Implementation of a custom time-domain firmware trigger for RADAR-based cosmic ray detection

Interest in Radio-based detection schemes for ultra-high energy cosmic rays (UHECR) has surged in recent years, owing to the potentially very low cost/detection ratio. The method of radio-frequency (RF) scatter has been proposed as potentially the most economical detection technology. Though the first dedicated experiment to employ this method, the Telescope Array RADAR experiment (TARA), reported no signal, efforts to develop more robust and sensitive trigger techniques continue. This paper details the development of a time-domain firmware trigger that exploits characteristics of the expected scattered signal from an UHECR extensive-air shower (EAS). The improved sensitivity of this trigger is discussed, as well as implementation in two separate field deployments from 2016-2017

Estimating Effectiveness of Identifying Human Trafficking via Data Envelopment Analysis

Transit monitoring is a preventative approach used to identify possible cases of human trafficking while an individual is in transit or before one crosses a border. Transit monitoring is often conducted by non-governmental organizations (NGOs) who train staff to identify and intercept suspicious activity. Love Justice International (LJI) is one such NGO that has been conducting transit monitoring for 14 years along the Nepal-India border at approximately 25-30 monitoring stations. In partnership with LJI, we developed a system that uses data envelopment analysis (DEA) to help LJI decision-makers evaluate the performance of these stations and make specific operational improvement recommendations. We identified efficient stations, compared rankings of station performance, and recommended strategies to improve efficiency. To the best of our knowledge, this is the first application of DEA in the anti-human trafficking domain

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-

Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps

The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new STS marker based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished using a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2,469 marker loci. In silico anchoring approaches employed genetic and physical maps from the diploid potato genotype RH and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules is closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal 'pseudomolecules'.Fil: Carboni, Martín Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires. Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: D'ambrosio, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional San Cristobal de Huamanga. Laboratorio de Genética y Biotecnología Vegetal; PerúFil: Sharma, Sanjeev Kumar. The James Hutton Institute; Reino UnidoFil: Bolser, Daniel. University of Dundee; Reino UnidoFil: de Boer, Jan. Wageningen University & Researc; Países BajosFil: Sønderkær, Mads . Aalborg University; DinamarcaFil: Amoros, Walter. International Potato Center; PerúFil: de la Cruz, Germán. Universidad Nacional San Cristobal de Huamanga; PerúFil: Di Genova, Alex. Universidad de Chile; ChileFil: Douches, David S.. Michigan State University; Estados UnidosFil: Eguiluz, Maria. Universidad Peruana Cayetano Heredia; PerúFil: Guo, Xiao. Shandong Academy of Agricultural Sciences; ChinaFil: Guzman, Frank. Universidad Peruana Cayetano Heredia; PerúFil: Hackett, Christine A.. Biomathematics and Statistics Scotland; Reino UnidoFil: Hamilton, John P.. Crops Environment and Land Use Programme; IrlandaFil: Li, Guangcun. Shandong Academy of Agricultural Sciences; ChinaFil: Li, Ying. The New Zealand Institute for Plant & Food Research; Nueva ZelandaFil: Lozano, Roberto. Universidad Peruana Cayetano Heredia; PerúFil: Maass, Alejandro. Universidad de Chile; ChileFil: Marshall, David. The James Hutton Institute; Reino UnidoFil: Martinez, Diana. Universidad Peruana Cayetano Heredia; PerúFil: McLean, Karen. The James Hutton Institute; Reino UnidoFil: Mejía, Nilo. Instituto de Investigaciones Agropecuarias. Centro Regional de Investigación La Platina; ChileFil: Milne, Linda. The James Hutton Institute; Reino UnidoFil: Munive, Susan. International Potato Center; PerúFil: Nagy, Istvan. Crops Environment and Land Use Programme; IrlandaFil: Ponce, Olga. Universidad Peruana Cayetano Heredia; PerúFil: Ramirez, Manuel. Universidad Peruana Cayetano Heredia; PerúFil: Simon, Reinhard. International Potato Center; PerúFil: Thomson, Susan J.. Chinese Academy of Agricultural Sciences; Chin

The Atlantic salmon genome provides insights into rediploidization

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.publishedVersio

The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations