Efficiency comparison of Markov Chain Monte Carlo simulation with subset simulation (MCMC/ss) to standard Monte Carlo Simulation (sMC) for extreme event scenarios

Standard Monte Carlo (sMC) simulation models have been widely used in AEC industry research to address system uncertainties. Although the benefits of probabilistic simulation analyses over deterministic methods are well documented, the sMC simulation technique is quite sensitive to the probability distributions of the input variables. This phenomenon becomes highly pronounced when the region of interest within the joint probability distribution (a function of the input variables) is small. In such cases, the standard Monte Carlo approach is often impractical from a computational standpoint. In this paper, a comparative analysis of standard Monte Carlo simulation to Markov Chain Monte Carlo with subset simulation (MCMC/ss) is presented. The MCMC/ss technique constitutes a more complex simulation method (relative to sMC), wherein a structured sampling algorithm is employed in place of completely randomized sampling. Consequently, gains in computational efficiency can be made. The two simulation methods are compared via theoretical case studies.

Alive SMC^2: Bayesian model selection for low-count time series models with intractable likelihoods

In this paper we present a new method for performing Bayesian parameter inference and model choice for low count time series models with intractable likelihoods. The method involves incorporating an alive particle filter within a sequential Monte Carlo (SMC) algorithm to create a novel pseudo-marginal algorithm, which we refer to as alive SMC^2. The advantages of this approach over competing approaches is that it is naturally adaptive, it does not involve between-model proposals required in reversible jump Markov chain Monte Carlo and does not rely on potentially rough approximations. The algorithm is demonstrated on Markov process and integer autoregressive moving average models applied to real biological datasets of hospital-acquired pathogen incidence, animal health time series and the cumulative number of poison disease cases in mule deer.

Effect of pulse profile variations on measurement of eccentricity in orbits of Cen X-3 and SMC X-1

It has long been argued that better timing precision allowed by satellites like Rossi X-ray Timing Explorer (RXTE) will allow us to measure the orbital eccentricity and the angle of periastron of some of the bright persistent high-mass X-ray binaries (HMXBs) and hence a possible measurement of apsidal motion in these system. Measuring the rate of apsidal motion allows one to estimate the apsidal motion constant of the mass losing companion star and hence allows for the direct testing of the stellar structure models for these giant stars present in the HMXBs. In the present paper, we use the archival RXTE data of two bright persistent sources, namely Cen X-3 and SMC X-1, to measure the very small orbital eccentricity and the angle of periastron. We find that the small variations in the pulse profiles of these sources, rather than the intrinsic time resolution provided by RXTE, limit the accuracy with which we can measure arrival time of the pulses from these sources. This influences the accuracy with which one can measure the orbital parameters, especially the very small eccentricity and the angle of periastron in these sources. The observations of SMC X-1 in the year 2000 were taken during the high-flux state of the source and we could determine the orbital eccentricity and omega using this data set.

SMC蛋白复合体的结构、功能和作用机制

染色体结构维持(SMC)蛋白是一类染色体ATP酶.以这类蛋白质为核心可形成三种多蛋白复合体:凝聚蛋白(condensin)、黏结蛋白(cohesin)和SMC5-SMC6复合体.这些复合体直接参与了染色质结构的组织、细胞分裂过程中遗传物质的准确分离和忠实遗传等重要功能活动,自发现至今,对该类复合体的结构、功能及作用机制等方面已有较多研究并取得一些重要进展.

