Scattering below ground state of 3D focusing cubic fractional Schordinger equation with radial data

The aim of this note is to adapt the strategy in [4][See,B.Dodson, J.Murphy, a new proof of scattering below the ground state for the 3D radial focusing cubic NLS, arXiv:1611.04195 ] to prove the scattering of radial solutions below sharp threshold for certain focusing fractional NLS with cubic nonlinearity. The main ingredient is to apply the fractional virial identity proved in [11][See,T.Boulenger, D.Himmelsbach,E.Lenzmann, Blow up for fractional NLS,J.Func.Anal,271(2016),2569-2603] to exclude the concentration of mass near the origin.Comment: This version is an extension of the last version by the first and fourth author, where the dimensional case $d=3$ is treate

Blade-Tip Vortex Noise Mitigation Traded-Off against Aerodynamic Design for Propellers of Future Electric Aircraft

We study noise generation at the blade tips of propellers designed for future electric aircraft propulsion and, furthermore, analyze the interrelationship between noise mitigation and aerodynamics improvement in terms of propeller geometric designs. Classical propellers with three or six blades and a conceptual propeller with three joined dual-blades are compared to understand the effects of blade tip vortices on the noise generation and aerodynamics. The dual blade of the conceptual propeller is constructed by joining the tips of two sub-blades. These propellers are designed to operate under the same freestream flow conditions and similar electric power consumption. The Improved Delayed Detached Eddy Simulation (IDDES) is adopted for the flow simulation to identify high-resolution time-dependent noise sources around the blade tips. The acoustic computations use a time-domain method based on the convective Ffowcs Williams–Hawkings (FW-H) equation. The thrust of the 3-blade conceptual propeller is\ua04%\ua0larger than the 3-blade classical propeller and\ua08%\ua0more than the 6-blade one, given that they have similar efficiencies. Blade tip vortices are found emitting broadband noise. Since the classical and conceptual 3-blade propellers have different geometries, especially at the blade tips, they introduce deviations in the vortex development. However, the differences are small regarding the broadband noise generation. As compared to the 6-blade classical propeller, both 3-blade propellers produce much larger noise. The reason is that the increased number of blades leads to the reduced strength of tip vortices. The findings indicate that the noise mitigation through the modification of the blade design and number can be traded-off by the changed aerodynamic performance

VitisExpDB: A database resource for grape functional genomics

<p>Abstract</p> <p>Background</p> <p>The family Vitaceae consists of many different grape species that grow in a range of climatic conditions. In the past few years, several studies have generated functional genomic information on different <it>Vitis </it>species and cultivars, including the European grape vine, <it>Vitis vinifera</it>. Our goal is to develop a comprehensive web data source for Vitaceae.</p> <p>Description</p> <p>VitisExpDB is an online MySQL-PHP driven relational database that houses annotated EST and gene expression data for <it>V. vinifera </it>and non-<it>vinifera </it>grape species and varieties. Currently, the database stores ~320,000 EST sequences derived from 8 species/hybrids, their annotation (BLAST top match) details and Gene Ontology based structured vocabulary. Putative homologs for each EST in other species and varieties along with information on their percent nucleotide identities, phylogenetic relationship and common primers can be retrieved. The database also includes information on probe sequence and annotation features of the high density 60-mer gene expression chip consisting of ~20,000 non-redundant set of ESTs. Finally, the database includes 14 processed global microarray expression profile sets. Data from 12 of these expression profile sets have been mapped onto metabolic pathways. A user-friendly web interface with multiple search indices and extensively hyperlinked result features that permit efficient data retrieval has been developed. Several online bioinformatics tools that interact with the database along with other sequence analysis tools have been added. In addition, users can submit their ESTs to the database.</p> <p>Conclusion</p> <p>The developed database provides genomic resource to grape community for functional analysis of genes in the collection and for the grape genome annotation and gene function identification. The VitisExpDB database is available through our website <url>http://cropdisease.ars.usda.gov/vitis_at/main-page.htm</url>.</p

Near-wall modeling of forests for atmosphere boundary layers using lattice Boltzmann method on GPU

In this paper, the simulation and modeling of the turbulent atmospheric boundary layers (ABLs) in the presence of forests are studied using a lattice Boltzmann method with large eddy simulation, which was implemented in the open-source program GASCANS with the use of Graphic Processing Units (GPU). A method of modeling forests in the form of body forces injected near the wall is revisited, while the effects of leaf area density (LAD) on the model accuracy is further addressed. Since a uniform cell size is applied throughout the computational domain, the wall-normal height of the near-wall cells is very large, theoretically requiring a wall function to model the boundary layer. However, the wall function is disregarded here when the forest is modeled. This approximation is validated based on the comparison with previous experimental and numerical data. It concludes that for the ABL conditions specified in this study as well as a large body of literature, the forest forces overwhelm the wall friction so that the modeling of the latter effect is trivial. Constant and varying LAD profiles across the forest zone are defined with the same total leaf area despite the varying one being studied previously. It is found that the two LAD profiles provide consistent predictions. The present forest modeling can therefore be simplified with the use of the constant LAD without degrading the model accuracy remarkably

