9,817 research outputs found
Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes
No full textComparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi
Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites
No full textParasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied model nematode parasite of rodents, which secretes products known to modulate host immunity
The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
No full textABSTRACT: BACKGROUND: Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic in its new host than in its native one, and is thought to threaten the endangered An. anguilla across its range. The molecular bases for the increased pathogenicity of the nematodes in their new hosts is not known. RESULTS: A reference transcriptome was assembled for A. crassus from Roche 454 pyrosequencing data. Raw reads (756,363 total) from nematodes from An. japonica and An. anguilla hosts were filtered for likely host contaminats and ribosomal RNAs. The remaining 353,055 reads were assembled into 11,372 contigs of a high confidence assembly (spanning 6.6 Mb) and an additional 21,153 singletons and contigs of a lower confidence assembly (spanning an additional 6.2 Mb). Roughly 55% of the high condence assembly contigs were annotated with domain- or protein sequence similarity derived functional information. Sequences conserved only in nematodes, or unique to A. crassus were more likely to have secretory signal peptides. Thousands of high quality single nucleotide polymorphisms were identified, and coding polymorphism was correlated with diffrential expression between individual nematodes. Transcripts identfied as being under positive selection were enriched in peptidases. Enzymes involved in energy metabolism were enriched in the set of genes differentially expressed between European and Asian A. crassus. CONCLUSIONS: The reference transcriptome of A. crassus is of high quality, and will serve as a basis for future work on the invasion biology of this important parasite. The polymorphisms identied will provide a key tool set for analysis of population structure and identication of genes likely to be involved in increased pathogenicity in European eel hosts. The identication of peptidases under positive selection is a first step in this programme
prot4EST: translating expressed sequence tags from neglected genomes
No full textThe genomes of an increasing number of species are being investigated through generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects
Metadata Representations for Queryable ML Model Zoos
No full textMachine learning (ML) practitioners and organizations are building model zoos of pre-trained models, containing metadata describing properties of the ML models and datasets that are useful for reporting, auditing, reproducibility, and interpretability purposes. The metatada is currently not standardised; its expressivity is limited; and there is no interoperable way to store and query it. Consequently, model search, reuse, comparison, and composition are hindered. In this paper, we advocate for standardized ML model metadata representation and management, proposing a toolkit supported to help practitioners manage and query that metadata.Web Information SystemsHuman-Centred Artificial Intelligenc
A Manifesto of Nodalism
No full textThis paper proposes the notion of Nodalism as a means describing contemporary culture and of understanding my own creative practice in electronic music composition. It draws on theories and ideas from Kirby, Bauman, Bourriaud, Deleuze, Guatarri, and Gochenour, to demonstrate how networks of ideas or connectionist neural models of cognitive behaviour can be used to contextualize, understand and become a creative tool for the creation of contemporary electronic music
The genome of Romanomermis culicivorax:revealing fundamental changes in the core developmental genetic toolkit in Nematoda
No full textThe genetics of development in the nematode Caenorhabditis elegans has been described in exquisitedetail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and theEnoplea. While the development of many chromadorean species resembles closely that of C. elegans,enoplean nematodes show markedly different patterns of early cell division and cell fate assignment.Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the geneticcircuitry underpinning development in this species has not been explored
Operon conservation and the evolution of trans-splicing in the phylum Nematoda
No full textThe nematode Caenorhabditis elegans is unique among model animals in that many of its genes are cotranscribed as polycistronic pre-mRNAs from operons. The mechanism by which these operonic transcripts are resolved into mature mRNAs includes trans-splicing to a family of SL2-like spliced leader exons. SL2-like spliced leaders are distinct from SL1, the major spliced leader in C. elegans and other nematode species. We surveyed five additional nematode species, representing three of the five major clades of the phylum Nematoda, for the presence of operons and the use of trans-spliced leaders in resolution of polycistronic pre-mRNAs. Conserved operons were found in Pristionchus pacificus, Nippostrongylus brasiliensis, Strongyloides ratti, Brugia malayi, and Ascaris suum. In nematodes closely related to the rhabditine C. elegans, a related family of SL2-like spliced leaders is used for operonic transcript resolution. However, in the tylenchine S. ratti operonic transcripts are resolved using a family of spliced leaders related to SL1. Non-operonic genes in S. ratti may also receive these SL1 variants. In the spirurine nematodes B. malayi and A. suum operonic transcripts are resolved using SL1. Mapping these phenotypes onto the robust molecular phylogeny for the Nematoda suggests that operons evolved before SL2-like spliced leaders, which are an evolutionary invention of the rhabditine lineage
Optimizing ML Inference Queries Under Constraints
No full textThe proliferation of pre-trained ML models in public Web-based model zoos facilitates the engineering of ML pipelines to address complex inference queries over datasets and streams of unstructured content. Constructing optimal plan for a query is hard, especially when constraints (e.g. accuracy or execution time) must be taken into consideration, and the complexity of the inference query increases. To address this issue, we propose a method for optimizing ML inference queries that selects the most suitable ML models to use, as well as the order in which those models are executed. We formally define the constraint-based ML inference query optimization problem, formulate it as a Mixed Integer Programming (MIP) problem, and develop an optimizer that maximizes accuracy given constraints. This optimizer is capable of navigating a large search space to identify optimal query plans on various model zoos.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Web Information SystemsHuman-Centred Artificial Intelligenc
Building a generalisable ML pipeline at ING
No full textAdvances in data science have caused an increase in the use of Artificial Intelligence (AI), specifically Machine Learning (ML), throughout various fields. Not only in research but in the industry as well, has ML been receiving increasing amounts of interest. Many companies rely on ML models to increase the efficiency of existing processes or offer new services and products. The industry, however, is facing several additional challenges compared to the academic context. One of those challenges is applying the Development Operations (DevOps) model to an ML application, also referred to as MLOps. This thesis sets out to find the specific challenges that practitioners encounter while operationalising ML models. To do so, we perform a single-case case study on an ML pipeline built by the Trade & Communication Surveillance team at the ING bank. This case study consists of conducting a set of interviews and performing a manual code inspection of the pipeline. The team faces challenges ranging from having insufficient time for operationalising each ML project individually to operating in the highlyregulated fintech context. Their pipeline is able to deploy a single ML model but it does not generalise well to other projects. We present the first version of an application that mitigates these challenges. The application is able to deploy ML models to the development environment at ING and can be operated by data scientists to reduce the effort of operationalising an ML model. Computer Science | Software Technolog
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