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Using whole-genome sequence (WGS) data are supposed to be optimal for genome-wide association studies and genomic predictions. However, sequencing thousands of individuals of interest is expensive. Imputation from single nucleotide polymorphisms panels to WGS data is an attractive approach to obtain highly reliable WGS data at low cost. Here, we conducted a genotype imputation study with a combined reference panel in yellow-feather dwarf broiler population. The combined reference panel was assembled by sequencing 24 key individuals of a yellow-feather dwarf broiler population (internal reference panel) and WGS data from 311 chickens in public databases (external reference panel). Three scenarios were investigated to determine how different factors affect the accuracy of imputation from 600 K array data to WGS data, including: genotype imputation with internal, external and combined reference panels; the number of internal reference individuals in the combined reference panel; and different reference sizes and selection strategies of an external reference panel. Results showed that imputation accuracy from 600 K to WGS data were 0.834±0.012, 0.920±0.007 and 0.982±0.003 for the internal, external and combined reference panels, respectively. Increasing the reference size from 50 to 250 improved the accuracy of genotype imputation from 0.848 to 0.974 for the combined reference panel and from 0.647 to 0.917 for the external reference panel. The selection strategies for the external reference panel had no impact on the accuracy of imputation using the combined reference panel. However, if only an external reference panel with reference size >50 was used, the selection strategy of minimizing the average distance to the closest leaf had the greatest imputation accuracy compared with other methods. Generally, using a combined reference panel provided greater imputation accuracy, especially for low-frequency variants. In conclusion, the optimal imputation strategy with a combined reference panel should comprehensively consider genetic diversity of the study population, availability and properties of external reference panels, sequencing and computing costs, and frequency of imputed variants. This work sheds light on how to design and execute genotype imputation with a combined external reference panel in a livestock population.
The discovery of the first electromagnetic counterpart to a gravitational wave signal has generated follow-up observations by over 50 facilities world-wide, ushering in the new era of multi-messenger astronomy. In this paper, we present follow-up observations of the gravitational wave event GW170817 and its electromagnetic counterpart SSS17a/DLT17ck (IAU label AT2017gfo) by 14 Australian telescopes and partner observatories as part of Australian-based and Australian-led research programs. We report early- to late-time multi-wavelength observations, including optical imaging and spectroscopy, mid-infrared imaging, radio imaging, and searches for fast radio bursts. Our optical spectra reveal that the transient source emission cooled from approximately 6 400 K to 2 100 K over a 7-d period and produced no significant optical emission lines. The spectral profiles, cooling rate, and photometric light curves are consistent with the expected outburst and subsequent processes of a binary neutron star merger. Star formation in the host galaxy probably ceased at least a Gyr ago, although there is evidence for a galaxy merger. Binary pulsars with short (100 Myr) decay times are therefore unlikely progenitors, but pulsars like PSR B1534+12 with its 2.7 Gyr coalescence time could produce such a merger. The displacement (~2.2 kpc) of the binary star system from the centre of the main galaxy is not unusual for stars in the host galaxy or stars originating in the merging galaxy, and therefore any constraints on the kick velocity imparted to the progenitor are poor.
G22 is a hub-filament system composed of four supercritical filaments. Velocity gradients are detected along three filaments. A total mass infall rate of 700 M⊙ Myr−1 would double the hub mass in about three free-fall times. The most massive clump C1 would be in global collapse with an infall velocity of 0.26 km s−1 and a mass infall rate of 5 × 10−4M⊙ yr−1, which is supported by the prevalent HCO+ (3-2) and 13CO (3-2) blue profiles. A hot molecular core (SMA1) was revealed in C1. At the SMA1 center, there is a massive protostar (MIR1) driving multipolar outflows which are associated with clusters of class I methanol masers. MIR1 may be still growing with an accretion rate of 7 × 10−5M⊙ yr−1. Filamentary flows, clump-scale collapse, core-scale accretion coexist in G22, suggesting that high-mass starless cores may not be prerequisite to form high-mass stars. In the high-mass star formation process, the central protostar, the core, and the clump can grow in mass simultaneously.
