stable TEAD1-deficient CCSMC lines derived from diabetic rat with ED were obtained. Western blotting confirmed that the protein expression of TEAD1 in TEAD1-sgRNA-2 group was the lowest (P < 0.05), and this cell line was used in subsequent experiment. The results of qRT-PCR and Western blotting showed significantly up-regulated expressions of SMMHC and calponin (all P < 0.05) and down-regulated expression of PCNA (all P < 0.05) at both the mRNA and protein levels in TEAD1-deficient CCSMCs from diabetic rats with ED. OBJECTIVE We successfully constructed a stable CCSMCs line with CRISPR/Cas9-mediated TEAD1 knockout from diabetic rats with ED. TEAD1 gene knockout can induce phenotype transformation of the CCSMCs from diabetic rats with ED from the synthetic to the contractile type.
Collapse
|
39
|
He JR, Ramakrishnan R, Wei XL, Lu JH, Lu MS, Xiao WQ, Tu S, Liu X, Zhou FJ, Zhang LF, Xia HM, Qiu X. Fetal growth at different gestational periods and risk of impaired childhood growth, low childhood weight and obesity: a prospective birth cohort study. BJOG 2021; 128:1615-1624. [PMID: 33690938 DOI: 10.1111/1471-0528.16698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To examine the longitudinal associations of fetal growth with adverse child growth outcomes and to assess whether maternal metabolic factors modify the associations. DESIGN Prospective cohort study. SETTING Born in Guangzhou Cohort Study, China. POPULATION A total of 4818 mother-child pairs. METHODS Fetal growth was assessed according to estimated fetal weight (EFW) from 22 weeks of gestation until birth and the measurement of the birthweight. Fetal growth Z-scores were computed from random effects in the multilevel linear spline models to represent fetal size in early pregnancy (22 weeks of gestation) and growth in mid-pregnancy (22-27 weeks of gestation), early third trimester (28-36 weeks of gestation) and late third trimester (≥37 weeks of gestation). MAIN OUTCOME MEASURES Z-scores for childhood stunting, low weight, overweight or obesity, length/height for age (LAZ/HAZ), weight for age (WAZ) and body mass index for age (BMIZ) at the age of 3 years. Adjusted associations were examined using multiple Poisson or linear regression models. RESULTS Increased Z-scores of fetal size in early pregnancy and growth in mid-pregnancy and early third trimester were associated with a higher risk of childhood overweight or obesity (risk ratios 1.25-1.45). Fetal growth in each period was negatively associated with stunting and low weight, with the strongest associations observed for fetal size in early pregnancy and growth in mid-pregnancy. The results for continuous outcomes (LAZ/HAZ, WAZ and BMIZ) were similar. The associations of fetal growth with overweight or obesity in childhood were stronger among mothers who were underweight and who were overweight or obese than among mothers of normal weight. CONCLUSIONS Accelerated fetal growth before 37 weeks of gestation is associated with children who are overweight or obese, whereas the critical period for stunting and low weight occurs before 28 weeks of gestation. TWEETABLE ABSTRACT Fetal growth during different periods is differentially associated with childhood stunting, underweight and overweight or obesity.
Collapse
|
40
|
Wang KS, Yu G, Xu C, Meng XH, Zhou J, Zheng C, Deng Z, Shang L, Liu R, Su S, Zhou X, Li Q, Li J, Wang J, Ma K, Qi J, Hu Z, Tang P, Deng J, Qiu X, Li BY, Shen WD, Quan RP, Yang JT, Huang LY, Xiao Y, Yang ZC, Li Z, Wang SC, Ren H, Liang C, Guo W, Li Y, Xiao H, Gu Y, Yun JP, Huang D, Song Z, Fan X, Chen L, Yan X, Li Z, Huang ZC, Huang J, Luttrell J, Zhang CY, Zhou W, Zhang K, Yi C, Wu C, Shen H, Wang YP, Xiao HM, Deng HW. Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence. BMC Med 2021; 19:76. [PMID: 33752648 PMCID: PMC7986569 DOI: 10.1186/s12916-021-01942-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Accurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients' treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on daily image analyses. METHODS Based on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC diagnosis using weakly labeled pathological whole-slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, > 14,680 WSIs, from > 9631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, the USA, and Germany. RESULTS Our innovative AI tool consistently and nearly perfectly agreed with (average Kappa statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multicenters. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.988 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells. CONCLUSIONS This first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. It will drastically alleviate the heavy clinical burden of daily pathology diagnosis and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.
