Probing Local Atomic Environments to Model RNA Energetics and Structure

Ribonucleic acids (RNA) are critical components of living systems. Understanding RNA structure and its interaction with other molecules is an essential step in understanding RNA-driven processes within the cell. Experimental techniques like X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and chemical probing methods have provided insights into RNA structures on the atomic scale. To effectively exploit experimental data and characterize features of an RNA structure, quantitative descriptors of local atomic environments are required. Here, I investigated different ways to describe RNA local atomic environments. First, I investigated the solvent-accessible surface area (SASA) as a probe of RNA local atomic environment. SASA contains information on the level of exposure of an RNA atom to solvents and, in some cases, is highly correlated to reactivity profiles derived from chemical probing experiments. Using Bayesian/maximum entropy (BME), I was able to reweight RNA structure models based on the agreement between SASA and chemical reactivities. Next, I developed a numerical descriptor (the atomic fingerprint), that is capable of discriminating different atomic environments. Using atomic fingerprints as features enable the prediction of RNA structure and structure-related properties. Two detailed examples are discussed. Firstly, a classification model was developed to predict Mg$^{2+}$ ion binding sites. Results indicate that the model could predict Mg$^{2+}$ binding sites with reasonable accuracy, and it appears to outperform existing methods. Secondly, a set of models were developed to identify cavities in RNA that are likely to accommodate small-molecule ligands. The models were also used to identify bound-like conformations from an ensemble of RNA structures. The frameworks presented here provide paths to connect the local atomic environment to RNA structure, and I envision they will provide opportunities to develop novel RNA modeling tools.PHDPhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/163135/1/jingrux_1.pd

Sharing tableware reduces waste generation, emissions and water consumption in China’s takeaway packaging waste dilemma

China has a rapidly growing online food delivery and takeaway market, serving 406 million customers with 10.0 billion orders and generating 323kilotonnes of tableware and packaging waste in 2018. Here we use a top-down approach with city-level takeaway order data to explore the packaging waste and life-cycle environmental impacts of the takeaway industry in China. The ten most wasteful cities, with just 7% of the population, in terms of per capita waste generation, were responsible for 30% of the country's takeaway waste, 27-34% of the country's pollutant emissions and 30% of the country's water consumption. We defined one paper substitution and two sharing tableware scenarios to simulate the environmental mitigation potentials. The results of the scenario simulations show that sharing tableware could reduce waste generation by up to 92%, and environmental emissions and water consumption by more than two-thirds. Such a mechanism provides a potential solution to address the food packaging waste dilemma and a new strategy for promoting sustainable and zero-waste lifestyles. The online food delivery and takeaway market is growing in China, serving 406 million customers with 10.0 billion orders in 2018. Here, data from an online food delivery platform, life-cycle environmental impacts of packaging and tableware waste generated across 353 cities in China, and scenarios for paper alternatives and tableware sharing are presented

Driving Mechanisms of Cropland Abandonment from the Perspectives of Household and Topography in the Poyang Lake Region, China

Cropland abandonment is driven by various mechanisms and is best viewed from multiple perspectives to suggest targeted policy changes which may change the status quo of abandonment. Here, we systematically analyze the characteristics of abandonment and its driving mechanisms by different farming households (pure, part-time, and non-farm) in three topographic regions of the Poyang Lake region using a binary logistic regression model. Results show that: (1) The overall abandonment probability in the Poyang Lake region is largest for non-farm households, followed by part-time households and pure households. In the mountainous region, abandonment is largest for non-farm households, followed by pure households and part-time households. Both the hilly and plain regions show the largest abandonment probability for pure households, followed by part-time households, and non-farm households. (2) The low agricultural economic benefits and the uneconomical investments of time in plots are the main abandonment determinants for pure households. Economic efficiency, both the time invested in plots and economic efficiency, are key abandonment determinants for pure households in the mountainous and plain regions, respectively. (3) Labor shortage and plots which are time-consuming and unfavorable to cultivation are the main abandonment determinants for part-time households, with different factors in different topographic regions. (4) For non-farm households, many factors can influence the occurrence of abandonment. Non-farm households in the mountainous and hilly regions are more influenced by non-farm work and the number of farming workers, respectively; in addition, the inconvenience of using agricultural machinery has a significant influence

Driving Mechanisms of Cropland Abandonment from the Perspectives of Household and Topography in the Poyang Lake Region, China

Cropland abandonment is driven by various mechanisms and is best viewed from multiple perspectives to suggest targeted policy changes which may change the status quo of abandonment. Here, we systematically analyze the characteristics of abandonment and its driving mechanisms by different farming households (pure, part-time, and non-farm) in three topographic regions of the Poyang Lake region using a binary logistic regression model. Results show that: (1) The overall abandonment probability in the Poyang Lake region is largest for non-farm households, followed by part-time households and pure households. In the mountainous region, abandonment is largest for non-farm households, followed by pure households and part-time households. Both the hilly and plain regions show the largest abandonment probability for pure households, followed by part-time households, and non-farm households. (2) The low agricultural economic benefits and the uneconomical investments of time in plots are the main abandonment determinants for pure households. Economic efficiency, both the time invested in plots and economic efficiency, are key abandonment determinants for pure households in the mountainous and plain regions, respectively. (3) Labor shortage and plots which are time-consuming and unfavorable to cultivation are the main abandonment determinants for part-time households, with different factors in different topographic regions. (4) For non-farm households, many factors can influence the occurrence of abandonment. Non-farm households in the mountainous and hilly regions are more influenced by non-farm work and the number of farming workers, respectively; in addition, the inconvenience of using agricultural machinery has a significant influence

Epidermal Stem Cells in Wound Healing and Regeneration

Skin stem cells distributed in the basal layer of the epidermis and hair follicles are important cell sources for skin development, metabolism, and injury repair. At present, great progress has been made in the study of epidermal stem cells at the cellular and molecular levels. Stem cell transplantation is reported to promote skin healing, endothelial cell transformation, and vascular formation. Local stem cells can also be transformed into keratinocytes, sebaceous gland, and other skin-associated tissues. However, the mechanism of action of epidermal stem cells on wound healing and regeneration is not completely clear. This review is aimed at briefly summarizing the biological characteristics of epidermal stem cells and their clinical application in wound healing and tissue regeneration. It further discussed the mechanism of action and the development direction in the future

A K-SVD Based Compressive Sensing Method for Visual Chaotic Image Encryption

The visually secure image encryption scheme is an effective image encryption method, which embeds an encrypted image into a visual image to realize a secure and secret image transfer. This paper proposes a merging compression and encryption chaos image visual encryption scheme. First, a dictionary matrix D is constructed with the plain image by the K-SVD algorithm, which can encrypt the image while sparsing. Second, an improved Zeraoulia-Sprott chaotic map and logistic map are employed to generate three S-Boxes, which are used to complete scrambling, diffusion, and embedding operations. The secret keys of this scheme contain the initial value of the chaotic system and the dictionary matrix D, which significantly increases the key space, plain image correlation, and system security. Simulation shows the proposed image encryption scheme can resist most attacks and, compared with the existing scheme, the proposed scheme has a larger key space, higher plain image correlation, and better image restoration quality, improving image encryption processing efficiency and security

Fault Estimation Method for Nonlinear Time-Delay System Based on Intermediate Observer-Application on Quadrotor Unmanned Aerial Vehicle

In this paper, the problem of actuator and sensor faults of a quadrotor unmanned aerial vehicle (QUAV) system is studied. In the system fault model, time delay, nonlinear term, and disturbances of QUAV during the flight are considered. A fault estimation algorithm based on an intermediate observer is proposed. To deal with a single actuator fault, an intermediate variable is introduced, and the intermediate observer is designed for the system to estimate fault. For simultaneous actuator and sensor faults, the system is first augmented, and then two intermediate variables are introduced, and an intermediate observer is designed for the augmented system to estimate the system state, faults, and disturbances. The Lyapunov–Krasovskii functional is used to prove that the estimation error system is uniformly eventually bounded. The simulation results verify the feasibility and effectiveness of the proposed fault estimation method

Preparation of Graphene Sponge Coated Iron Electrode for the Electrolytic Decoloration of Methylene Blue

Electrolysis is a widely adopted technology in water treatment, while the major challenge focuses on developing better electrode materials. In this study, we reported that the hydrothermal coating of graphene sponge (GS) on Fe electrode (GS-Fe electrode) could significantly improve the decoloration performance of Fe electrode. The decoloration kinetics constant of GS-Fe electrode was five times of that of Fe electrode at the same current density. Mechanistically, the electrolytic oxidation of MB was via indirect pathway, where Cl- was oxidized into ClO- for the oxidation of other substances. Moreover, the performance of GS-Fe electrode remained nearly unchanged in the recycling evaluations. The implication to the applications of GS-Fe electrode in water treatment is discussed