1
|
Pian E, Mazzali PA, Masetti N, Ferrero P, Klose S, Palazzi E, Ramirez-Ruiz E, Woosley SE, Kouveliotou C, Deng J, Filippenko AV, Foley RJ, Fynbo JPU, Kann DA, Li W, Hjorth J, Nomoto K, Patat F, Sauer DN, Sollerman J, Vreeswijk PM, Guenther EW, Levan A, O'Brien P, Tanvir NR, Wijers RAMJ, Dumas C, Hainaut O, Wong DS, Baade D, Wang L, Amati L, Cappellaro E, Castro-Tirado AJ, Ellison S, Frontera F, Fruchter AS, Greiner J, Kawabata K, Ledoux C, Maeda K, Møller P, Nicastro L, Rol E, Starling R. An optical supernova associated with the X-ray flash XRF 060218. Nature 2006; 442:1011-3. [PMID: 16943831 DOI: 10.1038/nature05082] [Citation(s) in RCA: 393] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Accepted: 07/10/2006] [Indexed: 11/09/2022]
Abstract
Long-duration gamma-ray bursts (GRBs) are associated with type Ic supernovae that are more luminous than average and that eject material at very high velocities. Less-luminous supernovae were not hitherto known to be associated with GRBs, and therefore GRB-supernovae were thought to be rare events. Whether X-ray flashes--analogues of GRBs, but with lower luminosities and fewer gamma-rays--can also be associated with supernovae, and whether they are intrinsically 'weak' events or typical GRBs viewed off the axis of the burst, is unclear. Here we report the optical discovery and follow-up observations of the type Ic supernova SN 2006aj associated with X-ray flash XRF 060218. Supernova 2006aj is intrinsically less luminous than the GRB-supernovae, but more luminous than many supernovae not accompanied by a GRB. The ejecta velocities derived from our spectra are intermediate between these two groups, which is consistent with the weakness of both the GRB output and the supernova radio flux. Our data, combined with radio and X-ray observations, suggest that XRF 060218 is an intrinsically weak and soft event, rather than a classical GRB observed off-axis. This extends the GRB-supernova connection to X-ray flashes and fainter supernovae, implying a common origin. Events such as XRF 060218 are probably more numerous than GRB-supernovae.
Collapse
|
|
19 |
393 |
2
|
Gal-Yam A, Mazzali P, Ofek EO, Nugent PE, Kulkarni SR, Kasliwal MM, Quimby RM, Filippenko AV, Cenko SB, Chornock R, Waldman R, Kasen D, Sullivan M, Beshore EC, Drake AJ, Thomas RC, Bloom JS, Poznanski D, Miller AA, Foley RJ, Silverman JM, Arcavi I, Ellis RS, Deng J. Supernova 2007bi as a pair-instability explosion. Nature 2009; 462:624-7. [DOI: 10.1038/nature08579] [Citation(s) in RCA: 357] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 10/08/2009] [Indexed: 11/09/2022]
|
|
16 |
357 |
3
|
Deng J, Kohda Y, Chiao H, Wang Y, Hu X, Hewitt SM, Miyaji T, McLeroy P, Nibhanupudy B, Li S, Star RA. Interleukin-10 inhibits ischemic and cisplatin-induced acute renal injury. Kidney Int 2001; 60:2118-28. [PMID: 11737586 DOI: 10.1046/j.1523-1755.2001.00043.x] [Citation(s) in RCA: 308] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Acute renal failure (ARF) is caused by ischemic and nephrotoxic insults acting alone or in combination. Anti-inflammatory agents have been shown to decrease renal ischemia-reperfusion and cisplatin-induced injury and leukocyte infiltration. Interleukin-10 (IL-10) is a potent anti-inflammatory cytokine that inhibits inflammatory and cytotoxic pathways implicated in acute renal injury. Therefore, we sought to determine if IL-10 inhibits acute renal injury. METHODS The effects of IL-10 were studied in mice following cisplatin administration and bilateral renal ischemia-reperfusion, in a rat model of renal transplantation, and in cultured mouse cortical tubule cells. RESULTS IL-10 significantly decreased renal injury following cisplatin administration and following renal ischemia/reperfusion. Delay of IL-10 treatment for one hour after cisplatin also significantly inhibited renal damage. IL-10 and alpha-melanocyte stimulating hormone (alpha-MSH) increased recovery following transplantation of a kidney subjected to warm ischemia. To explore the mechanism of action of IL-10, its effects were measured on mediators of leukocyte trafficking and inducible nitric oxide synthase (NOS-II). IL-10 inhibited cisplatin and ischemia-induced increases in mRNA for tumor necrosis factor-alpha (TNF-alpha), intercellular adhesion molecule-1 (ICAM-1), and NOS-II. IL-10 also inhibited staining for markers of apoptosis and cell cycle activity following cisplatin administration, and nitric oxide production in cultured mouse cortical tubules. CONCLUSIONS IL-10 protects against renal ischemic and cisplatin-induced injury. IL-10 may act, in part, by inhibiting the maladaptive activation of genes that cause leukocyte activation and adhesion, and induction of iNOS.
