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1
Tang, Shixing, Tsutomu Murakami, Naiqian Cheng, Alasdair C. Steven, Eric O. Freed, and Judith G. Levin. "Human Immunodeficiency Virus Type 1 N-Terminal Capsid Mutants Containing Cores with Abnormally High Levels of Capsid Protein and Virtually No Reverse Transcriptase." Journal of Virology 77, no. 23 (December 1, 2003): 12592–602. http://dx.doi.org/10.1128/jvi.77.23.12592-12602.2003.
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ABSTRACT We previously described the phenotype associated with three alanine substitution mutations in conserved residues (Trp23, Phe40, and Asp51) in the N-terminal domain of human immunodeficiency virus type 1 capsid protein (CA). All of the mutants produce noninfectious virions that lack conical cores and, despite having a functional reverse transcriptase (RT), are unable to initiate reverse transcription in vivo. Here, we have focused on elucidating the mechanism by which these CA mutations disrupt virus infectivity. We also report that cyclophilin A packaging is severely reduced in W23A and F40A virions, even though these residues are distant from the cyclophilin A binding loop. To correlate loss of infectivity with a possible defect in an early event preceding reverse transcription, we modeled disassembly by generating viral cores from particles treated with mild nonionic detergent; cores were isolated by sedimentation in sucrose density gradients. In general, fractions containing mutant cores exhibited a normal protein profile. However, there were two striking differences from the wild-type pattern: mutant core fractions displayed a marked deficiency in RT protein and enzymatic activity (<5% of total RT in gradient fractions) and a substantial increase in the retention of CA. The high level of core-associated CA suggests that mutant cores may be unable to undergo proper disassembly. Thus, taken together with the almost complete absence of RT in mutant cores, these findings can account for the failure of the three CA mutants to synthesize viral DNA following virus entry into cells.
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Guillen, Isabel Cristina Martins, and Ivaldo Marciano de França Lima. "História e Memória da Negritude Pernambucana em ritmos, cores e gestos: 1970-1990." Revista Territórios e Fronteiras 5, no. 2 (December 21, 2012): 261. http://dx.doi.org/10.22228/rt-f.v5i2.151.
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Resumo: Neste artigo, apresentamos o projeto de pesquisa Ritmos, cores e gestos da negritude pernambucana, desenvolvido no LAHOI - UFPE. Através dos depoimentos orais de militantes do movimento negro pernambucano, e da participação dos mesmos em grupos culturais, tais como afoxés e maracatus, discutimos a intrincada relação entre subjetividade e participação nos movimentos sociais na construção da identidade negra. Palavras chave: movimento negro, negritude, identidade
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Juvela, M., J. Malinen, J. Montillaud, V. M. Pelkonen, I. Ristorcelli, and L. V. Tóth. "Galactic cold cores." Astronomy & Astrophysics 614 (June 2018): A83. http://dx.doi.org/10.1051/0004-6361/201630304.
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Context. The Galactic Cold Cores (GCC) project has made Herschel photometric observations of interstellar clouds where Planck detected compact sources of cold dust emission. The fields are in different environments and stages of star formation. Aims. Our aim is to characterise the structure of the clumps and their parent clouds, and to study the connections between the environment and the formation of gravitationally bound objects. We also examine the accuracy to which the structure of dense clumps can be determined from sub-millimetre data. Methods. We use standard statistical methods to characterise the GCC fields. Individual clumps are extracted using column density thresholding. Based on sub-millimetre measurements, we construct a three-dimensional radiative transfer (RT) model for each field. These are used to estimate the relative radiation field intensities, to probe the clump stability, and to examine the uncertainty of column density estimates. We examine the structural parameters of the clumps, including their radial column density profiles. Results. In the GCC fields, the structure noise follows the relations previously established at larger scales and in lower-density clouds. The fractal dimension has no significant dependence on column density and the values DP = 1.25 ± 0.07 are only slightly lower than in typical molecular clouds. The column density probability density functions (PDFs) exhibit large variations, for example, in the case of externally compressed clouds. At scales r > 0.1 pc, the radial column density distributions of the clouds follow an average relation of N ~ r−1. In spite of a great variety of clump morphologies (and a typical aspect ratio of 1.5), clumps tend to follow a similar N ~ r−1 relation below r ~ 0.1 pc. RT calculations indicate only factor 2.5 variation in the local radiation field intensity. The fraction of gravitationally bound clumps increases significantly in regions with AV > 5 mag but most bound objects appear to be pressure-confined. Conclusions. The host clouds of the cold clumps in the GCC sample have statistical properties similar to general molecular clouds. The gravitational stability, peak column density, and clump orientation are connected to the cloud background while most other statistical clump properties (e.g. DP and radial profiles) are insensitive to the environment. The study of clump morphology should be continued with a comparison with numerical simulations.
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Pavlyuchenkov, Yaroslav, Dmitry Wiebe, Anna Fateeva, and Tatiana Vasyunina. "Radiative Transfer Simulations of Infrared Dark Clouds." Proceedings of the International Astronomical Union 6, S270 (May 2010): 455–58. http://dx.doi.org/10.1017/s1743921311000809.
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AbstractThe determination of prestellar core structure is often based on observations of (sub)millimeter dust continuum. However, recently the Spitzer Space Telescope provided us with IR images of many objects not only in emission but also in absorption. We developed a technique to reconstruct the density and temperature distributions of protostellar objects based on radiation transfer (RT) simulations both in mm and IR wavelengths. Best-fit model parameters are obtained with the genetic algorithm. We apply the method to two cores of Infrared Dark Clouds and show that their observations are better reproduced by a model with an embedded heating source despite the lack of 70 μm emission in one of these cores. Thus, the starless nature of massive cores can only be established with the careful case-by-case RT modeling.
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Ma, Ping, Zhiping Zhou, Jiangdong Dai, Ling Qin, Xubo Ye, Xiang Chen, Jinsong He, Atian Xie, Yongsheng Yan, and Chunxiang Li. "A biomimetic Setaria viridis-inspired imprinted nanoadsorbent: green synthesis and application to the highly selective and fast removal of sulfamethazine." RSC Advances 6, no. 12 (2016): 9619–30. http://dx.doi.org/10.1039/c5ra18715j.
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The preparation of biomimetic Setaria viridis-inspired hydrophilic magnetic imprinted nanoadsorbent, via a two-step surface-initiated ATRP in a green alcohol/water solvent at RT, with MHNTs used as nano-cores, was first reported.
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Öhagen, Åsa, and Dana Gabuzda. "Role of Vif in Stability of the Human Immunodeficiency Virus Type 1 Core." Journal of Virology 74, no. 23 (December 1, 2000): 11055–66. http://dx.doi.org/10.1128/jvi.74.23.11055-11066.2000.
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ABSTRACT The Vif protein of human immunodeficiency virus type 1 (HIV-1) is important for virion infectivity. Previous studies have shown thatvif-defective virions exhibit structural abnormalities in the virus core and are defective in the ability to complete proviral DNA synthesis in acutely infected cells. We developed novel assays to assess the relative stability of the core in HIV-1 virions. Using these assays, we examined the role of Vif in the stability of the HIV-1 core. The integrity of the core was examined following virion permeabilization or removal of the lipid envelope and treatment with various triggers, including S100 cytosol, deoxynucleoside triphosphates, detergents, NaCl, and buffers of different pH to mimic aspects of the uncoating and disassembly process which occurs after virus entry but preceding or during reverse transcription.vif mutant cores were more sensitive to disruption by all triggers tested than wild-type cores, as determined by endogenous reverse transcriptase (RT) assays, biochemical analyses, and electron microscopy. RT and the p7 nucleocapsid protein were released more readily from vif mutant virions than from wild-type virions, suggesting that the internal nucleocapsid is less stably packaged in the absence of Vif. Purified cores could be isolated from wild-type but not vif mutant virions by sedimentation through detergent-treated gradients. These results demonstrate that Vif increases the stability of virion cores. This may permit efficient viral DNA synthesis by preventing premature degradation or disassembly of viral nucleoprotein complexes during early events after virus entry.
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Huang, J., L. L. Kestin, F. A. Vicini, S. G. Williams, H. Ye, S. D. McGrath, M. Ghilezan, and A. Martinez. "Percentage of positive biopsy cores to predict distant metastasis of prostate cancer after definitive radiation therapy." Journal of Clinical Oncology 29, no. 7_suppl (March 1, 2011): 80. http://dx.doi.org/10.1200/jco.2011.29.7_suppl.80.
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80 Background: To assess the prognostic value of percentage of positive biopsy cores (PPC) and perineural invasion (PNI) in predicting clinical outcome following radiotherapy (RT) for prostate cancer. Methods: One thousand and fifty-six patients with clinical stage T1-T3 N0 M0 prostate cancer, who had ≥ 4 biopsy cores sampled and complete biopsy core data available, were treated with either adaptive image-guided RT (median 75.6 Gy, n=387), low-dose EBRT (median 66.6 Gy, n=393), or EBRT and high-dose rate brachytherapy boost (n=276) at William Beaumont Hospital (1993-2004). Neoadjuvant and/or adjuvant androgen deprivation (AD) were given to 253 patients (24%). Multivariate cox regression analysis included PPC, gleason score, PSA, T stage, PNI, RT dose, androgen deprivation, and age. Biochemical failure (BF) was scored according to the Phoenix definition. Clinical failure (CF) was defined as any locoregional recurrence (LRR) or distant metastasis (DM). Median follow-up was 7.6 years. Results: Median cores sampled was 7, median PPC was 33%, and 18% had PNI. On univariate Cox regression, both PPC and PNI were predicators of biochemical failure and clinical failure (all P<0.05). On multivariate Cox regression, PPC, either as continuous or categorical variable, remained an independent predicator of BF, CF, DM, cause-specific survival, and overall survival (all P<0.05). PPC of >50% was associated with significantly higher DM (HR 4.01, 95% CI 1.86-8.61), and its independent predicative value remained significant whether AD was given or not (all P<0.05). Combining ≤50% vs ≥50% PPC with NCCN risk group stratification demonstrated added prognostic value of DM for intermediate-risk (HR 5.44, 95% CI 1.78-16.6) and high-risk groups (HR 4.39, 95% CI 1.70-2.84), with or without AD (all P<0.05). On multivariate Cox regression, PNI was an independent predicator of LRR only (HR 2.51, 95% CI 1.18-5.33). Conclusions: PPC is an independent and powerful predicator of DM for intermediate- and high-risk prostate cancer, regardless the use of AD. It should be considered for risk stratification and when designing for future trials testing adjuvant treatment after definitive RT for prostate cancer. No significant financial relationships to disclose.
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Liao, Wei-Hao, Kuo-Jung Huang, Yu-Fen Chang, Shiu-Mei Wang, Ying-Tzu Tseng, Chien-Cheng Chiang, Jaang-Jiun Wang, and Chin-Tien Wang. "Incorporation of Human Immunodeficiency Virus Type 1 Reverse Transcriptase into Virus-Like Particles." Journal of Virology 81, no. 10 (March 7, 2007): 5155–65. http://dx.doi.org/10.1128/jvi.01796-06.
