Outlier Profiles of Atomic Structures Derived From X-ray Crystallography and From Cryo-electron Microscopy

Background: As more protein atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. Methods: We applied a histogram-based outlier score (HBOS) to six sets of cryo-EM atomic structures and five sets of X-ray atomic structures, including one derived from X-ray data with better than 1.5 Å resolution. Cryo-EM data sets contain structures released by December 2016 and those released between 2017 and 2019, derived from resolution ranges 0–4 Å and 4–6 Å respectively. Results: The distribution of HBOS values in five sets of X-ray structures show that HBOS is sensitive distinguishing sets of X-ray structures derived from different resolution ranges-higher than 1.5 Å, 1.5–2.0 Å, 2.0–2.5 Å, 2.5–3.0 Å, and 3.0–3.5 Å. The overall quality of cryo-EM structures is likely improved, as shown in a comparison of cryo-EM structures released before the end of 2016, those between 2017 and 2018, and those between 2018 and 2019. Our investigation shows that leucine (LEU) has a significantly higher rate of HBOS outliers than that of the reference data set (X-ray-1.5) and of other residue types in the cryo-EM data sets. HBOS was able to detect outliers for those residues that are currently marked as green in PDB validation reports. Conclusions: The HBOS profile of a dataset is a potential method to characterize the overall structural quality of the set. Residue LEU deserves special attention since it has a significantly higher HBOS outlier rate in sets of cryo-EM structures and those X-ray structures derived from X-ray data of lower than 2.5 Å resolutions. Most HBOS outlier residues from the EM-0-4-2019 set are located on loops for most types of residues

Magnetic properties of undoped Cu2O fine powders with magnetic impurities and/or cation vacancies

Fine powders of micron- and submicron-sized particles of undoped Cu2O semiconductor, with three different sizes and morphologies have been synthesized by different chemical processes. These samples include nanospheres 200 nm in diameter, octahedra of size 1 micron, and polyhedra of size 800 nm. They exhibit a wide spectrum of magnetic properties. At low temperature, T = 5 K, the octahedron sample is diamagnetic. The nanosphere is paramagnetic. The other two polyhedron samples synthesized in different runs by the same process are found to show different magnetic properties. One of them exhibits weak ferromagnetism with T_C = 455 K and saturation magnetization, M_S = 0.19 emu/g at T = 5 K, while the other is paramagnetic. The total magnetic moment estimated from the detected impurity concentration of Fe, Co, and Ni, is too small to account for the observed magnetism by one to two orders of magnitude. Calculations by the density functional theory (DFT) reveal that cation vacancies in the Cu2O lattice are one of the possible causes of induced magnetic moments. The results further predict that the defect-induced magnetic moments favour a ferromagnetically coupled ground state if the local concentration of cation vacancies, n_C, exceeds 12.5%. This offers a possible scenario to explain the observed magnetic properties. The limitations of the investigations in the present work, in particular in the theoretical calculations, are discussed and possible areas for further study are suggested.Comment: 20 pages, 5 figures 2 tables, submitted to J Phys Condense Matte

Distributed and Asynchronous Data Collection in Cognitive Radio Networks with Fairness Consideration

As a promising communication paradigm, Cognitive Radio Networks (CRNs) have paved a road for Secondary Users (SUs) to opportunistically exploit unused licensed spectrum without causing unacceptable interference to Primary Users (PUs). In this paper, we study the distributed data collection problem for asynchronous CRNs, which has not been addressed before. We study the Proper Carrier-sensing Range (PCR) for SUs. By working with this PCR, an SU can successfully conduct data transmission without disturbing the activities of PUs and other SUs. Subsequently, based on the PCR, we propose an Asynchronous Distributed Data Collection (ADDC) algorithm with fairness consideration for CRNs. ADDC collects a snapshot of data to the base station in a distributed manner without the time synchronization requirement. The algorithm is scalable and more practical compared with centralized and synchronized algorithms. Through comprehensive theoretical analysis, we show that ADDC is order-optimal in terms of delay and capacity, as long as an SU has a positive probability to access the spectrum. Furthermore, we extend ADDC to deal with the continuous data collection issue, and analyze the delay and capacity performances of ADDC for continuous data collection, which are also proven to be order-optimal. Finally, extensive simulation results indicate that ADDC can effectively accomplish a data collection task and significantly reduce data collection delay. [ABSTRACT FROM PUBLISHER

An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains

Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2-4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2-4 Å resolutions

NP and NS1 proteins of H5N1 virus significantly upregulated IFITM1, IFITM2, and IFITM3 in A549 cells

Background: Avian influence virus H5N1 causes serious public health concern with significant morbidity and mortality from poultry to humans. Interferon-induced transmembrane (IFITM) proteins usually protect cells from many virus infections by viral entry and replication.Objectives: The purpose of this study was to investigate whether H5N1 viral proteins involved in regulation IFITM1, IFITM2, and IFITM3 following H5N1 infection.Methods: NS1, M1, NP, PB2, HA and NA genes of H5N1 virus were generated by PCR and cloned into pcDNA3.1/myc-His (+) A vector for genes over-expression experiments. Gene expression levels was performed using Real-time PCR.Results: Research displayed that NS1, M1, NP, and PB2 proteins of H5N1 virus increased IFITM1, IFITM2, and IFITM3 expression in A549 cells, only IFITM1 was upregulated by M1 in HEK293T cells. However, our study did not find that HA and NA of H5N1 virus affected IFITM genes family or interferon genes expression.Conclusion: Taken together, our data suggested that IFITM1, IFITM2, and IFITM3 might be directly upregulated via NS1, M1, NP, and PB2 proteins during H5N1 avian influenza virus infection. This study provided new insights into the influence of NS1 and NP proteins on regulation of IFITM1, IFITM2, and IFITM3 expression following H5N1 infection.Keywords: Influenza Virus, H5N1, NS1 protein, NP protein, IFITMs

Analysis and optimization of a double-sided air-cored tubular generator

In this paper, the design and development of a double-sided air-cored tubular generator (DSTG) is presented. The characteristics of air-cored slot-less structures are investigated in terms of power density and efficiency. This is highly desirable for small- and medium-sized renewable energy conversion systems. In this paper, an analytical tool based on the magnetic vector potential method is built in order to achieve a fast but accurate method by which the machine is analyzed. The analytical model is validated by finite-element (FE) analysis. Further design improvements based on the analytical and FE models are then suggested in order to enhance the performance of the DSTG. The final design of the DSTG is validated by the test results from a developed prototype of the DSTG