Collapse
|
|
24 |
308 |
4
|
Pastorello A, Smartt SJ, Mattila S, Eldridge JJ, Young D, Itagaki K, Yamaoka H, Navasardyan H, Valenti S, Patat F, Agnoletto I, Augusteijn T, Benetti S, Cappellaro E, Boles T, Bonnet-Bidaud JM, Botticella MT, Bufano F, Cao C, Deng J, Dennefeld M, Elias-Rosa N, Harutyunyan A, Keenan FP, Iijima T, Lorenzi V, Mazzali PA, Meng X, Nakano S, Nielsen TB, Smoker JV, Stanishev V, Turatto M, Xu D, Zampieri L. A giant outburst two years before the core-collapse of a massive star. Nature 2007; 447:829-32. [PMID: 17568740 DOI: 10.1038/nature05825] [Citation(s) in RCA: 279] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Accepted: 04/02/2007] [Indexed: 11/08/2022]
Abstract
The death of massive stars produces a variety of supernovae, which are linked to the structure of the exploding stars. The detection of several precursor stars of type II supernovae has been reported (see, for example, ref. 3), but we do not yet have direct information on the progenitors of the hydrogen-deficient type Ib and Ic supernovae. Here we report that the peculiar type Ib supernova SN 2006jc is spatially coincident with a bright optical transient that occurred in 2004. Spectroscopic and photometric monitoring of the supernova leads us to suggest that the progenitor was a carbon-oxygen Wolf-Rayet star embedded within a helium-rich circumstellar medium. There are different possible explanations for this pre-explosion transient. It appears similar to the giant outbursts of luminous blue variable stars (LBVs) of 60-100 solar masses, but the progenitor of SN 2006jc was helium- and hydrogen-deficient (unlike LBVs). An LBV-like outburst of a Wolf-Rayet star could be invoked, but this would be the first observational evidence of such a phenomenon. Alternatively, a massive binary system composed of an LBV that erupted in 2004, and a Wolf-Rayet star exploding as SN 2006jc, could explain the observations.
Collapse
|
Research Support, Non-U.S. Gov't |
18 |
279 |
5
|
McLaurin J, Franklin T, Zhang X, Deng J, Fraser PE. Interactions of Alzheimer amyloid-beta peptides with glycosaminoglycans effects on fibril nucleation and growth. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 266:1101-10. [PMID: 10583407 DOI: 10.1046/j.1432-1327.1999.00957.x] [Citation(s) in RCA: 204] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Proteoglycans and their constituent glycosaminoglycans are associated with all amyloid deposits and may be involved in the amyloidogenic pathway. In Alzheimer's disease, plaques are composed of the amyloid-beta peptide and are associated with at least four different proteoglycans. Using CD spectroscopy, fluorescence spectroscopy and electron microscopy, we examined glycosaminoglycan interaction with the amyloid-beta peptides 1-40 (Abeta40) and 1-42 (Abeta42) to determine the effects on peptide conformation and fibril formation. Monomeric amyloid-beta peptides in trifluoroethanol, when diluted in aqueous buffer, undergo a slow random to amyloidogenic beta sheet transition. In the presence of heparin, heparan sulfate, keratan sulfate or chondroitin sulfates, this transition was accelerated with Abeta42 rapidly adopting a beta-sheet conformation. This was accompanied by the appearance of well-defined amyloid fibrils indicating an enhanced nucleation of Abeta42. Incubation of preformed Abeta42 fibrils with glycosaminoglycans resulted in extensive lateral aggregation and precipitation of the fibrils. The glycosaminoglycans differed in their relative activities with the chondroitin sulfates producing the most pronounced effects. The less amyloidogenic Abeta40 isoform did not show an immediate structural transition that was dependent upon the shielding effect by the phosphate counter ion. Removal or substitution of phosphate resulted in similar glycosaminoglycan-induced conformational and aggregation changes. These findings clearly demonstrate that glycosaminoglycans act at the earliest stage of fibril formation, namely amyloid-beta nucleation, and are not simply involved in the lateral aggregation of preformed fibrils or nonspecific adhesion to plaques. The identification of a structure-activity relationship between amyloid-beta and the different glycosaminoglycans, as well as the condition dependence for glycosaminoglycan binding, are important for the successful development and evaluation of glycosaminoglycan-specific therapeutic interventions.