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ABSTRACT We demonstrate that a genetically engineered human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) composed mainly of p66 or p51 subunits can be incorporated into virus-like particles (VLPs) when coexpressed with HIV-1 Pr55 gag . VLP-associated RT exhibited a detergent-resistant association with immature cores during sucrose gradient equilibrium centrifugation, suggesting that RT is incorporated into VLPs. However, RT that retains downstream integrase (IN) is severely inhibited in terms of incorporation into VLPs. Results from immunofluorescence tests reveal that RT-IN is primarily localized at the perinuclear area and exhibits poor colocalization with Gag. IN removal leads to a redistribution of RT throughout the cytoplasm and improved RT incorporation into VLPs. Similar results were observed for RT-IN in which alanine was substituted for 186-Lys-Arg-Lys-188 residues of the IN putative nuclear localization signal, suggesting that IN karyophilic properties may partly account for the inhibitory effect of IN on RT incorporation. Although the membrane-binding capacity of RT was markedly reduced compared to that of wild-type Gag or Gag-Pol, the correlation of membrane-binding ability with particle incorporation efficiency was incomplete. Furthermore, we observed that membrane-binding-defective myristylation-minus RT can be packaged into VLPs at the same level as its normal myristylated counterpart. This suggests that the incorporation of RT into VLPs is independent of membrane affinity but very dependent on RT-Gag interaction. Results from a genetic analysis suggest that the Gag-interacting regions of RT mainly reside in the thumb subdomain and that the RT-binding domains of Gag are located in the matrix (MA) and p6 regions.
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Buchschacher, Gary L., Lei Yu, Fukashi Murai, Theodore Friedmann, and Atsushi Miyanohara. "Association of Murine Leukemia Virus Pol with Virions, Independent of Gag-Pol Expression." Journal of Virology 73, no. 11 (November 1, 1999): 9632–37. http://dx.doi.org/10.1128/jvi.73.11.9632-9637.1999.
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ABSTRACT During the replication cycle of murine leukemia virus (MLV), Pol is normally synthesized as part of a Gag-Pol fusion protein. In this study, the ability of free MLV Pol to be incorporated into virions was examined. When MLV Gag and MLV Pol were coexpressed from separate plasmids in cells, reverse transcriptase (RT) activity associated with Gag core particles at a slightly lower level than did RT activity generated from wild-type Gag-Pol expression. Particles produced in this manner were somewhat less infectious than those produced with wild-type Gag-Pol. A smaller amount of MLV Pol also associated with heterologous human immunodeficiency virus type 1 Gag cores.
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Qian, Y., F. Y. Feng, S. Halverson, K. Blas, H. M. Sandler, and D. A. Hamstra. "Use of percent positive biopsy cores to predict prostate cancer–specific death in patients treated with dose-escalated radiotherapy." Journal of Clinical Oncology 29, no. 7_suppl (March 1, 2011): 35. http://dx.doi.org/10.1200/jco.2011.29.7_suppl.35.
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35 Background: The percent of positive biopsy cores (PPC)-considered a surrogate of local disease burden-has been shown to predict biochemical failure (BF) after external beam radiation therapy (EBRT), but most series have used conventional dose RT. Dose-escalated RT has been demonstrated to improve prostate cancer outcomes, but the value of PPC is unclear in the setting of RT doses high enough to decrease local failure. Methods: A retrospective evaluation was performed of 651 patients treated to ≥75 Gy with biopsy core information available. Patients were stratified for PPC by quartile, and differences by quartile in BF, freedom from metastasis (FFM), cause specific survival (CSS), and overall survival (OS) were assessed using the log-rank test. Receiver operated characteristic (ROC) curve analysis was utilized to determine an optimal cut-point for PPC. Cox proportional hazards multivariate regression was utilized to assess the impact of PPC on clinical outcome when adjusting for risk group. Results: With median follow-up of 62 months the median number of cores sampled was 7 (IQR: 6–12) with median PPC in 38% (IQR: 17%-67%). On log-rank test, BF, FFM, and CSS were all associated with PPC (p < 0.005 for all), with worse outcomes only for the highest PPC quartile (>67%). There was no observed difference in OS based upon PPC. ROC curve analysis confirmed a cut-point of 67% as most closely associated with CSS (p<0.001, AUC=0.71). On multivariate analysis after adjusting for NCCN risk group and ADT use, PPC>67% increased the risk for BF (p<0.0001, HR:2.1 [1.4–3.0]), FFM (p<0.05, HR:1.7 [1.1 to 2.9]), and CSS (p<0.06 (HR:2.1 [1.0–4.6]). When analyzed as a continuous variable controlling for risk group and ADT use, increasing PPC increased the risk for BF (p < 0.002), metastasis (p < 0.05), and CSS (p < 0.02), with a 1–2% increase in relative risk of recurrence for each 1% increase in the PPC. Conclusions: For patients treated with dose-escalated RT, the PPC adds prognostic value but at a higher cut-point then previously utilized. Patients with PPC >67% remain at increased risk for failure even with dose-escalated EBRT and may receive benefit from further intensification of therapy. No significant financial relationships to disclose.
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Shehu-Xhilaga, M., M. Hill, J. A. Marshall, J. Kappes, S. M. Crowe, and J. Mak. "The Conformation of the Mature Dimeric Human Immunodeficiency Virus Type 1 RNA Genome Requires Packaging of Pol Protein." Journal of Virology 76, no. 9 (May 1, 2002): 4331–40. http://dx.doi.org/10.1128/jvi.76.9.4331-4340.2002.
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ABSTRACT The packaging of a mature dimeric RNA genome is an essential step in human immunodeficiency virus type 1 (HIV-1) replication. We have previously shown that overexpression of a protease (PR)-inactive HIV-1 Gag-Pro-Pol precursor protein generates noninfectious virions that contain mainly monomeric RNA (M. Shehu-Xhilaga, S. M. Crowe, and J. Mak, J. Virol. 75:1834-1841, 2001). To further define the contribution of HIV-1 Gag and Gag-Pro-Pol to RNA maturation, we analyzed virion RNA dimers derived from Gag particles in the absence of Gag-Pro-Pol. Compared to wild-type (WT) dimeric RNAs, these RNA dimers have altered mobility and low stability under electrophoresis conditions, suggesting that the HIV-1 Gag precursor protein alone is not sufficient to stabilize the dimeric virion RNA structure. The inclusion of an active viral PR, without reverse transcriptase (RT) and integrase (IN), rescued the stability of the virion RNA dimers in the Gag particles but did not restore the mobility of the RNAs, suggesting that RT and IN are also required for virion RNA dimer maturation. Thin-section electron microscopy showed that viral particles deficient in RT and IN contain empty cone-shaped cores. The abnormal core structure indicates a requirement for Gag-Pro-Pol packaging during core maturation. Supplementing viral particles with either RT or IN via Vpr-RT or Vpr-IN alone did not correct the conformation of the dimer RNAs, whereas expression of both RT and IN in trans as a Vpr-RT-IN fusion restored RNA dimer conformation to that of the WT virus and also restored the electron-dense, cone-shaped virion core characteristic of WT virus. Our data suggest a role for RT-IN in RNA dimer conformation and the formation of the electron-dense viral core.
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Mauritz, M., and D. L. Lipson. "Altered phenology and temperature sensitivity of invasive annual grasses and forbs changes autotrophic and heterotrophic respiration rates in a semi-arid shrub community." Biogeosciences Discussions 10, no. 4 (April 3, 2013): 6335–75. http://dx.doi.org/10.5194/bgd-10-6335-2013.
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Abstract. Many invasions, like the wide-spread establishment of annual grasses and forbs in semi-arid shrublands, are associated with climate change. In order to predict ecosystem carbon (C) storage it is critical that we understand how invasion affects soil respiration (Rt). Because plants and microbes have different seasonal dynamics, determining the relative contribution of autotrophic (Ra) and heterotrophic (Rh) respiration provides critical insight into soil C processes. Using automated soil respiration measurements and root exclusion cores we evaluated the moisture and temperature sensitivity of Rt and Rh and calculated the contribution of Ra in native shrub and invaded areas. Invasion increased cumulative Rt by 40% from 695 (±51) g C m−2 under shrubs to 1050 g C m−2 (±44) in invaded areas. Cumulative Rh did not change but invasion altered the seasonal pattern of Rh. Throughout the season Rt and Rh responded positively to temperature increases when soils were wet and negatively when soils were dry. Invasion increased temperature sensitivity of Rt and Rh in wet soils and decreased temperature sensitivity in dry soils. The altered temperature sensitivity of invasives was attributed largely to differences in phenology. Early phenology of invasive grasses caused rapid Ra increases early in the season; late phenology of invasive forbs resulted in the surprising maintenance of diurnal Ra and Rh signals despite high temperatures and low soil moisture. Invasion extended the respiration season of the system. Ability of the invasive community to withstand high temperatures and drought could confer greater resilience if temperature and precipitation patterns in the region change. The high contribution of Ra by invasive annuals means ecosystem C storage will depend heavily on seasonal rainfall dynamics and productivity of invasive annuals. In semi-arid ecosystems even small scale changes in plant community composition alter Rt, Ra and Rh and should be considered when attempting to predict Rt.
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Imrich, Horst, Martin Heinkelein, Ottmar Herchenröder, and Axel Rethwilm. "Primate foamy virus Pol proteins are imported into the nucleus." Journal of General Virology 81, no. 12 (December 1, 2000): 2941–47. http://dx.doi.org/10.1099/0022-1317-81-12-2941.
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Mouse monoclonal antibodies (MAbs) that specifically detect the 127 kDa Pol precursor and the 85 kDa reverse transcriptase/RNase H (RT/RN) or pr127 and the 40 kDa integrase (IN) in immunoblot and immunofluorescence assays (IFA) were used to investigate the subcellular localization of primate foamy virus (PFV) proteins. IFA of cells infected with PFV using the anti-Pol MAbs and rabbit anti-capsid (Gag) serum revealed that both the Gag and Pol proteins are transported into the nucleus. Transfection of cells with eukaryotic expression constructs for pr127Pol, p85RT/RN and p40IN served to show Gag-independent subcellular localization of Pol proteins. Interestingly, not only the Pol precursor and IN molecules were found to be localized to the nucleus, but also the RT/RN subdomain. It is therefore suggested that PFV cores bear at least three separate nuclear localization signals, one in Gag and two in Pol. The latter appear to be localized to the two Pol subdomains.
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Moret-Fernández, D., C. Peña-Sancho, and M. V. López. "Influence of the wetting process on estimation of the water-retention curve of tilled soils." Soil Research 54, no. 7 (2016): 840. http://dx.doi.org/10.1071/sr15274.
