Positive selection analysis reveals the deep-sea adaptation of a hadal sea cucumber ( Paelopatides sp.) to the Mariana Trench

The Mariana Trench,the deepest trench on the earth,is ideal for deep-sea adaptation research due to its unique characters,such as the highest hydrostatic pressure on the Earth,constant ice-cold temperature,and eternal darkness.In this study,tissues of a the hadal holothurian(Paelopatides sp.)were fi xed with RNA later in situ at~6501-m depth in the Mariana Trench,which,to our knowledge,is the deepest in-situ fi xed animal sample.A high-quality transcript was obtained by de-novo transcriptome assembly.A maximum likelihood tree was constructed based on the single copy orthologs across nine species with their available omics data.To investigate deep-sea adaptation,113 positively selected genes(PSGs)were identifi ed in Paelopatides sp.Some PSGs such as microphthalmia-associated transcription factor(MITF)may contribute to the distinct phenotype of Paelopatides sp.,including its translucent white body and degenerated ossicles.At least eight PSGs(transcription factor 7-like 2[TCF7L2],ETS-related transcription factor Elf-2-like[ELF2],PERQ amino acid-rich with GYF domain-containing protein[GIGYF],cytochrome c oxidase subunit 7a,[COX7A],type I thyroxine 5′-deiodinase[DIO1],translation factor GUF1[GUF1],SWI/SNF related-matrix-associated actin-dependent regulator of chromatin subfamily C and subfamily E,member 1[SMARCC]and[SMARCE1])might be related to cold adaptation.In addition,at least nine PSGs(cell cycle checkpoint control protein[RAD9A],replication factor A3[RPA3],DNA-directed RNA polymerases I/II/III subunit RPABC1[POLR2E],putative TAR DNA-binding protein 43 isoform X2[TARDBP],ribonucleoside-diphosphate reductase subunit M1[RRM1],putative serine/threonine-protein kinase[SMG1],transcriptional regulator[ATRX],alkylated DNA repair protein alkB homolog 6[ALKBH6],and PLAC8 motif-containing protein[PLAC8])may facilitate the repair of DNA damage induced by the high hydrostatic pressure,coldness,and high concentration of cadmium in the upper Mariana Trench.

Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding

Cotton fiber is one of the main raw materials for the textile industry.In recent years,many cotton fiber quality QTL have been identified,but few were applied in breeding.In this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 QTL.Most of these QTL were ignored by only using GWAS.The CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain extent.Then these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in breeding.Additionally,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated currently.These findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

Genome-Wide Characterization of the Hyaluronidase Gene Family and Their Potential Roles in Viviparous Black Rockfish(Sebastes schlegeli)

Black rockfish(Sebastes schlegelii)has evolved viviparous reproduction mode.Different from the oviparous fishes,the spermatozoa of black rockfish are stored on the surface of ovarian follicle for over four months until the egg mature in ovary,while the adaptive evolution of fertilization-related genes remains to be studied.In the present study,based on the genome and transcriptome information of black rockfish,a total of 10 hyaluronidase genes were identified by phylogenetic and sequence analyses,including hyal1,hyal2,hyal3,hyal4,hyal6 and spam1a,spam1b,spam1c and spam1d.The spam1 subfamilies,including spam1a,spam1b,spam1c and spam1d,were significantly expanded compared to other species.The adaptive evolution of hyaluronidase was further investigated by selection pressure analysis of branch model and branch site model.The results showed that only spam1 subfamily was positively selected with a large number of positive selection sites,and the evolution rate was significantly higher thanthose of other teleosts.Two positively selected sites,LYS-171 and GLY-164,were located in the neutral hyaluronidase activity domain,which was pivotal for SPAM1 to participate in enzymatic hydrolysis of the extracellular hyaluronic acid matrix and mediate acrosome reaction in mammals.Furthermore,spam1 was mainly expressed in spermatocytes,secondary spermatocytes,and spermatids of testis,whereas it was not found in metamorphic sperm and mature sperm based on the spatiotemporal expression analysis.All results indicated that spam1 might originate from the testis and might be an adaptation of viviparous trait in black rockfish.