Collapse
|
|
26 |
204 |
6
|
Hsing AW, Chua S, Gao YT, Gentzschein E, Chang L, Deng J, Stanczyk FZ. Prostate cancer risk and serum levels of insulin and leptin: a population-based study. J Natl Cancer Inst 2001; 93:783-9. [PMID: 11353789 DOI: 10.1093/jnci/93.10.783] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND In a previous study of Chinese men, we found that men with a higher waist-to-hip ratio (WHR) have a higher prostate cancer risk. Because leptin and insulin are related to body fat distribution, we examined whether leptin and insulin were associated with prostate cancer risk. METHODS Blood samples were collected from 128 case patients with incident prostate cancer and from 306 healthy control subjects randomly selected from residents of Shanghai, CHINA: Epidemiologic information and anthropometric measurements were collected in personal interviews. Serum leptin, insulin, and sex hormone levels were measured by radioimmunoassay, and insulin-like growth factor-I (IGF-I) was measured by enzyme-linked immunosorbent assay. Multiple logistic regression analyses were used to estimate odds ratios for prostate cancer in relation to serum insulin and leptin levels. All statistical tests were two-sided. RESULTS After adjustment for body mass index, WHR, IGF-I, and sex hormone levels, higher serum insulin levels were associated with a statistically significantly elevated risk of prostate cancer (P<.001). Men in the highest tertile of insulin levels had a 2.56-fold (95% confidence interval [CI] = 1.38 to 4.75) risk of prostate cancer compared with men in the lowest tertile. Regardless of the tertile level of WHR, higher serum insulin levels were associated with an increased risk of prostate cancer: Men in the highest tertiles of WHR (>0.900) and insulin (>8.83 microU/mL) had 8.55 times (95% CI = 2.80 to 26.10) the prostate cancer risk of men in the lowest tertiles of both, and those in the lowest tertile of WHR (<0.873) and highest tertile of insulin had 4.30 times (95% CI = 1.17 to 15.70) the risk. By contrast, the association between leptin levels and prostate cancer risk was not statistically significant. CONCLUSION Our results suggest that serum insulin levels may influence the risk of prostate cancer in Chinese men. Further research, especially prospective studies, is needed to confirm these findings in high-risk populations and to clarify the underlying mechanisms involved.
Collapse
|
Journal Article |
24 |
190 |
7
|
Yan H, Wu QL, Sun CY, Ai LS, Deng J, Zhang L, Chen L, Chu ZB, Tang B, Wang K, Wu XF, Xu J, Hu Y. piRNA-823 contributes to tumorigenesis by regulating de novo DNA methylation and angiogenesis in multiple myeloma. Leukemia 2014; 29:196-206. [PMID: 24732595 DOI: 10.1038/leu.2014.135] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 03/05/2014] [Accepted: 04/09/2014] [Indexed: 12/17/2022]
Abstract
Aberrant DNA hypermethylation contributes to myelomagenesis by silencing tumor-suppressor genes. Recently, a few reports have suggested that a novel class of small non-coding RNAs, called Piwi-interacting RNAs (piRNAs), may be involved in the epigenetic regulation of cancer. In this study, for the first time we provided evidence that the expression of piRNA-823 was upregulated in multiple myeloma (MM) patients and cell lines, and positively correlated with clinical stage. Silencing piRNA-823 in MM cells induced deregulation of cell cycle regulators and apoptosis-related proteins expression, accompanied by inhibition of tumorigenicity in vitro and in vivo. Moreover, piRNA-823 was directly relevant to de novo DNA methyltransferases, DNMT3A and 3B, in primary CD138(+) MM cells. The inhibited expression of piRNA-823 in MM cells resulted in marked reduction of DNMT3A and 3B at both mRNA and protein levels, which in turn led to decrease in global DNA methylation and reexpression of methylation-silenced tumor suppressor, p16(INK4A). In addition, piRNA-823 abrogation in MM cells induced reduction of vascular endothelial growth factor secretion, with consequent decreased proangiogenic activity. Altogether, these data support an oncogenic role of piRNA-823 in the biology of MM, providing a rational for the development of piRNA-targeted therapeutic strategies in MM.
Collapse
|
Research Support, Non-U.S. Gov't |
11 |
156 |
8
|
Deng J, Gurnis M, Kanamori H, Hauksson E. Viscoelastic flow in the lower crust after the 1992 landers, california, earthquake. Science 1998; 282:1689-92. [PMID: 9831556 DOI: 10.1126/science.282.5394.1689] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Space geodesy showed that broad-scale postseismic deformation occurred after the 1992 Landers earthquake. Three-dimensional modeling shows that afterslip can only explain one horizontal component of the postseismic deformation, whereas viscoelastic flow can explain the horizontal and near-vertical displacements. The viscosity of a weak, about 10-km-thick layer, in the lower crust beneath the rupture zone that controls the rebound is about 10(18) pascal seconds. The viscoelastic behavior of the lower crust may help to explain the extensional structures observed in the Basin and Range province and it may be used for the analysis of earthquake hazard.