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Correct estimation of the soil-water retention curve (WRC) is of paramount importance to characterise the hydraulic behaviour of soils. This paper studies the influence of two different soil-wetting processes (waterlogging soil, WP; capillary rise to saturation, CRP) on the estimate of the WRC. The two procedures were applied on undisturbed loam soil samples with three degrees of soil structure: (i) consolidated soils under conventional tillage (CT), reduced tillage (RT) and no tillage (NT); (ii) freshly tilled soil under CT and RT; and (iii) CT and RT after secondary tillage plus some intense rainfalls events. WRCs were estimated with time-domain reflectometry (TDR) pressure cells and volumetric water content was measured at saturation conditions (for the WP method) and at pressure heads of 0.5, 1.5, 3, 5, 10, 50, 100, 500 and 1500 kPa. The same cores were used to determine the soil bulk density (ρb), which was subsequently used to estimate the saturated water content under CRP. The ρb value of the consolidated soil under NT was significantly higher (P < 0.001) than under CT and RT. No effect of the wetting process on the WRC of consolidated soils was observed. Only the freshly tilled soil samples under RT were significantly affected by the wetting process. In these cases, the water draining after WP collapsed the more unstable soil macropores and increased the volume of the smaller ones. However, this effect was minimised by the CRP method, which prevented the collapse of the more unstable soil pores. This work demonstrates that the soil-wetting process may have an important effect on the characterisation of the water-holding capacity on freshly tilled soils.
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Ahmad, Ardalan, Melvin Chua, Jure Murgic, Hamid Reza Raziee, Ali Hosni, Fabio Ynoe De Moraes, Narhari Timilshina, Robert G. Bristow, Alejandro Berlin, and Antonio Finelli. "Oncologic outcomes of radiation therapy following active surveillance for low- and intermediate-risk localized prostate cancer." Journal of Clinical Oncology 35, no. 6_suppl (February 20, 2017): 42. http://dx.doi.org/10.1200/jco.2017.35.6_suppl.42.
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42 Background: To evaluate the oncologic outcomes and potential impact of delayed radical treatment in the form of radiotherapy (RT), in men with localized prostate cancer progressing after active surveillance (AS). Methods: We identified patients on AS subsequently treated with state-of-the-art RT (either dose-escalated image-guided intensity modulated radiotherapy [IG-IMRT] or low-dose-rate brachytherapy [LDR-BT]). Based on the clinical characteristics at time of AS progression, we compared the oncologic outcomes to matched patients treated with upfront RT after diagnose. One to two matching patients per AS case were identified from existing RT databases based on: age (+/- 3 years), clinical prognostic factors (NCCN risk group; PSA +/- 2ng/mL; cT category; primary and secondary Gleason score; percentage of diagnostic cores involved dichotomized at < or > 50%), and treatment modality (IG-IMRT or LDR-BT). We aimed to determine whether patients on AS have potentially compromised outcomes. Results: We identified 215 patients (out of 1070 AS cohort) undergoing RT after a median of 26 months (IQR 16-52.5) on AS. Median follow-up post RT was 4.8 years (IQR 2.9-7.2). No patient died of prostate cancer. At 5-years, the biochemical relapse free-, metastases free- and overall-survival rate were respectively 98.6%, 99.1%, 98.6% in the AS cohort. Matched cohort comprised 400 patients treated with IG-IMRT (71%) or LDR-BT (29%). Adequate matching was confirmed. The median follow-up post RT was 8.2 years (IQR 4.7-10). At 5-years, biochemical relapse free-, metastases free- and overall-survival rates of 98.5%, 98.7%, 93.7% respectively, which were not statistically different compared to those patients treated upon AS progression. Conclusions: Curative-intent radiotherapy (i.e. dose-escalated IG-IMRT or LDR-BT) after a period of AS renders excellent oncologic outcomes at 5 years. Moreover, the delay of therapy after a period of AS does not appear to result in inferior oncologic outcomes compared to patients with similar risk characteristics undergoing upfront radical radiotherapy.
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Xu, Gaogui, Chunzhu Dong, Tao Zhao, Hongcheng Yin, and Xuan Chen. "Acceleration of shooting and bouncing ray method based on OptiX and normal vectors correction." PLOS ONE 16, no. 6 (June 25, 2021): e0253743. http://dx.doi.org/10.1371/journal.pone.0253743.
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The present paper deals with a new efficient shooting and bouncing ray (SBR) method based on OptiX and normal vectors correction. The basic idea is to make full use of the computing resources of the RTX series graphics cards. For ray tracing, the algorithm uses OptiX to invoke the built-in RT Cores of hardware. Thus, a fast intersection test can be implemented. To reduce the error of ray tracing caused by the facetted surface characterizing the curved surface, the direction of the reflected ray is corrected by normal vectors correction. Additionally, multiple GPU cores are invoked to accelerate the calculation of far-field integration of millions of ray tubes, which can improve the efficiency of the algorithm while reducing the data transmission time of heterogeneous devices. Simulation results show that the ray path after normal vectors correction is consistent with the theoretical results, and the algorithm can predict the RCS of arbitrary facetted geometries, which is 60 times faster than the SBR method based on kd-tree.
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Hall, Douglas S. "The Relation Between RS CVn and Algol." International Astronomical Union Colloquium 107 (1989): 219–33. http://dx.doi.org/10.1017/s0252921100087807.
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AbstractLate-type secondaries in Algol binaries are rapidly rotating convective stars and thus should be chromospherically active (CA). They are examined with respect to observational manifestations which characterize already known CA stars: Ca II H and K emission cores, photometric variability attributable to starspots, soft x-ray emission, non-thermal radio emission, ultraviolet and infrared excess, and alternating period changes. The conclusion is that they can be regarded as another class of CA stars. In most respects they are literally indistinguishable from other CA stars. Ca II H and K emission cores are observed in the lobe-filling component of six semi-detached binaries: U Cep, RT Lac, RV Lib, AR Mon, S Vel, HR 5110. Alternating period changes are shown to occur only in Algols containing a late-type (convective) star. It is proposed, therefore, that the Matese-Whitmire mechanism explains these changes. Specifically, the interval from one increase (or decrease) to the next can be equated with the star’s magnetic cycle. Cycle lengths for 31 stars, derived in this way, range between 7 years and 109 years, with a median of 50 years.
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Krichbaum, T. P., K. J. Standke, D. A. Graham, A. Witzel, C. J. Schalinski, and J. A. Zensus. "mm-VLBI: Jets in the Vicinity of Galaxy-Cores." Symposium - International Astronomical Union 159 (1994): 187–88. http://dx.doi.org/10.1017/s007418090017500x.
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Millimeter-VLBI provides an angular resolution of up to a few tens of microarcseconds and allows imaging of compact radio sources, self-absorbed at longer wavelengths, with unsurpassed angular resolution. At 43 GHz the participation of the VLBA and the 30 m-MRT at Pico Veleta (e.g. Krichbaum et al., 1993 a&b), and at 86 GHz the addition of the 100 m-RT at Effelsberg and the 30 m-MRT (Schalinski et al., 1993, and this volume) have improved the imaging capabilities of mm-VLBI observations.Results: The increased sensitivity of mm-VLBI observations allows the investigation of fainter objects, previously not accessible. As one example we show in Fig.1 the first detection of the compact radio source Sgr A∗ in the Galactic Center with VLBI at 43 GHz in May 1992 (Krichbaum et al., 1993d) and at 86 GHz in April 1993 (Krichbaum et al., 1994). In both observations the size of Sgr A∗ appeared to be larger than its expected scattering size, indicative of intrinsic source structure showing up at mm-wavelengths. Future monitoring with mm-VLBI is necessary to search for (not unexpected) structural variability.Monitoring of AGN with mm-VLBI reveals in all cases observed in sufficient detail jet curvatures of increasing amplitude towards the self-absorbed VLBI-cores (e.g. in 18034-784: Krichbaum, 1990, OJ 287: Krichbaum et al., 1993c), and sub- or superluminal motion along ‘quasi-helically’ bent trajectories (e.g. 3C 84: Krichbaum et al., 1993b; 3C 273: Krichbaum et al., 1993c), which differ sometimes for adjacent jet components (e.g. 3C 345: Krichbaum & Witzel, 1992, Krichbaum et al., 1992&1993a). In 3C 84, 3C 273 and 3C 345 the apparent velocity of jet components varies systematically along the jet axis, in 4C 39.25 (Alberdi et al., 1993) a moving component decelerates and brightens, all of this suggesting differential Doppler boosting and motion along three-dimensionally curved trajectories. In 3C 345 the complex kinematics of C4 and C5 (Zensus, this volume) has been geometrically modeled by motion along a helical path on the surface of a conical jet (Qian et al., 1992, Steffen et al., 1993, and this volume; see also Camenzind, this volume). As a new example, the oscillations of the inner jet and its velocity variations βapp(r) are shown for the BL Lac object 1803+784 in Fig. 2 (see the maps in: Krichbaum et al., 1993b). The frequent occurence of ‘quasi-sinusoidal’ bends in the inner jets of very different classes of AGN (QSO's, BL Lac's, Seyfert's) suggests that this effect is common in a large fraction of AGN and that the underlying jet-physical process may be fundamental for the understanding of the creation of jets.
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Yao, Zhi-Gang, Hai-Bo Wu, Ying-Hua Hao, Xing-Fu Wang, Guang-Zhen Ma, Jia Li, Ji-Feng Li, et al. "Papillary Solitary Fibrous Tumor/Hemangiopericytoma: An Uncommon Morphological Form With NAB2-STAT6 Gene Fusion." Journal of Neuropathology & Experimental Neurology 78, no. 8 (July 4, 2019): 685–93. http://dx.doi.org/10.1093/jnen/nlz053.
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Abstract Solitary fibrous tumor/hemangiopericytomas (SFT/HPCs) are mesenchymal tumors characterized by “staghorn” blood vessels and collagen deposition. Little is known about SFT/HPCs with papillary architecture. We summarized the clinicopathologic features of 12 patients with papillary SFT/HPCs (8 males and 4 females; median age: 59 years), including 8 previously reported cases. Tumors were present in the meninges (75%, 9/12), adrenal gland (8%, 1/12), orbit (8%, 1/12), or spinal canal (8%, 1/12). Six tumors (50%) had a true papillary architecture with fibrovascular cores and 6 tumors (50%) had a pseudopapillary architecture with vascular cores. Nuclear staining for STAT6 was present in all tested tumors (10/10). RT-PCR indicated NAB2 ex6-STAT6 ex17 fusion in 4 tumors (80%, 4/5) and NAB2 ex4-STAT6 ex2 fusion in 1 tumor (20%, 1/5). Five patients (42%, 5/12), all with tumors in the meninges, developed local recurrence at a median of 61 months after surgery (range: 56–165 months; mean: 88.6 months). These results indicated that the papillary architecture is a morphological form of SFT/HPCs. The recognition of this pattern, with appropriate immunohistochemical analysis and assessment of NAB2-STAT6 fusion, should facilitate the distinction of these rare neoplasms from morphologically similar tumors in the meninges, lung, pleura, and soft tissue.