Reducing the aerodynamic drag of high-speed trains by air blowing from the nose part: Effect of blowing speed

To reduce the aerodynamic drag of high-speed trains, this work proposes an air blowing configuration on the head and tail cars of high-speed trains. The variation in the aerodynamic drag and slipstream velocity is analyzed under different blowing velocities, and the flow mechanism for train aerodynamic performance alteration is explained. The results show that under the blowing speeds of Ub = 0.05Ut, 0.10Ut, 0.15Ut, and 0.20Ut, where Ut is the train speed, the total drag coefficient (Cd) decreases by 5.81%, 10.78%, 13.70%, and 15.43% compared to the without-blowing case, respectively. However, with the increase in the blowing speed, the reduction trend of Cd tends to be smoother; namely, the decrement ratio compared to the previous blowing speed for the head car is 9.08%, 0.11%, 0.60%, and 1.14% for Ub = 0.05Ut, 0.10Ut, 0.15Ut, and 0.20Ut, respectively. The blowing measure generates an air gap between the coming flow and train surface, consequently causing a reduction in the viscous and pressure drag. In addition, the structure size and strength of the wake flow under different blowing cases show a decreasing trend from Ub = 0.00Ut to 0.10Ut and then an increasing trend from Ub = 0.10Ut to 0.20Ut. Thus, considering the blowing cost, efficiency, and flow structure evolution comprehensively, the case of Ub = 0.10Ut is recommended. Under this blowing speed, the reduction ratio of the aerodynamic drag is 9.18%, 12.77%, 10.90%, and 10.78% for the head, middle, tail car, and total train, respectively

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

BACKGROUND: Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes. RESULTS: Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F(1)-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80–120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were designed for the identified markers. The assembly was annotated by Blast2GO and 14,740 (12%) of annotated contigs were associated with functional proteins. CONCLUSIONS: Before availability of pepper genome sequence, assembling transcriptomes of this economically important crop was required to generate thousands of high-quality molecular markers that could be used in breeding programs. In order to have a better understanding of the assembled sequences and to identify candidate genes underlying QTLs, we annotated the contigs of Sanger-EST and Illumina transcriptome assemblies. These and other information have been curated in a database that we have dedicated for pepper project

PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

<p>Abstract</p> <p>Background</p> <p>The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the identification of the few loci in the genome that can serve as unique markers for strain differentiation. PrimerSNP attempts to identify reliable strain-specific markers, on which specific primers are designed for pathogen detection purpose.</p> <p>Results</p> <p>PrimerSNP is an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. The allele-specific primers could distinguish query sequences of one strain from other homologous sequences by standard PCR reaction. Additionally, PrimerSNP provides a feature for designing common primers that can amplify all the homologous sequences of multiple strains/species of microorganisms. PrimerSNP is freely available at <url>http://cropdisease.ars.usda.gov/~primer</url>.</p> <p>Conclusion</p> <p>PrimerSNP is a high-throughput specific primer generation tool for the differentiation of phylogenetically-related strains/species. Experimental validation showed that this software had a successful prediction rate of 80.4 – 100% for strain specific primer design.</p

Tumor exome sequencing and copy number alterations reveal potential predictors of intrinsic resistance to multi-targeted tyrosine kinase inhibitors

Multi-targeted tyrosine kinase inhibitors (TKIs) have broad efficacy and similar FDA-approved indications, suggesting shared molecular drug targets across cancer types. Irrespective of tumor type, 20-30% of patients treated with multi-targeted TKIs demonstrate intrinsic resistance, with progressive disease as a best response. We conducted a retrospective cohort study to identify tumor (somatic) point mutations, insertion/deletions, and copy number alterations (CNA) associated with intrinsic resistance to multi-targeted TKIs. Using a candidate gene approach (n=243), tumor next-generation sequencing and CNA data was associated with resistant and non-resistant outcomes. Resistant individuals (n=11) more commonly harbored somatic point mutations in NTRK1, KDR, TGFBR2, and PTPN11 and CNA in CDK4, CDKN2B, and ERBB2 compared to non-resistant (n=26, p<0.01). Using a random forest classification model for variable reduction and a decision tree classification model, we were able to differentiate intrinsically resistant from non-resistant patients. CNA in CDK4 and CDKN2B were the most important analytical features, implicating the cyclin D pathway as a potentially important factor in resistance to multi-targeted TKIs. Replication of these results in a larger, independent patient cohort has potential to inform personalized prescribing of these widely utilized agents