Whole-genome resequencing reveals molecular imprints of anthropogenic and natural selection in wild and domesticated sheep

The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying phenotypic variation induced by the domestication and improvement of sheep. In this study, to explore genomic diversity and selective regions at the genome level, we sequenced the genomes of 100 sheep across 10 breeds and combined these results with publicly available genomic data from 225 individuals, including improved breeds, Chinese indigenous breeds,African indigenous breeds, and their Asian mouflon ancestor. Based on population structure, the domesticated sheep formed a monophyletic group,while the Chinese indigenous sheep showed a clear geographical distribution trend. Comparative genomic analysis of domestication identified several selective signatures, including IFI44 and IFI44L genes and PANK2 and RNF24 genes, associated with immune response and visual function.Population genomic analysis of improvement demonstrated that candidate genes of selected regions were mainly associated with pigmentation,energy metabolism, and growth development.Furthermore, the IFI44 and IFI44L genes showed a common selection signature in the genomes of 30domesticated sheep breeds. The IFI44 c. 54413058C>G mutation was selected for genotyping and population genetic validation. Results showed that the IFI44 polymorphism was significantly associated with partial immune traits. Our findings identified the population genetic basis of domesticated sheep at the whole-genome level, providing theoretical insights into the molecular mechanism underlying breed characteristics and phenotypic changes during sheep domestication and improvement.

Isolation and phylogenetic analysis of feline calicivirus strains from various region of China

Feline calicivirus(FCV)is an important feline pathogen mainly causing upper respiratory tract disease,conjunctivitis,and stomatitis,and it is classifed into genotype I and genotype II.To investigate the prevalence and molecular characteristics of FCV,this study collected 337 cat swab samples from animal hospitals in diferent regions of China from 2019 to 2021.The positive detection rate of FCV was 29.9%(101/337)by RT-PCR.Statistical analysis showed that FCV prevalence was signifcantly associated with living environment(p=0.0004),age(p=0.031)and clinical symptoms(p=0.00),but not with sex(p=0.092)and breed(p=0.171).The 26 strains of FCV were isolated using F81 cells.Phylogenetic analysis showed that 10 isolates belonged to genotype I,and 16 isolates belonged to genotype II.These 26 isolates were highly genetically diverse,of which HB7 isolate had three same virulence-related amino acid loci with VSD strains.Potential loci distinguishing diferent genotypes were identifed from 26 isolates,suggesting the genetic relationship between diferent genotypes.In addition,selection pressure analysis based on capsid protein of 26 isolates revealed that the protein is under diversifying selection.This study reveals the genetic diversity of FCV and provides a reference for the screening of vaccine candidate strains and the development of vaccines with better cross-protection efects.

Scenario-based approach for project portfolio selection in army engineering and manufacturing development

The decisions concerning portfolio selection for army engineering and manufacturing development projects determine the benefit of those projects to the country concerned.Projects are typically selected based on ex ante estimates of future return values,which are usually difficult to specify or only generated after project launch.A scenario-based approach is presented here to address the problem of selecting a project portfolio under incomplete scenario information and interdependency constraints.In the first stage,the relevant dominance concepts of scenario analysis are studied to handle the incomplete information.Then,a scenario-based programming approach is proposed to handle the interdependencies to obtain the projects,whose return values are multi-criteria with interval data.Finally,an illustrative example of army engineering and manufacturing development shows the feasibility and advantages of the scenario-based multi-objective programming approach.

S. E. M. analysis of quartz sand grains from selected Hong Kong and Chinese littoral environments

This pilot study attempts to demonstrate some underlying scanning electron microscopy themes of quartz grain surface textures. A variety of textural patterns and individual features are described for grains selected from various littoral environments. An attempt was made to differentiate samples on surface textures alone, but limitations of using this technique in sedimentological isolation were apparent. Statistical analysis of checklist data and photographic evidence revealed some of the more important feature combinations used in environmental diagnosis. The use of discriminant analysis provided quantitative sample separation.