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Forster, Linda, Anthony B. Davis, David J. Diner, and Bernhard Mayer. "Toward Cloud Tomography from Space Using MISR and MODIS: Locating the “Veiled Core” in Opaque Convective Clouds." Journal of the Atmospheric Sciences 78, no. 1 (January 2021): 155–66. http://dx.doi.org/10.1175/jas-d-19-0262.1.
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AbstractFor passive satellite imagers, current retrievals of cloud optical thickness and effective particle size fail for convective clouds with 3D morphology. Indeed, being based on 1D radiative transfer (RT) theory, they work well only for horizontally homogeneous clouds. A promising approach for treating clouds as fully 3D objects is cloud tomography, which has been demonstrated for airborne observations. However, more efficient forward 3D RT solvers are required for cloud tomography from space. Here, we present a path forward by acknowledging that optically thick clouds have “veiled cores” (VCs). Sunlight scattered into and out of this deep region does not contribute significant information about the inner structure of the cloud to the spatially detailed imagery. We investigate the VC location for the MISR and MODIS imagers. While MISR provides multiangle imagery in the visible and near-infrared (IR), MODIS includes channels in the shortwave IR, albeit at a single view angle. This combination will enable future 3D retrievals to disentangle the cloud’s effective particle size and extinction fields. We find that, in practice, the VC is located at an optical distance of ~5, starting from the cloud boundary along the line of sight. For MODIS’s absorbing wavelengths the VC covers a larger volume, starting at smaller optical distances. This concept will not only lead to a reduction in the number of unknowns for the tomographic reconstruction but also significantly increase the speed and efficiency of the 3D RT solver at the heart of the algorithm by applying, say, the photon diffusion approximation inside the VC.
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Lin, Min-Hsuan, Ann Apolloni, Vincent Cutillas, Haran Sivakumaran, Sally Martin, Dongsheng Li, Ting Wei, et al. "A Mutant Tat Protein Inhibits HIV-1 Reverse Transcription by Targeting the Reverse Transcription Complex." Journal of Virology 89, no. 9 (February 11, 2015): 4827–36. http://dx.doi.org/10.1128/jvi.03440-14.
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ABSTRACTPreviously, we reported that a mutant of Tat referred to as Nullbasic inhibits HIV-1 reverse transcription although the mechanism of action is unknown. Here we show that Nullbasic is a reverse transcriptase (RT) binding protein that targets the reverse transcription complex rather than directly inhibiting RT activity. An interaction between Nullbasic and RT was observed by using coimmunoprecipitation and pulldown assays, and a direct interaction was measured by using a biolayer interferometry assay. Mixtures of recombinant 6×His-RT and Nullbasic-FLAG-V5-6×His at molar ratios of up to 1:20,000 did not inhibit RT activity in standard homopolymer primer template assays. An analysis of virus made by cells that coexpressed Nullbasic showed that Nullbasic copurified with virus particles, indicating that it was a virion protein. In addition, analysis of reverse transcription complexes (RTCs) isolated from cells infected with wild type or Nullbasic-treated HIV-1 showed that Nullbasic reduced the levels of viral DNA in RTC fractions. In addition, a shift in the distribution of viral DNA and CAp24 to less-dense non-RTC fractions was observed, indicating that RTC activity from Nullbasic-treated virus was impaired. Further analysis showed that viral cores isolated from Nullbasic-treated HIV undergo increased disassemblyin vitrocompared to untreated HIV-1. To our knowledge, this is the first description of an antiviral protein that inhibits reverse transcription by targeting the RTC and affecting core stability.IMPORTANCEHIV-1 infection is treated by using combinations of antiretroviral drugs that target independent steps of virus replication. A newly described antiviral protein called Nullbasic can also inhibit a combination of different steps in virus replication (transcription, reverse transcription, and Rev-mediated viral mRNA transport), although the precise mechanism of action is unknown. This study shows that Nullbasic can inhibit reverse transcription by binding to the viral enzyme called reverse transcriptase, which results in accelerated uncoating of the viral core and instability of the viral apparatus called the reverse transcription complex (RTC). This unique antiviral activity may inform development of other RTC inhibitors, as well as providing a unique investigative tool for dissecting the RTC cellular composition.
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Blyth, Simon. "Meeting the challenge of JUNO simulation with Opticks: GPU optical photon acceleration via NVIDIA® OptiXTM." EPJ Web of Conferences 245 (2020): 11003. http://dx.doi.org/10.1051/epjconf/202024511003.
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Opticks is an open source project that accelerates optical photon simulation by integrating NVIDIA GPU ray tracing, accessed via NVIDIA OptiX, with Geant4 toolkit based simulations. A single NVIDIA Turing architecture GPU has been measured to provide optical photon simulation speedup factors exceeding 1500 times single threaded Geant4 with a full JUNO analytic GPU geometry automatically translated from the Geant4 geometry. Optical physics processes of scattering, absorption, scintillator reemission and boundary processes are implemented within CUDA OptiX programs based on the Geant4 implementations. Wavelength-dependent material and surface properties as well as inverse cumulative distribution functions for reemission are interleaved into GPU textures providing fast interpolated property lookup or wavelength generation. Major recent developments enable Opticks to benefit from ray trace dedicated RT cores available in NVIDIA RTX series GPUs. Results of extensive validation tests are presented.
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Skupio, Rafal. "Portable XRF spectrometer with helium flow as a tool for lithological interpretation." Geology, Geophysics and Environment 46, no. 4 (January 29, 2021): 315–20. http://dx.doi.org/10.7494/geol.2020.46.4.315.
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Portable EDXRF (Energy Dispersive X-Ray Fluorescence) spectrometer with the ability to perform rock tests in a helium atmosphere was applied to prepare unique calibration coefficients and mineralogical models. These data could be used for the chemical profiling, chemostratigraphy, gamma-ray, TOC and lithological interpretation of borehole geological profile. The measurements were conducted on 19 samples of sandstones and compared to the XRF data without helium flow. The acquired dataset was calibrated to the chemical laboratory tests (ICP-MS), gamma-ray spectrometry measurements (RT-50) and combined with the mineralogical data (XRD). The new methodology enables the measurement of sodium and enhances the possibility of detecting magnesium, thorium and uranium, compared to standard handheld XRF spectrometers. The applied method is dedicated to whole cores (without sample preparation) or cuttings which must be cleaned, dried, milled and pressed.
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Zhuang, Xin-jie, Xue Feng, Wen-hao Tang, Jin-liang Zhu, Ming Li, Jun-sheng Li, Xiao-ying Zheng, Rong Li, Ping Liu, and Jie Qiao. "FAM9B serves as a novel meiosis-related protein localized in meiotic chromosome cores and is associated with human gametogenesis." PLOS ONE 16, no. 9 (September 10, 2021): e0257248. http://dx.doi.org/10.1371/journal.pone.0257248.
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Meiosis is a complex process involving the expression and interaction of numerous genes in a series of highly orchestrated molecular events. Fam9b localized in Xp22.3 has been found to be expressed in testes. However, FAM9B expression, localization, and its role in meiosis have not been previously reported. In this study, FAM9B expression was evaluated in the human testes and ovaries by RT-PCR, qPCR, and western blotting. FAM9B was found in the nuclei of primary spermatocytes in testes and specifically localized in the synaptonemal complex (SC) region of spermatocytes. FAM9B was also evident in the follicle cell nuclei and diffusely dispersed in the granular cell cytoplasm. FAM9B was partly co-localized with SYCP3, which is essential for both formation and maintenance of lateral SC elements. In addition, FAM9B had a similar distribution pattern and co-localization as γH2AX, which is a novel biomarker for DNA double-strand breaks during meiosis. All results indicate that FAM9B is a novel meiosis-associated protein that is co-localized with SYCP3 and γH2AX and may play an important role in SC formation and DNA recombination during meiosis. These findings offer a new perspective for understanding the molecular mechanisms involved in meiosis of human gametogenesis.
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Shah, C., L. L. Kestin, M. Ghilezan, F. A. Vicini, G. S. Gustafson, D. Brabbins, M. Wallace, K. Marvin, H. Ye, and A. Martinez. "A matched-pair analysis of dose-escalated adaptive image-guided radiotherapy (IGRT) versus pelvic irradiation with brachytherapy boost for intermediate- and high-risk prostate cancer." Journal of Clinical Oncology 29, no. 7_suppl (March 1, 2011): 71. http://dx.doi.org/10.1200/jco.2011.29.7_suppl.71.
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71 Background: The purpose of this study was to compare clinical outcomes in a cohort of intermediate- and high-risk prostate cancer patients treated with either dose-escalated adaptive IGRT or pelvic external beam RT with high-dose rate brachytherapy boost (EBRT+HDR). Methods: 1,520 patients with clinical stage T1-T3 N0 M0 prostate cancer were treated with either CT-based offline adaptive IGRT (n=1,037) or EBRT+HDR, n=438) at William Beaumont Hospital. For IGRT, the CTV included the prostate and proximal seminal vesicles only. Median dose (minimum to cl-PTV) delivered via 3D conformal RT or intensity-modulated RT was 75.6 Gy (range: 73.8-79.2 Gy). For EBRT+HDR, the whole pelvis was treated to 46 Gy + 2 HDR implants with a median of 10.5 Gy (8.75-11.5 Gy) per implant. 208 patients from each group were matched based on criteria of pretreatment PSA ± 4 ng/mL, same Gleason score, T stage ± 2 sublevels, and use of neoadjuvant androgen deprivation therapy (ADT). Results: Mean follow-up was 5.1 years for IGRT vs 7.0 years for EBRT+HDR. Mean pretreatment PSA was 9 for both groups. Mean Gleason was 7 for both groups. EBRT+HDR patients were younger (67 vs 71 years, p<0.01) with a higher percentage of positive biopsy cores (51% vs 39%, p<0.01). Intermediate risk patients comprised 78% and 76% for IGRT and EBRT+HDR, respectively (p=0.56). 42% in each treatment group received neoadjuvant or concurrent ADT. 5-year biochemical control (BC) based on the Phoenix definition was 91% for IGRT vs 87% for EBRT+HDR (p=0.60). For intermediate-risk, 5-year BC was 94% vs 87% (p=0.71) and was 86% vs 86% (p=0.83) for high-risk patients. No significant differences were noted between the 2 groups for local recurrence, distant metastasis, clinical failure, overall survival, and cause-specific survival. Conclusions: In this matched-pair analysis of 416 patients, treatment of intermediate and high-risk prostate cancer with either offline adaptive IGRT or EBRT+HDR yielded excellent clinical outcomes without significant differences. The omission of pelvic radiotherapy in the IGRT patients did not appear to be associated with poorer clinical outcomes with modern high-dose RT. No significant financial relationships to disclose.
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Scoca, Viviana, and Francesca Di Nunzio. "The HIV-1 Capsid: From Structural Component to Key Factor for Host Nuclear Invasion." Viruses 13, no. 2 (February 10, 2021): 273. http://dx.doi.org/10.3390/v13020273.
