Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm

Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the image can be captured using a single segmentation. In this paper, we present a segmentation-free approach to extract the gray-scale curve-like skeletons. The approach relies on a novel representation of the 3D image, where the image is modeled as a graph and a set of volume trees. A test containing 36 synthesized maps and one authentic map shows that our approach can improve the performance of the two tested tools used in de novo modeling. The improvements were 62 and 13 percent for Gorgon and DP-TOSS, respectively

A novel adaptive particle swarm optimization algorithm based high precision parameter identification and state estimation of lithium-ion battery.

Lithium-ion batteries are widely used in new energy vehicles, energy storage systems, aerospace and other fields because of their high energy density, long cycle life and high-cost performance. Accurate equivalent modeling, adaptive internal state characterization and accurate state of charge estimation are the cornerstones of expanding the application market of lithium-ion batteries. According to the highly nonlinear operating characteristics of lithium-ion batteries, the Thevenin equivalent model is used to characterize the operating characteristics of lithium-ion batteries, particle swarm optimization algorithm is used to process the measured data, and adaptive optimization strategy is added to improve the global search ability of particles, and the parameters of the model are identified innovatively. Combined with extended Kalman algorithm and Sage-Husa filtering algorithm, the state-of-charge estimation model of lithium ion battery is constructed. Aiming at the influence of fixed and inaccurate noise initial value in traditional Kalman filtering algorithm on SOC estimation results, Sage-Husa algorithm is used to adaptively correct system noise. The experimental results under HPPC condition show that the maximum error of the model is less than 1.5%. Simulation results of SOC estimation algorithm under two different operating conditions show that the maximum estimation error of adaptive extended Kalman algorithm is less than 0.05, which realizes high-precision lithium battery model parameter identification and high-precision state-of-charge estimation

Molecular genetic analysis of phosphomannomutase genes in Triticum monococcum

AbstractIn higher plants, phosphomannomutase (PMM) is essential for synthesizing the antioxidant ascorbic acid through the Smirnoff–Wheeler pathway. Previously, we characterized six PMM genes (TaPMM-A1, A2, B1, B2, D1 and D2) in common wheat (Triticum aestivum, AABBDD). Here, we report a molecular genetic analysis of PMM genes in Triticum monococcum (AmAm), a diploid wheat species whose Am genome is closely related to the A genome of common wheat. Two distinct PMM genes, TmPMM-1 and TmPMM-2, were found in T. monococcum. The coding region of TmPMM-1 was intact and highly conserved. In contrast, two main TmPMM-2 alleles were identified, with TmPMM-2a possessing an intact coding sequence and TmPMM-2b being a pseudogene. The transcript level of TmPMM-2a was much higher than that of TmPMM-2b, and a bacterially expressed TmPMM-2a recombinant protein displayed relatively high PMM activity. In general, the total transcript level of PMM was substantially higher in accessions carrying TmPMM-1 and TmPMM-2a than those harboring TmPMM-1 and TmPMM-2b. However, total PMM protein and activity levels did not differ drastically between the two genotypes. This work provides new information on PMM genes in T. monococcum and expands our understanding on Triticeae PMM genes, which may aid further functional and applied studies of PMM in crop plants

Theoretical Study on Relaxed Surrounding Rock Pressure on Shallow Bias Neighborhood Tunnels under Seismic Load

To study the distribution of relaxed surrounding rock pressure on the shallow bias neighborhood tunnels under the combined action of horizontal and vertical earthquake force, finite element software was used for failure mode analysis. Moreover, with the pseudo-static method, the calculation formula for the relaxed pressure on the shallow bias neighborhood tunnels was derived and used to analyze the variation of the rupture angle of these tunnels under the action of the seismic force. The study shows that: shallow bias neighborhood tunnels basically follow a “W” failure pattern under the combined action of horizontal and vertical seismic force, and the failure scope of the surrounding rock is controlled by four rupture angles. Rupture angles β2 and β3 between the deep and shallow tunnels of the shallow bias neighborhood tunnels are not affected by the surface slope. For tunnels with the same grade of the surrounding rock, the greater the seismic intensity, the smaller the value of β2, and the greater the value of β3. While at the same seismic intensity, the higher the grade of the surrounding rock, the smaller the β2 and β3. Ruptures angles β1 and β4 are influenced by the surface slope, seismic intensity and surrounding rock grades. A steeper surface slope leads to a smaller β1 and a greater β4; β1 increase and β4 decrease with increasing seismic intensity; while, β1 and β4 both show a decreasing trend with an increasing rock grade

