LRBmat: A Novel Gut Microbial Interaction and Individual Heterogeneity Inference Method for Colorectal Cancer

Many diseases are considered to be closely related to the changes in the gut microbial community, including colorectal cancer (CRC), which is one of the most common cancers in the world. The diagnostic classification and etiological analysis of CRC are two critical issues worthy of attention. Many methods adopt gut microbiota to solve it, but few of them simultaneously take into account the complex interactions and individual heterogeneity of gut microbiota, which are two common and important issues in genetics and intestinal microbiology, especially in high-dimensional cases. In this paper, a novel method with a Binary matrix based on Logistic Regression (LRBmat) is proposed to deal with the above problem. The binary matrix can directly weakened or avoided the influence of heterogeneity, and also contain the information about gut microbial interactions with any order. Moreover, LRBmat has a powerful generalization, it can combine with any machine learning method and enhance them. The real data analysis on CRC validates the proposed method, which has the best classification performance compared with the state-of-the-art. Furthermore, the association rules extracted from the binary matrix of the real data align well with the biological properties and existing literatures, which are helpful for the etiological analysis of CRC. The source codes for LRBmat are available at https://github.com/tsnm1/LRBmat

Regulation of High-Temperature Stress Response by Small RNAs

Temperature extremes constitute one of the most common environmental stresses that adversely affect the growth and development of plants. Transcriptional regulation of temperature stress responses, particularly involving protein-coding gene networks, has been intensively studied in recent years. High-throughput sequencing technologies enabled the detection of a great number of small RNAs that have been found to change during and following temperature stress. The precise molecular action of some of these has been elucidated in detail. In the present chapter, we summarize the current understanding of small RNA-mediated modulation of high- temperature stress-regulatory pathways including basal stress responses, acclimation, and thermo-memory. We gather evidence that suggests that small RNA network changes, involving multiple upregulated and downregulated small RNAs, balance the trade-off between growth/development and stress responses, in order to ensure successful adaptation. We highlight specific characteristics of small RNA-based tem- perature stress regulation in crop plants. Finally, we explore the perspectives of the use of small RNAs in breeding to improve stress tolerance, which may be relevant for agriculture in the near future

Decoupled Adaptive Motion Control for Unmanned Tracked Vehicles in the Leader-Following Task

As a specific task for unmanned tracked vehicles, leader-following imposes high-precision requirements on the vehicle’s motion control, especially the steering control. However, due to characteristics such as the frequent changes in off-road terrain and steering resistance coefficients, controlling tracked vehicles poses significant challenges, making it difficult to achieve stable and precise leader-following. This paper decouples the leader-following control into speed and curvature control to address such issues. It utilizes model reference adaptive control to establish reference models for the speed and curvature subsystems and designs corresponding parameter adaptive control laws. This control method enables the actual vehicle speed and curvature to effectively track the response of the reference model, thereby addressing the impact of frequent changes in the steering resistance coefficient. Furthermore, this paper demonstrates significant improvements in leader-following performance through a series of simulations and experiments. Compared with the traditional PID control method, the results shows that the maximum following distance has been reduced by at least approximately 12% (ensuring the ability to keep up with the leader), the braking distance has effectively decreased by 22% (ensuring a safe distance in an emergency braking scenario and improving energy recovery), the curvature tracking accuracy has improved by at least 11% (improving steering performance), and the speed tracking accuracy has increased by at least 3.5% (improving following performance)

In vivo nuclear capture and molecular profiling identifies Gmeb1 as a transcriptional regulator essential for dopamine neuron function

Midbrain dopamine (mDA) neurons play a central role in reward signaling and are widely implicated in psychiatric and neurodegenerative disorders. To understand how mDA neurons perform these functions, it is important to understand how mDA-specific genes are regulated. However, cellular heterogeneity in the mammalian brain presents a major challenge to obtaining this understanding. To this end, we developed a virus-based approach to label and capture mDA nuclei for transcriptome (RNA-Seq), and low-input chromatin accessibility (liDNase-Seq) profiling, followed by predictive modeling to identify putative transcriptional regulators of mDA neurons. Using this method, we identified Gmeb1, a transcription factor predicted to regulate expression of Th and Dat, genes critical for dopamine synthesis and reuptake, respectively. Gmeb1 knockdown in mDA neurons resulted in downregulation of Th and Dat, as well as in severe motor deficits. This study thus identifies Gmeb1 as a master regulator of mDA gene expression and function, and provides a general method for identifying cell type-specific transcriptional regulators

A novel source/drain on void (SDOV) MOSFET implemented by local co-implantation of hydrogen and helium

In this paper a novel device named as SDOV MOSFET is proposed for the first time. This structure features localized void layers under the source and drain regions. The short channel effects of this device can be improved due to the SOI-like source/drain structure. In addition, witliout the dielectric layer under the channel region, this device can avoid some weaknesses of UTB SOI devices caused by the thin silicon film and the underlying buried oxide, such as mobility degradation, film thickness fluctuation and self-heating effect. Based on self-aligned hydrogen and helium co-implantation technology, the new device can be fabricated by a process compatible with the standard CMOS process. The SDOV MOSFETs with 50 nm gate length are experimentally demonstrated for verification. (C) 2008 Elsevier B.V. All rights reserved

Evaluation of a Mycobacterium avium subsp. paratuberculosis leuD mutant as a vaccine candidate against challenge in a caprine model

Johne's disease (JD) is prevalent worldwide and has a significant impact on the global agricultural economy. In the present study, we evaluated the protective efficacy of a leuD (Δleud) mutant and gained insight into differential immune responses after challenge with virulent M. avium subsp. paratuberculosis in a caprine colonization model. The immune response and protective efficacy were compared with those of the killed vaccine Mycopar. In vitro stimulation of peripheral blood mononuclear cells with johnin purified protein derivative showed that Mycopar and ΔleuD generated similar levels of gamma interferon (IFN-γ) but significantly higher levels than unvaccinated and challenged phosphate-buffered saline controls. However, only with ΔleuD was the IFN-γ response maintained. Flow cytometric analysis showed that the increase in IFN-γ correlated with proliferation and activation (increased expression of CD25) of CD4, CD8, and γδT cells, but this response was significantly higher in ΔleuD-vaccinated animals at some time points after challenge. Both Mycopar and ΔleuD vaccines upregulated Th1/proinflammatory and Th17 cytokines and downregulated Th2/anti-inflammatory and regulatory cytokines at similar levels at almost all time points. However, significantly higher levels of IFN-γ (at weeks 26 and 30), interleukin-2 (IL-2; week 18), IL-1b (weeks 14 and 22), IL-17 (weeks 18 and 22), and IL-23 (week 18) and a significantly lower level of IL-10 (weeks 14 and 18) and transforming growth factor β (week 18) were detected in the ΔleuD-vaccinated group. Most importantly, ΔleuD elicited an immune response that significantly limited colonization of tissues compared to Mycopar upon challenge with wild-type M. avium subsp. paratuberculosis. In conclusion, the ΔleuD mutant is a promising vaccine candidate for development of a live attenuated vaccine for JD in ruminants