A select link analysis method based on logit–weibit hybrid model

Select link analysis provides information of where traffic comes from and goes to at selected links.This disaggregate information has wide applications in practice.The state-of-the-art planning software packages often adopt the user equilibrium(UE) model for select link analysis.However,empirical studies have repeatedly revealed that the stochastic user equilibrium model more accurately predicts observed mean and variance of choices than the UE model.This paper proposes an alternative select link analysis method by making use of the recently developed logit–weibit hybrid model,to alleviate the drawbacks of both logit and weibit models while keeping a closed-form route choice probability expression.To enhance the applicability in large-scale networks,Bell’s stochastic loading method originally developed for logit model is adapted to the hybrid model.The features of the proposed method are twofold:(1) unique O–D-specific link flow pattern and more plausible behavioral realism attributed to the hybrid route choice model and(2) applicability in large-scale networks due to the link-based stochastic loading method.An illustrative network example and a case study in a large-scale network are conducted to demonstrate the efficiency and effectiveness of the proposed select link analysis method as well as applications of O–D-specific link flow information.A visualizationmethod is also proposed to enhance the understanding of O–D-specific link flow originally in the form of a matrix.

Optimization of Selecting Air Conditioning Cold/Heat Sources with Grey Relation Analysis

Selection of air conditioning（AC） cold/heat sources generally concerns about certain aspects and cannot reveal the whole profile of the problems. Grey relation analysis （GRA） is a data processing method to categorize the correlation extent of compared sequences and a certain reference sequence in a system with uncertain information. It is applied to evaluating and selecting AC cold/heat sources from four main aspects, which are technology, economy, reliability, and operation and management. Case study shows that the result for selecting AC cold/heat sources with the GRA method can be more reasonable and convincible. Thus it offers a new approach for designers in heating, ventilating and air conditioning field to compare and evaluate different AC cold/heat sou rces.

SELECTIVE SULFUR DIOXIDE DETERMINATION BY GAS DIFFUSION FLOW INJECTION ANALYSIS WITH CHEMILUMINESCENT DETECTION

Sulfur dioxide has been found to decrease the chemiluminescence of luminol-iodine system.A new determination method for sulfur dioxide in atmosphere is developed by applying this reaction to a flow injection gas diffusion separation system.This permits the determination of sulfur dioxide selectively and rapidly.

Identifying QTL and candidate genes for prolificacy in maize

In maize,prolificacy,the number of ears per plant,is a trait of interest to maize breeders for breeding high grain-yielding cultivars or specialty corn,as well as being a model trait for decoding the molecular mechanism of maize evolution.Its genetic basis remains largely unknown.We identified a stable quantitative trait locus,qEN7,for ear number on chromosome 7 in both F2 and F2:3 populations derived from a single cross between the nonprolific inbred line Mo17 and the prolific inbred line LAN404 derived from the landrace PI217404.qEN7 explained 10.7%-11.9%of phenotypic variation,and the LAN404 allele at this locus was associated with an increase of around one ear per plant.qEN7 was confined by fine-mapping to a 0.56-Mb region containing eight annotated genes.Analysis of selection,gene expression patterns in various maize tissues,and sequence polymorphisms between the two parental lines suggested that Zm00001d020683,which encodes a putative INDETERMINATE DOMAIN(IDD)transcription factor,is the most likely candidate gene underlying qEN7.Zm00001d020683 is expressed mainly in the vegetative meristem,immature ears,and internodes and has undergone selection during maize improvement.The identification of qEN7 and the prediction of its candidate gene sheds some light on the evolution of maize ear number and provides a novel resource for breeding of multi-ear maize cultivars.

