On Weight Matrix and Free Energy Models for Sequence Motif Detection

The problem of motif detection can be formulated as the construction of a discriminant function to separate sequences of a specific pattern from background. In computational biology, motif detection is used to predict DNA binding sites of a transcription factor (TF), mostly based on the weight matrix (WM) model or the Gibbs free energy (FE) model. However, despite the wide applications, theoretical analysis of these two models and their predictions is still lacking. We derive asymptotic error rates of prediction procedures based on these models under different data generation assumptions. This allows a theoretical comparison between the WM-based and the FE-based predictions in terms of asymptotic efficiency. Applications of the theoretical results are demonstrated with empirical studies on ChIP-seq data and protein binding microarray data. We find that, irrespective of underlying data generation mechanisms, the FE approach shows higher or comparable predictive power relative to the WM approach when the number of observed binding sites used for constructing a discriminant decision is not too small.Comment: 23 pages, 1 figure and 4 table

Extrapolation Theory and the Pricing of REIT Stocks

This paper is the winner of the best paper on Real Estate Investment Trusts award (sponsored by the National Association of Real Estate Investment Trusts (NAREIT)] presented at the 2005 American Real Estate Society Annual Meeting. This study evaluates the investment prospects of value stocks in the real estate investment trust (REIT) market. Value stocks are defined as those that carry low prices relative to their earnings, dividends, book assets, or other measures of fundamental value. The empirical results show that from 1990 onwards, value REITs provide superior returns without exposing investors to higher risks. The evidence is consistent with the extrapolation theory, which attributes the mispricing to investors over extrapolating past corporate results into the future. Interestingly, the findings reveal that such extrapolation is asymmetric in the REIT market. While value REITs are underpriced in accordance with the extrapolation theory, no evidence is found that growth REITs are overpriced. The value anomaly also exhibited several temporal traits. Firstly, the value premium varies over time. Secondly, the magnitude of the premium is inversely associated with the market performance. Finally, the value anomaly is not evident in the pricing of REITs in the 1980s.

Three-dimensional flow structure behind an Ahmed vehicle model

Paper presented at the 9th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, Malta, 16-18 July, 2012.The lasting high fuel cost has recently inspired resurgence in drag reduction research for vehicles, which calls for a thorough understanding of the vehicle wake. The simplified Ahmed vehicle model is characterized by controllable flow separation, thus especially suitable for this purpose. In spite of a considerable number of previous investigations, our knowledge of flow around this model remains incomplete. This work aims to revisit turbulent flow structure behind this model. Two rear slant angles, i.e., α = 25º and 35º, of the model were examined, representing two distinct flow regimes. The Reynolds number was 5.26×104 based on the model height (H) and incident flow velocity. Using particle image velocimetry (PIV), flow was measured with and without a gap (g/H = 0.174) between the vehicle underside and ground in three orthogonal planes, viz. the x-z, x-y and y-z planes, where x, y and z are the coordinates along longitudinal, transverse and spanwise directions, respectively. The flow at g/H = 0 serves as an important reference for the understanding of the highly complicated vehicle wake (g/H ≠ 0). While reconfirming the well documented major characteristics of the mean flow structure, both instantaneous and time-averaged PIV data unveil a number of important features of the flow structure, which have not been previously reported. As such, considerably modified flow structure models are proposed for both regimes. The time-averaged velocities, second moments of fluctuating velocities and vorticity components are presented and discussed, along with their dependence on g/H in the two distinct flow regimes.dc201

Skyrmion Excitation in Two-Dimensional Spinor Bose-Einstein Condensate

We study the properties of coreless vortices(skyrmion) in spinor Bose-Einstein condensate. We find that this excitation is always energetically unstable, it always decays to an uniform spin texture. We obtain the skyrmion energy as a function of its size and position, a key quantity in understanding the decay process. We also point out that the decay rate of a skyrmion with high winding number will be slower. The interaction between skyrmions and other excitation modes are also discussed.Comment: 5 pages, 4 figures, final version published in Phys. Rev.