SiO2 nanoparticles induce cytotoxicity and protein expression alteration in HaCaT cells

<p>Abstract</p> <p>Background</p> <p>Nanometer silicon dioxide (nano-SiO₂) has a wide variety of applications in material sciences, engineering and medicine; however, the potential cell biological and proteomic effects of nano-SiO₂exposure and the toxic mechanisms remain far from clear.</p> <p>Results</p> <p>Here, we evaluated the effects of amorphous nano-SiO₂(15-nm, 30-nm SiO₂). on cellular viability, cell cycle, apoptosis and protein expression in HaCaT cells by using biochemical and morphological analysis, two-dimensional differential gel electrophoresis (2D-DIGE) as well as mass spectrometry (MS). We found that the cellular viability of HaCaT cells was significantly decreased in a dose-dependent manner after the treatment of nano-SiO₂and micro-sized SiO₂particles. The IC₅₀value (50% concentration of inhibition) was associated with the size of SiO₂particles. Exposure to nano-SiO₂and micro-sized SiO₂particles also induced apoptosis in HaCaT cells in a dose-dependent manner. Furthermore, the smaller SiO₂particle size was, the higher apoptotic rate the cells underwent. The proteomic analysis revealed that 16 differentially expressed proteins were induced by SiO₂exposure, and that the expression levels of the differentially expressed proteins were associated with the particle size. The 16 proteins were identified by MALDI-TOF-TOF-MS analysis and could be classified into 5 categories according to their functions. They include oxidative stress-associated proteins; cytoskeleton-associated proteins; molecular chaperones; energy metabolism-associated proteins; apoptosis and tumor-associated proteins.</p> <p>Conclusions</p> <p>These results showed that nano-SiO₂exposure exerted toxic effects and altered protein expression in HaCaT cells. The data indicated the alterations of the proteins, such as the proteins associated with oxidative stress and apoptosis, could be involved in the toxic mechanisms of nano-SiO₂exposure.</p

Effect of Empoasca onukii Puncturing Aroma- and Taste-Active Metabolites of Qingxindamao Beauty Tea

To explore the effects of Empoasca onukii puncturing on metabolites in beauty tea produced from the cultivar Qingxindamao, sensory evaluation, ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and gas chromatography-mass spectrometry (GC-MS) were used to compare the sensory quality and metabolites of beauty tea processed from fresh tea leaves punctured or not punctured by E. onukii. The results showed that the quality of beauty tea with E. onukii puncturing was better. The contents of flavones, flavanols and their glycosides, phenolic acids, theaflavins, glycoside derivatives and tannins increased compared with beauty tea without E. onukii puncturing, while the contents of amino acids, saccharides and lipids decreased. Based on odor activity value (OAV) and partial least squares discriminant analysis (PLS-DA), a total of five characteristic volatile components, including geraniol, linalool, β-myrcene, methyl salicylate and D-limonene, were identified

Activation of Serotonin 2C Receptors in Dopamine Neurons Inhibits Binge-like Eating in Mice

Acknowledgments and Disclosures This work was supported by the National Institutes of Health (Grant Nos. R01DK093587 and R01DK101379 [to YX], R01DK092605 to [QT], R01DK078056 [to MM]), the Klarman Family Foundation (to YX), the Naman Family Fund for Basic Research (to YX), Curtis Hankamer Basic Research Fund (to YX), American Diabetes Association (Grant Nos. 7-13-JF-61 [to QW] and 1-15-BS-184 [to QT]), American Heart Association postdoctoral fellowship (to PX), Wellcome Trust (Grant No. WT098012 [to LKH]), and Biotechnology and Biological Sciences Research Council (Grant No. BB/K001418/1 [to LKH]). The anxiety tests (e.g., open-field test, light-dark test, elevated plus maze test) were performed in the Mouse Neurobehavior Core, Baylor College of Medicine, which was supported by National Institutes of Health Grant No. P30HD024064. PX and YH were involved in experimental design and most of the procedures, data acquisition and analyses, and writing the manuscript. XC assisted in the electrophysiological recordings; LV-T assisted in the histology study; XY, KS, CW, YY, AH, LZ, and GS assisted in surgical procedures and production of study mice. MGM, QW, QT, and LKH were involved in study design and writing the manuscript. YX is the guarantor of this work and, as such, had full access to all the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. The authors report no biomedical financial interests or potential conflicts of interest.Peer reviewedPublisher PD

