Finding Transition Pathways on Manifolds

We consider noise-induced transition paths in randomly perturbed dynami- cal systems on a smooth manifold. The classical Freidlin-Wentzell large devia- tion theory in Euclidean spaces is generalized and new forms of action functionals are derived in the spaces of functions and the space of curves to accommodate the intrinsic constraints associated with the manifold. Numerical meth- ods are proposed to compute the minimum action paths for the systems with constraints. The examples of conformational transition paths for a single and double rod molecules arising in polymer science are numerically investigated

A statistical normalization method and differential expression analysis for RNA-seq data between different species

Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved transcriptional responses. To remove systematic variation between different species for a fair comparison, the normalization procedure serves as a crucial pre-processing step that adjusts for the varying sample sequencing depths and other confounding technical effects. Results: In this paper, we propose a scale based normalization (SCBN) method by taking into account the available knowledge of conserved orthologous genes and hypothesis testing framework. Considering the different gene lengths and unmapped genes between different species, we formulate the problem from the perspective of hypothesis testing and search for the optimal scaling factor that minimizes the deviation between the empirical and nominal type I errors. Conclusions: Simulation studies show that the proposed method performs significantly better than the existing competitor in a wide range of settings. An RNA-seq dataset of different species is also analyzed and it coincides with the conclusion that the proposed method outperforms the existing method. For practical applications, we have also developed an R package named "SCBN" and the software is available at http://www.bioconductor.org/packages/devel/bioc/html/SCBN.html

Table-to-Text: Describing Table Region with Natural Language

In this paper, we present a generative model to generate a natural language sentence describing a table region, e.g., a row. The model maps a row from a table to a continuous vector and then generates a natural language sentence by leveraging the semantics of a table. To deal with rare words appearing in a table, we develop a flexible copying mechanism that selectively replicates contents from the table in the output sequence. Extensive experiments demonstrate the accuracy of the model and the power of the copying mechanism. On two synthetic datasets, WIKIBIO and SIMPLEQUESTIONS, our model improves the current state-of-the-art BLEU-4 score from 34.70 to 40.26 and from 33.32 to 39.12, respectively. Furthermore, we introduce an open-domain dataset WIKITABLETEXT including 13,318 explanatory sentences for 4,962 tables. Our model achieves a BLEU-4 score of 38.23, which outperforms template based and language model based approaches.Comment: 9 pages, 4 figures. This paper has been published by AAAI201

On the Mathematics of RNA Velocity II: Algorithmic Aspects

In a previous paper [CSIAM Trans. Appl. Math. 2 (2021), 1-55], the authors proposed a theoretical framework for the analysis of RNA velocity, which is a promising concept in scRNA-seq data analysis to reveal the cell state-transition dynamical processes underlying snapshot data. The current paper is devoted to the algorithmic study of some key components in RNA velocity workflow. Four important points are addressed in this paper: (1) We construct a rational time-scale fixation method which can determine the global gene-shared latent time for cells. (2) We present an uncertainty quantification strategy for the inferred parameters obtained through the EM algorithm. (3) We establish the optimal criterion for the choice of velocity kernel bandwidth with respect to the sample size in the downstream analysis and discuss its implications. (4) We propose a temporal distance estimation approach between two cell clusters along the cellular development path. Some illustrative numerical tests are also carried out to verify our analysis. These results are intended to provide tools and insights in further development of RNA velocity type methods in the future.Comment: 32 pages, 5 figure

Unusual Sign Reversal of Field-like Spin-Orbit Torque in Pt/Ni/Py with an Ultrathin Ni Spacer