几类特殊进化地位原生生物 SMC 及其复合成分的分析鉴定与SMC 的起源进化研究

真核细胞有丝分裂过程中染色体的动态变化是细胞生物学研究的基本问题 之一。虽然人们早就观察到了有丝分裂过程中染色体的这种变化，但对其中所涉 及到的蛋白及机制问题只是在近二十年来才陆续有些研究。现已知SMC 家族蛋 白在染色体的组织、分离过程中扮演了至为关键的角色。但这类蛋白的进化研究 相对较少，尤其是在进化地位特殊的原生生物中的情况尚未有研究报道。本文对 SMC 及其复合体成分在几种原生生物中的存在情况进行了调查，进而对该蛋白 在整个原核生物和真核生物中的起源和演化问题进行了探讨。 通过基因组搜索等生物信息学手段，我们鉴定了四种原生生物中的全部的 SMC 同源序列，并对这些序列进行了分析。结果显示除贾第虫缺少典型的SMC5， 锥虫中缺少SMC5、SMC6 的同源序列外，其它SMC 的同源序列均在这些生物 中找到。还发现毛滴虫中SMC 同源序列表现出明显的多拷贝现象，其编码序列 （ORF）具有明显的核苷酸A 偏好性。对这些蛋白进行的二级结构预测显示出 一些与高等真核生物有所不同的特征，尤其是贾第虫中的SMC 蛋白更表现了独 特的二级结构特征。这些特点可能与这些生物核分裂过程中某些独特的染色体动 态变化特征相关联。对与SMC 形成复合体的蛋白在这些生物中的存在情况也做 了调查，发现它们在这些生物中只有小部分存在。这表明由SMC 组成的 “SMC/Kleisin/non-SMC﹠Kleisin”复合体在这几种生物可能较为简单或者在非 SMC 亚基方面有较大的分化。 为了进一步研究与形成典型中期染色体密切相关的两种蛋白SMC2 和 TopoII 在未发现凝聚染色体的贾第虫中的功能，本文还对贾第虫的这两个基因进 行了原核表达载体的克隆构建和表达。成功构建了重组质粒，并在相应的菌种中 得到了大量的包涵体表达。经过纯化进行兔子免疫制备出了抗血清，为后续研究 这两种蛋白在贾第虫细胞周期中的定位分布和贾第虫的核分裂打下了基础。 最后，我们对SMC 及同功蛋白MukB 在原核中的存在情况以及它们与真核 生物SMC 的分子系统关系进行了系统研究。发现MukB 及其组成的复合体仅存 在于γ 蛋白菌中的 Enterobacteriale、Pasteurellaceae 和Vibrionaceae 中，且在物 种间非常保守，应是较晚时期进化形成的；衣原体类、α蛋白菌中的立克次氏体、 ε 蛋白菌中没有任何SMC 或MukB 同源序列，也没有与其形成复合体的蛋白。 II 由于这些原核生物均为高度寄生菌，推测应该是由于寄生完全丢失了这类蛋白， 而利用宿主的相应装置完成对自身基因的组织。分子系统分析的结果显示MukB 与SMC 距离较远，不是同源蛋白，应是趋同进化的结果。真核的SMC 与原细 菌SMC 距离最近，应有最近的共同祖先。

Role of KLF4 in regulation of myocardin induced SMC differentiation in human smooth muscle stem progenitor cells (hSMSPC)

The differentiation of stem cells into multiple lineages has been explored in vascular regenerative medicine. However, in the case of smooth muscle cells (SMC), issues exist concerning inefficient rates of differentiation. In stem cells, multiple repressors potentially downregulate myocardin, the potent SRF coactivator induced SMC transcription including Krüppel like zinc finger transcription factor-4 (KLF4). This thesis aimed to explore the role of KLF4 in the regulation of myocardin gene expression in human smooth muscle stem/progenitor cells (hSMSPC), a novel circulating stem cell identified in our laboratory which expresses low levels of myocardin and higher levels of KLF4. hSMSPC cells cultured in SmGM2 1% FBS with TGF-β1 (5 ng/ml “differentiation media”) show limited SMC cell differentiation potential. Furthermore, myocardin transduced hSMSPC cells cultured in differentiation media induced myofilamentous SMC like cells with expression of SM markers. Five potential KLF4 binding sites were identified in silico within 3.9Kb upstream of the translational start site of the human myocardin promoter. Chromatin immunoprecipitation assays verified that endogenous KLF4 binds the human myocardin promoter at -3702bp with Respect to the translation start site (-1). Transduction of lentiviral vectors encoding either myocardin cDNA (LV_myocardin) or KLF4 targeting shRNA (LV_shKLF4 B) induced human myocardin promoter activity in hSMSPCs. Silencing of KLF4 expression in differentiation media induced smooth muscle like morphology by day 5 in culture and increased overtime with expression of SMC markers in hSMSPCs. Implantation of silastic tubes into the rat peritoneal cavity induces formation of a tissue capsule structure which may be used as vascular grafts. Rat SMSPCs integrate into, strengthen and enhance the SMC component of such tubular capsules. These data demonstrate that KLF4 directly represses myocardin gene expression in hSMSPCs, which when differentiated, provide a potential source of SMCs in the development of autologous vascular grafts in regenerative medicine.

