Predicting RNA polymerase II transcriptional elongation pausing and associated histone code.

RNA Polymerase II (Pol II) transcriptional elongation pausing is an integral part of the dynamic regulation of gene transcription in the genome of metazoans. It plays a pivotal role in many vital biological processes and disease progression. However, experimentally measuring genome-wide Pol II pausing is technically challenging and the precise governing mechanism underlying this process is not fully understood.

Delay induced stability switch in a mathematical model of CD8 T-cell response to SARS-CoV-2 mediated by receptor ACE2.

The pathogen SARS-CoV-2 binds to the receptor angiotensin-converting enzyme 2 (ACE2) of the target cells and then replicates itself through the host, eventually releasing free virus particles. After infection, the CD8 T-cell response is triggered and appears to play a critical role in the defense against virus infections. Infected cells and their activated CD8 T-cells can cause tissue damage.

SpecLoop predicts cell type-specific chromatin loop via transcription factor cooperation.

Cell-type-Specific Chromatin Loops (CSCLs) are crucial for gene regulation and cell fate determination. However, the mechanisms governing their establishment remain elusive. Here, we present SpecLoop, a network regularization-based machine learning framework, to investigate the role of transcription factors (TFs) cooperation in CSCL formation.

Stability and persistence analysis of a microorganism flocculation model with infinite delay.

In this paper, we study the global stability and persistence of a microorganism flocculation model with infinite delay. First, we make a complete theoretical analysis on the local stability of the boundary equilibrium (microorganism-free equilibrium) and the positive equilibrium (microorganism co-existent equilibrium), and give a sufficient condition for the global stability of the boundary equilibrium (applicable to the forward bifurcation and the backward bifurcation). Then, for the persistence of the model, we present an explicit estimate of the eventual lower bound of any positive solution for which only the parameter threshold $ R_0 > 1 $ is required.

A COVID-19 Infection Model Considering the Factors of Environmental Vectors and Re-Positives and Its Application to Data Fitting in Japan and Italy.

COVID-19, which broke out globally in 2019, is an infectious disease caused by a novel strain of coronavirus, and its spread is highly contagious and concealed. Environmental vectors play an important role in viral infection and transmission, which brings new difficulties and challenges to disease prevention and control. In this paper, a type of differential equation model is constructed according to the spreading functions and characteristics of exposed individuals and environmental vectors during the virus infection process.

Global asymptotic stability of a delay differential equation model for SARS-CoV-2 virus infection mediated by ACE2 receptor protein.

The COVID-19 pandemic has brought a serious threat to human life safety worldwide. SARS-CoV-2 virus mainly binds to the target cell surface receptor ACE2 (Angiotensin-converting enzyme 2 ) through the S protein expressed on the surface of the virus, resulting in infection of target cells. During this infection process, the target cell ACE2 receptor plays a very important mediating role.

Periodic oscillation for a class of in-host MERS-CoV infection model with CTL immune response.

The purpose of this paper is to give some sufficient conditions for the existence of periodic oscillation of a class of in-host MERS-Cov infection model with cytotoxic T lymphocyte (CTL) immune response. A new technique is developed to obtain a lower bound of the state variable characterizing CTL immune response in the model. Our results expand on some previous works.

Global dynamics of an SI epidemic model with nonlinear incidence rate, feedback controls and time delays.

In this paper, we consider a class of SI epidemic model with nonlinear incidence, feedback controls and four different discrete time delays. By skillfully constructing appropriate Lyapunov functionals, and combining Lyapunov-LaSalle invariance principle and Barbalat's lemma, the global dynamics of the model are established. Our results extend and improve related works in the existing literatures.

The differential equation model of pathogenesis of Kawasaki disease with theoretical analysis.

Fever is a extremely common symptom in infants and young children. Due to the lowresistance of infants and young, long-term fever may cause damage to the child's body. Clinically,some children with long-term fever was eventually diagnosed with Kawasaki disease (KD).

Corrigendum to "Modeling Inhibitory Effect on the Growth of Uninfected T Cells Caused by Infected T Cells: Stability and Hopf Bifurcation".

