Systematic Effects on the Genus Topology of Large Scale Structure of the Universe

Large-scale structure of the universe is a useful cosmological probe of the primordial non-Gaussianity and the expansion history of the universe because its topology does not change with time in the linear regime in the standard paradigm of structure formation. However, when the topology of iso-density contour surfaces is measured from an observational data, many systematic effects are introduced due to the finite size of pixels used to define the density field, non-linear gravitational evolution, redshift-space distortion, shot noise (discrete sampling), and bias in the distribution of the density field tracers. We study the various systematic effects on the genus curve to a great accuracy by using the Horizon Run 2 simulation of a {\Lambda}CDM cosmology. We numerically measure the genus curve from the gravitationally evolved matter and dark matter halo density fields. It is found that all the non-Gaussian deviations due to the systematic effects can be modeled by using a few low-order Hermite polynomials from H0 to H4. We compare our results with the analytic theories whenever possible, and find many new terms in the Hermite series that are making significant contributions to the non-Gaussian deviations. In particular, it is found that the amplitude drop of the genus curve due to the non-linear gravitational evolution can be accurately modeled by two terms H0 and H2 with coefficients both proportional to \sigma_0^2, the mean-square density fluctuation.Comment: 44 pages, 13 figures, 8 tables, Accepted for publication in ApJ

Topology of Luminous Red Galaxies from the Sloan Digital Sky Survey

We present measurements of the genus topology of luminous red galaxies (LRGs) from the Sloan Digital Sky Survey (SDSS) Data Release 7 catalog, with unprecedented statistical significance. To estimate the uncertainties in the measured genus, we construct 81 mock SDSS LRG surveys along the past light cone from the Horizon Run 3, one of the largest N-body simulations to date that evolved 7210^3 particles in a 10815 Mpc/h size box. After carefully modeling and removing all known systematic effects due to finite pixel size, survey boundary, radial and angular selection functions, shot noise and galaxy biasing, we find the observed genus amplitude to reach 272 at 22 Mpc/h smoothing scale with an uncertainty of 4.2%; the estimated error fully incorporates cosmic variance. This is the most accurate constraint of the genus amplitude to date, which significantly improves on our previous results. In particular, the shape of the genus curve agrees very well with the mean topology of the SDSS LRG mock surveys in the LCDM universe. However, comparison with simulations also shows small deviations of the observed genus curve from the theoretical expectation for Gaussian initial conditions. While these discrepancies are mainly driven by known systematic effects such as those of shot noise and redshift-space distortions, they do contain important cosmological information on the physical effects connected with galaxy formation, gravitational evolution and primordial non-Gaussianity. We address here the key role played by systematics on the genus curve, and show how to accurately correct for their effects to recover the topology of the underlying matter. In a forthcoming paper, we provide an interpretation of those deviations in the context of the local model of non-Gaussianity.Comment: 23 pages, 18 figures. APJ Supplement Series 201

The value of chest CT for prediction of breast tumor size: comparison with pathology measurement

BACKGROUND: Little information is available on the use of chest computed tomography (CT) to predict breast tumor size in breast cancer, despite the fact that chest CT examinations are being increasingly used. The purpose of this study was to evaluate the value of chest CT for predicting breast tumor size using pathology measurements as reference standards. METHODS: Tumor sizes (defined as greatest diameter) were retrospectively measured on the preoperative chest CT images of 285 patients with surgically proven unifocal, invasive breast carcinoma. Greatest tumor diameters as determined by chest CT and pathologic examinations were compared by linear regression and Spearman’s rho correlation analysis. Concordance between CT and pathology results was defined as a diameter difference of <5 mm. Subgroup analyses were also performed with respect to tumor size (<20 mm or ≥20 mm) and histological subtype (invasive ductal carcinoma(IDC) or non-IDC). RESULTS: CT and pathology measured diameters were found to be linearly related (size at pathology = 1.086 × CT determined tumor size - 1.141; Spearman’s rho correlation coefficient = 0.84, P<0.001). Most tumors (n = 228, 80.0%) were concordant by chest CT and pathology, but 36 tumors (12.7%) were underestimated by CT (average underestimation, 11 mm; range, 6–36 mm) and 21 tumors (7.4%) were overestimated (average overestimation by CT, 10 mm; range, 6–19 mm). The concordance rate between the two sets of measurements was greater for tumor of <20 mm and for IDC (P<0.001 and P = 0.011, respectively). CONCLUSIONS: Tumor size by chest CT is well correlated with pathology determined tumor size in breast cancer patients, and the diameters of the majority of tumors by chest CT and pathology differed by <5 mm. In addition, the concordance rate was higher for breast tumors of <20 mm and for tumors of the IDC histologic subtype

Principal factors that determine the extension of detection range in molecular beacon aptamer/conjugated polyelectrolyte bioassays.