Collapse
|
41
|
Lu S, Yu Y, Barnes G, Qiu X, Bao Y, Li J, Tang B. MO01.43 Examining the Impact of Tislelizumab Added to Platinum Doublet Chemotherapy on Health-Related Quality of Life in Patients with Non-Squamous NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2020.10.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
42
|
Wang X, Zhou H, Du P, Lan R, Chen D, Dong A, Lin X, Qiu X, Xu S, Ji X, Li M, Hou X, Sun L, Li D, Han L, Li Z. Genomic epidemiology of Corynebacterium striatum from three regions of China: an emerging national nosocomial epidemic. J Hosp Infect 2020; 110:67-75. [PMID: 33166588 DOI: 10.1016/j.jhin.2020.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/27/2020] [Accepted: 10/03/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Corynebacteritum straitum has been considered as an emerging multi-drug-resistant (MDR) pathogen. Isolation of MDR C. striatum as the only organism from respiratory samples from hospitalized patients is increasing in China. AIM To elucidate the genomic epidemiology and evolution of C. striatum in China. METHODS A total of 260 isolates from 2016 to 2018 were collected from three hospitals in three regions of China. Antibiotic sensitivity testing was performed on all isolates. Whole-genome sequencing was applied to all isolates to assess their genomic diversity and relationships and detect the presence of antimicrobial resistance genes (ARG) and ARG cassettes. FINDINGS Almost all isolates (96.2%, 250/260) showed multi-drug-resistance. Genome sequencing revealed four major lineages with lineage IV emerging as the epidemic lineage. Most of the diversity was developed in the last 6 years. Each hospital has its own predominant clones with potential spread between Hebei and Guangdong hospitals. Genomic analysis further revealed multiple antimicrobial resistance genes. CONCLUSIONS Our results suggested that four lineages of C. striatum have spread in parallel across China, causing persistent and extensive transmissions within hospitals. MDR C. striatum infection has become a national epidemic. Antibiotic-driven selection pressure may have played significant roles in forming persistent and predominant clones. Our data provide the basis for surveillance and prevention strategies to control the epidemic caused by MDR C. striatum.
Collapse
|
43
|
Hu J, Hu W, Gao J, Yang J, Huang Q, Qiu X, Kong L, Lu J. Particle-Beam Radiation Therapy In The Treatment Of Nasopharyngeal Carcinoma. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
44
|
Yang J, Gao J, Qiu X, Hu J, Hu W, Huang Q, Kong L, Lu J. Excellent Local Control and Survivals after Particle Beam Radiation Therapy for Skull Base Malignancies. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.354] [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]
|
45
|
Lu J, Zhao YJ, Zhou Y, He Q, Tian Y, Hao H, Qiu X, Jiang L, Zhao G, Huang CM. Modified staging system for gastric neuroendocrine carcinoma based on American Joint Committee on Cancer and European Neuroendocrine Tumor Society systems. Br J Surg 2020; 107:248-257. [PMID: 31971627 DOI: 10.1002/bjs.11408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/04/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND The prognostic values of the AJCC staging system for gastric cancer (GC-AJCC), the AJCC staging system for gastric neuroendocrine tumours (NET-AJCC) and the European Neuroendocrine Tumor Society (ENETS) system for gastric neuroendocrine carcinoma and mixed adenoneuroendocrine carcinoma (MA)NEC remain controversial. METHODS Data on patients with (MA)NEC from 21 centres in China were analysed. Different staging systems were evaluated by performing Kaplan-Meier survival analysis and calculating the concordance index (C-index) and Akaike information criterion (AIC). Based on three existing systems, a modified staging system (mTNM) was developed. RESULTS A total of 871 patients were included. In the GC-AJCC system, an overlap was noticed for pT2 and pT3 categories. Patients with stage IIIC disease had a similar prognosis to those with stage IV disease. The pT categories of the NET-AJCC system had a lower C-index and higher AIC than those of the other systems. In the ENETS system, there was a low proportion (0·2 per cent) of patients with stage IIIA and a high proportion (67·6 per cent) of stage IIIB disease. The mTNM system adopted the NET-AJCC pT and GC-AJCC pN and pM definitions, and was developed based on the ENETS stage definitions. The proportion of patients in each stage was better distributed and the mTNM system showed improved prognostic performance in predicting overall and disease-free survival. CONCLUSION The mTNM system offers more accurate prognostic value for gastric (MA)NEC than the AJCC or ENETS staging systems.