Biomimetic motions are helpful to underwater vehicles and new conception airplanes design. The lattice Boltzmann method with an immersed boundary method technique is used to reveal the propulsion and lift enhancement mechanism of biomimetic motions. The flow past a sphere and an ellipsoidal flapping wing were validated respectively by comparing with other numerical methods. Then a single flapping wing and three flapping wings in a tandem arrangement are accomplished respectively. It founds that the mean thrust coefficient of three plate wings is bigger than the one of the single plate wing. Three ellipsoidal wings and single ellipsoidal wing are compared. It shows that the single ellipsoidal wing has larger thrust coefficients than the three ellipsoidal wings. Ellipsoidal flapping wing and plate wing were further compared to investigate the influence of wing shape. It indicates the mean thrust coefficient of the ellipsoidal wing is bigger than the plate wing.
Using the spectroscopic distances of over 0.12 million A-type stars selected from the LAMOST Spectroscopic Survey of the Galactic Anti-center (LSS-GAC), we map their three-dimensional number density distributions in the Galaxy. These stellar number density maps allow an investigation of the Galactic young age thin disk structure with no a priori assumptions about the functional form of its components. The data show strong evidence for a significant flaring young disk. A more detail analysis show that the stellar flaring have different behaviours between the Northern and the Southern Galactic disks. The maps also reveal spatially coherent, kpc-scale stellar substructure in the thin disk. Finally, we detect the Perseus arm stellar overdensity at R ~ 10 kpc.
The pressure oscillation and terminal shock motion in a two dimensional inlet, which was designed for tandem configuration turbine-based combined cycle propulsion systems was investigated experimentally and numerically, respectively. The inlet was characterised by a bleed cavity upstream the inlet throat, an S-shape rectangular-to-circular diffuser and flowpaths for a turbine and a ramjet engine. The terminal shock motion was calculated through a second-order unsteady Reynolds-averaged Navier-Stokes scheme. The pressure and the terminal shock were unsteady when the combined cycle inlet operated at different conditions. With the terminal shock located in the throat and at the shoulder of the third ramp of the TBCC inlet, the pressure oscillation was significant and the shock exhibited unsteady streamwise motion with an oscillatory pattern. The amplitude of shock oscillation at these two conditions was 6mm and 12mm, respectively. When the shock was located downstream of the throat and upstream of the cowl lip, it oscillated in a small range. We defined this motion as the “shake” of the shock. This unsteady behaviour of the shock was caused by flow separation in the combined cycle inlet diffuser.
Foxtail millet (Setaria italica (L.) P. Beauv.) is a naturally stress-tolerant plant, a major reserve crop and a model for panicoid grasses. The recent completion of the S. italica genome facilitates identification and characterization of WRKY transcription factor family proteins that are important regulators of major plant processes, including growth, development and stress response. The present study identified 103 WRKY transcription factor-encoding genes in the S. italica genome. The genes were named SiWRKY1–SiWRKY103 according to their order on the chromosomes. A comprehensive expression analysis of SiWRKY genes among four different tissues was performed using publicly available RNA sequencing data. Eighty-four SiWRKY genes were more highly expressed in root tissue than in other tissues and nine genes were only expressed in roots. Additionally, real-time quantitative polymerase chain reaction was performed to comprehensively analyse the expression of all SiWRKY genes in response to dehydration. Results indicated that most SiWRKY genes (over 0.8) were up-regulated by drought stress. In conclusion, genome-wide identification and expression profiling of SiWRKY genes provided a set of candidates for cloning and functional analyses in plants’ response to drought stress.
Ectropis grisescens Warren and Ectropis obliqua (Prout) are two morphologically similar sibling species with overlapping ranges. In this study, manipulative laboratory experiments were conducted to examine the possibility of reproductive interference in sympatric populations of E. grisescens and E. obliqua and the potential consequences of the mating interaction. Our results showed that the presence of males or females of different species could incur mating interference and significant reduction of F1 offspring. The reduction was not significant relevant to the initial relative abundance of E. grisescens and E. obliqua. Detailed observations of mating opportunity showed that female mating frequencies of both species were not significantly affected by the absolute species density, but the mating success of E. obliqua females with conspecific males depended on species ratio. In addition, adding males to the other species resulted in lower number of offspring suggesting that the males’ behaviour might be linked with mating interference. Males of both E. grisescens and E. obliqua could interfere the intraspecific mating of the other species, but the impact of the mating interference differed. These combined data indicated that asymmetric reproductive interference existed in E. grisescens and E. obliqua under laboratory conditions, and the offspring of the mixed species were significantly reduced. The long term outcome of this effect is yet to be determined since additional reproductive factors such as oviposition rate and progeny survival to adulthood may reduce the probability of demographic displacement of one species by the other in overlapping niches.
The analysis method is developed to obtain dynamic characteristics of the rotating cantilever plate with thermal shock and tip-rub. Based on the variational principle, equations of motion are derived considering the differences between rubbing forces in the width direction of the plate. The transverse deformation is decomposed into quasi-static deformation of the cantilever plate with thermal shock and dynamic deformation of the rubbing plate under thermal shock. Then deformations are obtained through the calculation of modal characteristics of rotating cantilever plate and temperature distribution function. Special attention is paid to the influence of tip-rub and thermal shock on the plate. The results show that tip-rub has the characteristics of multiple frequency vibrations, and high frequency vibrations are significant. On the contrary, thermal shock shows the low frequency vibrations. The thermal shock makes the rubbing plate gradually change into low frequency vibrations. Because rub-induced vibrations are more complicated than those caused by thermal shock, tip-rub is easier to result in the destruction of the blade. The increasing friction coefficient intensifies vibrations of the rubbing plate. Minimizing friction coefficients can be an effective way to reduce rub-induced damage through reducing the surface roughness between the blade tip and the inner surface of the casing.
Peripheral blood viral load is an important indicator of viral production and clearance. Previous studies have suggested that viral load might predict the rate of decrease in CD4+ cell count and progression to AIDS and death. Here, we conducted a retrospective analysis of the trends in HIV-1 viral load in southeast China. Among inpatients newly diagnosed with HIV infection, we found that viral load has increased over the past decade from 4·20 log10 copies/ml in 2002 to 6·61 log10 copies/ml in 2014, with a mean increase of 0·19 log10 copies/ml each year. However, the CD4+ cell count was stable and insensitive to changes in viral load. Thus, increasing viral load appears to be an emerging trend in newly diagnosed HIV-infected inpatients.
We compiled a sample of 57 galaxies with spectroscopically confirmed redshifts and SPIRE detections in all three bands at z = 2.5-6.4, and compared their SPIRE colors with SED templates from local and high-z libraries. We find that local calibrations are inconsistent with high-z observations. For high-z libraries, the templates with an evolution from z = 0 to 3 can describe the average colors of the observations at high redshift well. Based on the templates, we defined color cuts to divide the SPIRE color-color diagram into different regions with different mean redshifts. We tested this method and two other color cut methods using a larger sample (783 galaxies) with photometric redshifts. We find that these color cuts can separate the sample into subsamples with different mean redshifts, but the dispersion of redshifts in each subsample is considerably large. Additional information is needed for better sampling.
Gray matter (GM) atrophy and disrupted intrinsic functional connectivity (IFC) are often present in patients with amnestic mild cognitive impairment (aMCI), which shows high risk of developing into Alzheimer's disease. Little is known, however, about the relationship between GM atrophy and altered IFC, and whether they are related to cognitive decline.
A total of 30 aMCI and 26 cognitively normal (CN) subjects were recruited for this study. Optimized voxel-based morphometric and resting-state functional connectivity magnetic resonance imaging approaches were performed to measure the GM volumes (GMVs) and atrophy-related IFC, respectively. Multivariate linear regression analysis was used to examine the effects of GM atrophy and IFC on cognitive performance across subjects, after controlling for the effects of age, education, gender and group.