A strategy to extend the detection range of weakly-binding targets is reported that takes advantage of fluorescence resonance energy transfer (FRET)-based bioassays based on molecular beacon aptamers (MBAs) and cationic conjugated polyelectrolytes (CPEs). In comparison to other aptamer-target pairs, the aptamer-based adenosine triphosphate (ATP) detection assays are limited by the relatively weak binding between the two partners. In response, a series of MBAs were designed that have different stem stabilities while keeping the constant ATP-specific aptamer sequence in the loop part. The MBAs are labeled with a fluorophore and a quencher at both termini. In the absence of ATP, the hairpin MBAs can be opened by CPEs via a combination of electrostatic and hydrophobic interactions, showing a FRET-sensitized fluorophore signal. In the presence of ATP, the aptamer forms a G-quadruplex and the FRET signal decreases due to tighter contact between the fluorophore and quencher in the ATP/MBA/CPE triplex structure. The FRET-sensitized signal is inversely proportional to [ATP]. The extension of the detection range is determined by the competition between opening of the ATP/MBA G-quadruplex by CPEs and the composite influence by ATP/aptamer binding and the stem interactions. With increasing stem stability, the weak binding of ATP and its aptamer is successfully compensated to show the resistance to disruption by CPEs, resulting in a substantially broadened detection range (from millimolar up to nanomolar concentrations) and a remarkably improved limit of detection. From a general perspective, this strategy has the potential to be extended to other chemical- and biological-assays with low target binding affinity

Clinical disease characteristics according to karyotype in Turner syndrome

Purpose : Turner syndrome (TS) is a disorder in which various anomalies can be accompanied, especially cardiovascular, renal, thyroid and auditory problems. The aim of this study is to identify the incidence of these disorders in patients with TS according to karyotype. Methods : We reviewed medical records of 90 patients with TS diagnosed by chromosomal analysis in 4 hospitals from Jan 1998 to Dec 2007. We evaluated these cases by prepared protocol of 4 medical problems. Results : The distribution of karyotype was 45,X (47.8&#37;), mosaic pattern (34.4&#37;) and structural aberration group (17.8 &#37;). Renal anomalies, cardiovascular anomalies, thyroid disorders and auditory problems are accompanied in 4.4&#37;, 10.0 &#37;, 11.1&#37; and 5.6&#37;, respectively. 45,X group had renal anomalies (7.0&#37;), cardiovascular anomalies (18.6&#37;), thyroid disorders (9.3&#37;) and auditory problems (11.6&#37;). Mosaic group had renal anomalies (3.2&#37;), thyroid disorders (12.9&#37;), no cardiovascular anomalies and auditory problems. Structural aberration group had cardiovascular anomalies (6.3&#37;), thyroid disorders (12.5&#37;) and no other 2 problems. Patients with 45,X group had a significant higher incidence of cardiovascular anomalies (P&#61;0.025). Conclusion : Our results indicate that there are differences clinically according to karyotype of TS, especially in incidence of cardiovascular anomalies

Arctic-North Pacific Coupled Impacts on the Late Autumn Cold in North America

The Pacific Decadal Oscillation (PDO) is known to bring an anomalously cold (warm) period to southeastern (northwestern) North America during the cold season of its positive phase through a Rossby wave linkage. This study provides evidence that the remote connection between the North Pacific and the downstream temperature over central North America is strengthened by the warm arctic conditions over the Chukchi and East Siberian Sea, especially in the late autumn season. The modulation effect of the Arctic manifests itself as an altered Rossby wave response to a transient vorticity forcing that results from an equatorward storm track shift, which is induced collaboratively by the PDO and the warm Arctic. This observational finding is supported by two independent modeling experiments: 1) an idealized coupled GCM experiment being nudged toward the warm arctic surface condition and 2) a simple stationary wave model (SWM) experiment forced by transient eddy forcing

A Preliminary Report of Crosslinguistic Evidence on Efficacy of Semantic-Complexity Based Naming Treatment in Korean Aphasics

The current study investigated the efficacy of semantic-complexity based naming treatment in Korean participants with aphasia. Results suggested that both participants showed small to medium effect sizes in the trained items. However, generalization effects were greater in the participant who received treatment on the atypical items first, than the participant who was initiated on the typical items. These results are consistent with the previous findings in English-speaking aphasic participants (Kiran & Thompson, 2003; Kiran, 2008). Preliminary findings of two Korean participants with aphasia added crosslinguistic evidence on efficacy of the semantic complexity based naming treatment