[This corrects the article DOI: 10.1155/2018/3176893.].

Modeling Inhibitory Effect on the Growth of Uninfected T Cells Caused by Infected T Cells: Stability and Hopf Bifurcation.

We consider a class of viral infection dynamic models with inhibitory effect on the growth of uninfected T cells caused by infected T cells and logistic target cell growth. The basic reproduction number is derived. It is shown that the uninfected equilibrium is globally asymptotically stable if < 1.

Remarks on a variant of Lyapunov-LaSalle theorem.

The aim of this paper is to give some global stability criteria on a variant of Lyapunov-LaSalle theorem for a class of delay di erential system.

A Novel Dynamic Model Describing the Spread of the MERS-CoV and the Expression of Dipeptidyl Peptidase 4.

The Middle East respiratory syndrome (MERS) coronavirus, a newly identified pathogen, causes severe pneumonia in humans. MERS is caused by a coronavirus known as MERS-CoV, which attacks the respiratory system. The recently defined receptor for MERS-CoV, dipeptidyl peptidase 4 (DPP4), is generally expressed in endothelial and epithelial cells and has been shown to be present on cultured human nonciliated bronchiolar epithelium cells.

Stability and Hopf Bifurcation in a Delayed HIV Infection Model with General Incidence Rate and Immune Impairment.

We investigate the dynamical behavior of a delayed HIV infection model with general incidence rate and immune impairment. We derive two threshold parameters, the basic reproduction number R 0 and the immune response reproduction number R 1. By using Lyapunov functional and LaSalle invariance principle, we prove the global stability of the infection-free equilibrium and the infected equilibrium without immunity.

[Advances in the pathway and molecular mechanism for the biodegradation of microcystins].

With increasing discharge of wastewater containing nitrogen and phosphorus into rivers and lakes, harmful cyanobacterial blooms have become more frequent worldwide. The main harm of cyanobacterial blooms is producing and releasing a great amount of algal toxins mainly containing microcystins (MCs). Since MCs are extremely harmful to plants and animals and difficult to be removed efficiently by the traditional processing methods, how to control harmful cyanobacterial blooms and remove MCs have become an unsolved problem in the field of environmental science all over the world.

Analysis of SIR epidemic models with nonlinear incidence rate and treatment.

This paper deals with the nonlinear dynamics of a susceptible-infectious-recovered (SIR) epidemic model with nonlinear incidence rate, vertical transmission, vaccination for the newborns of susceptible and recovered individuals, and the capacity of treatment. It is assumed that the treatment rate is proportional to the number of infectives when it is below the capacity and constant when the number of infectives reaches the capacity. Under some conditions, it is shown that there exists a backward bifurcation from an endemic equilibrium, which implies that the disease-free equilibrium coexists with an endemic equilibrium.

A dynamic model describing heterotrophic culture of Chlorella and its stability analysis.

Chlorella is an important species of microorganism, which includes about 10 species. Chlorella USTB01 is a strain of microalga which is isolated from Qinghe River in Beijing and has strong ability in the utilization of organic compounds and was identified as Chlorella sp. (H.

Global stability for delay SIR and SEIR epidemic models with nonlinear incidence rate.

In this paper, based on SIR and SEIR epidemic models with a general nonlinear incidence rate, we incorporate time delays into the ordinary differential equation models. In particular, we consider two delay differential equation models in which delays are caused (i) by the latency of the infection in a vector, and (ii) by the latent period in an infected host. By constructing suitable Lyapunov functionals and using the Lyapunov-LaSalle invariance principle, we prove the global stability of the endemic equilibrium and the disease-free equilibrium for time delays of any length in each model.

An improved model of T cell development in the thymus and its stability analysis.

Based on some important experimental dates, in this paper we shall introduce time delays into Mehrs's non-linear differential system model which is used to describe proliferation, differentiation and death of T cells in the thymus (see, for example, [3], [6], [7] and [9]) and give a revised nonlinear differential system model with time delays. By using some classical analysis techniques of functional differential equations, we also consider local and global asymptotic stability of the equilibrium and the permanence of the model.