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Since the discovery of HIV-1, the viral capsid has been recognized to have an important role as a structural protein that holds the viral genome, together with viral proteins essential for viral life cycle, such as the reverse transcriptase (RT) and the integrase (IN). The reverse transcription process takes place between the cytoplasm and the nucleus of the host cell, thus the Reverse Transcription Complexes (RTCs)/Pre-integration Complexes (PICs) are hosted in intact or partial cores. Early biochemical assays failed to identify the viral CA associated to the RTC/PIC, possibly due to the stringent detergent conditions used to fractionate the cells or to isolate the viral complexes. More recently, it has been observed that some host partners of capsid, such as Nup153 and CPSF6, can only bind multimeric CA proteins organized in hexamers. Those host factors are mainly located in the nuclear compartment, suggesting the entrance of the viral CA as multimeric structure inside the nucleus. Recent data show CA complexes within the nucleus having a different morphology from the cytoplasmic ones, clearly highlighting the remodeling of the viral cores during nuclear translocation. Thus, the multimeric CA complexes lead the viral genome into the host nuclear compartment, piloting the intranuclear journey of HIV-1 in order to successfully replicate. The aim of this review is to discuss and analyze the main discoveries to date that uncover the viral capsid as a key player in the reverse transcription and PIC maturation until the viral DNA integration into the host genome.
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Farinha, Pedro, Giovanna Roncador, Abdul Al-Tourah, Joseph M. Connors, and Randy D. Gascoyne. "Combined FOXP3+ and PD1+ T Cell Density and Architectural Patterns Predict Overall Survival and Risk of Transformation in Uniformly Treated Patients with Follicular Lymphoma." Blood 112, no. 11 (November 16, 2008): 2815. http://dx.doi.org/10.1182/blood.v112.11.2815.2815.
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Abstract Background: Follicular lymphoma (FL) is an indolent heterogeneous lymphoid neoplasm with a variable clinical course. Transformation into an aggressive lymphoma is a dominant clinical event frequently associated with inferior survival. No consistent biological markers are predictive of survival or risk of transformation (RT). Recent studies have highlighted the role of the microenvironment, including regulatory T cells (Treg) as important prognostic factors in FL. Using tissue microarrays (TMA), we previously identified FOXP3+ T cell distribution but not cell density within the tumor is an independent adverse prognostic factor for both overall survival (OS), progression-free (PFS) survival and RT in advanced-stage FL pts treated uniformly with an aggressive treatment regimen (ASH 2007). Programmed death-1(PD1) belongs to the immunoglobulin CD28 receptor family and is characteristically expressed by germinal center associated T cells. They have imunoregulatory activity and are FOXP3-negative. Using the same cohort we assessed the role of PD1+ cells alone and in combination with FOXP3+ cells in FL prognosis. Methods: Between 1987 and 1993, 126 pts were enrolled on a phase II study of BP-VACOP chemotherapy with involved region radiotherapy. All patients were treatment naive, < 61y and had advanced-stage FL. Paraffin blocks were available for 105 pts. TMAs consisted of duplicate 1.0mm cores of diagnostic biopsies and were immunostained with both FOXP3 and PD1 (NAT105) specific antibodies. Both cell content and immuno-architectural patterns were determined and correlated with OS and RT including univariate and multivariate analysis. Results: There were 101 evaluable cases. The median follow-up of the living pts was 14 years. Histologic grade included 78 grade 1, 17 grade 2 and 6 grade 3a FLs. The IPI was predictive of OS (RR = 2.5, 95% CI =1.5–4.4, p = 0.002), but not RT (p = 0.14). Cases revealed zero to 731 FOXP3+ cells per core (median of 242 cells per core) and zero to 654 PD1+ cells per core (median of 102 cells per core). There was a predominantly intrafollicular or perifollicular localization of positive cells (“follicular pattern”) in 38 and 43 pts for FOXP3 and PD1, respectively. There was no significant correlation between cell density (χ2=0.1) or pattern (χ2=0.8) between markers. Separately, cell density did not impact prognosis. Yet, when quartiles were combined and dichotomized, cases with high cell content of FOXP3+/PD1+ cells correlated with inferior OS and increased RT in univariate (p = 0.002 and p = 0.01) and multivariate Cox models (RR = 2.18, 95% CI =1.2–3.9, p = 0.01 & RR = 3.4, 95% CI =1.3–8.8, p = 0.015). In univariate analysis, a PD1 follicular pattern correlated with inferior OS (p=0.027) but did not impact RT. When combined with follicular FOXP3+ cases, a subset of 15 “double follicular” FOXP3 & PD1 cases correlated with inferior OS in univariate (p=0.0016) and multivariate Cox models (RR = 2.1, 95% CI =1–4.3, p = 0.04). This subset of cases also showed a trend for increased RT (p = 0.09). Conclusions: Combined cell density and distribution within FL of immuno-regulatory T cell subsets are important predictors of OS & RT in advanced-stage FL patients treated uniformly with an aggressive treatment regimen. Our results reinforce the importance of the microenvironment in FL biology and further suggest an active role for immuno-modulatory T cells in pro-tumoral immunity.
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Klein, Eric A., Tara Maddala, Carl Millward, Diana B. Cherbavaz, Sara Moscovita Falzarano, Dejan Knezevic, William F. Novotny, Mark Lee, and Cristina Magi-Galluzzi. "Development of a needle biopsy-based genomic test to improve discrimination of clinically aggressive from indolent prostate cancer." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): 4560. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.4560.
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4560 Background: Standardized, quantitative tools are needed to improve discrimination of clinically aggressive from indolent prostate cancer at diagnosis. We previously identified multiple genes and biological pathways in radical prostatectomy (RP) specimens associated with clinical recurrence and adverse pathology. We evaluated whether measurement of these genes in prostate needle biopsy (Bx) specimens predicts adverse pathology - high grade (GS ≥ 4+3) and/or non-organ-confined disease (pT3) - in a separate study of AUA low-intermed risk pts treated w/ RP. Methods: All AUA low-intermed risk (cT1-T2a, GS 3+3/3+4) pts treated w/ RP <6 mos from Bx at Cleveland Clinic (1999-2007) w/ available Bx tissue and <3 pos cores were evaluated. Expression of 81 prognostic genes identified in previous RP studies and 5 reference genes was quantitated by RT-PCR in 60 µm manually microdissected FPE prostate needle Bx tissue. Association of gene expression w/ adverse pathology was analyzed by logistic regression controlling false discovery rate (FDR) using Storey’s method. Results: RT-PCR was successful for 167 of 171 (98%) pts (92 AUA low, 75 intermed). At RP, 58 pts (35%) had high-grade and/or non-organ confined disease. 58 of 81(72%) genes predicted high grade and/or non-organ-confined disease (FDR<10%), including all stromal response and androgen genes and the majority of cellular organization genes (82%). Proportionately fewer proliferation (40%), stress response (29%), and basal epithelial (25%) genes were associated w/ adverse path. Androgen and cellular organization genes consistently predicted lower risk; stromal response and proliferation genes predicted higher risk; (majority of std odds ratios >1.5, comparable to the prognostic strength of ER in breast cancer). Conclusions: Genes and biological pathways associated w/ clinically aggressive prostate cancer in RP specimens can be reliably measured by RT-PCR from fixed prostate needle biopsies and predict high-grade, non-organ-confined disease. These results support the potential value of a Bx-based assay to inform selection of immediate treatment or active surveillance for pts diagnosed with prostate cancer on needle Bx.
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Han, Dongyan, Ziming Wang, Qilin Wang, Bohao Wu, Tao Yu, and Dayong Wang. "Analysis of the Kozeny–Carman model based on pore networks." Journal of Geophysics and Engineering 16, no. 6 (October 18, 2019): 1191–99. http://dx.doi.org/10.1093/jge/gxz089.
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Abstract The Kozeny–Carman (KC) model is commonly used to predict permeability (k) but sometimes presents obvious predictive deviations. Comparatively, k prediction based on pore networks could more effectively describe the dependence of k on porous structure and accordingly shows high accuracy and reliability. This triggers us to examine the rationality of the KC assumptions about the pore structure and analyze the model applicability according to the pore networks. Two glass bead packs, a sintered glass bead plate and a Berea core are measured using computed tomography imaging and their pore parameters are accordingly calculated. Their pore parameters are obviously distinct, generally reflecting the progressively stronger roles of particle size, compaction-alike sintering and weak cementation in reducing porosity (ϕ), k, pore and pore throat radii (rp and rt). When correlating the pore parameters of the KC model to those of the pore networks, it is found that the specific surface area (av) has no specific relation to rp and rt and that pore structures could be distinct despite the equivalent av. Thus, av is insufficient to distinguish the differences in pore geometry and reflects their influence on k. An analysis of the modified KC equations of our cores and the ϕ−k relationships of some relative homogeneous reservoir rocks (e.g. silty sandstone and Fontainebleau sands) indicates that the variety of the ϕ−k relationships induced by such factors as particle size and pore radius could not be fully predicted by the KC model in some cases, especially when the ϕ is relatively low.
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Tauchi, Lisa, Takahiro Nakagaki, Masahiro Shimizu, Eiji Itoh, Mikio Yasutake, and Kazuchika Ohta. "Discotic liquid crystals of transition metal complexes 49: establishment of helical structure of fullerene moieties in columnar mesophase of phthalocyanine-fullerene dyads." Journal of Porphyrins and Phthalocyanines 17, no. 11 (November 2013): 1080–93. http://dx.doi.org/10.1142/s1088424613500752.
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A homologous series of the phthalocyanine-fullerene dyads, Cn-PcM(OFbaC60) (n = 6, 8, 10, 12; M = Cu , Ni , Co : 3a–3f) have been synthesized to obtain homeotropic alignment at rt and investigate the effects of spacer chain length (n = 6, 8, 10, 12) and central metal ( M = Cu , Ni , Co ) on the mesomorphism. Interestingly, the shorter-spacer-substituted (n = 6, 8; M = Cu ) dyads 3a and 3b showed a hexagonal columnar mesophase (Colh), whereas the longer-spacer-substituted (n = 10, 12; M = Cu , Ni , Co ) dyads 3c–3f showed a tetragonal columnar mesophase (Coltet). Moreover, each of the homologs 3a–3e shows perfect homeotropic alignment in both the Colh and Coltet mesophases at rt. More interestingly, these columnar mesophases gave a very unique XRD reflection peak denoted as Peak H in a very small angle region of 0.8 < 2θ < 2.0 degree. We have established at the first time from our developed two new XRD sample preparation techniques that the Peak H is due to the helical structure of fullerenes around columns formed by one-dimensionally stacked Pc cores. 1D nano array structure of donor and acceptor between two electrodes is recently proposed to obtain higher photoelectric conversion efficiency for organic thin film solar cells. This 1D nano array structure is almost compatible with the present homeotropically aligned Pc- C 60 dyads 3a–3f between two glass plates. Hence, these novel Pc- C 60 dyads 3a–3f may be very suitable to organic thin film solar cells.