Collapse
|
46
|
Adamson P, Anghel I, Aurisano A, Barr G, Blake A, Cao SV, Carroll TJ, Castromonte CM, Chen R, Childress S, Coelho JAB, De Rijck S, Evans JJ, Feldman GJ, Flanagan W, Gabrielyan M, Germani S, Gomes RA, Gouffon P, Graf N, Grzelak K, Habig A, Hahn SR, Hartnell J, Hatcher R, Holin A, Huang J, Koerner LW, Kordosky M, Kreymer A, Lang K, Lucas P, Mann WA, Marshak ML, Mayer N, Mehdiyev R, Meier JR, Miller WH, Mills G, Naples D, Nelson JK, Nichol RJ, O'Connor J, Pahlka RB, Pavlović Ž, Pawloski G, Perch A, Pfützner MM, Phan DD, Plunkett RK, Poonthottathil N, Qiu X, Radovic A, Sail P, Sanchez MC, Schneps J, Schreckenberger A, Sharma R, Sousa A, Tagg N, Thomas J, Thomson MA, Timmons A, Todd J, Tognini SC, Toner R, Torretta D, Vahle P, Weber A, Whitehead LH, Wojcicki SG. Precision Constraints for Three-Flavor Neutrino Oscillations from the Full MINOS+ and MINOS Dataset. PHYSICAL REVIEW LETTERS 2020; 125:131802. [PMID: 33034464 DOI: 10.1103/physrevlett.125.131802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
We report the final measurement of the neutrino oscillation parameters Δm_{32}^{2} and sin^{2}θ_{23} using all data from the MINOS and MINOS+ experiments. These data were collected using a total exposure of 23.76×10^{20} protons on target producing ν_{μ} and ν[over ¯]_{μ} beams and 60.75 kt yr exposure to atmospheric neutrinos. The measurement of the disappearance of ν_{μ} and the appearance of ν_{e} events between the Near and Far detectors yields |Δm_{32}^{2}|=2.40_{-0.09}^{+0.08}(2.45_{-0.08}^{+0.07})×10^{-3} eV^{2} and sin^{2}θ_{23}=0.43_{-0.04}^{+0.20}(0.42_{-0.03}^{+0.07}) at 68% C.L. for normal (inverted) hierarchy.
Collapse
|
47
|
Zeng H, Deng S, Zhou Z, Qiu X, Jia X, Li Z, Wang J, Duan H, Tu L, Wang J. Diagnostic value of combined nucleic acid and antibody detection in suspected COVID-19 cases. Public Health 2020; 186:1-5. [PMID: 32731151 PMCID: PMC7351380 DOI: 10.1016/j.puhe.2020.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Nucleic acid testing is the gold standard method for the diagnosis of coronavirus disease 2019 (COVID-19); however, large numbers of false-negative results have been reported. In this study, nucleic acid detection and antibody detection (IgG and IgM) were combined to improve the testing accuracy of patients with suspected COVID-19. STUDY DESIGN The positive rate of nucleic acid detection and antibody detection (IgG and IgM) were compared in suspected COVID-19 patients. METHODS A total of 71 patients with suspected COVID-19 were selected to participate in this study, which included a retrospective analysis of clinical features, imaging examination, laboratory biochemical examination and nucleic acid detection and specific antibody (IgM and IgG) detection. RESULTS The majority of participants with suspected COVID-19 presented with fever (67.61%) and cough (54.93%), and the imaging results showed multiple small patches and ground-glass opacity in both lungs, with less common infiltration and consolidation opacity (23.94%). Routine blood tests were mostly normal (69.01%), although only a few patients had lymphopenia (4.23%) or leucopenia (12.68%). There was no statistical difference in the double-positive rate between nucleic acid detection (46.48%) and specific antibody (IgG and IgM) detection (42.25%) (P = 0.612), both of which were also poorly consistent with each other (kappa = 0.231). The positive rate of combined nucleic acid detection and antibody detection (63.38%) was significantly increased, compared with that of nucleic acid detection (46.48%) and that of specific antibody (IgG and IgM) detection (42.25%), and the differences were statistically significant (P = 0.043 and P = 0.012, respectively). CONCLUSIONS Nucleic acid detection and specific antibody (IgG and IgM) detection had similar positive rates, and their combination could improve the positive rate of COVID-19 detection, which is of great significance for diagnosis and epidemic control.
