PCalign: a method to quantify physicochemical similarity of protein-protein interfaces

Abstract Background Structural comparison of protein-protein interfaces provides valuable insights into the functional relationship between proteins, which may not solely arise from shared evolutionary origin. A few methods that exist for such comparative studies have focused on structural models determined at atomic resolution, and may miss out interesting patterns present in large macromolecular complexes that are typically solved by low-resolution techniques. Results We developed a coarse-grained method, PCalign, to quantitatively evaluate physicochemical similarities between a given pair of protein-protein interfaces. This method uses an order-independent algorithm, geometric hashing, to superimpose the backbone atoms of a given pair of interfaces, and provides a normalized scoring function, PC-score, to account for the extent of overlap in terms of both geometric and chemical characteristics. We demonstrate that PCalign outperforms existing methods, and additionally facilitates comparative studies across models of different resolutions, which are not accommodated by existing methods. Furthermore, we illustrate potential application of our method to recognize interesting biological relationships masked by apparent lack of structural similarity. Conclusions PCalign is a useful method in recognizing shared chemical and spatial patterns among protein-protein interfaces. It outperforms existing methods for high-quality data, and additionally facilitates comparison across structural models with different levels of details with proven robustness against noise.http://deepblue.lib.umich.edu/bitstream/2027.42/110905/1/12859_2015_Article_471.pd

Road Crack Detection Using Deep Convolutional Neural Network and Adaptive Thresholding

Crack is one of the most common road distresses which may pose road safety hazards. Generally, crack detection is performed by either certified inspectors or structural engineers. This task is, however, time-consuming, subjective and labor-intensive. In this paper, we propose a novel road crack detection algorithm based on deep learning and adaptive image segmentation. Firstly, a deep convolutional neural network is trained to determine whether an image contains cracks or not. The images containing cracks are then smoothed using bilateral filtering, which greatly minimizes the number of noisy pixels. Finally, we utilize an adaptive thresholding method to extract the cracks from road surface. The experimental results illustrate that our network can classify images with an accuracy of 99.92%, and the cracks can be successfully extracted from the images using our proposed thresholding algorithm.Comment: 6 pages, 8 figures, 2019 IEEE Intelligent Vehicles Symposiu

Fire performance of cold-formed steel sections

Thin-walled cold-formed steel (CFS) has exhibited inherent structural and architectural advantages over other constructional materials, for example, high strength-to-weight ratio, ease of fabrication, economy in transportation and the flexibility of sectional profiles, which make CFS ideal for modern residential and industrial buildings. They have been increasingly used as purlins as the intermediate members in a roof system, or load-bearing components in low- and mid-rise buildings. However, using CFS members in building structures has been facing challenges due to the lack of knowledge to the fire performance of CFS at elevated temperatures and the lack of fire design guidelines. Among all available design specifications of CFS, EN1993-1-2 is the only one which provided design guidelines for CFS at elevated temperatures, which, however, is based on the same theory and material properties of hot-rolled steel. Since the material properties of CFS are found to be considerably different from those of hot-rolled steel, the applicability of hot-rolled steel design guidelines into CFS needs to be verified. Besides, the effect of non-uniform temperature distribution on the failure of CFS members is not properly addressed in literature and has not been specified in the existing design guidelines. Therefore, a better understanding of fire performance of CFS members is of great significance to further explore the potential application of CFS. Since CFS members are always with thin thickness (normally from 0.9 to 8 mm), open cross-section, and great flexural rigidity about one axis at the expense of low flexural rigidity about a perpendicular axis, the members are usually susceptible to various buckling modes which often govern the ultimate failure of CFS members. When CFS members are exposed to a fire, not only the reduced mechanical properties will influence the buckling capacity of CFS members, but also the thermal strains which can lead additional stresses in loaded members. The buckling behaviour of the member can be analysed based on uniformly reduced material properties when the member is unprotected or uniformly protected surrounded by a fire that the temperature distribution within the member is uniform. However if the temperature distribution in a member is not uniform, which usually happens in walls and/or roof panels when CFS members are protected by plaster boards and exposed to fire on one side, the analysis of the member becomes very complicated since the mechanical properties such as Young’s modulus and yield strength and thermal strains vary within the member. This project has the aim of providing better understanding of the buckling performance of CFS channel members under non-uniform temperatures. The primary objective is to investigate the fire performance of plasterboard protected CFS members exposed to fire on one side, in the aspects of pre-buckling stress distribution, elastic buckling behaviour and nonlinear failure models. Heat transfer analyses of one-side protected CFS members have been conducted firstly to investigate the temperature distributions within the cross-section, which have been applied to the analytical study for the prediction of flexural buckling loads of CFS columns at elevated temperatures. A simplified numerical method based on the second order elastic – plastic analysis has also been proposed for the calculation of the flexural buckling load of CFS columns under non-uniform temperature distributions. The effects of temperature distributions and stress-strain relationships on the flexure buckling of CFS columns are discussed. Afterwards a modified finite strip method combined with the classical Fourier series solutions have been presented to investigate the elastic buckling behaviour of CFS members at elevated temperatures, in which the effects of temperatures on both strain and mechanical properties have been considered. The variations of the elastic buckling loads/moments, buckling modes and slenderness of CFS columns/beams with increasing temperatures have been examined. The finite element method is also used to carry out the failure analysis of one-side protected beams at elevated temperatures. The effects of geometric imperfection, stress-strain relationships and temperature distributions on the ultimate moment capacities of CFS beams under uniform and non-uniform temperature distributions are examined. At the end the direct strength method based design methods have been discussed and corresponding recommendations for the designing of CFS beams at elevated temperatures are presented. This thesis has contributed to improve the knowledge of the buckling and failure behaviour of CFS members at elevated temperatures, and the essential data provided in the numerical studies has laid the foundation for further design-oriented studies.School of Marine Science and Engineering, Plymouth University; China Scholarship Counci

Arrayed van der Waals Vertical Heterostructures based on 2D GaSe Grown by Molecular Beam Epitaxy

Vertically stacking two dimensional (2D) materials can enable the design of novel electronic and optoelectronic devices and realize complex functionality. However, the fabrication of such artificial heterostructures in wafer scale with an atomically-sharp interface poses an unprecedented challenge. Here, we demonstrate a convenient and controllable approach for the production of wafer-scale 2D GaSe thin films by molecular beam epitaxy. In-situ reflection high-energy electron diffraction oscillations and Raman spectroscopy reveal a layer-by-layer van der Waals epitaxial growth mode. Highly-efficient photodetector arrays were fabricated based on few-layer GaSe on Si. These photodiodes show steady rectifying characteristics and a relatively high external quantum efficiency of 23.6%. The resultant photoresponse is super-fast and robust with a response time of 60 us. Importantly, the device shows no sign of degradation after 1 million cycles of operation. Our study establishes a new approach to produce controllable, robust and large-area 2D heterostructures and presents a crucial step for further practical applications

Long-term culture captures injury-repair cycles of colonic stem cells

The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. The responsive stem cell that mediates this process is unclear, in part because of a lack of in vitro models that recapitulate key epithelial changes that occur in vivo during damage and repair. Here, we identify a Hop