Chemical compositions of four B-type supergiants in the SMC wing

High-resolution UCLES/AAT spectra of four B-type supergiants in the SMC South East Wing have been analysed using non-LTE model atmosphere techniques to determine their atmospheric parameters and chemical compositions. The principle aim of this analysis was to determine whether the very low metal abundances (-1.1 dex compared with Galactic value) previously found in the Magellanic Inter Cloud region (ICR) were also present in the SMC Wing. The chemical compositions of the four targets are similar to those found in other SMC objects and appear to be incompatible with those deduced previously for the ICR. Given the close proximity of the Wing to the ICR, this is difficult to understand and some possible explanations are briefly discussed.

B-type supergiants in the SMC: Chemical compositions and comparison of static and unified models

High-resolution UCLES/AAT spectra are presented for nine B-type supergiants in the SMC, chosen on the basis that they may show varying amounts of nuclear-synthetically processed material mixed to their surface. These spectra have been analysed using a new grid of approximately 12 000 non-LTE line blanketed tlusty model atmospheres to estimate atmospheric parameters and chemical composition. The abundance estimates for O, Mg and Si are in excellent agreement with those deduced from other studies, whilst the low estimate for C may reflect the use of the C II doublet at 4267 Å. The N estimates are approximately an order of magnitude greater than those found in unevolved B-type stars or H II regions but are consistent with the other estimates in AB-type supergiants. These results have been combined with results from a unified model atmosphere analysis of UVES/VLT spectra of B-type supergiants (Trundle et al. 2004, A&A, 417, 217) to discuss the evolutionary status of these objects. For two stars that are in common with those discussed by Trundle et al., we have undertaken a careful comparison in order to try to understand the relative importance of the different uncertainties present in such analyses, including observational errors and the use of static or unified models. We find that even for these relatively luminous supergiants, tlusty models yield atmospheric parameters and chemical compositions similar to those deduced from the unified code fastwind.

A non-LTE analysis of the spectra of two narrow lined main sequence stars in the SMC

An analysis of high-resolution VLT/UVES spectra of two B-type main sequence stars, NGC 346-11 and AV 304, in the Small Magellanic Cloud (SMC), has been undertaken, using the non-LTE tlusty model atmospheres to derive the stellar parameters and chemical compositions of each star. The chemical compositions of the two stars are in reasonable agreement. Moreover, our stellar analysis agrees well with earlier analyses of H II regions. The results derived here should be representative of the current base-line chemical composition of the SMC interstellar medium as derived from B-type stars.

A Be star with a low nitrogen abundance in the SMC cluster NGC330

High- resolution UVES/ VLT spectra of B 12, an extreme pole- on Be star in the SMC cluster NGC 330, have been analysed using non-LTE model atmospheres to obtain its chemical composition relative to the SMC standard star AV304. We find a general underabundance of metals which can be understood in terms of an extra contribution to the stellar continuum due to emission from a disk which we estimate to be at the similar to 25% level. When this is corrected for, the nitrogen abundance for B12 shows no evidence of enhancement by rotational mixing as has been found in other non-Be B-type stars in NGC 330, and is inconsistent with evolutionary models which include the effects of rotational mixing. A second Be star, NGC330-B 17, is also shown to have no detectable nitrogen lines. Possible explanations for the lack of rotational mixing in these rapidly rotating stars are discussed, one promising solution being the possibility that magnetic fields might inhibit rotational mixing.