Collapse
|
48
|
Qiu Q, Hu P, Qiu X, Govek KW, Cámara PG, Wu H. Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq. Nat Methods 2020; 17:991-1001. [PMID: 32868927 PMCID: PMC8103797 DOI: 10.1038/s41592-020-0935-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/22/2020] [Indexed: 12/31/2022]
Abstract
Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal RNA dynamics. Here we present single-cell metabolically labeled new RNA tagging sequencing (scNT-seq), a method for massively parallel analysis of newly transcribed and pre-existing mRNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking newly transcribed mRNAs with T-to-C substitutions. Using scNT-seq, we jointly profiled new and old transcriptomes in ~55,000 single cells. These data revealed time-resolved transcription factor activities and cell-state trajectories at the single-cell level in response to neuronal activation. We further determined rates of RNA biogenesis and decay to uncover RNA regulatory strategies during stepwise conversion between pluripotent and rare totipotent two-cell embryo (2C)-like stem cell states. Finally, integrating scNT-seq with genetic perturbation identifies DNA methylcytosine dioxygenase as an epigenetic barrier into the 2C-like cell state. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms.
Collapse
|
49
|
Adamson P, An FP, Anghel I, Aurisano A, Balantekin AB, Band HR, Barr G, Bishai M, Blake A, Blyth S, Cao GF, Cao J, Cao SV, Carroll TJ, Castromonte CM, Chang JF, Chang Y, Chen HS, Chen R, Chen SM, Chen Y, Chen YX, Cheng J, Cheng ZK, Cherwinka JJ, Childress S, Chu MC, Chukanov A, Coelho JAB, Cummings JP, Dash N, De Rijck S, Deng FS, Ding YY, Diwan MV, Dohnal T, Dolzhikov D, Dove J, Dvořák M, Dwyer DA, Evans JJ, Feldman GJ, Flanagan W, Gabrielyan M, Gallo JP, Germani S, Gomes RA, Gonchar M, Gong GH, Gong H, Gouffon P, Graf N, Grzelak K, Gu WQ, Guo JY, Guo L, Guo XH, Guo YH, Guo Z, Habig A, Hackenburg RW, Hahn SR, Hans S, Hartnell J, Hatcher R, He M, Heeger KM, Heng YK, Higuera A, Holin A, Hor YK, Hsiung YB, Hu BZ, Hu JR, Hu T, Hu ZJ, Huang HX, Huang J, Huang XT, Huang YB, Huber P, Jaffe DE, Jen KL, Ji XL, Ji XP, Johnson RA, Jones D, Kang L, Kettell SH, Koerner LW, Kohn S, Kordosky M, Kramer M, Kreymer A, Lang K, Langford TJ, Lee J, Lee JHC, Lei RT, Leitner R, Leung JKC, Li F, Li HL, Li JJ, Li QJ, Li S, Li SC, Li SJ, Li WD, Li XN, Li XQ, Li YF, Li ZB, Liang H, Lin CJ, Lin GL, Lin S, Ling JJ, Link JM, Littenberg L, Littlejohn BR, Liu JC, Liu JL, Liu Y, Liu YH, Lu C, Lu HQ, Lu JS, Lucas P, Luk KB, Ma XB, Ma XY, Ma YQ, Mann WA, Marshak ML, Marshall C, Martinez Caicedo DA, Mayer N, McDonald KT, McKeown RD, Mehdiyev R, Meier JR, Meng Y, Miller WH, Mills G, Mora Lepin L, Naples D, Napolitano J, Naumov D, Naumova E, Nelson JK, Nichol RJ, O'Connor J, Ochoa-Ricoux JP, Olshevskiy A, Pahlka RB, Pan HR, Park J, Patton S, Pavlović Ž, Pawloski G, Peng JC, Perch A, Pfützner MM, Phan DD, Plunkett RK, Poonthottathil N, Pun CSJ, Qi FZ, Qi M, Qian X, Qiu X, Radovic A, Raper N, Ren J, Reveco CM, Rosero R, Roskovec B, Ruan XC, Sail P, Sanchez MC, Schneps J, Schreckenberger A, Shaheed N, Sharma R, Sousa A, Steiner H, Sun JL, Tagg N, Thomas J, Thomson MA, Timmons A, Tmej T, Todd J, Tognini SC, Toner R, Torretta D, Treskov K, Tse WH, Tull CE, Vahle P, Viren B, Vorobel V, Wang CH, Wang J, Wang M, Wang NY, Wang RG, Wang W, Wang W, Wang X, Wang Y, Wang YF, Wang Z, Wang Z, Wang ZM, Weber A, Wei HY, Wei LH, Wen LJ, Whisnant K, White C, Whitehead LH, Wojcicki SG, Wong HLH, Wong SCF, Worcester E, Wu