Collapse
|
|
27 |
149 |
9
|
Ma CM, Li JS, Pawlicki T, Jiang SB, Deng J, Lee MC, Koumrian T, Luxton M, Brain S. A Monte Carlo dose calculation tool for radiotherapy treatment planning. Phys Med Biol 2002; 47:1671-89. [PMID: 12069086 DOI: 10.1088/0031-9155/47/10/305] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A Monte Carlo user code, MCDOSE, has been developed for radiotherapy treatment planning (RTP) dose calculations. MCDOSE is designed as a dose calculation module suitable for adaptation to host RTP systems. MCDOSE can be used for both conventional photon/electron beam calculation and intensity modulated radiotherapy (IMRT) treatment planning. MCDOSE uses a multiple-source model to reconstruct the treatment beam phase space. Based on Monte Carlo simulated or measured beam data acquired during commissioning, source-model parameters are adjusted through an automated procedure. Beam modifiers such as jaws, physical and dynamic wedges, compensators, blocks, electron cut-outs and bolus are simulated by MCDOSE together with a 3D rectilinear patient geometry model built from CT data. Dose distributions calculated using MCDOSE agreed well with those calculated by the EGS4/DOSXYZ code using different beam set-ups and beam modifiers. Heterogeneity correction factors for layered-lung or layered-bone phantoms as calculated by both codes were consistent with measured data to within 1%. The effect of energy cut-offs for particle transport was investigated. Variance reduction techniques were implemented in MCDOSE to achieve a speedup factor of 10-30 compared to DOSXYZ.
Collapse
|
|
23 |
146 |
10
|
Deng J, Isik E, Fernandes SM, Brown JR, Letai A, Davids MS. Bruton's tyrosine kinase inhibition increases BCL-2 dependence and enhances sensitivity to venetoclax in chronic lymphocytic leukemia. Leukemia 2017; 31:2075-2084. [PMID: 28111464 PMCID: PMC5555835 DOI: 10.1038/leu.2017.32] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/05/2017] [Accepted: 01/13/2017] [Indexed: 02/07/2023]
Abstract
Although the BTK inhibitor ibrutinib has transformed the management of patients with CLL, it does not induce substantial apoptosis in vitro, and as such the mechanisms underlying its ability to kill CLL cells are not well understood. Acalabrutinib, a more specific BTK inhibitor now in development, also appears to be highly effective in CLL, but the connection of its mechanism with CLL cell death is also unclear. Using dynamic BH3 profiling, we analyzed alterations in the function of the mitochondrial apoptotic pathway induced by ibrutinib and acalabrutinib. We studied CLL patient samples treated ex vivo with both drugs, as well as primary samples from CLL patients on clinical trials of both drugs. We found that BTK inhibition enhances mitochondrial BCL-2 dependence without significantly altering overall mitochondrial priming. Enhancement of BCL-2 dependence was accompanied by an increase in the pro-apoptotic protein BIM. In contrast, treatment with the selective BCL-2 inhibitor venetoclax enhanced overall mitochondrial priming without increasing BCL-2 dependence. Pre-treatment of CLL cells with either BTK inhibitor, whether ex vivo or in vivo in patients, enhanced killing by venetoclax. Our data suggest that BTK inhibition enhances mitochondrial BCL2 dependence, supporting the ongoing development of clinical trials combining BTK and BCL-2 inhibition.
Collapse
|
Journal Article |
8 |
139 |
11
|
Liu Z, Liu B, Kong J, Deng J. Probing trace phenols based on mediator-free alumina sol--gel-derived tyrosinase biosensor. Anal Chem 2000; 72:4707-12. [PMID: 11028635 DOI: 10.1021/ac990490h] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel tyrosinase biosensor has been developed for the subnanomolar detection of phenols, based on the immobilization of tyrosinase in a positively charged Al2O3 sol-gel membrane on a glassy carbon electrode. It has been found that Al2O3 sol-gel is perfectly beneficial to the immobilization of tyrosinase, because it not only possesses the general advantages of sol-gel but it also is an effective promoter of the biosensor. The large microscopic surface area, porous morphology, and hydrophilic property of the sol-gel matrix result in high enzyme loading, and the enzyme entrapped in this matrix retains its activity to a large extent. The Al2O3 sol-gel-containing surface also displays an intrinsic electrocatalytic o-quinone response and, hence, offers a high-sensitivity (127 microA mM(-1)) monitoring of phenols. The detection limit is 0.2 nM at a signal-to-noise ratio of 3, the response time is less than 4 s reaching 95% of the steady-state value, and 70% of the activity is retained after 3 months.