New Upper Limit of Terrestrial Equivalence Principle Test for Rotating Extended Bodies

Improved terrestrial experiment to test the equivalence principle for rotating extended bodies is presented, and a new upper limit for the violation of the equivalence principle is obtained at the level of 1.6$10^{\text{-7}}$, which is limited by the friction of the rotating gyroscope. It means the spin-gravity interaction between the extended bodies has not been observed at this level.Comment: 4 page

Exploring morphological correlations among H2CO, 12CO, MSX and continuum mappings

There are relatively few H2CO mappings of large-area giant molecular cloud (GMCs). H2CO absorption lines are good tracers for low-temperature molecular clouds towards star formation regions. Thus, the aim of the study was to identify H2CO distributions in ambient molecular clouds. We investigated morphologic relations among 6-cm continuum brightness temperature (CBT) data and H2CO (111-110; Nanshan 25-m radio telescope), 12CO (1--0; 1.2-m CfA telescope) and midcourse space experiment (MSX) data, and considered the impact of background components on foreground clouds. We report simultaneous 6-cm H2CO absorption lines and H110\alpha radio recombination line observations and give several large-area mappings at 4.8 GHz toward W49 (50'\times50'), W3 (70'\times90'), DR21/W75 (60'\times90') and NGC2024/NGC2023 (50'\times100') GMCs. By superimposing H2CO and 12CO contours onto the MSX color map, we can compare correlations. The resolution for H2CO, 12CO and MSX data was about 10', 8' and 18.3", respectively. Comparison of H2CO and 12CO contours, 8.28-\mu m MSX colorscale and CBT data revealed great morphological correlation in the large area, although there are some discrepancies between 12CO and H2CO peaks in small areas. The NGC2024/NGC2023 GMC is a large area of HII regions with a high CBT, but a H2CO cloud to the north is possible against the cosmic microwave background. A statistical diagram shows that 85.21% of H2CO absorption lines are distributed in the intensity range from -1.0 to 0 Jy and the \Delta V range from 1.206 to 5 km/s.Comment: 18 pages, 22 figures, 5 tables. Accepted to be published in Astrophysics and Space Scienc

Exercise SBP response and incident depressive symptoms: The Maastricht Study

Objective : An exaggerated exercise SBP, which is potentially modifiable, may be associated with incident depressive symptoms via an increased pulsatile pressure load on the brain. However, the association between exaggerated exercise SBP and incident depressive symptoms is unknown. Therefore, we examined whether exaggerated exercise SBP is associated with a higher risk of depressive symptoms over time. Methods : We used longitudinal data from the population-based Maastricht Study, with only individuals free of depressive symptoms at baseline included (n = 2121; 51.3% men; age 59.5 +/- 8.5 years). Exercise SBP was measured at baseline with a submaximal exercise cycle test. We calculated a composite score of exercise SBP based on four standardized exercise SBP measures: SBP at moderate workload, SBP at peak exercise, SBP change per minute during exercise and SBP 4 min after exercise. Clinically relevant depressive symptoms were determined annually at follow-up and defined as a Patient Health Questionnaire score of at least 10. Results : After a mean follow-up of 3.9 years, 175 participants (8.3%) had incident clinically relevant depressive symptoms. A 1 SD higher exercise SBP composite score was associated with a higher incidence of clinically relevant depressive symptoms [hazard ratio: 1.27 (95% confidence interval: 1.04-1.54)]. Results were adjusted for age, sex, education level, glucose metabolism status, lifestyle, cardiovascular risk factors, resting SBP and cardiorespiratory fitness. Conclusion : A higher exercise SBP response is associated with a higher incidence of clinically relevant depressive symptoms

Crystallization Characteristics of CaO-Al2O3-Based Mold Flux and Their Effects on In-Mold Performance during High-Aluminum TRIP Steels Continuous Casting