Compared with CN subjects, aMCI subjects showed significantly reduced GMVs and decreased IFC in the frontal-parietal and medial temporal lobe systems. Multivariate regression analysis further demonstrated that the GMVs and decreased IFC simultaneously affected the cognitive function. Specifically, GMVs were positively correlated with cognitive performances, including global cognition and episodic memory, and showed a strong trend in correlation between GMVs and non-episodic memory, whilst IFC was positively correlated with the above three cognitive measures, across all subjects. In addition, significant correlation was found between GMVs and altered IFC strength across all subjects.
Our findings demonstrated that GMVs and IFC jointly contribute to cognitive performance, and combining quantitative information about GMVs and the strength of functional connectivity may serve as an indicator of cognitive deficits in non-demented elderly.
The first human infection with avian influenza A(H7N9) virus was reported in Shanghai, China in March 2013. An additional 32 cases of human H7N9 infection were identified in the following months from March to April 2013 in Shanghai. Here we conducted a case-control study of the patients with H7N9 infection (n = 25) using controls matched by age, sex, and residence to determine risk factors for H7N9 infection. Our findings suggest that chronic disease and frequency of visiting a live poultry market (>10 times, or 1–9 times during the 2 weeks before illness onset) were likely to be significantly associated with H7N9 infection, with the odds ratios being 4·07 [95% confidence interval (CI) 1·32–12·56], 10·61 (95% CI 1·85–60·74), and 3·76 (95% CI 1·31–10·79), respectively. Effective strategies for live poultry market control should be reinforced and ongoing education of the public is warranted to promote behavioural changes that can help to eliminate direct or indirect contact with influenza A(H7N9) virus.
In this talk, we will show the beaming effect for Fermi/LAT blazars, then we discuss the correlations between γ-ray luminosity and other parameters, such as radio Doppler factors, superluminal motions, and core-dominance parameters. We also compare the Doppler factors determined from the γ-ray luminosity, X-ray emissions, and the short-term time scales with those from other methods. Our discussions suggest that γ-ray emissions may be strongly beamed.
Variability is one of the extreme observational properties of BL Lacertae objects. AO 0235+164 is a well studied BL Lac through the whole electro-magnetic wavebands, it is violently variable in the optical bands. In the present work, we show its optical R band photometric observations carried out during the period of Nov. 2006 to Dec. 2012 using the Ap6E CCD camera attached to the primary focus of the 70 cm meniscus telescope at Abastumani Observatory, Georgia. It shows a large variation of ΔR = 4.88 mag (14.20 - 19.08 mag) during our monitoring period. When periodicity analysis methods are adopted to its R observations from our Abastumani monitoring programme and those in the literature, the signs of some periods, P1 = 8.26 yr, P2 = 0.55 yr, P3 = 0.85 yr, P4 = 1.99 yr are found.
In this work, we reported the optical photometry monitoring results for two brightest nearby quasars, PHL 1811 and 3C 273 using the ST-6 camera at Abastumani Observatory, Georgia. For PHL 1811, we found 3 microvariability events with time scale of ΔT = 6.0 min. For 3C273, we found that the largest variations are ΔV = 0.369 ± 0.028 mag, ΔR = 0.495 ± 0.076 mag, and ΔI = 0.355 ± 0.009 mag. When periodicity analysis methods are adopted to the available data, a period of p = 5.80 ± 1.12 years is obtained for PHL 1811, and p = 21.10 ± 0.14, 10.00 ± 0.14, 7.30 ± 0.09, 13.20 ± 0.09, 2.10 ± 0.06, and 0.68 ± 0.05 years are obtained for 3C 273.