Collapse
|
|
25 |
133 |
12
|
Cui X, Wang Y, Tang Y, Liu Y, Zhao L, Deng J, Xu G, Peng X, Ju S, Liu G, Yang H. Seipin ablation in mice results in severe generalized lipodystrophy. Hum Mol Genet 2011; 20:3022-30. [DOI: 10.1093/hmg/ddr205] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
|
14 |
132 |
13
|
Wang JYJ, Zhou DHD, Li J, Zhang M, Deng J, Tang M, Gao C, Li J, Lian Y, Chen M. Leisure activity and risk of cognitive impairment: The Chongqing aging study. Neurology 2005; 66:911-3. [PMID: 16291928 DOI: 10.1212/01.wnl.0000192165.99963.2a] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The authors followed 5,437 people aged 55 years and older with normal baseline Mini-Mental State Examination score annually for 5 years. The mean incidence of cognitive impairment was 2.3% per year. Cognitive activities in both the individual item (playing board games and reading) and the composite measure were associated with the reduced risk of cognitive impairment, while watching television was associated with an increased risk of cognitive impairment.
Collapse
|
|
20 |
130 |
14
|
Lei C, Deng J. Hydrogen peroxide sensor based on coimmobilized methylene green and horseradish peroxidase in the same montmorillonite-modified bovine serum albumin-glutaraldehyde matrix on a glassy carbon electrode surface. Anal Chem 1996; 68:3344-9. [PMID: 8843134 DOI: 10.1021/ac960291n] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A new approach to construct a second-generation amperometric biosensor is described. The classical dye methylene green as a probing-needle mediator and horseradish peroxidase as a base enzyme were coimmobilized in the same montmorillonite-modified bovine serum albumin (BSA)-glutaraldehyde matrix to construct a H2O2 sensor. The immobilization matrix was formed from the pretreated sodium montmorillonite colloid in which the enzyme and the cross-linker were dissolved. Immobilization of methylene green from the dye mother solution was attributed to the adsorption function of the montmorillonite, whereas immobilization of horseradish peroxidase was attributed to the cross-linking function of the BSA-glutaraldehyde as usual. Cyclic voltammetry and potentiostatic measurements indicated that methylene green efficiently mediated electrons from the base electrode to the enzyme in the matrix. The sensor responded rapidly to low H2O2 concentration and achieved 95% of the steady-state current in less than 20 s, with a detection limit of 4.0 x 10(-7) M H2O2.
Collapse
|
|
29 |
128 |
15
|
Ma CM, Pawlicki T, Jiang SB, Li JS, Deng J, Mok E, Kapur A, Xing L, Ma L, Boyer AL. Monte Carlo verification of IMRT dose distributions from a commercial treatment planning optimization system. Phys Med Biol 2000; 45:2483-95. [PMID: 11008950 DOI: 10.1088/0031-9155/45/9/303] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The purpose of this work was to use Monte Carlo simulations to verify the accuracy of the dose distributions from a commercial treatment planning optimization system (Corvus, Nomos Corp., Sewickley, PA) for intensity-modulated radiotherapy (IMRT). A Monte Carlo treatment planning system has been implemented clinically to improve and verify the accuracy of radiotherapy dose calculations. Further modifications to the system were made to compute the dose in a patient for multiple fixed-gantry IMRT fields. The dose distributions in the experimental phantoms and in the patients were calculated and used to verify the optimized treatment plans generated by the Corvus system. The Monte Carlo calculated IMRT dose distributions agreed with the measurements to within 2% of the maximum dose for all the beam energies and field sizes for both the homogeneous and heterogeneous phantoms. The dose distributions predicted by the Corvus system, which employs a finite-size pencil beam (FSPB) algorithm, agreed with the Monte Carlo simulations and measurements to within 4% in a cylindrical water phantom with various hypothetical target shapes. Discrepancies of more than 5% (relative to the prescribed target dose) in the target region and over 20% in the critical structures were found in some IMRT patient calculations. The FSPB algorithm as implemented in the Corvus system is adequate for homogeneous phantoms (such as prostate) but may result in significant under or over-estimation of the dose in some cases involving heterogeneities such as the air-tissue, lung-tissue and tissue-bone interfaces.
