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Articles by Y. Zhu
Total Records ( 6 ) for Y. Zhu
  A. E Hoffman , T Zheng , C. H Yi , R. G Stevens , Y Ba , Y Zhang , D Leaderer , T Holford , J Hansen and Y. Zhu

As transcriptional regulators, circadian genes have the potential to influence a variety of biological pathways, including many cancer-related processes. Cryptochrome 2 (CRY2) is essential for proper circadian timing and is a key component of the circadian regulatory feedback loop. Here, we report findings from genetic, epigenetic, loss-of-function, and transcriptional profiling analyses of CRY2 in breast cancer. Six single-nucleotide polymorphisms in CRY2 were identified for genotyping in a case-control population (n = 441 cases and n = 479 controls), and three single-nucleotide polymorphisms (rs11038689, rs7123390, and rs1401417) were significantly associated with postmenopausal breast cancer risk, with significant effect modification by menopausal status [dominant model for rs11038689: odds ratio (OR), 0.71; 95% confidence interval (95% CI), 0.51-0.99; P for trend = 0.028; homozygous variants for rs7123390: OR, 0.44; 95% CI, 0.22-0.86; P for trend = 0.028; and rs1401417: OR, 0.44; 95% CI, 0.21-0.92; P for trend = 0.017]. Interestingly, this association was only evident in women with estrogen and progesterone receptor (ER/PR)–negative breast tumors but not with ER/PR-positive tumors. Breast cancer patients also had significantly higher levels of CRY2 promoter methylation relative to controls, which is consistent with tissue array data showing lower levels of CRY2 expression in tumor tissue relative to adjacent normal tissue. Furthermore, in vitro analyses identified several breast cancer–relevant genes that displayed altered expression following CRY2 knockdown. These findings suggest a role for CRY2 in breast tumorigenesis and provide further evidence that the circadian system may be an important modulator of hormone-related cancer susceptibility. Cancer Prev Res; 3(4); 539–48. ©2010 AACR.

  X He , Z Gu and Y. Zhu

We consider the task model of periodic tasks running on a network of processor nodes connected by a bus based on the time-triggered protocol, an industry-standard bus protocol designed for safety-critical automotive and avionics distributed embedded systems, and present an integrated optimization framework that jointly considers one or more of the following attributes: task-to-processor allocation, task priority assignment, task period assignment and bus access configuration. We adopt a hierarchical optimization framework, where each possible task allocation and priority assignment is treated as one top-level coarse-grained state, which may contain many lower-level fine-grained states defined by different task period assignments and bus access configurations. Simulated annealing is used to explore the top-level states, which calls a geometric programming solver as a subroutine to explore the lower-level states contained within a given top-level state. Performance evaluation shows that our framework has good performance in terms of solution quality and scalability.

  H Inada , L Wu , J Wall , D Su and Y. Zhu

We report the performance of the first aberration-corrected scanning transmission electron microscope (STEM) manufactured by Hitachi. We describe its unique features and versatile capabilities in atomic-scale characterization and its applications in materials research. We also discuss contrast variation of the STEM images obtained from different annular dark-field (ADF) detectors of the instrument, and the increased complexity in contrast interpretation and quantification due to the increased convergent angles of the electron probe associated with the aberration corrector. We demonstrate that the intensity of atomic columns in an ADF image depends strongly on a variety of imaging parameters, sample thickness, as well as the nuclear charge and the deviation from their periodic position of the atoms we are probing. Image simulations are often required to correctly interpret the atomic structure of an ADF-STEM image.

  M Zhou , F Carlotti and Y. Zhu

A zooplankton closure model is developed by combining the size-based growth and mortality rates and size (biomass) spectrum theory. The new growth rate model, developed based on both Huntley and Boyd [(1984) Food-limited growth of marine zooplankton. Am. Nat., 124, 455–478.] and Hirst and Bunker [(2003) Growth of marine planktonic copepods: Global rates and patterns in relation to chlorophyll a, temperature, and body weight. Limnol. Oceanogr., 48, 1988–2010.], avoids overestimating zooplankton growth at the high temperature and food concentration condition; the mortality rate model developed based on the slope of observed biomass spectra and assimilation efficiency; and the biomass spectrum theory is a conservation equation of biomass fluxes between size classes in terms of growth and mortality. The zooplankton closure model is applied to simulate particular organic carbon and mesozooplankton biomass concentrations from 5 January 1999 to 12 July 2007 forced by temperature and chlorophyll, all of which were observed at the Service d'Observation du Frioul du Centre d'Océanologie de Marseille (SOFCOM) long-term monitoring station in the Gulf of Lions, northwestern Mediterranean Sea. The modelled zooplankton biomass and size spectra imitate the seasonal variations and responses of zooplankton communities to phytoplankton blooms. The carbon fluxes of total grazing, grazing on phytoplankton, feeding on zooplankton and removal from the zooplankton community are analyzed equal to 78, 40, 38 and 14 mg C m–3 day–1, respectively. This zooplankton closure model is intended to provide a link between lower and higher trophic level models in ecosystem modelling.

  Non-agricultural lands are surveyed sparsely in general. Meanwhile, soils in these areas usually exhibit strong spatial variability which requires more samples for producing acceptable estimates. Capulin Volcano National Monument, as a typical sparsely-surveyed area, was chosen to assess spatial variability of a variety of soil properties, and furthermore, to investigate its implications for sampling design. One hundred and forty one composited soil samples were collected across the Monument and the surrounding areas. Soil properties including pH, organic matter content, extractable elements such as calcium (Ca), magnesium (Mg), potassium (K), sodium (Na), phosphorus (P), sulfur (S), zinc (Zn), and copper (Cu), as well as sand, silt, and clay percentages were analyzed for each sample. Semivariograms of all properties were constructed, standardized, and compared to estimate the spatial variability of the soil properties in the area. Based on the similarity among standardized semivariograms, we found that the semivariograms could be generalized for physical and chemical properties, respectively. The generalized semivariogram for physical properties had a much greater sill value (2.635) and effective range (7 500 m) than that for chemical properties. Optimal sampling density (OSD), which is derived from the generalized semivariogram and defines the relationship between sampling density and expected error percentage, was proposed to represent, interpret, and compare soil spatial variability and to provide guidance for sample scheme design. OSDs showed that chemical properties exhibit a stronger local spatial variability than soil texture parameters, implying more samples or analysis are required to achieve a similar level of precision.
  D.C. Weindorf , N. Bakr , Y. Zhu , B. Haggard , S. Johnson and J. Daigle
  Placic horizons, defined as thin, wavy, hardened layers of iron and organic matter, are rare within the United States, occurring only in Washington, Alaska, and Hawaii. While ironstone is common in many soils of the southeastern United States, it is not known to contain appreciable organic matter. As a pilot study evaluating the justification for a larger study on ironstone in Louisiana, a 40 m lateral exposure with suspected placic horizons was evaluated in Vernon Parish, Louisiana. Results of laboratory analysis show elevated levels of iron and organic matter in the suspect horizons that meet the criteria of placic horizons as defined by the Soil Survey Staff. Based on the results of this study, additional evaluation of multiple pedons with similar features is warranted. Should additional pedons demonstrate similar properties, a new great group of ‘Petrudepts’ would be needed to describe both the placic horizons in the pedon and the udic moisture regime in which they occur.
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