Preservation of Simmental bull sperm at 0°C in Tris dilution: effect of dilution ratio and long-distance transport

Objective This study aimed to assess the impact of the dilution ratio of Tris diluent, storage at 0°C, and long-distance transportation on the spermatozoa of Simmental cattle. It also validated the feasibility of the regional distribution of fresh semen. Methods In experiment 1, semen was diluted at four dilution ratios (1:6, 1:9, 1:12, and 1:15) to determine the optimal dilution ratio of Tris diluent. In experiment 2, we assessed sperm viability, progressive motility (objectively assessed by computer-assisted sperm analyzer), and acrosome intactness in Tris dilutions kept at constant 0°C for 1, 3, 6, 9, and 12 days. We compared them to Tianshan livestock dilutions (Commercial diluent). In experiment 3, semen was diluted using Tris diluent, and sperm quality was measured before and after long-distance transport. Artificial insemination of 177 Simmental heifers compared to 156 using Tianshan Livestock dilution. Results The outcomes demonstrated that 1:9 was the ideal Tris diluent dilution ratio. The sperm viability, Progressive Motility, and acrosome integrity of both Tris and Tianshan dilutions preserved at 0°C gradually decreased over time. sperm viability was above 50% for both dilutions on d 9, with a flat rate of decline. The decrease in acrosome integrity rate was faster for Tianshan livestock dilutions than for Tris dilutions when stored at 0°C for 1 to 6 days. There was no significant difference (p>0.05) in sperm viability between semen preserved in Tris diluent after long-distance transportation and semen preserved in resting condition. The conception rates for Tris dilution and Tianshan livestock dilution were 49.15% and 46.15% respectively, with no significant difference (p>0.05). Conclusion This shows that Tris diluent is a good long-term protectant. It has been observed that fresh semen can be successfully preserved for long-distance transport when stored under 0°C conditions. Additionally, it is feasible to distribute semen regionally

Sociodemographic and obstetric characteristics of stillbirths in China: a census of nearly 4 million health facility births between 2012 and 2014

Background Very little is known about the burden and determinants of stillbirths in China. We used data from a national surveillance system for health facility births to compute a stillbirth rate representative of all facility births in China and to explore sociodemographic and obstetric factors associated with variation in the stillbirth rate. Methods We used data from China’s National Maternal Near Miss Surveillance System between Jan 1, 2012, and Dec 31, 2014, which covers 441 hospitals in 326 urban districts and rural counties. The surveillance aimed to enumerate all maternal deaths and near misses in health facilities, and collected data prospectively for all pregnant or post-partum women admitted to the obstetric department. We restricted the analysis to births of 28 or more completed weeks of gestation or 1000 g or heavier birthweight. We examined the strength of association between sociodemographic characteristics, gestational age, and obstetric complications and stillbirths using logistic regression, taking account of the sampling strategy and clustering of births within hospitals and in cases of more than one birth per woman. Findings There were 3 956 836 births and 37 855 stillbirths, giving a stillbirth rate of 8·8 per 1000 births (95% CI 8·8–8·9). The stillbirth rate was particularly high for women younger than 15 years of age (59·9 stillbirths per 1000 births), those who had not sought antenatal care (38·3 per 1000), the unmarried (32·5 per 1000), those with no education (26·9 per 1000), or those who had had four or more births (23·2 per 1000). A high proportion (29 319 [78·2%] of 37 514) of stillbirths occurred at gestational ages of younger than 37 weeks, and about two thirds (24 787 [66·1%] of 37 514) were in women without any maternal complication at the time of birth. Of babies born at normal gestations (37–41 weeks), maternal complications substantially increased the risk of stillbirth (odds ratio comparing antepartum or intrapartum complications with no complication 3·96 [95% CI 3·66–4·29]), but only a small proportion (1638 [4·4%] of 37 514) of stillbirths fell into this group. Interpretation Our analysis of nearly 4 million births in 441 health facilities in China suggests a stillbirth rate of 8·8 per 1000 births between 2012 and 2014. Stillbirths do not feature in the Chinese Government’s 5 year plans and most information systems do not include stillbirths. The Government need to start paying attention to stillbirths and invest strategically in antenatal care, particularly for the most disadvantaged women, including the very young, unmarried, and illiterate, and those at high parity