The magnetization manipulation by spin-orbit torques (SOTs) in nonmagnetic-metal (NM)/ferromagnet (FM) heterostructures has provided great opportunities for spin devices. Besides the conventional spin Hall effect (SHE) in heavy metals with strong spin-orbit coupling, the orbital currents have been proposed to be another promising approach to generate strong SOTs. Here, we systematically study the SOTs efficiency and its dependence on the FM thickness and different NM/FM interfaces in two prototypical Pt/Py and Ta/Py systems by inserting an ultrathin magnetic layer (0.4 nm thick ML = Co, Fe, Gd, and Ni). The dampinglike (DL) torque efficiency $\xi_{DL}$ is significantly enhanced by inserting ultrathin Co, Fe, and Ni layers and is noticeably suppressed for the Gd insertion. Moreover, the Ni insertion results in a sign change of the field-like (FL) torque in Pt/Py and substantially reduces $\xi_{DL}$ in Ta/Py. These results are likely related to the additional spin currents generated by combining the orbital Hall effect (OHE) in the NM and orbital-to-spin conversion in the ML insertion layer and/or their interfaces, especially for the Ni insertion. Our results demonstrate that inserting ultrathin ML can effectively manipulate the strength and sign of the SOTs, which would be helpful for spintronics applications

Characteristics of HCV Co-Infection among HIV Infected Individuals from an Area with High Risk of Blood-Borne Infections in Central China

Objective: Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) co-infection has been proved to be a growing public health concern. The prevalence and genotypic pattern vary with geographic locations. Limited information is available to date with regard to HCV genotype and its clinical implications among those former commercial blood donor communities. The aims of this study were to genetically define the HCV genotype and associated clinical characteristics of HIV/HCV co-infected patients from a region with commercial blood donation history in central China. Methods: A cross sectional study, including 164 HIV infected subjects, was conducted in Shanxi province central China. Serum samples were collected and HCV antibody testing, AST and ALT testing were performed. Seropositive samples were further subjected to RT-PCR followed by direct sequence coupled with phylogenetic analysis of Core-E1 and NS5B regions performed in comparison with known reference genotypes. Findings: A total of 139 subjects were HCV antibody positive. Genotype could be determined for 88 isolates. Phylogenetic analysis revealed that the predominant circulating subtype was HCV 1b (65.9%), followed by HCV 2a (34.1%). The HCV viral load in the subjects infected with HIV1b was significantly higher than those infected with HCV 2a (P = 0.006). No significant difference for HCV RNA level was detected between ART status, CD4+ cell count level and HIV RNA level. Serum AST and ALT level were likely to increase with HCV RNA level, although no significance was observed. Those who had conducted commercial donation later than 1991 (OR 3.43, 95% CI: 1.12–10.48) and had a short duration of donation (OR 0.35, 95% CI: 0.13–0.96) were more likely to be infected with HCV 1b. Conclusion: These results suggest that HCV subtype 1b predominates in this population, and the impact of HIV status and ART on HCV disease progression is not significantly correlated

The effect of migration on transmission of Wolbachia in Nilaparvata lugens

Brown planthopper Nilaparvata lugens, which can transmit rice ragged stunt virus, is a serious and damaging pest to rice plants. Rice plants can protect themselves from the associated diseases of N.lugens by either suppressing or replacing N.lugens by releasing N.lugens infected by a special strain of Wolbachia wStri. The long-distance migration habit of N.lugens is one of the important precursors leading up to the large-scale occurrence of N.lugens. To study the effect of migration on the transmission of Wolbachia in N.lugens, a Wolbachia spreading dynamics model with migration of N.lugens between two patches is put forward. The existence and local stability conditions of equilibrium points of the system and its subsystems are obtained. Moreover, the effects of migration on the dynamic properties and the control of N.lugens are analyzed; the results show that the system can exhibit a bistable phenomenon, and the migration can change the stability of equilibrium infected with wStri from stable to unstable. The quantitative control methods for the migration of the insect N.lugens are proposed, which provide a theoretical guidance for future field experiments. Lastly, we use the Markov chain Monte Carlo (MCMC) method to estimate the parameters of the wild N.lugens migration model based on limited observational data; the numerical simulation results show that migration can increase the quantity of N.lugens, which is consistent with the relevant experimental results