Stars are tidally disrupted and accreted when they approach massive black holes (MBHs) closely, producing a flare of electromagnetic radiation. The majority of the (approximately two dozen) tidal disruption events (TDEs) identified so far have been discovered by their luminous, transient X-ray emission. Once TDEs are detected in much larger numbers, in future dedicated transient surveys, a wealth of new applications will become possible. Here, we present the proposed Einstein Probe mission, which is a dedicated time-domain soft X-ray all-sky monitor aiming at detecting X-ray transients including TDEs in large numbers. The mission consists of a wide-field micro-pore Lobster-eye imager (60° × 60°), and is designed to carry out an all-sky transient survey at energies of 0.5-4 keV. It will also carry a more sensitive telescope for X-ray follow-ups, and will be capable of issuing public transient alerts rapidly. Einstein Probe is expected to revolutionise the field of TDE research by detecting several tens to hundreds of events per year from the early phase of flares, many with long-term, well sampled lightcurves.
Narrow-line Seyfert 1 (NLS1) galaxies are a sub-class of active galactic nuclei (AGN) with relatively low-mass black holes, accreting near the Eddington rate. A small fraction of them is radio-loud and harbors relativistic jets. As a class, these provide us with new insights into the cause(s) of radio-loudness, the blazar phenomenon at low black hole masses, and the operation of radio-mode feedback. The NLS1 galaxy RXJ2314.9+2243 is remarkable for its multi-wavelength properties. We present new radio observations taken at Effelsberg, and a summary of the recent results from our multi-wavelength study. RXJ2314.9+2243 is radio-loud, luminous in the infrared, has a flat X-ray spectrum and peculiar UV spectrum, and hosts an exceptionally broad and blueshifted [OIII]λ5007 emission line, indicating the presence of a strong outflow. RXJ2314.9+2243 likely represents an extreme case of AGN induced feedback in the local universe.
In 2006 we initiated an enhanced laboratory-based surveillance of Salmonella and Shigella infections in Shanghai, China. A total of 4483 Salmonella and 2226 Shigella isolates were recovered from stool specimens by 2012. In 80 identified Salmonella serovars, Enteritidis (34·5%) and Typhimurium (26·2%) were the most common. Shigella (S.) sonnei accounted for 63·9% of human Shigella infections over the same time period, and replaced S. flexneri to become the primary cause of shigellosis since 2010. Overall, a high level of antimicrobial resistance was observed in Salmonella and Shigella, particularly to nalidixic acid, ampicillin, and tetracycline. Ciprofloxacin resistance was common in Salmonella Typhimurium (21·0%) and S. flexneri (37·6%). The cephalosporin resistance in both pathogens also increased over the years, ranging from 3·4% to 7·0% in Salmonella, and from 10·4% to 28·6% in Shigella. Resistance to multiple antimicrobials was also identified in a large number of the isolates. This study provides insight into the distribution of Salmonella and Shigella in diarrhoeal diseases.
The Beijing/W lineage strains are the major prevalent strains in China. The prevalence, mortality and drug-resistant rates of tuberculosis in Xinjiang, Northwestern China are higher than in other parts of the country. Our previous study results showed that the dominant strains of Mycobacterium tuberculosis (MTB) were ‘Beijing/W lineage’ MTB in Xinjiang; those strains had no significant correlation with drug resistance. We investigated whether the prevalence of ‘Beijing/W lineage’ sublineage strains was associated with drug resistance. We collected 478 sputum specimens from patients with pulmonary tuberculosis. Beijing/W strains and their sublineages were identified by distinguishing five specific large sequence polymorphisms, using polymerase chain reaction. All strains were subjected to a drug susceptibility test using the proportion method on Löwenstein–Jensen culture medium. In total, 379 clinical isolates of MTB were isolated and identified, 57·26% of these isolates were identified as Beijing/W strains, of which 11·06% isolates were in sublineage 105, 14·74% isolates in sublineage 207, 69·59% isolates in sublineage 181, and 4·61% isolates in sublineage 150. None of the isolates was in sublineage 142. Our data showed there were four sublineages of Beijing/W isolates in Xinjiang province, China. However, there were no correlations between drug resistance and the sublineages of Beijing/W strains.