Reprogramming of mesenchymal stem cells and adult fibroblasts following nuclear transfer in rabbits

The main aim of this thesis was to find out which donor cells would be most suitable for production of cloned rabbits with a targeted modification of their genome, and their corresponding patterns of reprogramming hetero- and euchromatic histone modifications (H3K4m2/3 and H3K27m3). For these purposes, we carried out NT with rabbit mesenchymal stem cells (MSCs) and adult fibroblasts (RAFs). As totally 13 cell lines of MSCs have been tested, they didn’t show stably higher development potential than RAFs, even though the blastocyst rate of embryos cloned from MSC A/B reached to 76%. Finally two cloned rabbits were produced from meschnymal stem cells. H3K27m3 was undetectable in all stages of nuclear transfer embryos except for one cell stage and blastocysts. It seems that H3K27m3 is faithfully reprogrammed in transferred nuclei of all donor cell types, with minor differences in zygotes and blastocysts. Strong signals for H3K4m2/3 were detected at the one to two-cell stages of in vivo embryos with a slight decrease at the 4-cell stage, followed by a more drastic decrease at the 8-cell stage, where the signal minimum was reached. In 16-cell embryos signals slightly increased and then reached in morulae and blastocysts the levels observed in one-two cell embryos. In all types of nuclear transfer embryos fluorescence intensity ratios differed from that of in vivo embryos. The minimum was not reached at the 8-cell stage but at the 4-cell stage. Reprogramming of H3K4m2/3 modification occurred quite differently with either type of cells irrespective of the cell origin or type and no close similarities in the patterns of this reprogramming was observed between in vivo and nuclear transfer embryos. Embryos cloned from MSC A/B differed from all others in the way that H3K4m2/3 was generally lower and remained in the range of the donor cells. This suggests that reprogramming of H3K4m2/3 modification is more aberrant with MSC A/B cells than with any other cell type used in this study. However, with MSC A/B cells, a significantly higher or similar proportion of cloned embryos developed to blastocysts indicating that reprogramming of H3K4m2/3 modification does not correlate with developmental potential of donor cells. In conclusion, our study provides evidence that histone modifications for heterochromatin are faithfully reprogrammed during NT of rabbit somatic cells, while patterns of epigenetic reprogramming of euchromatic histone modifications differ between individual cell lines irrespective of their origin or type and are not correlated with their developmental potential. Although MSCs were not superior to RAFs in respect to the criteria tested in our study they may be suitable nuclear donors for generating transgenic cloned rabbits due to their high developmental plasticity

SCOPE: Scalable Composite Optimization for Learning on Spark

Many machine learning models, such as logistic regression~(LR) and support vector machine~(SVM), can be formulated as composite optimization problems. Recently, many distributed stochastic optimization~(DSO) methods have been proposed to solve the large-scale composite optimization problems, which have shown better performance than traditional batch methods. However, most of these DSO methods are not scalable enough. In this paper, we propose a novel DSO method, called \underline{s}calable \underline{c}omposite \underline{op}timization for l\underline{e}arning~({SCOPE}), and implement it on the fault-tolerant distributed platform \mbox{Spark}. SCOPE is both computation-efficient and communication-efficient. Theoretical analysis shows that SCOPE is convergent with linear convergence rate when the objective function is convex. Furthermore, empirical results on real datasets show that SCOPE can outperform other state-of-the-art distributed learning methods on Spark, including both batch learning methods and DSO methods

Approximating First Hitting Point Distribution in Milestoning for Rare Event Kinetics

Milestoning is an efficient method for rare event kinetics calculation using short trajectory parallelization. The phase space is partitioned into small compartments, and interfaces of compartments are called milestones. Local kinetics between milestones are aggregated to compute the flux through the entire reaction space. Besides the accuracy of force fields, the accuracy of Milestoning crucially depends on two factors: the initial distribution of a short trajectory ensemble and statistical adequacy of trajectory sampling. The latter can be improved by increasing the number of trajectories while the true initial distribution, i.e., first hitting point distribution (FHPD), has no analytic expression in the general case. Here, we propose two algorithms, local passage time weighted Milestoning (LPT-M) and Bayesian inference Milestoning (BI-M), to accurately and efficiently approximate FHPD in Milestoning for systems at equilibrium condition, leading to accurate mean first passage time (MFPT) computation. Starting from equilibrium Boltzmann distribution on milestones, we calculate the proper weighting factor for FHPD approximation and consequently trajectories. The method is tested on two model examples for illustration purpose. The results show that LPT-M is especially advantageous in terms of computational costs and robustness with respect to the increasing number of intermediate milestones. The MFPT estimation achieves the same accuracy as a long equilibrium trajectory simulation while the consumed wall-clock time is as cheap as the widely used classical Milestoning. BI-M also improves over classical Milestoning and covers the directional Milestoning method as a special case in the deterministic Hamiltonian dynamics. Iterative correction on FHPD can be further performed for exact MFPT calculation

Health-Related Quality of Life in Chinese Patients with Chronic Liver Disease

Aim. To investigate the factors contributing to health-related quality of life (HRQOL) in Chinese patients with chronic liver disease (CLD). Methods. HRQOL was measured with SF-36v2 Chinese version. Demographic and clinical data were collected, and patients with liver cirrhosis were divided into Child's Class A, B, and C according to Child-Turcotte-Pugh scoring system. Results. A total of 392 Chinese patients with CLD and 91 healthy controls were enrolled. HRQOL in patients with CLD was lower than that in healthy controls. Score of PCS in healthy controls was 54.6 ± 5.5 and in CLD was 47.8 ± 8.8 (P = 0.000). Score of MCS in healthy controls was 56.4 ± 8.1 and in CLD was 51.7 ± 7.4 (P = 0.000). Increasing severity of CLD from no cirrhosis to advanced cirrhosis was associated with a decrease on all domains of the SF-36 (P < 0.05). Stepwise linear regression analysis showed that severity of disease, age, present ascites, present varices, and prothrombin time had significant effect on physical health area. Severity of disease, female, present varices, total bilirubin, prothrombin time, and hemoglobin had significant effect on mental health area. Conclusions. Patients with CLD had impaired HRQOL. Increasing severity of CLD was associated with a decrease on HRQOL. Old age, female gender, advanced stage of CLD, present ascites, hyperbilirubinemia, and prolonging prothrombin time were important factors reducing HRQOL