Tomato Expression Database (TED): a suite of data presentation and analysis tools

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150 000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at

PanScales showers for hadron collisions: all-order validation

We carry out extensive tests of the next-to-leading logarithmic (NLL) accuracy of the PanScales parton showers, as introduced recently for colour-singlet production in hadron collisions. The tests include comparisons to (semi-)analytic NLL calculations of a wide range of hadron-collider observables: the colour-singlet boson transverse momentum distribution; global and non-global hadronic energy flow variables related to jet vetoes and analogues of jettiness distributions; (sub)jet multiplicities; and observables sensitive to the DGLAP evolution of the incoming momentum fractions. In the tests, we also include an implementation of a standard transverse-momentum ordered dipole shower, to establish the size of missing NLL effects in such showers, which, depending on the observable, can reach $100\%$. This paper, together with arXiv:2205.02237, constitutes the first step towards process-independent NLL-accurate parton showers for hadronic collisions.Comment: 29 pages, 8 figure

Global gene expression analysis of apple fruit development from the floral bud to ripe fruit

<p>Abstract</p> <p>Background</p> <p>Apple fruit develop over a period of 150 days from anthesis to fully ripe. An array representing approximately 13000 genes (15726 oligonucleotides of 45–55 bases) designed from apple ESTs has been used to study gene expression over eight time points during fruit development. This analysis of gene expression lays the groundwork for a molecular understanding of fruit growth and development in apple.</p> <p>Results</p> <p>Using ANOVA analysis of the microarray data, 1955 genes showed significant changes in expression over this time course. Expression of genes is coordinated with four major patterns of expression observed: high in floral buds; high during cell division; high when starch levels and cell expansion rates peak; and high during ripening. Functional analysis associated cell cycle genes with early fruit development and three core cell cycle genes are significantly up-regulated in the early stages of fruit development. Starch metabolic genes were associated with changes in starch levels during fruit development. Comparison with microarrays of ethylene-treated apple fruit identified a group of ethylene induced genes also induced in normal fruit ripening. Comparison with fruit development microarrays in tomato has been used to identify 16 genes for which expression patterns are similar in apple and tomato and these genes may play fundamental roles in fruit development. The early phase of cell division and tissue specification that occurs in the first 35 days after pollination has been associated with up-regulation of a cluster of genes that includes core cell cycle genes.</p> <p>Conclusion</p> <p>Gene expression in apple fruit is coordinated with specific developmental stages. The array results are reproducible and comparisons with experiments in other species has been used to identify genes that may play a fundamental role in fruit development.</p

Irony Detection in Twitter: The Role of Affective Content

© ACM 2016. This is the author's version of the work. It is posted here for your personal use. Not for redistribution. The definitive Version of Record was published in ACM Transactions on Internet Technology, Vol. 16. http://dx.doi.org/10.1145/2930663.[EN] Irony has been proven to be pervasive in social media, posing a challenge to sentiment analysis systems. It is a creative linguistic phenomenon where affect-related aspects play a key role. In this work, we address the problem of detecting irony in tweets, casting it as a classification problem. We propose a novel model that explores the use of affective features based on a wide range of lexical resources available for English, reflecting different facets of affect. Classification experiments over different corpora show that affective information helps in distinguishing among ironic and nonironic tweets. Our model outperforms the state of the art in almost all cases.The National Council for Science and Technology (CONACyT Mexico) has funded the research work of Delia Irazu Hernandez Farias (Grant No. 218109/313683 CVU-369616). The work of Viviana Patti was partially carried out at the Universitat Politecnica de Valencia within the framework of a fellowship of the University of Turin cofunded by Fondazione CRT (World Wide Style Program 2). The work of Paolo Rosso has been partially funded by the SomEMBED TIN2015-71147-C2-1-P MINECO research project and by the Generalitat Valenciana under the grant ALMAMATER (PrometeoII/2014/030).Hernandez-Farias, DI.; Patti, V.; Rosso, P. (2016). Irony Detection in Twitter: The Role of Affective Content. ACM Transactions on Internet Technology. 16(3):19:1-19:24. https://doi.org/10.1145/2930663S19:119:24163Rob Abbott, Marilyn Walker, Pranav Anand, Jean E. Fox Tree, Robeson Bowmani, and Joseph King. 2011. 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Bioengineering an osteoinductive treatment for bone healing disorders: a small animal case series

The aim of this article was to study clinical and radiographic outcomes following treatment of bone healing disorders with a novel osteoinductive system that utilizes poly (ethyl acrylate), fibronectin and an ultra-low concentration of recombinant human bone morphogenetic protein-2. A case series of nine dogs and two cats were treated, and clinical records and radiographs were reviewed. Radiographs were scored by two blinded observers using the modified Radiographic Union Score for Tibial Fractures. Long-term follow-up was obtained using the Canine Orthopaedic Index and Feline Musculoskeletal Pain Index. Follow-up data were available for 11 treatments (10 cases). Complications: three minor, three major, one catastrophic (non-union requiring amputation). Lameness median 320 (range: 42–1,082) days postoperatively: ‘sound’ (three cases), ‘subtle’ (two), ‘mild’ (three), ‘moderate’ (one), and ‘non-weightbearing’ (one). The attending clinician judged 9 of 11 treatments achieved radiographic union; modified Radiographic Union Score for Tibial Fractures observers 1 and 2 agreed with the clinician in 8/9 and 5/9 treatments respectively. Long-term Canine Orthopaedic Index scores for five dogs median 650 (range: 544–1,724) days postoperatively: 15/64 (median) for four dogs with acceptable outcomes, 30/64 in one dog with a poor outcome. Feline Musculoskeletal Pain Index scores for two cats 433 and 751 days postoperatively: 48/60 and 60/60. Eight of 10 cases were sound or showed subtle or mild lameness in the short- or long-term, and radiographic union occurred in the majority of treatments

ESTs, cDNA microarrays, and gene expression profiling : tools for dissecting plant physiology and development

Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit

Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I:Wet lab procedure

Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols