Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model

The two-phase thermodynamic (2PT) model is used to determine the absolute entropy and energy of carbon dioxide over a wide range of conditions from molecular dynamics trajectories. The 2PT method determines the thermodynamic properties by applying the proper statistical mechanical partition function to the normal modes of a fluid. The vibrational density of state (DoS), obtained from the Fourier transform of the velocity autocorrelation function, converges quickly, allowing the free energy, entropy, and other thermodynamic properties to be determined from short 20-ps MD trajectories. The anharmonic effects in the vibrations are accounted for by the broadening of the normal modes into bands from sampling the velocities over the trajectory. The low frequency diffusive modes, which lead to finite DoS at zero frequency, are accounted for by considering the DoS as a superposition of gas-phase and solid-phase components (two phases). The analytical decomposition of the DoS allows for an evaluation of properties contributed by different types of molecular motions. We show that this 2PT analysis leads to accurate predictions of entropy and energy of CO_2 over a wide range of conditions (from the triple point to the critical point of both the vapor and the liquid phases along the saturation line). This allows the equation of state of CO_2 to be determined, which is limited only by the accuracy of the force field. We also validated that the 2PT entropy agrees with that determined from thermodynamic integration, but 2PT requires only a fraction of the time. A complication for CO_2 is that its equilibrium configuration is linear, which would have only two rotational modes, but during the dynamics it is never exactly linear, so that there is a third mode from rotational about the axis. In this work, we show how to treat such linear molecules in the 2PT framework

Marching velocity of capillary meniscuses in microchannels

[[abstract]]This paper describes a new method and an analytical model for characterizing the surface energy inside a microchannel using the measurement of the marching velocity of a capillary meniscus. This method is based on the fact that surface tension of a liquid meniscus in a hydrophilic case produces pressure to pull liquid into the channel and the velocity of the meniscus is related to the surface energy. Both Parylene and silicon nitride microchannels with different surface conditions were fabricated to perform the liquid-filling experiments. It is shown that our model agrees well with the data and this is a valid method.[[conferencetype]]國際[[conferencedate]]20020120~20020124[[iscallforpapers]]Y[[conferencelocation]]Las Vegas, NV, US

Multiwavelength stellar polarimetry of the filamentary cloud IC5146. I. Dust properties

We present optical and near-infrared stellar polarization observations toward the dark filamentary clouds associated with IC5146. The data allow us to investigate the dust properties (this paper) and the magnetic field structure (Paper II). A total of 2022 background stars were detected in the Rc, i¢, H, and/or K bands to AV 25 mag. The ratio of the polarization percentage at different wavelengths provides an estimate of lmax, the wavelength of the peak polarization, which is an indicator of the small-size cutoff of the grain size distribution. The grain size distribution seems to significantly change at AV ~ 3 mag, where both the average and dispersion of P P R H c decrease. In addition, we found lmax ~ 0.6 0.9 – μm for AV > 2.5 mag, which is larger than the ∼0.55 μm in the general interstellar medium (ISM), suggesting that grain growth has already started in low-AV regions. Our data also reveal that polarization efficiency (PE º P A l V ) decreases with AV as a power law in the Rc, i¢, and K bands with indices of −0.71 ± 0.10, −1.23 ± 0.10, and −0.53 ± 0.09. However, H-band data show a power index change; the PE varies with AV steeply (index of −0.95 ± 0.30) when AV < 2.88 0.67 mag, but softly (index of −0.25 ± 0.06) for greater AV values. The soft decay of PE in high-AV regions is consistent with the radiative alignment torque model, suggesting that our data trace the magnetic field to AV ~ 20 mag. Furthermore, the breakpoint found in the H band is similar to that for AV, where we found the P P R H c dispersion significantly decreased. Therefore, the flat PE–AV in high-AV regions implies that the power-index changes result from additional grain growth.We acknowledge support from the Aryabhatta Research Institute of Observational Sciences and Lulin Observatory concerning the data collected using AIMPOL and TRIPOL. This research was conducted in part using the Mimir instrument, jointly developed at Boston University and Lowell Observatory and supported by NASA, NSF, and the W.M. Keck Foundation. This work and the analysis software for Mimir data were developed under NSF grants AST 06-07500, 09-07790, and 14-12269 to Boston University. We thank Brian Taylor, Tao-Chung Ching, and Lauren Cashman for their help in the smooth operations of Mimir observations. This research has made use of the Herchel Science Archive (HSA), and the data are based on the observations performed with the ESA Herschel. Space Observatory (Pilbratt et al. 2010). J.W.W., S.P.L., and C.E. are grateful for the support from the Ministry of Science and Technology (MOST) of Taiwan through grants NSC 99-2923-M-008-002-MY3, NSC 101-2119-M-007-004, MOST 102-2119-M-007-004-MY3, 105-2119-M-007-022-MY3, and 105-2119-M-007-024. (NASA; NSF; W.M. Keck Foundation; AST 06-07500 - NSF; 09-07790 - NSF; 14-12269 - NSF; NSC 99-2923-M-008-002-MY3 - Ministry of Science and Technology (MOST) of Taiwan; NSC 101-2119-M-007-004 - Ministry of Science and Technology (MOST) of Taiwan; MOST 102-2119-M-007-004-MY3 - Ministry of Science and Technology (MOST) of Taiwan; 105-2119-M-007-022-MY3 - Ministry of Science and Technology (MOST) of Taiwan; 105-2119-M-007-024 - Ministry of Science and Technology (MOST) of Taiwan

