ALBERT

Description: Background: In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity. Results: Analyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency 〉 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies. Conclusions: In this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.

Description: The physicochemical properties of soils might be affected by the addition of biomass black carbon, a special black carbon produced by incomplete combustion of biomass. Therefore, this study performed experiments to explore the effects of yak dung biomass black carbon (YBC) on physicochemical properties of soils in the northeastern Qinghai-Tibet Plateau. Three YBCs (pyrolyzed at 300, 500, and 700 °C) were separately added into four typical soils with three addition amounts (1%, 5%, and 10%). Changes of soil texture, pH, electrical conductivity (EC), cation exchange capacity (CEC), CHN contents, morphologies, functional groups, and mineral constituents of soils were comparatively studied. The results showed that addition of YBCs affected physicochemical properties of soils. Soil pH, EC, CEC, and carbon/nitrogen content were positively related with addition amount of YBCs. YBC particles were unevenly distributed among soil particles and positively related with addition amount. Addition of YBCs did not change texture, functional groups, and mineral constituents of soils. These results indicated that addition of YBC would be beneficial to stability of the soil ecosystem and sustainability of the northeastern Qinghai-Tibet Plateau.

Description: Background: As a major economic trait in chickens, egg weight (EW) receives widespread interests in breeding, production and consumption. However, limited information is available for underlying genetic architecture of longitudinal trend in EW. Herein, we measured EWs at nine time points from onset of laying to 60 week of age, and conducted comprehensive genome-wide association studies (GWAS) in 1,534 F 2 hens derived from reciprocal crosses between White Leghorn and Dongxiang chickens. Results: Egg weights at all ages except the first egg weight (FEW) exhibited high SNP-based heritability estimates (0.47 ~ 0.60). Strong pair-wise genetic correlations (0.77 ~ 1.00) were found among all EWs. Nine separate univariate genome-wide screens suggested 73 signals showing significant associations with longitudinal EWs. After multivariate and conditional analyses, four variants on three chromosomes remained independent contributions. The minor alleles at two loci exerted consistent and positive substitution effects on EWs, and other two were negative. The four loci together accounted for 3.84 % of the phenotypic variance for FEW and 7.29 ~ 11.06 % for EWs from 32 to 60 week of age. We obtained five candidate genes, of which NCAPG harbors a non-synonymous SNP (rs14491030) causing a valine-to-alanine amino-acid substitution. Genome partitioning analysis indicated a strong linear correlation between the variance explained by each chromosome and its length, which provided evidence that EW follows a highly polygenic nature of inheritance. Conclusions: Identification of significant genetic causes that together implicate EWs at different ages will greatly advance our understanding of the genetic basis behind longitudinal EWs, and would be helpful to illuminate the future breeding direction on how to select desired egg size.

Description: Understanding the risk factors of e-bike collisions can improve e-bike riders’ safety awareness and help traffic professionals to develop effective countermeasures. This study investigates risk factors that significantly contribute to the severity of e-bike collisions. Two months of e-bike collision data were collected in the city of Ningbo, China. A random parameters multinomial logit regression (RP-MNL) is proposed to account for the unobserved heterogeneity across observations. A fixed parameters multinomial logit regression (FP-MNL) is estimated and compared with the RP-MNL under the Bayesian framework. The full Bayesian approach based on Markov chain Monte Carlo simulation is employed to estimate the model parameters. Both parameter estimates and odds ratio (OR) are used to interpret the impact of risk factors on the severity of e-bike collisions. The model comparison results show that RP-MNL outperforms FP-MNL, indicating that accommodating the unobserved heterogeneity across observations could improve the model fit. The model estimation results show that age, gender, e-bike behavior, license plate, bicycle type, location, and speed limit are statistically significant and associated with the severity of e-bike collisions. Furthermore, four risk factors, i.e., gender, e-bike behavior, bicycle type, and speed limit, are found to have heterogeneous effects on severity of e-bike collisions, appearing in the form of random parameters in the statistical model.

Description: Intoxicated driving is a threat to both drivers and other road users. Exploring the association between intoxicated driving factors and traffic crashes is essential for taking effective countermeasures. Most previous works have studied the relation between intoxicated driving and traffic crash based on some large-sized cities. The current study aims to evaluate the effect of driving factors on traffic crashes among intoxicated drivers in a small-sized city in China. Descriptive statistics and binary logistic regression analysis are performed to guide the study, and the data (N = 1010) for the period 2016–2017 in Wujiang (i.e., a small-sized city in China) are employed as the target samples. The results demonstrate age, years of driving experience, road position, week, hour and blood alcohol concentration (BAC) are associated with traffic crashes in Wujiang. Specifically, the age of “18–25”, the years of driving experience of “≤2”, the “road intersection”, the “weekend”, the period of “0:00–6:59” and the BAC of “above 150 mg/100 mL” are more likely to cause traffic crashes among intoxicated drivers. The findings can be referred to make some targeted policies or measures to relieve Wujiang’s intoxicated driving situation and reduce the number of crashes caused by intoxicated driving.

Description: The Resistance-Harary index of a connected graph G is defined as R H ( G ) = ∑ { u , v } ⊆ V ( G ) 1 r ( u , v ) , where r ( u , v ) is the resistance distance between vertices u and v in G. A graph G is called a unicyclic graph if it contains exactly one cycle and a fully loaded unicyclic graph is a unicyclic graph that no vertex with degree less than three in its unique cycle. Let U ( n ) and U ( n ) be the set of unicyclic graphs and fully loaded unicyclic graphs of order n, respectively. In this paper, we determine the graphs of U ( n ) with second-largest Resistance-Harary index and determine the graphs of U ( n ) with largest Resistance-Harary index.