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Albertine, Kurt H., Mar Janna Dahl, Linda W. Gonzales, Zheng-ming Wang, Drew Metcalfe, Dallas M. Hyde, Charles G. Plopper, Barry C. Starcher, David P. Carlton, and Richard D. Bland. "Chronic lung disease in preterm lambs: effect of daily vitamin A treatment on alveolarization." American Journal of Physiology-Lung Cellular and Molecular Physiology 299, no. 1 (July 2010): L59—L72. http://dx.doi.org/10.1152/ajplung.00380.2009.
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Neonatal chronic lung disease is characterized by failed formation of alveoli and capillaries, and excessive deposition of matrix elastin, which are linked to lengthy mechanical ventilation (MV) with O2-rich gas. Vitamin A supplementation has improved respiratory outcome of premature infants, but there is little information about the structural and molecular manifestations in the lung that occur with vitamin A treatment. We hypothesized that vitamin A supplementation during prolonged MV, without confounding by antenatal steroid treatment, would improve alveolar secondary septation, decrease thickness of the mesenchymal tissue cores between distal air space walls, and increase alveolar capillary growth. We further hypothesized that these structural advancements would be associated with modulated expression of tropoelastin and deposition of matrix elastin, phosphorylated Smad2 (pSmad2), cleaved caspase 3, proliferating cell nuclear antigen (PCNA), VEGF, VEGF-R2, and midkine in the parenchyma of the immature lung. Eight preterm lambs (125 days' gestation, term ∼150 days) were managed by MV for 3 wk: four were treated with daily intramuscular Aquasol A (vitamin A), 5,000 IU/kg, starting at birth; four received vehicle alone. Postmortem lung assays included quantitative RT-PCR and in situ hybridization, immunoblot and immunohistochemistry, and morphometry and stereology. Daily vitamin A supplementation increased alveolar secondary septation, decreased thickness of the mesenchymal tissue cores between the distal air space walls, and increased alveolar capillary growth. Associated molecular changes were less tropoelastin mRNA expression, matrix elastin deposition, pSmad2, and PCNA protein localization in the mesenchymal tissue core of the distal air space walls. On the other hand, mRNA expression and protein abundance of VEGF, VEGF-R2, midkine, and cleaved caspase 3 were increased. We conclude that vitamin A treatment partially improves lung development in chronically ventilated preterm neonates by modulating expression of tropoelastin, deposition of elastin, and expression of vascular growth factors.
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Marina, O., G. S. Gustafson, D. S. Brabbins, P. Y. Chen, M. Wallace, H. Ye, and D. J. Krauss. "Prognostic Value of Diagnostic Prostate Biopsy Percent Carcinoma Volume (PCV) and Percent Positive Cores (PPC) on Treatment Outcomes Following Radiation Therapy (RT): A Retrospective Analysis of 1731 Patients." International Journal of Radiation Oncology*Biology*Physics 90, no. 1 (September 2014): S404—S405. http://dx.doi.org/10.1016/j.ijrobp.2014.05.1289.
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Aizer, Ayal A., John Phillips, Ming-Hui Chen, Danjie Zhang, Marian Loffredo, and Anthony Victor D'Amico. "Detecting lower in addition to the highest Gleason score prostate cancer on core biopsy and the risk of prostate cancer-specific mortality." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): 5051. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.5051.
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5051 Background: We evaluated the risk of prostate cancer-specific mortality (PCSM) following definitive treatment in men with at least one prostate biopsy core with a Gleason score (GS) lower than the highest GS identified. This pattern termed “ComboGS” in a concurrent submission was shown to be associated with a significant reduction in the odds of upgrading at radical prostatectomy (RP). Methods: In this validation cohort 666 men with localized or locally advanced prostate cancer, men were diagnosed via a transrectal, ultrasound-guided needle prostate biopsy (median 6, IQR 5-6 cores) and treated definitively between 1989-2000 with either RP or radiation (RT) or RT and hormones (HT) at a regional radiation oncology center. Patients could be referred into this center from 6 community based hospitals in Southeastern Massachusetts and Rhode Island. Community based pathologists from these 6 health care facilities assigned the biopsy GS used for the analyses in this study. Multivariable competing risks regression was performed (Table) to assess the impact of ComboGS on the risk of PCSM adjusting for age, established PC prognostic factors, and treatment. Results: After a median follow up of 4.6 years (IQR 2.5-6.7 years), 168 men (25.2%) died, 41 (24.4%) of PC. ComboGS was associated with a decreased risk of PCSM (Adjusted Hazard Ratio (AHR) 0.40, 95% Confidence Interval (CI) 0.19-0.85, p=.017). Estimates of PCSM were significantly lower in men with versus without ComboGS when the highest GS was ≥7 (p<.001) but not 6 or less (p=.71). Specifically these 5-year estimates were 14.4% and 4.8% versus 1.9% and 2.7% respectively. Conclusions: In addition to lower odds of upgrading at RP, using an independent data set the ComboGS assessed by community based pathologists serving 6 hospitals was found to also be associated with a decreased risk of PCSM. [Table: see text]
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Martinez, A., R. Pio, J. Lopez, and F. Cuttitta. "Expression of the adrenomedullin binding protein, complement factor H, in the pancreas and its physiological impact on insulin secretion." Journal of Endocrinology 170, no. 3 (September 1, 2001): 503–11. http://dx.doi.org/10.1677/joe.0.1700503.
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Adrenomedullin (AM) is a ubiquitous peptide hormone which, among other functional roles, reduces insulin secretion in the pancreas. Recently we have described the interaction between AM and the complement regulator protein factor H, which results in mutual modulation of their respective functions. Here we identify the expression of factor H in the beta cells of the rat pancreatic islets by immunohistochemistry and multiple immunofluorescence followed by confocal microscopy. In addition, double immunogold staining under the electron microscope showed coexistence of insulin and factor H immunoreactivities within the same secretory granules; interestingly, factor H staining was found in the electron-lucent haloes whereas the insulin antibody labeled preferentially the dense cores. The existence of factor H mRNA in the pancreas was confirmed by RT-PCR and in situ hybridization. The function of factor H in the pancreas was investigated with an insulin secretion assay. Addition of factor H to freshly isolated islets in the presence of AM resulted in a further reduction in insulin secretion with a concomitant elevation of cAMP, suggesting that factor H increases AM function in glucose homeostasis. The expression of factor H in the pancreas may play other important roles such as protection against complement-mediated cell lysis.
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Rewari, A., H. Lu, Q. Yang, Z. Shen, and B. Haffty. "BCCIP: A novel marker for radiotherapy benefit in patients with laryngeal cancer." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 6006. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.6006.
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6006 Background: It has been well established that the functionality of the p53 pathway is related to radiosensitivity in various human cancers. The status of proteins regulating p53 activity may also be valuable markers for radiosensitivity. Recent studies have shown that BCCIP (BRCA2 & CDKN1A interacting protein) is essential for maintaining the transactivation activity of wild type p53. We hypothesize that functional BCCIP may contribute to effective radiotherapy in the clinical setting. To test this hypothesis, we analyzed the expression of BCCIP and p53 in a cohort of laryngeal cancer treated with radiotherapy and assessed whether BCCIP and p53, alone or in combination, would correlate with local control and overall survival. Methods: One hundred thirty-five patients treated between 1975 and 2000 for early stage (stage I & II) squamous cell carcinoma of the larynx were included in the study. Treatment consisted of definitive radiation therapy (RT) with standard fields and fractionation to a median dose of 6,590 cGY. Tissue was collected from pre-RT biopsies and constructed in a tissue microarray, with duplicate cores created for each case. BCCIP and p53 expression was analyzed by immunohistochemistry and qualitatively scored with greater than 10% nuclear reactivity the cutoff for positive staining. Results: Expression of BCCIP and wild type p53 in combination was associated with significant improvements in 5-year local control (68.75% vs. 46.27%, p = .04) and 5-year overall survival (67.68% vs. 34.62%, p = .006) compared to patients who did not express BCCIP. Expression of BCCIP or p53 alone was not found to be independently associated with benefits in local control or overall survival. Conclusions: This study provides clinical evidence that BCCIP contributes to effective local control and overall survival in patients with laryngeal cancer treated with radiation. This benefit may be a result of increased radiosensitivity in patients who have functional BCCIP and p53. Using immunohistochemical methods, BCCIP and p53 co-expression can act as markers to identify sub-groups of laryngeal cancer patients who are more likely to be cured with radiotherapy. No significant financial relationships to disclose.
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Nishimura, Hiroshi, and Norikazu Maeno. "Characteristic Growth Processes of Ice Crystals on the Antarctic Ice Sheet." Annals of Glaciology 11 (1988): 104–8. http://dx.doi.org/10.1017/s0260305500006418.
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Characteristic growth processes were investigated by measuring cross-sectional areas of ice crystals for four 30 m snow cores drilled in Mizuho Plateau, Antarctica. Considerable difference was found in the growth rate of crystals between a temperature-gradient layer above 6 m depth and an isothermal layer below 10 m depth: the growth rate in the temperature-gradient layer was much larger than that in the isothermal layer. In the isothermal layer, temperature dependence of the growth rate K was expressed by an equation K = K 0 exp(−E/RT), where R and T are the gas constant and absolute temperature respectively. The apparent activation energy E is 44.7 kJ mol−1. On the other hand, in the temperature-gradient layer, the apparent activation energy was as small as 12 kJ mol−1: the difference was explained as due to the temperature gradient. Using the temperature profiles in snow that have been estimated from the meteorological data from several stations, the growth rates in the temperature-gradient layer were calculated. The calculated temperature dependence of the growth rates, taking into consideration vertical flux of water vapor between ice particles caused by the temperature gradient, showed good agreement with measured results. It is concluded that the growth process in the layer above 6 m depth is mainly due to vapor transport under the vertical temperature gradient.
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Nishimura, Hiroshi, and Norikazu Maeno. "Characteristic Growth Processes of Ice Crystals on the Antarctic Ice Sheet." Annals of Glaciology 11 (1988): 104–8. http://dx.doi.org/10.3189/s0260305500006418.
Full textAbstract:
Characteristic growth processes were investigated by measuring cross-sectional areas of ice crystals for four 30 m snow cores drilled in Mizuho Plateau, Antarctica. Considerable difference was found in the growth rate of crystals between a temperature-gradient layer above 6 m depth and an isothermal layer below 10 m depth: the growth rate in the temperature-gradient layer was much larger than that in the isothermal layer. In the isothermal layer, temperature dependence of the growth rate K was expressed by an equation K = K0 exp(−E/RT), where R and T are the gas constant and absolute temperature respectively. The apparent activation energy E is 44.7 kJ mol−1.On the other hand, in the temperature-gradient layer, the apparent activation energy was as small as 12 kJ mol−1: the difference was explained as due to the temperature gradient. Using the temperature profiles in snow that have been estimated from the meteorological data from several stations, the growth rates in the temperature-gradient layer were calculated. The calculated temperature dependence of the growth rates, taking into consideration vertical flux of water vapor between ice particles caused by the temperature gradient, showed good agreement with measured results. It is concluded that the growth process in the layer above 6 m depth is mainly due to vapor transport under the vertical temperature gradient.