Collapse
|
Comparative Study |
25 |
123 |
16
|
Deng J, Xiong Y, Sundaralingam M. X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A). Proc Natl Acad Sci U S A 2001; 98:13665-70. [PMID: 11707581 PMCID: PMC61098 DOI: 10.1073/pnas.241374798] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four-stranded guanine tetraplexes in RNA have been identified to be involved in crucial biological functions, such as dimerization of retroviral RNA, translational repression, and mRNA turnover. However, the structural basis for these biological processes is still largely unknown. Here we report the RNA tetraplex structure (UGGGGU)(4) at ultra-high resolution (0.61 A). The space group is P42(1)2, and cell constants are a = b = 36.16 A and c = 74.09 A. The structure was solved by the multiple-wavelength anomalous dispersion method using a set of three-wavelength data of the isomorphous bromo derivative (br)UGGGGU and refined to 0.61-A resolution. Each of the four strands in the asymmetric unit forms a parallel tetraplex with symmetry-related molecules. The tetraplex molecules stack on one another in opposite polarity (head-to-head or tail-to-tail) to form a pseudocontinuous column. All of the 5'-end uridines rotate around the backbone of G2, swing out, and form unique octaplexes with the neighboring G tetraplexes, whereas the 3'-end uridines are stacked-in and form uridine tetrads. All of the bases are anti, and the riboses are in the mixed C2'- and C3'-puckering mode. Strontium ions are observed in every other guanine tetrad plane, sitting on the fourfold axis and associated to the eight O6 atoms of neighboring guanine bases in a bipyramidal-antiprism geometry. The hydrogens are clearly observed in the structure.
Collapse
|
research-article |
24 |
117 |
17
|
Deng J, Jiang SB, Kapur A, Li J, Pawlicki T, Ma CM. Photon beam characterization and modelling for Monte Carlo treatment planning. Phys Med Biol 2000; 45:411-27. [PMID: 10701512 DOI: 10.1088/0031-9155/45/2/311] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Photon beams of 4, 6 and 15 MV from Varian Clinac 2100C and 2300C/D accelerators were simulated using the EGS4/BEAM code system. The accelerators were modelled as a combination of component modules (CMs) consisting of a target, primary collimator, exit window, flattening filter, monitor chamber, secondary collimator, ring collimator, photon jaws and protection window. A full phase space file was scored directly above the upper photon jaws and analysed using beam data processing software, BEAMDP, to derive the beam characteristics, such as planar fluence, angular distribution, energy spectrum and the fractional contributions of each individual CM. A multiple-source model has been further developed to reconstruct the original phase space. Separate sources were created with accurate source intensity, energy, fluence and angular distributions for the target, primary collimator and flattening filter. Good agreement (within 2%) between the Monte Carlo calculations with the source model and those with the original phase space was achieved in the dose distributions for field sizes of 4 cm x 4 cm to 40 cm x 40 cm at source surface distances (SSDs) of 80-120 cm. The dose distributions in lung and bone heterogeneous phantoms have also been found to be in good agreement (within 2%) for 4, 6 and 15 MV photon beams for various field sizes between the Monte Carlo calculations with the source model and those with the original phase space.
Collapse
|
Comparative Study |
25 |
117 |
18
|
Apsel SE, Emmert JW, Deng J, Bloomfield LA. Surface-enhanced magnetism in nickel clusters. PHYSICAL REVIEW LETTERS 1996; 76:1441-1444. [PMID: 10061724 DOI: 10.1103/physrevlett.76.1441] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
|
|
29 |
110 |
19
|
Liu B, Hu R, Deng J. Characterization of immobilization of an enzyme in a modified Y zeolite matrix and its application to an amperometric glucose biosensor. Anal Chem 1997; 69:2343-8. [PMID: 9212705 DOI: 10.1021/ac960930u] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A new approach to construct an amperometric biosensor is described. Without using bovine serum albumin-glutaraldehyde, glucose oxidase (GOx) was immobilized on a dealuminized Y zeolite (DAY)-modified platinum electrode to construct a glucose sensor. The large specific surface area of the zeolite substrate resulted in high enzyme loading. The immobilized GOx in this manner was stable and could maintain its high activity for at least 3 months. The interactions between the zeolite and the enzyme were investigated by means of Fourier transform infrared spectra, and the pore distribution and the surface acid property of DAY were preliminarily studied. The results showed that the hydrophilic property and the existing mesopores of DAY played important roles in the enzyme immobilization. This resulting biosensor exhibited good reproducibility and selectivity, owing to the uniform pore structure and unique ion-exchange property of the zeolite. The biosensor responded rapidly to glucose in the linear range from 2.0 x 10(-6) to 3.0 x 10(-3) M, with a detection limit of 0.5 microM.