A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken

Background:Egg production is economically important in the meat-type chicken industry.To better understand the molecular genetic mechanism of egg production in meat-type chicken,genetic parameter estimation,genome-wide association analyses combined with meta-analyses,Bayesian analyses,and selective sweep analyses were performed to screen single nucleotide polymorphisms(SNPs)and other genetic loci that were significantly associated with egg number traits in 11,279 chickens from seven material lines.Results:Yellow-feathered meat-type chickens laid 115 eggs at 43 weeks of age and white-feathered chickens laid 143 eggs at 60 weeks of age,with heritability ranging from 0.034–0.258.Based on meta-analyses and selective sweep analyses,one region(10.81–13.05 Mb)on chromosome Z was associated with egg number in all lines.Further analyses using the W2 line was also associated with the same region,and 29 SNPs were identified that significantly affected estimation of breeding value of egg numbers.The 29 SNPs were identified as having a significant effect on the egg number EBV in 3194 birds in line W2.There are 36 genes in the region,with glial cell derived neurotrophic factor,DAB adaptor protein 2,protein kinase AMP-activated catalytic subunit alpha 1,NAD kinase 2,mitochondrial,WD repeat domain 70,leukemia inhibitory factor receptor alpha,complement C6,and complement C7 identified as being potentially affecting to egg number.In addition,three SNPs(rs318154184,rs13769886,and rs313325646)associated with egg number were located on or near the prolactin receptor gene.Conclusion:Our study used genomic information from different chicken lines and populations to identify a genomic region(spanning 2.24 Mb)associated with egg number.Nine genes and 29 SNPs were identified as the most likely candidate genes and variations for egg production.These results contribute to the identification of candidate genes and variants for egg traits in poultry.

PRECIPITATION HARDENING OF ELINVAR ALLOY

The microstructural evolution and precipitation hardening of an Elinvar alloy doped with Ti and Al during isothermal aging at 700℃ have been investigated by atom probe field ion microscopy and microhardness measurements.The γ′ precipiates are spherical and coherent with the matrix.The chemical composition of the precipitates are(Ni_(0.53)Fe_(0.47)_3 (Ti_(0.(?))Al_(0.4)). During aging,a Lifshitz-Wagner type dissolution and coarsening reaction of the precipitates has been observed,The hardness of the material varies with the aging time and reaches maxi- mum when the average diameter of the precipitates was about 11 nm.

Geographical classification of Nanfeng mandarin by near infrared spectroscopy coupled with chemometrics methods

Near infrared spectroscopy(NIRS),coupled with principal component analysis and wavelength selection techniques,has been sed to develop a robust and reliable reduced-spectrum classifi-cation model for determining the geographical origins of Nanfeng mandarins.The application of the changeable size moving window principal component analysis(CSMWPCA)provided a notably improved lassification model,with correct classification rates of 92.00%,100.00%,90.00%,100.00%,100.00%,100.00%and 100.00%for Fujian,Guangxi,Hunan,Baishe,Baofeng,Qiawan,Sanxi samples,respectively,as well as,a total dassification rate of 97.52%in the wavelength range from 1007 to 1296 nm.To test and apply the proposed method,the procedure was applied to the analysis of 59 samples in an independent test set.Good identification results(correct rate of 96.61%)were also received.The improvement achieved by the application of CSMWPCA method was particularly remarkable when taking the low complexities of the final model(290 variables)into account.The results of the study showed the great potential of NIRS as a fast,nondestructive and environmentally acceptable method for the rapid and reliable determination for geographical classifcation of Nanfeng mandarins.

Motion capability analysis of a quadruped robot as a parallel manipulator

This paper presents the forward and inverse displacement analysis of a quadruped robot MANA as a parallel manipulator in quadruple stance phase, which is used to obtain the workspace and control the motion of the body. The robot MANA designed on the basis of the structure of quadruped mammal is able to not only walk and turn in the uneven terrain, but also accomplish various manipulating tasks as a parallel manipulator in quadruple stance phase. The latter will be the focus of this paper, however. For this purpose, the leg kinematics is primarily analyzed, which lays the foundation on the gait planning in terms of locomotion and body kinematics analysis as a parallel manipulator. When all four feet of the robot contact on the ground, by assuming there is no slipping at the feet, each contacting point is treated as a passive spherical joint and the kinematic model of parallel manipulator is established. The method for choosing six non-redundant actuated joints for the parallel manipulator from all twelve optional joints is elaborated. The inverse and forward displacement analysis of the parallel manipulator is carried out using the method of coordinate transformation. Finally, based on the inverse and forward kinematic model, two issues on obtaining the reachable workspace of parallel manipulator and planning the motion of the body are implemented and verified by ADAMS simulation.