Description: In the ridesourcing industry, drivers are often unable to quickly and accurately locate the waiting position of riders, but patrol or wait on the road, which will seriously affect the management of the road traffic order. It may be a good idea to provide an online virtual site for the taxi to facilitate convergence of the rider and driver. The concept of recommended pick-up point is presented in this paper. At present, ridesourcing service platforms on the market have similar functions, but they do not take into account whether the setting of the pick-up point is compatible with the actual traffic environment, resulting in some problems. We have invented a method to select the recommended pick-up point by integrating various traffic influencing factors, so as to ensure that the setting of the pick-up point is compatible with the actual traffic situation, which consists of three steps. Firstly, we studied the rider’s maximum tolerable waiting time and defined an attractive walking range for riders based on the huge amount of data. In the second step, we analyzed spatial distribution characteristics of the taxi demand hotspot and determined candidate pick-up locations. Lastly, the fuzzy analytic hierarchy method was used to select the recommended pick-up point that is most conducive to traffic management from multiple candidate points. A case study was conducted to validate the proposed approach and experimental evidence showed that recommended results based on the approach are in line with the actual situation of the road, and conducive to road traffic management. This recommendation method is based on real ridesourcing orders data.

Description: Road traffic safety is a key concern of transport management as it has severely restricted Chinese economic and social development. With the objective to prevent and reduce road traffic crashes, this study proposes a comprehensive spatiotemporal analysis method that integrates the time-space cube analysis, spatial autocorrelation analysis, and emerging hot spot analysis for exploring the traffic crash evolution characteristics and identifying crash hot spots. These analyses are all conducted by the corresponding toolbox of ArcGIS 10.5. Then, a small sized-city of China (i.e., Wujiang) is selected as the case study, and the historical traffic crash data occurring at the road intersections of Wujiang for the year 2016 are analyzed by the proposed method. The analysis process identifies the high incidence locations of traffic crashes, then presents the spatial change trend and statistical significance of the crash locations. Finally, different types of crash hotspots, as well as their evolution patterns over time, are determined. The results illustrate that the traffic crash hotspots of road intersections are primarily distributed in the Northeast area of Wujiang’s major urban area, while the crash cold spots are concentrated in the Southwest of Wujiang, which points out the direction for crash prevention. In addition, the finding has a potential engineering application value, and it is of great significance to the sustainable development of Wujiang.

Description: Synaptic devices with bipolar analog resistive switching behavior are the building blocks for memristor-based neuromorphic computing. In this work, a fully complementary metal-oxide semiconductor (CMOS)-compatible, forming-free, and non-filamentary memristive device (Pd/Al2O3/TaOx/Ta) with bipolar analog switching behavior is reported as an artificial synapse for neuromorphic computing. Synaptic functions, including long-term potentiation/depression, paired-pulse facilitation (PPF), and spike-timing-dependent plasticity (STDP), are implemented based on this device; the switching energy is around 50 pJ per spike. Furthermore, for applications in artificial neural networks (ANN), determined target conductance states with little deviation (〈1%) can be obtained with random initial states. However, the device shows non-linear conductance change characteristics, and a nearly linear conductance change behavior is obtained by optimizing the training scheme. Based on these results, the device is a promising emulator for biology synapses, which could be of great benefit to memristor-based neuromorphic computing.

Description: Background: There is growing evidence supporting a role for microRNAs (miRNA) as targets in aberrant mechanisms of DNA hypermethylation. Epigenetic silencing of tumor suppressor miRNAs, including miR-663, which has recently been reported to be inactivated by hypermethylation in several cancers, may play important roles in pediatric acute myeloid leukemia (AML). However, expression of miR-663 and its promoter methylation remain status unclear in childhood leukemia. Methods: Promoter methylation status of miR-663 was investigated by methylation specific PCR (MSP) and bisulfate genomic sequencing (BGS). Transcriptional expression of miR-663 was evaluated by semi-quantitative and real-time PCR, and the relationship between expression of miR-663 and promoter methylation was confirmed using 5-aza-2[prime]-deoxycytidine (5-Aza) demethylation reagent. Results: MiR-663 was aberrantly methylated in 45.5% (5/11) leukemia cell lines; BGS showed that the promoter was significantly methylated in three AML cell lines; methylation of miR-663 was significantly higher in Chinese pediatric AML patients [41.4% (29/70)] compared to normal bone marrow (NBM) control samples [10.0% (3/30)]. These results were confirmed by both BGS and 5-Aza demethylation analysis. In addition, miR-663 transcript expression was significantly lower in AML patients, both with and without miR-663 methylation, compared to controls; however, there were no significant differences in clinical features or French-American-British (FAB) classification between patients with and without miR-663 methylation. Conclusions: Expression of miR-663 was significantly lower in pediatric AML cells compared to NBM controls; furthermore, a high frequency of miR-663 promoter hypermethylation was observed in both AML cell lines and pediatric AML samples. Inactivation of miR-663 by promoter hypermethylation could be affected by 5-Aza demethylation. These findings suggest that hypermethylation of the miR-663 promoter may be an early event in the development of pediatric AML.