Collapse
|
|
28 |
106 |
20
|
|
|
15 |
104 |
21
|
Ma CM, Ding M, Li JS, Lee MC, Pawlicki T, Deng J. A comparative dosimetric study on tangential photon beams, intensity-modulated radiation therapy (IMRT) and modulated electron radiotherapy (MERT) for breast cancer treatment. Phys Med Biol 2003; 48:909-24. [PMID: 12701895 DOI: 10.1088/0031-9155/48/7/308] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recently, energy- and intensity-modulated electron radiotherapy (MERT) has garnered a growing interest for the treatment of superficial targets. In this work. we carried out a comparative dosimetry study to evaluate MERT, photon beam intensity-modulated radiation therapy (IMRT) and conventional tangential photon beams for the treatment of breast cancer. A Monte Carlo based treatment planning system has been investigated, which consists of a set of software tools to perform accurate dose calculation, treatment optimization, leaf sequencing and plan analysis. We have compared breast treatment plans generated using this home-grown treatment optimization and dose calculation software forthese treatment techniques. The MERT plans were planned with up to two gantry angles and four nominal energies (6, 9, 12 and 16 MeV). The tangential photon treatment plans were planned with 6 MV wedged photon beams. The IMRT plans were planned using both multiple-gantry 6 MV photon beams or two 6 MV tangential beams. Our results show that tangential IMRT can reduce the dose to the lung, heart and contralateral breast compared to conventional tangential wedged beams (up to 50% reduction in high dose volume or 5 Gy in the maximum dose). MERT can reduce the maximum dose to the lung by up to 20 Gy and to the heart by up to 35 Gy compared to conventional tangential wedged beams. Multiple beam angle IMRT can significantly reduce the maximum dose to the lung and heart (up to 20 Gy) but it induces low and medium doses to a large volume of normal tissues including lung, heart and contralateral breast. It is concluded that MERT has superior capabilities to achieve dose conformity both laterally and in the depth direction, which will be well suited for treating superficial targets such as breast cancer.
Collapse
|
Comparative Study |
22 |
93 |
22
|
Blanco FF, Jimbo M, Wulfkuhle J, Gallagher I, Deng J, Enyenihi L, Meisner-Kober N, Londin E, Rigoutsos I, Sawicki JA, Risbud MV, Witkiewicz AK, McCue PA, Jiang W, Rui H, Yeo CJ, Petricoin E, Winter JM, Brody JR. The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells. Oncogene 2015; 35:2529-41. [PMID: 26387536 DOI: 10.1038/onc.2015.325] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/08/2015] [Accepted: 07/10/2015] [Indexed: 12/15/2022]
Abstract
Previously, it has been shown that pancreatic ductal adenocarcinoma (PDA) tumors exhibit high levels of hypoxia, characterized by low oxygen pressure (pO2) and decreased O2 intracellular perfusion. Chronic hypoxia is strongly associated with resistance to cytotoxic chemotherapy and chemoradiation in an understudied phenomenon known as hypoxia-induced chemoresistance. The hypoxia-inducible, pro-oncogenic, serine-threonine kinase PIM1 (Proviral Integration site for Moloney murine leukemia virus 1) has emerged as a key regulator of hypoxia-induced chemoresistance in PDA and other cancers. Although its role in therapeutic resistance has been described previously, the molecular mechanism behind PIM1 overexpression in PDA is unknown. Here, we demonstrate that cis-acting AU-rich elements (ARE) present within a 38-base pair region of the PIM1 mRNA 3'-untranslated region mediate a regulatory interaction with the mRNA stability factor HuR (Hu antigen R) in the context of tumor hypoxia. Predominantly expressed in the nucleus in PDA cells, HuR translocates to the cytoplasm in response to hypoxic stress and stabilizes the PIM1 mRNA transcript, resulting in PIM1 protein overexpression. A reverse-phase protein array revealed that HuR-mediated regulation of PIM1 protects cells from hypoxic stress through phosphorylation and inactivation of the apoptotic effector BAD and activation of MEK1/2. Importantly, pharmacological inhibition of HuR by MS-444 inhibits HuR homodimerization and its cytoplasmic translocation, abrogates hypoxia-induced PIM1 overexpression and markedly enhances PDA cell sensitivity to oxaliplatin and 5-fluorouracil under physiologic low oxygen conditions. Taken together, these results support the notion that HuR has prosurvival properties in PDA cells by enabling them with growth advantages in stressful tumor microenvironment niches. Accordingly, these studies provide evidence that therapeutic disruption of HuR's regulation of PIM1 may be a key strategy in breaking an elusive chemotherapeutic resistance mechanism acquired by PDA cells that reside in hypoxic PDA microenvironments.
Collapse
|
Journal Article |
10 |
92 |
23
|
Shao R, Karunagaran D, Zhou BP, Li K, Lo SS, Deng J, Chiao P, Hung MC. Inhibition of nuclear factor-kappaB activity is involved in E1A-mediated sensitization of radiation-induced apoptosis. J Biol Chem 1997; 272:32739-42. [PMID: 9407046 DOI: 10.1074/jbc.272.52.32739] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The adenoviral E1A protein has been implicated in the potentiation of apoptosis induced by various external stimuli, but the exact mechanism of that potentiation is not clear. In this study, we compared the sensitivity to ionizing gamma-irradiation of E1A transfectants with that of parental cells in a human ovarian cancer cell line (SKOV3.ip1); we found that the E1A transfectants became sensitive to radiation-induced apoptosis. Recently, activation of the transcription factor nuclear factor-kappaB (NF-kappaB) has been shown to play a key role in the anti-apoptotic pathway of radiation-induced apoptosis. In an attempt to determine whether NF-kappaB was involved in the E1A-mediated sensitization of radiation-induced apoptosis, we found that radiation-induced activation of NF-kappaB occurred in the parental cells but was blocked in the E1A transfectants. Furthermore, parental cells cotransfected with NF-kappaB and E1A were better protected from undergoing apoptosis upon irradiation than those transfected with E1A alone. Thus, our results suggest that inhibition of NF-kappaB activation by E1A is a plausible mechanism for E1A-mediated sensitization of radiation-induced apoptosis.