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Rybár, Samuel, Eva Halásová, Natália Hudáčková, Michal Kováč, Marianna Kováčová, Katarína Šarinová, and Michal Šujan. "Biostratigraphy, sedimentology and paleoenvironments of the northern Danube Basin: Ratkovce 1 well case study." Geologica Carpathica 66, no. 1 (February 1, 2015): 51–67. http://dx.doi.org/10.1515/geoca-2015-0010.
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Abstract The Ratkovce 1 well, drilled in the Blatné depocenter of the northern Danube Basin penetrated the Miocene sedimentary record with a total thickness of 2000 m. Biostratigraphically, the NN4, NN5 and NN6 Zones of calcareous nannoplankton were documented; CPN7 and CPN8 foraminifer Zones (N9, 10, 11 of the global foraminiferal zonation; and MMi4a; MMi5 and MMi6 of the Mediterranean foraminiferal zonation were recognized. Sedimentology was based on description of well core material, and together with SP and RT logs, used to characterize paleoenvironmental conditions of the deposition. Five sedimentary facies were reconstructed: (1) fan-delta to onshore environment which developed during the Lower Badenian; (2) followed by the Lower Badenian proximal slope gravity currents sediments; (3) distal slope turbidites were deposited in the Lower and Upper Badenian; (4) at the very end of the Upper Badenian and during the Sarmatian a coastal plain of normal marine to brackish environment developed; (5) sedimentation finished with the Pannonian-Pliocene shallow lacustrine to alluvial plain deposits. The provenance analysis records that the sediment of the well-cores was derived from crystalline basement granitoides and gneisses and from the Permian to Lower Cretaceous sedimentary cover and nappe units of the Western Carpathians and the Eastern Alps. Moreover, the Lower Badenian volcanism was an important source of sediments in the lower part of the sequence.
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McBride, Sean Matthew, Daniel Eidelberg Spratt, Marisa Kollmeier, Wassim Abida, Han Xiao, Susan F. Slovin, Channing Judith Paller, et al. "Interim results of aasur: A single arm, multi-center phase 2 trial of apalutamide (A) + abiraterone acetate + prednisone (AA+P) + leuprolide with stereotactic ultra-hypofractionated radiation (UHRT) in very high risk (VHR), node negative (N0) prostate cancer (PCa)." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): 5012. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.5012.
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5012 Background: Standard of care in VHR PCa is radiation therapy (RT) with 18-36 months (mos) of androgen-deprivation therapy (ADT). With this regimen, chronic ADT toxicity is significant and biochemical recurrence (BCR) frequent. We sought to improve tumor control and minimize toxicity with intensified short course ADT with dual androgen receptor signaling inhibitors (ARSI) and UHRT. Methods: 64 patients (pts) with VHR, N0 PCa were enrolled from 4 centers. VHR PCa was defined as Gleason score (GS) 9-10, >4 cores of GS 8 disease, or 2 high-risk features (including rT3/T4 disease). Treatment (tx) involved 6 mos of A, AA+P, and leuprolide with prostate/seminal vesicle-directed RT (7.5-8 Gy x 5 fractions). The primary endpoint was BCR defined as nadir PSA + 2ng/mL. Biochemical recurrence-free survival (bRFS) is reported herein. Our hypothesized reduction in BCR from 25% to 10% at 3 years (yrs) required 53 pts to provide a power of 0.84 and an alpha of 0.03. Undetectable PSA was defined as <0.10 ng/mL. Non-castrate testosterone (T) was a post-tx value >150 ng/mL. All analyses were intention-to-treat. Toxicity and health-related quality of life measures were evaluated using CTCAEv4.0 and the EPIC-26 questionnaire. Results: Baseline characteristics are summarized in the Table; 63 of 64 pts completed protocol tx. Median time to nadir PSA from tx start was 2 mos (range, 1-9); 63 of 64 pts (98.4%) achieved an undetectable nadir PSA. Median time to post-tx, non-castrate T was 6.5 mos (range, 2.5-25.5). Median follow-up (f/u) for pts without BCR was 30 mos (range, 15-44). Seven pts had BCR; 2-yr bRFS was 95.0% (95% CI, 89.7-100); 3-yr bRFS was 89.7% (95 CI, 81.0-99.3). For the 57 pts without BCR, 56 (98.2%) had T > 150ng/mL at last f/u; median PSA at last f/u was 0.10 ng/mL (IQR, <0.10-0.30); of these, 40 (70.2%) pts had PSAs ≤ 0.20 ng/mL with 24 (42.1%) undetectable. Fifteen pts experienced transient Grade 3 toxicities: 12 (18.8%) with hypertension and 3 with rash (4.7%). EPIC-26 scores for a subset of pts (n=21) at baseline and 12 mos showed no significant decline in urinary or bowel domains; declines in sexual (-11.9) and hormone (-5.7) domains met significance. Conclusions: Compared to historic controls with the long course ADT, AASUR demonstrated impressive 3-yr bRFS, rapid T recovery, and limited toxicities; the safety profile of this regimen was consistent with the known AE profile of the ARSI and RT. This regimen warrants further, randomized evaluation. Funded by Janssen Pharmaceuticals. Managed by the Prostate Cancer Clinical Trials Consortium. Clinical trial information: NCT02772588. [Table: see text]
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D’Agostino, Fabio, Daniele Kaza, Michele Martelli, Giacomo-Piero Schiapparelli, Federico Silvestro, and Carlo Soldano. "Development of a Multiphysics Real-Time Simulator for Model-Based Design of a DC Shipboard Microgrid." Energies 13, no. 14 (July 11, 2020): 3580. http://dx.doi.org/10.3390/en13143580.
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Recent and strict regulations in the maritime sector regarding exhaust gas emissions has led to an evolution of shipboard systems with a progressive increase of complexity, from the early utilization of electric propulsion to the realization of an integrated shipboard power system organized as a microgrid. Therefore, novel approaches, such as the model-based design, start to be experimented by industries to obtain multiphysics models able to study the impact of different designing solutions. In this context, this paper illustrates in detail the development of a multiphysics simulation framework, able to mimic the behaviour of a DC electric ship equipped with electric propulsion, rotating generators and battery energy storage systems. The simulation platform has been realized within the retrofitting project of a Ro-Ro Pax vessel, to size components and to validate control strategies before the system commissioning. It has been implemented on the Opal-RT simulator, as the core component of the future research infrastructure of the University of Genoa, which will include power converters, storage systems, and a ship bridge simulator. The proposed model includes the propulsion plant, characterized by propellers and ship dynamics, and the entire shipboard power system. Each component has been detailed together with its own regulators, such as the automatic voltage regulator of synchronous generators, the torque control of permanent magnet synchronous motors and the current control loop of power converters. The paper illustrates also details concerning the practical deployment of the proposed models within the real-time simulator, in order to share the computational effort among the available processor cores.
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McBride, Sean Matthew, Michael J. Zelefsky, Daniel Eidelberg Spratt, Channing Judith Paller, Marisa Kollmeier, Susan F. Slovin, Jahan Aghalar, et al. "Baseline genomic and circulating tumor cell (CTC) correlative data from very high-risk (VHR), localized, node-negative prostate cancer patients." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): e16563-e16563. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e16563.
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e16563 Background: Few data exist on CTC frequency and number, genetic landscape, and tumor mutational burden (TMB) in VHR, node negative, localized prostate cancer (PCa). Methods: We are conducting a single-arm phase 2 trial of ultra-hypofractionated radiation (RT) with 6 months of abiraterone, apalutamide and leuprolide in VHR PCa, defined as: Gleason (Gl) 9-10 or 2 high risk features (including radiographic (r) T3/T4 disease) or > 4 cores of Gl8. We report baseline correlatives in the first 38 screened patients (pts). CTCs were isolated using a non-selection based platform (EPIC Sciences). Additional analyses were conducted using MSK IMPACT, a next generation sequencing assay. Results: Median PSA was 14.8 ng/mL (IQR, 7.7-28.1); Gl7 was present in 5% (n = 2), Gl8 in 32% (n = 12), Gl9 in 61% (n = 23) and Gl10 in 2% (n = 1) of pts; on MR, 42% of pts were rT2 (n = 16), 39% had rT3a disease (n = 15) and 18% had rT3b disease (n = 7). CTC data were available on 31 pts; 74% (n = 23) had ≥1 detectable CTC (range, 0.8-14.6 cells per mL); 29% (n = 9) had CK+ clusters (range, 0.8-7.1 clusters per mL). IMPACT was available for 20 pts: KMT2D/C mutations were present in 25% (n = 4), TP53 missense mutations in 20% (n = 4), FOXA1 mutations in 20% (n = 4), PTEN truncating or missense mutations in 15% (n = 3), SPOP missense mutations in 15% (n = 3), PIK3CA activating mutations in 15% (n = 3), APC deletions in 15% (n = 3); 85% (17/20) had alterations in one of these genes. No clinically significant germline mutations were present. Median TMB was 2.63 mutations/mB (range, 0.87-60.56); the TMB-highest pt had an in-frame deletion in MSH2. Among IMPACTed pts with normalized testosterone post-protocol treatment (n = 16), there was a trend towards an association with SPOP/FOXA1 mutations and undetectable ( < 0.05 ng/mL) PSA; 5/6 pts with mutations had undetectable PSA (83.3%) vs 3/10 without (30%) (p = 0.12). The trial is managed by the PCCTC and funded by Janssen. Conclusions: The genetic profile and TMB of VHR, localized PCa resembles non-castrate, metastatic disease. The frequency of detectable CTCs is high with implications for post-treatment surveillance. SPOP/FOXA1 mutations may predict initial response to RT with total androgen blockade. Clinical trial information: NCT02772588.
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Morris, W. James, Scott Tyldesley, Howard H. Pai, Ross Halperin, Michael R. McKenzie, Graeme Duncan, Gerard Morton, Nevin Murray, and Jeremy Hamm. "ASCENDE-RT*: A multicenter, randomized trial of dose-escalated external beam radiation therapy (EBRT-B) versus low-dose-rate brachytherapy (LDR-B) for men with unfavorable-risk localized prostate cancer." Journal of Clinical Oncology 33, no. 7_suppl (March 1, 2015): 3. http://dx.doi.org/10.1200/jco.2015.33.7_suppl.3.
