MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants

Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named "MORPH bulk" (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest

Modeling Target-Side Inflection in Neural Machine Translation

NMT systems have problems with large vocabulary sizes. Byte-pair encoding (BPE) is a popular approach to solving this problem, but while BPE allows the system to generate any target-side word, it does not enable effective generalization over the rich vocabulary in morphologically rich languages with strong inflectional phenomena. We introduce a simple approach to overcome this problem by training a system to produce the lemma of a word and its morphologically rich POS tag, which is then followed by a deterministic generation step. We apply this strategy for English-Czech and English-German translation scenarios, obtaining improvements in both settings. We furthermore show that the improvement is not due to only adding explicit morphological information.Comment: Accepted as a research paper at WMT17. (Updated version with corrected references.

Integrating body scanning solutions into virtual dressing rooms

The world is entering its 4th Industrial Revolution, a new era of manufacturing characterized by ubiquitous digitization and computing. One industry to benefit and grow from this revolution is the fashion industry, in which Europe (and Italy in particular) has long maintained a global lead. To evolve with the changes in technology, we developed the IT- SHIRT project. In the context of this project, a key challenge relies on developing a virtual dressing room in which the final users (customers) can virtually try different clothes on their bodies. In this paper, we tackle the aforementioned issue by providing a critical analysis of the existing body scanning solutions, identifying their strengths and weaknesses towards their integration within the pipeline of virtual dressing rooms

Odour-mediated orientation of beetles is influenced by age, sex and morph

The behaviour of insects is dictated by a combination of factors and may vary considerably between individuals, but small insects are often considered en masse and thus these differences can be overlooked. For example, the cowpea bruchid Callosobruchus maculatus F. exists naturally in two adult forms: the active (flight) form for dispersal, and the inactive (flightless), more fecund but shorter-lived form. Given that these morphs show dissimilar biology, it is possible that they differ in odour-mediated orientation and yet studies of this species frequently neglect to distinguish morph type, or are carried out only on the inactive morph. Along with sex and age of individual, adult morph could be an important variable determining the biology of this and similar species, informing studies on evolution, ecology and pest management. We used an olfactometer with motion-tracking to investigate whether the olfactory behaviour and orientation of C. maculatus towards infested and uninfested cowpeas and a plant-derived repellent compound, methyl salicylate, differed between morphs or sexes. We found significant differences between the behaviour of male and female beetles and beetles of different ages, as well as interactive effects of sex, morph and age, in response to both host and repellent odours. This study demonstrates that behavioural experiments on insects should control for sex and age, while also considering differences between adult morphs where present in insect species. This finding has broad implications for fundamental entomological research, particularly when exploring the relationships between physiology, behaviour and evolutionary biology, and the application of crop protection strategies