DR, Wu FL, Wu Q, Wu WJ, Xia DM, Xie ZQ, Xing ZZ, Xu JL, Xu T, Xue T, Yang CG, Yang L, Yang YZ, Yao HF, Ye M, Yeh M, Young BL, Yu HZ, Yu ZY, Yue BB, Zeng S, Zeng Y, Zhan L, Zhang C, Zhang FY, Zhang HH, Zhang JW, Zhang QM, Zhang XT, Zhang YM, Zhang YX, Zhang YY, Zhang ZJ, Zhang ZP, Zhang ZY, Zhao J, Zhou L, Zhuang HL. Improved Constraints on Sterile Neutrino Mixing from Disappearance Searches in the MINOS, MINOS+, Daya Bay, and Bugey-3 Experiments. PHYSICAL REVIEW LETTERS 2020; 125:071801. [PMID: 32857527 DOI: 10.1103/physrevlett.125.071801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Searches for electron antineutrino, muon neutrino, and muon antineutrino disappearance driven by sterile neutrino mixing have been carried out by the Daya Bay and MINOS+ collaborations. This Letter presents the combined results of these searches, along with exclusion results from the Bugey-3 reactor experiment, framed in a minimally extended four-neutrino scenario. Significantly improved constraints on the θ_{μe} mixing angle are derived that constitute the most constraining limits to date over five orders of magnitude in the mass-squared splitting Δm_{41}^{2}, excluding the 90% C.L. sterile-neutrino parameter space allowed by the LSND and MiniBooNE observations at 90% CL_{s} for Δm_{41}^{2}<13 eV^{2}. Furthermore, the LSND and MiniBooNE 99% C.L. allowed regions are excluded at 99% CL_{s} for Δm_{41}^{2}<1.6 eV^{2}.
Collapse
|
50
|
Mi X, Lai K, Yan L, Xie S, Qiu X, Xiao S, Wei S. miR-18a expression in basal cell carcinoma and regulatory mechanism on autophagy through mTOR pathway. Clin Exp Dermatol 2020; 45:1027-1034. [PMID: 32485050 DOI: 10.1111/ced.14322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/11/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Basal cell carcinoma (BCC) is the most common form of skin carcinoma. AIM To investigate the function of key micro(mi)RNAs and to explore the potential molecular mechanisms involved in BCC. METHODS The microarray dataset GSE34535, which comprises seven BCC samples and seven control samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed miRNAs (DE-miRNAs) were identified. We collected tissue samples from 20 patients with BCC and 20 healthy controls (HCs), to compare the miR-18a expression in their tissue samples. Expression of miR-18a in A431 and HaCaT cells was also assayed. Following this, we upregulated and downregulated miR-18a expression in A431 cells to examine the effects on cell proliferation, migration and apoptosis. To further investigate the relative mechanism, the proteins LC3, Beclin 1, Akt and mammalian target of rapamycin (mTOR) were examined by quantitative real-time PCR and Western blotting. For further verification, we examined the expression of LC3 in the 20 BCC and 20 HC tissue samples. RESULTS In total, 19 DE-miRNAs (13 upregulated and 6 downregulated) that were common to the BCC and HC groups were identified. Levels of miR-18a were about three-fold higher in BCC tissues and A431 cells compared with their respective control groups. In vitro, downregulation of miR-18a was shown to inhibit cell proliferation and activate autophagy via the Akt/mTOR signalling pathway, while upregulation of miR-18a promoted proliferation of these cells. LC3 was decreased in BCC compared with HC tissue samples. CONCLUSIONS Our data support an oncogenic role of miR-18a through a novel Akt/mTOR/Beclin 1/LC3 axis, and suggest that the antitumour effects of miR-18a inhibitor may make it suitable for BCC therapy.
Collapse
|