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3 Background: This trial compared the efficacy of DE-EBRT and LDR-B for National Comprehensive Cancer Network (NCCN) high and intermediate-risk disease. Methods: A planned sample size of 400 patients were randomized to one of two treatment arms and stratified by risk group. Both arms received 12 months of androgen deprivation therapy (ADT) with luteinizing hormone releasing hormone (LHRH) agonist plus a non-steroidal anti-androgen for at least 1 month. After 8 months of neo-adjuvant ADT, both arms received whole pelvis EBRT (46Gy/23#). Patients assigned to DE-EBRT (standard arm) then received a conformal EBRT boost (32Gy/16#). Patients assigned to LDR-B (experimental arm) received an Iodine-125 LDR boost prescribed to a minimum peripheral dose of 115Gy. The primary endpoint was relapse free survival (RFS) defined by biochemical criteria using the nadir+2 ng/mL threshold. Time zero was the date of the first LHRH injection. Results: Between Dec 2002 and Sep 2011, 276 high-risk and 122 intermediate-risk patients were accrued at 6 cancer treatment centers. 200 men were assigned to DE-EBRT and 198 to LDR-B. The treatment arms were well balanced in terms of age and known prognostic factors. Median follow up (FU) is 6.5 years; 65 men have >9 years FU. There were 12 major protocol violations in each arm. By intent-to-treat analysis, the 3-, 5-, 7-, and 9-year Kaplan-Meier RFS estimates are 94% vs 94%, 77% vs 89%, 71% vs 86%, and 63% vs 83% for DE-EBRT and LDR-B respectively (hazard ratio = 0.473; 95% CI 0.292 – 0.765; P = 0.0022). Randomization (p<0.001), percent positive cores (p=0.005), initial PSA (p=0.006) and clinical T-stage (p=0.013) were predictive of RFS in a multivariable Cox model. The median PSA at latest FU for non-relapsing patients assigned to LDR-B is 0.02 vs 0.24 ng/mL for DE-EBRT. Conclusions: In a randomized trial, an Iodine-125 LDR boost was much more effective than an EBRT boost in rendering unfavorable-risk prostate cancer patients biochemically disease free. *ASCENDE-RT- Androgen Suppression Combined with Elective Nodal and Dose Escalated Radiation Therapy is an NCI registered trial (NCT00175396). Clinical trial information: NCT00175396.
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Kuznetsov, A. A., O. A. Smirnov, and T. Y. Kuznetsova. "Noise-like discrete signals for asynchronous code division radio systems." Radiotekhnika, no. 205 (July 2, 2021): 175–83. http://dx.doi.org/10.30837/rt.2021.2.205.19.
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This article discusses noise-like discrete signals (pseudo-random sequences) for asynchronous code division systems for radio channels. Asynchrony implies the use of sequences that are statistically uncorrelated for an arbitrary cyclically shifted copy of the signals, i.e. their cross-correlation coefficient for arbitrarily chosen starting points is close to zero. The fundamental theoretical limit for this characteristic is the well-known Welch boundary. In this paper, we compare the correlation properties of various sets (Gold codes, Kasami sequences, etc.) with this fundamental limit. The parameters of different codes are estimated, the corresponding bound is shown and compared with the real correlation characteristics of the codes. For the approximation, the Laurent series expansion and the Puiseau series were used. The asymptotic properties were also estimated. The paper also considers new ensembles of noise-like discrete signals for asynchronous systems. These codes are statistically uncorrelated, asymptotically the square of their cross-correlation for arbitrary starting points tends to the theoretical Welch bound. Moreover, the cardinality (power of the set) of new signal ensembles is much higher than that of Gold codes and Kasami sets. Consequently, the practical use of such noise-like discrete signals will increase the capacity of asynchronous code division systems for radio channels and reduce the cost of communication services. In addition, new sets of spreading signals will be useful for the implementation of the so-called. soft capacity, i.e. when, if necessary, the base station can increase the subscriber capacity with a slight decrease in the quality of service.
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Шевчук, О. С. "Randomized symmetric McEliece cryptosystem based on generalized Reed-Solomon codes." Radiotekhnika 1, no. 200 (April 30, 2020): 25–36. http://dx.doi.org/10.30837/rt.2020.1.200.03.
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Tsujino, Noriyoshi, Andreea Mârza, and Daisuke Yamazaki. "Pressure dependence of Si diffusion in γ-Fe." American Mineralogist 105, no. 3 (March 1, 2020): 319–24. http://dx.doi.org/10.2138/am-2020-7197.
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Abstract The pressure dependence of Si diffusion in γ-Fe was investigated at pressures of 5–15 GPa and temperatures of 1473–1673 K using the Kawai-type multi-anvil apparatus to estimate the rate of mass transportation for the chemical homogenization of the Earth's inner core and those of small terrestrial planets and large satellites. The obtained diffusion coefficients D were fitted to the equation D = D0 exp[−(E* + PV*)/(RT)], where D0 is a constant, E* is the activation energy, P is the pressure, V* is the activation volume, R is the gas constant, and T is the absolute temperature. The least-squares analysis yielded D0 = 10-1.17±0.54 m2/s, E* = 336 ± 16 kJ/mol, and V* = 4.3 ± 0.2 cm3/mol. Moreover, the pressure and temperature dependences of diffusion coefficients of Si in γ-Fe can also be expressed well using homologous temperature scaling, which is expressed as D = D0exp{–g[Tm(P)]/T}, where g is a constant, Tm(P) is the melting temperature at pressure P, and D0 and g are 10-1.0±0.3 m2/s and 22.0 ± 0.7, respectively. The present study indicates that even for 1 billion years, the maximum diffusion length of Si under conditions in planetary and satellite cores is less than ∼1.2 km. Additionally, the estimated strain of plastic deformation in the Earth's inner core, caused by the Harper–Dorn creep, reaches more than 103 at a stress level of 103–104 Pa, although the inner core might be slightly deformed by other mechanisms. The chemical heterogeneity of the inner core can be reduced only via plastic deformation by the Harper–Dorn creep.
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McDonough, Jill. "Cindy Comes to Hear Me Read and Gay Freaking Assholes: On Tolerance." Radical Teacher 109 (September 12, 2017): 54–56. http://dx.doi.org/10.5195/rt.2017.416.
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Si, Qilin, Santosh Shetty, and Benjamin Carrion Schaefer. "Building Complete Heterogeneous Systems-on-Chip in C: From Hardware Accelerators to CPUs." Electronics 10, no. 14 (July 20, 2021): 1746. http://dx.doi.org/10.3390/electronics10141746.
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High-Level Synthesis (HLS) dramatically accelerates the design and verification of individual components within larger VLSI systems. With most complex Integrated Circuits (ICs) being now heterogeneous Systems-on-Chip (SoCs), HLS has been traditionally used to design the dedicated hardware accelerators such as encryption cores and Digital Signal Processing (DSP) image processing accelerators. Unfortunately, HLS is a single process (component) synthesis method. Thus, the integration of these accelerators has to be performed at the RT level (Verilog or VHDL). This implies that the system-level verification needs to be performed at lower levels of abstraction, which significantly diminishes the benefits of using HLS. To address this, this work presents a methodology to generate entire heterogeneous SoCs in C. This work introduces two main contributions that enable this: first, an automatic bus generator that generates a synthesizable behavioral description of standard on-chip buses and, second, a library of synthesizable bus interfaces that allow any component in the system to send or receive data through the bus. Moreover, this work investigates the generation of processors and interfaces (peripherals) at the behavioral level as these are important parts of any SoCs, but have long been thought not to be efficiently synthesizable using HLS. Generating complete SoCs in C has significant advantages over traditional approaches. First, it enables the generation of fast cycle-accurate simulation models of the entire SoC, making the verification faster and easier. Second, it allows completely isolating the bus implementation details from the developers’ view, allowing the change between bus protocols with only minor changes in the designers’ code. Thirdly, it allows generating different SoC variants quickly by only changing the HLS synthesis options. Experimental results highlight these benefits.
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Selvaraj, R. S., and Venkatrajam Marka. "On Normal q-Ary Codes in Rosenbloom-Tsfasman Metric." ISRN Combinatorics 2014 (April 2, 2014): 1–5. http://dx.doi.org/10.1155/2014/237915.
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The notion of normality of codes in Hamming metric is extended to the codes in Rosenbloom-Tsfasman metric (RT-metric, in short). Using concepts of partition number and l-cell of codes in RT-metric, we establish results on covering radius and normality of q-ary codes in this metric. We also examine the acceptability of various coordinate positions of q-ary codes in this metric. And thus, by exploring the feasibility of applying amalgamated direct sum method for construction of codes, we analyze the significance of normality in RT-metric.
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Meyerson, Greg. "“It’s Not Personal, It’s Business: or Teaching Structural Explanation” (at an HBCU)." Radical Teacher 101 (February 23, 2015): 9–14. http://dx.doi.org/10.5195/rt.2015.197.
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Needless to say, the dominant explanatory framework among our students generally is still individualism, and when it comes to their career trajectories, American dreams and equal opportunities predominate. Where I currently teach, the Historically Black University (HBCU) of civil rights fame North Carolina A and T University, it is more complicated.
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Valladares Ayerbes, Manuel, Vanessa Medina Villaamil, Sara Martinez Breijo, Isabel Santamarina Cainzos, Guadalupe Aparicio, Jose Gonzalez Dacal, Paula Portela Pereira, Dario Vazquez Pazos, Francisco Gomez-Veiga, and Luis M. Antón Aparicio. "Circulating miR-337-3p as a novel biomarker for prostate cancer." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): 5087. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.5087.
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5087 Background: Recent studies have demonstrated that the aberrant expression of microRNAs (miRNAs)is related with the development of prostate cancer (PCa). Detection of circulating tumor cells (CTC) may provide diagnostic and prognostic information inPCa. The purpose is identifying circulating miRNAs potentially useful for CTC detection in patients with PCa. Methods: In the first study phase we examined blood levels of 92 miRNAs in 49 patients grouped in pools by risk classification: low-risk 42.8%, intermediate-risk 22.5% and high-risk 34.7% and healthy volunteers (N=10) using SYBR-green-based microARN RT-qPCR arrays (Exiqon). Prostate cancer diagnosis was obtained by transrectalultrasound guided biopsy of 10 cores, PSA and digital rectal examination was done previously. In the second study phase using quantitative real-time polymerase chain reaction (qPCR) by TaqMan Human MicroRNAAssays (Life Technologies), we compared the expression levels of miRNAs in blood samples from 34 patients of low-risk, 31 of intermediate-risk, 18 of high-risk localized disease and 22 healthy volunteers paired by age with cases. Receiver-operator characteristic (ROC) curve was used. Results: Blood samples from patients with low, intermediate, high-risk and healthy controls exhibit distinct circulating miRNA signatures. microRNAsdifferential expressed between risk groups (p<0.01) (low, intermediate and high) and control group: 0microARNs upregulated (MU), 12 MU and 68 MU respectively. Highlight the significantlyoverexpression in the intermediate risk group and maintained at the high-risk of microRNAs: 337-3p[247 PicTar predictions (PTP)], 330-3p (307 PTP) and 218 (551 PTP). Preliminary results of the second study phase showed that the median level of miRNA,337-3p was significantly higher in patients with high-risk than that in healthy controls (p=.001). ROC curve analyses indicated that this blood miRNA may beuseful for discriminating patients with high-risk from healthy controls (AUC=.724). Conclusions: miRNAs in the circulation are relatively stable, very accessible, low invasive and easily testable biomarkers. Our preliminary promisingresults suggest miR-337-3p as novel stable blood-based marker for PCa detection.