Microstructure and Fracture Behavior of 316L Austenitic Stainless Steel Produced by Selective Laser Melting

Selective laser melting is an additive manufacturing method based on local melting of a metal powder bed by a high power laser beam. Fast laser scans are responsible for severe thermal gradients and high cooling rates which produce complex hydrodynamic fluid flow. These phenomena affect crystal growth and orientation and are believed to be the cause of material spattering and microstructural defects, e.g. pores and incompletely melted particles. In this work, the microstructure and texture of 316L bars built along two different orientations and the effect of different distribution of defects on their mechanical response and failure mechanisms were investigated. Partially molten powder particles are believed to be responsible for the scattering in elongation to failure, reduced strength, and premature failure of vertical samples.

Research on a forecasting model of tourism traffic volume in theme parks in China

In this study,a model based on multiple regression analysis is developed to forecast the tourism traffic volume of theme parks.First,the macro,meso and micro factors affecting traffic passenger volume are analysed.Second,SPSS software is used for multivariate regression analysis on data for 10 theme parks from 2014.A tourism traffic volume forecasting model is then proposed.Finally,related data for 2015 is used to validate the model,with results showing a prediction error of 14.1%.All results show that the model has a high predictive ability.

Measuring air traffic complexity based on small samples

Air traffic complexity is an objective metric for evaluating the operational condition of the airspace. It has several applications, such as airspace design and traffic flow management.Therefore, identifying a reliable method to accurately measure traffic complexity is important. Considering that many factors correlate with traffic complexity in complicated nonlinear ways,researchers have proposed several complexity evaluation methods based on machine learning models which were trained with large samples. However, the high cost of sample collection usually results in limited training set. In this paper, an ensemble learning model is proposed for measuring air traffic complexity within a sector based on small samples. To exploit the classification information within each factor, multiple diverse factor subsets（FSSs） are generated under guidance from factor noise and independence analysis. Then, a base complexity evaluator is built corresponding to each FSS. The final complexity evaluation result is obtained by integrating all results from the base evaluators. Experimental studies using real-world air traffic operation data demonstrate the advantages of our model for small-sample-based traffic complexity evaluation over other stateof-the-art methods.

Surface composition change of chlorine-doped catalyst Ni(Clx)/CeO2 in methanation reaction

The oxide sample NiO/CeO_2 with feed atomic ratio of Ni/Ce at 40%, prepared by co-precipitation method and calcination at 500 oC for 2 h, was impregnated by aqueous solution of NH_4Cl to dope chlorine ions. After the impregnated samples were dried and calcined at 400 oC for 2 h, the calcined samples NiO（Cl_x）/CeO_2（x=0.1–0.5） were characterized by means of X-ray diffraction（XRD） and temperature programmed reduction（TPR） techniques. It was comfirmed that the doped chlorine ions hindered reduction of Ni^（2＋） ions in the calcined samples, and suppressed adsorption of CO_2 and CO on the reduced sample Ni（Cl_（0.3））/CeO_2. The reduced samples Ni（Cl_x）/CeO_2（x=0.0–0.5） were used as catalysts for selective methanation of CO in H_2-rich gas. When chlorine ions were doped at the feed atomic ratio of Cl/Ce（x） equal to 0.3–0.5, CO in the H_2-rich gas could be removed to below 10 ppm with a high selectivity more than 50% in a wide reaction temperature range of 220–280 oC. However, the selectivity of CO methanation decreased with reaction time in the durability tests over the catalyst Ni（Cl_（0.3））/CeO_2 at the reaction temperature of 260 oC and even at 220 oC. The lowering of the selectivity was found to be related with the surface composition change of the catalyst in the catalytic reaction.

Analyzing Electricity Consumption via Data Mining

This paper proposes a model to analyze the massive data of electricity.Feature subset is determined by the correla-tion-based feature selection and the data-driven methods.The attribute season can be classified successfully through five classi-fiers using the selected feature subset,and the best model can be determined further.The effects on analyzing electricity consump-tion of the other three attributes,including months,businesses,and meters,can be estimated using the chosen model.The data used for the project is provided by Beijing Power Supply Bureau.We use WEKA as the machine learning tool.The models we built are promising for electricity scheduling and power theft detection.