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.

The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3'-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3'-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation

The nucleolar protein NIFK promotes cancer progression via CK1α/β-catenin in metastasis and Ki-67-dependent cell proliferation.

Nucleolar protein interacting with the FHA domain of pKi-67 (NIFK) is a Ki-67-interacting protein. However, its precise function in cancer remains largely uninvestigated. Here we show the clinical significance and metastatic mechanism of NIFK in lung cancer. NIFK expression is clinically associated with poor prognosis and metastasis. Furthermore, NIFK enhances Ki-67-dependent proliferation, and promotes migration, invasion in vitro and metastasis in vivo via downregulation of casein kinase 1α (CK1α), a suppressor of pro-metastatic TCF4/β-catenin signaling. Inversely, CK1α is upregulated upon NIFK knockdown. The silencing of CK1α expression in NIFK-silenced cells restores TCF4/β-catenin transcriptional activity, cell migration, and metastasis. Furthermore, RUNX1 is identified as a transcription factor of CSNK1A1 (CK1α) that is negatively regulated by NIFK. Our results demonstrate the prognostic value of NIFK, and suggest that NIFK is required for lung cancer progression via the RUNX1-dependent CK1α repression, which activates TCF4/β-catenin signaling in metastasis and the Ki-67-dependent regulation in cell proliferation

An unusual Wittig reaction with sugar derivatives: exclusive formation of a 4-deoxy analogue of α-galactosyl ceramide

The Wittig reaction of reducing sugars undergoes an unexpected formation of dienes in the presence of base t-BuOK.</p

Ice Cloud Properties in Ice-Over-Water Cloud Systems Using TRMM VIRS and TMI Data

A multi-layered cloud retrieval system (MCRS) is updated and used to estimate ice water path in maritime ice-over-water clouds using Visible and Infrared Scanner (VIRS) and TRMM Microwave Imager (TMI) measurements from the Tropical Rainfall Measuring Mission spacecraft between January and August 1998. Lookup tables of top-of-atmosphere 0.65- m reflectance are developed for ice-over-water cloud systems using radiative transfer calculations with various combinations of ice-over-water cloud layers. The liquid and ice water paths, LWP and IWP, respectively, are determined with the MCRS using these lookup tables with a combination of microwave (MW), visible (VIS), and infrared (IR) data. LWP, determined directly from the TMI MW data, is used to define the lower-level cloud properties to select the proper lookup table. The properties of the upper-level ice clouds, such as optical depth and effective size, are then derived using the Visible Infrared Solar-infrared Split-window Technique (VISST), which matches the VIRS IR, 3.9- m, and VIS data to the multilayer-cloud lookup table reflectances and a set of emittance parameterizations. Initial comparisons with surface-based radar retrievals suggest that this enhanced MCRS can significantly improve the accuracy and decrease the IWP in overlapped clouds by 42% and 13% compared to using the single-layer VISST and an earlier simplified MW-VIS-IR (MVI) differencing method, respectively, for ice-over-water cloud systems. The tropical distribution of ice-over-water clouds is the same as derived earlier from combined TMI and VIRS data, but the new values of IWP and optical depth are slightly larger than the older MVI values, and exceed those of single-layered layered clouds by 7% and 11%, respectively. The mean IWP from the MCRS is 8-14% greater than that retrieved from radar retrievals of overlapped clouds over two surface sites and the standard deviations of the differences are similar to those for single-layered clouds. Examples of a method for applying the MCRS over land without microwave data yield similar differences with the surface retrievals. By combining the MCRS with other techniques that focus primarily on optically thin cirrus over low water clouds, it will be possible to more fully assess the IWP in all conditions over ocean except for precipitating systems

