ALBERT

Description: Background: A genome-wide association study (GWAS) is the foremost strategy used for finding genes that control human diseases and agriculturally important traits, but it often reports false positives. In contrast, its complementary method, linkage analysis, provides direct genetic confirmation, but with limited resolution. A joint approach, using multiple linkage populations, dramatically improves resolution and statistical power. For example, this approach has been used to confirm that many complex traits, such as flowering time controlling adaptation in maize, are controlled by multiple genes with small effects. In addition, genotyping by sequencing (GBS) at low coverage not only produces genotyping errors, but also results in large datasets, making the use of high-throughput sequencing technologies computationally inefficient or unfeasible. Results: In this study, we converted raw SNPs into effective recombination bins. The reduced bins not only retain the original information, but also correct sequencing errors from low-coverage genomic sequencing. To further increase the statistical power and resolution, we merged a new temperate maize nested association mapping (NAM) population derived in China (CN-NAM) with the existing maize NAM population developed in the US (US-NAM). Together, the two populations contain 36 families and 7,000 recombinant inbred lines (RILs). One million SNPs were generated for all the RILs with GBS at low coverage. We developed high-quality recombination maps for each NAM population to correct genotyping errors and improve the computational efficiency of the joint linkage analysis. The original one million SNPs were reduced to 4,932 and 5,296 recombination bins with average interval distances of 0.34 cM and 0.28 cM for CN-NAM and US-NAM, respectively. The quantitative trait locus (QTL) mapping for flowering time (days to tasseling) indicated that the high-density, recombination bin map improved resolution of QTL mapping by 50 % compared with that using a medium-density map. We also demonstrated that combining the CN-NAM and US-NAM populations improves the power to detect QTL by 50 % compared to single NAM population mapping. Among the QTLs mapped by joint usage of the US-NAM and CN-NAM maps, 25 % of the QTLs overlapped with known flowering-time genes in maize. Conclusion: This study provides directions and resources for the research community, especially maize researchers, for future studies using the recombination bin strategy for joint linkage analysis. Available resources include efficient usage of low-coverage genomic sequencing, detailed positions for genes controlling maize flowering, and recombination bin maps and flowering- time data for both CN and US NAMs. Maize researchers even have the opportunity to grow both CN and US NAM populations to study the traits of their interest, as the seeds of both NAM populations are available from the seed repository in China and the US.

Description: In this paper, we discuss the existence of the positive time periodic mild solutions for the evolution equation in an ordered Banach space E, u ′ ( t ) + A u ( t ) = f ( t , u ( t ) ) , t ∈ R , where A : D ( A ) ⊂ E → E is a closed linear operator and −A generates a positive compact semigroup T ( t ) ( t ≥ 0 ) in E, the nonlinear function f : R × E → E is continuous and f ( t , x ) is ω-periodic in t. We apply the operator semigroup theory and the Leray-Schauder fixed point theorem to obtain the existence of a positive ω-periodic mild solution under the condition that the nonlinear function satisfies a linear growth condition concerning the growth exponent of the semigroup T ( t ) ( t ≥ 0 ). In the end, an example is given to illustrate the applicability of our abstract results.MSC: 34K30, 47H07, 47H08.

Description: Article Structural variations in crop genomes are thought to be responsible for significant differences in phenotype and they can be well-represented by a ‘pan-genome’. Here, Lu et al. develop an approach to genetically map pan-genome sequence anchors using 14,129 inbred lines of maize, showing structural variation is a significant source of adaptive variation. Nature Communications doi: 10.1038/ncomms7914 Authors: Fei Lu, Maria C. Romay, Jeffrey C. Glaubitz, Peter J. Bradbury, Robert J. Elshire, Tianyu Wang, Yu Li, Yongxiang Li, Kassa Semagn, Xuecai Zhang, Alvaro G. Hernandez, Mark A. Mikel, Ilya Soifer, Omer Barad, Edward S. Buckler

Description: In this paper, we discuss the continuous dependence of mild solutions on initial values and orders for the initial value problem of fractional evolution equations in infinite dimensional spaces. The results obtained in this paper improve and extend some related conclusions on this topic. This paper can be considered as a contribution to this emerging field.MSC: 35R11, 47J35.

Description: Using tape-casting technology, 35  μ m free-standing (100)-textured Li doped KNN (KNLN) thick film was prepared by employing NaNbO 3 (NN) as template. It exhibited similar piezoelectric behavior to lead containing materials: a longitudinal piezoelectric coefficient (d 33 ) of ∼150 pm/V and an electromechanical coupling coefficient ( k t ) of 0.44. Based on this thick film, a 52 MHz side-looking miniature transducer with a bandwidth of 61.5% at −6 dB was built for Intravascular ultrasound (IVUS) imaging. In comparison with 40 MHz PMN-PT single crystal transducer, the rabbit aorta image had better resolution and higher noise-to-signal ratio, indicating that lead-free (100)-textured KNLN thick film may be suitable for IVUS (〉50 MHz) imaging.