Collapse
|
|
28 |
90 |
24
|
Ma CM, Pawlicki T, Lee MC, Jiang SB, Li JS, Deng J, Yi B, Mok E, Boyer AL. Energy- and intensity-modulated electron beams for radiotherapy. Phys Med Biol 2000; 45:2293-311. [PMID: 10958195 DOI: 10.1088/0031-9155/45/8/316] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This work investigates the feasibility of optimizing energy- and intensity-modulated electron beams for radiation therapy. A multileaf collimator (MLC) specially designed for modulated electron radiotherapy (MERT) was investigated both experimentally and by Monte Carlo simulations. An inverse-planning system based on Monte Carlo dose calculations was developed to optimize electron beam energy and intensity to achieve dose conformity for target volumes near the surface. The results showed that an MLC with 5 mm leaf widths could produce complex field shapes for MERT. Electron intra- and inter-leaf leakage had negligible effects on the dose distributions delivered with the MLC, even at shallow depths. Focused leaf ends reduced the electron scattering contributions to the dose compared with straight leaf ends. As anticipated, moving the MLC position toward the patient surface reduced the penumbra significantly. There were significant differences in the beamlet distributions calculated by an analytic 3-D pencil beam algorithm and the Monte Carlo method. The Monte Carlo calculated beamlet distributions were essential to the accuracy of the MERT dose distribution in cases involving large air gaps, oblique incidence and heterogeneous treatment targets (at the tissue-bone and bone-lung interfaces). To demonstrate the potential of MERT for target dose coverage and normal tissue sparing for treatment of superficial targets, treatment plans for a hypothetical treatment were compared using photon beams and MERT.
Collapse
|
Comparative Study |
25 |
90 |
25
|
Jiang J, Meng S, Huang S, Ruan Y, Lu X, Li JZ, Wu N, Huang J, Xie Z, Liang B, Deng J, Zhou B, Chen X, Ning C, Liao Y, Wei W, Lai J, Ye L, Wu F, Liang H. Effects of Talaromyces marneffei infection on mortality of HIV/AIDS patients in southern China: a retrospective cohort study. Clin Microbiol Infect 2018; 25:233-241. [PMID: 29698815 DOI: 10.1016/j.cmi.2018.04.018] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 10/17/2022]
Abstract
OBJECTIVE Talaromyces marneffei is an opportunistic infection with high morbidity among human immunodeficiency virus (HIV)/AIDS patients in Southeast Asia and southern China. Its effects on mortality in HIV/AIDS patients has not been clearly elucidated. METHODS We conducted a retrospective cohort study of hospitalized HIV-infected individuals at the Fourth People's Hospital of Nanning, Guangxi, China during 2012-2015. Kaplan-Meier analyses were used to calculate the cumulative mortality. Cox proportional hazard models and 1:1 propensity score matching (PSM) were used to evaluate the effects of T. marneffei infection on mortality of HIV/AIDS patients. RESULTS In total, 6791 HIV/AIDS patients were included, 1093 of them (16.1%) with documented T. marneffei co-infection. The mortality of T. marneffei-infected patients (25.0 per 100 person-months, 95% CI 21.5-26.7) was the highest among all AIDS-associated complications and was significantly higher than that of T. marneffei-uninfected HIV/AIDS patients (13.8 per 100 person-months, 95% CI 12.5-15.1; adjusted hazard ratio (AHR) 1.80, 95% CI 1.48-2.16). The results using PSM were similar (AHR 4.52 95% CI 2.43-8.42). The mortality of T. marneffei-infected patients was also significantly higher than that of patients without any complications. When stratified by demographic characteristics, T. marneffei infection has higher mortality risk in all stratifications. Co-infection with T. marneffei carries a higher mortality risk in patients at any CD4+ T-cell count. CONCLUSIONS Talaromyces marneffei infection is commonly found in hospitalized HIV/AIDS patients in southern China and was associated with a higher mortality rate than most HIV-associated complications. These results highlight the need for improved diagnosis, treatment and prevention of infection by this neglected fungal pathogen in southern China.
Collapse
|
Journal Article |
7 |
87 |