Hypermethylation of the TGF-β target, ABCA1 is associated with poor prognosis in ovarian cancer patients

Background The dysregulation of transforming growth factor-β (TGF-β) signaling plays a crucial role in ovarian carcinogenesis and in maintaining cancer stem cell properties. Classified as a member of the ATP-binding cassette (ABC) family, ABCA1 was previously identified by methylated DNA immunoprecipitation microarray (mDIP-Chip) to be methylated in ovarian cancer cell lines, A2780 and CP70. By microarray, it was also found to be upregulated in immortalized ovarian surface epithelial (IOSE) cells following TGF-β treatment. Thus, we hypothesized that ABCA1 may be involved in ovarian cancer and its initiation. Results We first compared the expression level of ABCA1 in IOSE cells and a panel of ovarian cancer cell lines and found that ABCA1 was expressed in HeyC2, SKOV3, MCP3, and MCP2 ovarian cancer cell lines but downregulated in A2780 and CP70 ovarian cancer cell lines. The reduced expression of ABCA1 in A2780 and CP70 cells was associated with promoter hypermethylation, as demonstrated by bisulfite pyro-sequencing. We also found that knockdown of ABCA1 increased the cholesterol level and promoted cell growth in vitro and in vivo. Further analysis of ABCA1 methylation in 76 ovarian cancer patient samples demonstrated that patients with higher ABCA1 methylation are associated with high stage (P = 0.0131) and grade (P = 0.0137). Kaplan-Meier analysis also found that patients with higher levels of methylation of ABCA1 have shorter overall survival (P = 0.019). Furthermore, tissue microarray using 55 ovarian cancer patient samples revealed that patients with a lower level of ABCA1 expression are associated with shorter progress-free survival (P = 0.038). Conclusions ABCA1 may be a tumor suppressor and is hypermethylated in a subset of ovarian cancer patients. Hypermethylation of ABCA1 is associated with poor prognosis in these patients

Targeting nuclear transporters in cancer: Diagnostic, prognostic and therapeutic potential

The Karyopherin superfamily is a major class of soluble transport receptors consisting of both import and export proteins. The trafficking of proteins involved in transcription, cell signalling and cell cycle regulation among other functions across the nuclear membrane is essential for normal cellular functioning. However, in cancer cells, the altered expression or localization of nuclear transporters as well as the disruption of endogenous nuclear transport inhibitors are some ways in which the Karyopherin proteins are dysregulated. The value of nuclear transporters in the diagnosis, prognosis and treatment of cancer is currently being elucidated with recent studies highlighting their potential as biomarkers and therapeutic targets

General approach of causal mediation analysis with causally ordered multiple mediators and survival outcome

Causal mediation analysis with multiple mediators (causal multi-mediation analysis) is critical in understanding why an intervention works, especially in medical research. Deriving the path-specific effects (PSEs) of exposure on the outcome through a certain set of mediators can detail the causal mechanism of interest. However, the existing models of causal multi-mediation analysis are usually restricted to partial decomposition, which can only evaluate the cumulative effect of several paths. Moreover, the general form of PSEs for an arbitrary number of mediators has not been proposed. In this study, we provide a generalized definition of PSE for partial decomposition (partPSE) and for complete decomposition, which are extended to the survival outcome. We apply the interventional analogues of PSE (iPSE) for complete decomposition to address the difficulty of non-identifiability. Based on Aalen’s additive hazards model and Cox’s proportional hazards model, we derive the generalized analytic forms and illustrate asymptotic property for both iPSEs and partPSEs for survival outcome. The simulation is conducted to evaluate the performance of estimation in several scenarios. We apply the new methodology to investigate the mechanism of methylation signals on mortality mediated through the expression of three nested genes among lung cancer patients