Description: Apart from electric vehicles, most internal combustion (IC) engines are powered while burning petroleum-based fossil or alternative fuels after mixing with inducted air. Thereby the operations of mixing and combustion evolve in a turbulent flow environment created during the intake phase and then intensified by the piston motion and influenced by the shape of combustion chamber. In particular, the swirl and turbulence levels existing immediately before and during combustion affect the evolution of these processes and determine engine performance, noise and pollutant emissions. Both the turbulence characteristics and the bulk flow pattern in the cylinder are strongly affected by the inlet port and valve design. In the present paper, large eddy simulation (LES) is appraised and applied to studying the turbulent fluid flow around the intake valve of a single cylinder IC-engine as represented by the so called magnetic resonance velocimetry (MRV) flow bench configuration with a relatively large Reynolds number of 45,000. To avoid an intense mesh refinement near the wall, various subgrid scale models for LES; namely the Smagorinsky, wall adapting local eddy (WALE) model, SIGMA, and dynamic one equation models, are employed in combination with an appropriate wall function. For comparison purposes, the standard RANS (Reynolds-averaged Navier–Stokes) k- ε model is also used. In terms of a global mean error index for the velocity results obtained from all the models, at first it turns out that all the subgrid models show similar predictive capability except the Smagorinsky model, while the standard k- ε model experiences a higher normalized mean absolute error (nMAE) of velocity once compared with MRV data. Secondly, based on the cost-accuracy criteria, the WALE model is used with a fine mesh of ≈39 millions control volumes, the averaged velocity results showed excellent agreement between LES and MRV measurements, revealing the high prediction capability of the suggested LES tool for valve flows. Thirdly, the turbulent flow across the valve curtain clearly featured a back flow resulting in a high speed intake jet in the middle. Comprehensive LES data are generated to carry out statistical analysis in terms of (1) evolution of the turbulent morphology across the valve passage relying on the flow anisotropy map, (2) integral turbulent scales along the intake-charge stream, (3) turbulent flow properties such as turbulent kinetic energy, turbulent velocity and its intensity within the most critical zone in intake-port and along the port length, it further transpires that the most turbulence are generated across the valve passage and these are responsible for the in-cylinder turbulence.

Description: This work reports a novel wireless microfluidic biosensor based on low temperature co-fired ceramic (LTCC) technology. The wireless biosensor consists of a planar spiral inductor and parallel plate capacitor (LC) resonant antenna, which integrates with microchannel bends in the LTCC substrate. The wireless response of the biosensor was associated to the changes of its resonant frequency due to the alteration in the permittivity of the liquid flow in the microchannel. The wireless sensing performance to different organic liquids with permittivity from 3 to 78.5 was presented. The measured results are in good agreement with the theoretical calculation. The wireless detection for the concentration of glucose in water solution was investigated, and an excellent linear response and repeatability were obtained. This kind of LC wireless microfluidic sensor is very promising in establishing wireless lab-on-a-chip for biomedical and chemical applications.

Description: Background: Exploring genetic differentiation and genomic variation is important for both the utilization of heterosis and the dissection of the genetic bases of complex traits. Methods: We integrated 1857 diverse maize accessions from America, Africa, Europe and Asia to investigatetheir genetic differentiation, genomic variation using 43,252 high-quality single-nucleotide polymorphisms(SNPs),combing GWAS and linkage analysis strategy to exploring the function of relevant genetic segments. Results: We uncovered many more subpopulations that recently or historically formed during the breeding process. These patterns are represented by the following lines: Mo17, GB, E28, Ye8112, HZS, Shen137, PHG39, B73, 207, A634, Oh43, Reid Yellow Dent, and the Tropical/subtropical (TS) germplasm. A total of 85 highly differentiated regions with a D EST of more than 0.2 were identified between the TS and temperate subpopulations. These regions comprised 79 % of the genetic variation, and most were significantly associated with adaptive traits. For example, the region containing the SNP tag PZE.108075114 was highly differentiated, and this region was significantly associated with flowering time (FT)-related traits, as supported by a genome-wide association study (GWAS) within the interval of FT-related quantitative trait loci (QTL). This region was also closely linked to zcn8 and vgt1, which were shown to be involved in maize adaptation. Most importantly, 197 highly differentiated regions between different subpopulation pairs were located within an FT- or plant architecture-related QTL. Conclusions: Here we reported that 700–1000 SNPs were necessary needed to robustly estimate the genetic differentiation of a naturally diverse panel. In addition, 13 subpopulations were observed in maize germplasm, 85 genetic regions with higher differentiation between TS and temperate maize germplasm, 197 highly differentiated regions between different subpopulation pairs, which contained some FT- related QTNs/QTLs/genes supported by GWAS and linkage analysis, and these regions were expected to play important roles in maize adaptation.