Crystallization behaviors of the newly developed lime-alumina-based mold fluxes for high-aluminum transformation induced plasticity (TRIP) steels casting were experimentally studied, and compared with those of lime-silica-based mold fluxes. The effects of mold flux crystallization characteristics on heat transfer and lubrication performance in casting high-Al TRIP steels were also evaluated. The results show that the crystallization temperatures of lime-alumina-based mold fluxes are much lower than those of lime-silica-based mold fluxes. Increasing B2O3 addition suppresses the crystallization of lime-alumina-based mold fluxes, while Na2O exhibits an opposite effect. In continuous cooling of lime-alumina-based mold fluxes with high B2O3 contents and a CaO/Al2O3 ratio of 3.3, faceted cuspidine precipitates first, followed by needle-like CaO center dot B2O3 or 9CaO center dot 3B(2)O(3)center dot CaF2. In lime-alumina-based mold flux with low B2O3 content (5.4 mass pct) and a CaO/Al2O3 ratio of 1.2, the formation of fine CaF2 takes place first, followed by blocky interconnected CaO center dot 2Al(2)O(3) as the dominant crystalline phase, and rod-like 2CaO center dot B2O3 precipitates at lower temperature during continuous cooling of the mold flux. In B2O3-free mold flux, blocky interconnected 3CaO center dot Al2O3 precipitates after CaF2 and 3CaO center dot 2SiO(2) formation, and takes up almost the whole crystalline fraction. The casting trials show that the mold heat transfer rate significantly decreases near the meniscus during the continuous casting using lime-alumina-mold fluxes with higher crystallinity, which brings a great reduction of surface depressions on cast slabs. However, excessive crystallinity of mold flux causes poor lubrication between mold and solidifying steel shell, which induces various defects such as drag marks on cast slab. Among the studied mold fluxes, lime-alumina-based mold fluxes with higher B2O3 contents and a CaO/Al2O3 ratio of 3.3 show comparatively improved performance.ope

Medical costs associated with metastatic breast cancer in younger, midlife, and older women

Purpose: We estimated average medical costs due to metastatic breast cancer (mBC) among younger (aged 18–44), midlife (aged 45–64), and older women (aged 65 and older) by phase of care: initial, continuing, and terminal. Methods: We used 2003–2014 North Carolina cancer registry data linked with administrative claims from public and private payers. We developed a claims-based algorithm to identify breast cancer patients who progressed to metastatic disease. We matched breast cancer patients (mBC and earlier stage) to non-cancer patients on age group, county of residence, and insurance plan. Outcomes were average monthly medical expenditures and expected medical expenditures by phase. We used regression to estimate excess costs attributed to mBC as the difference in mean payments between patients with mBC (N = 4806) and patients with each earlier-stage breast cancer (stage 1, stage 2, stage 3, and unknown stage; N = 21,772) and non-cancer controls (N = 109,631) by treatment phase and age group. Results: Adjusted monthly costs for women with mBC were significantly higher than for women with earlier-stage breast cancer and non-cancer controls for all age groups and treatment phases except the initial treatment among women with stage 3 breast cancer at diagnosis. The largest expected total costs were for women aged 18–44 with mBC during the continuing phase ($209,961 95$165,736–254,186). Conclusions: We found substantial excess costs for mBC among younger women and during the continuing and terminal phases of survivorship. It is important to assess whether this care is high value for these women

Functional diversity of chemokines and chemokine receptors in response to viral infection of the central nervous system.

Encounters with neurotropic viruses result in varied outcomes ranging from encephalitis, paralytic poliomyelitis or other serious consequences to relatively benign infection. One of the principal factors that control the outcome of infection is the localized tissue response and subsequent immune response directed against the invading toxic agent. It is the role of the immune system to contain and control the spread of virus infection in the central nervous system (CNS), and paradoxically, this response may also be pathologic. Chemokines are potent proinflammatory molecules whose expression within virally infected tissues is often associated with protection and/or pathology which correlates with migration and accumulation of immune cells. Indeed, studies with a neurotropic murine coronavirus, mouse hepatitis virus (MHV), have provided important insight into the functional roles of chemokines and chemokine receptors in participating in various aspects of host defense as well as disease development within the CNS. This chapter will highlight recent discoveries that have provided insight into the diverse biologic roles of chemokines and their receptors in coordinating immune responses following viral infection of the CNS