Towards Interactive Multidimensional Visualisations for Corpus Linguistics

We propose the novel application of dynamic and interactive visualisation techniques to support the iterative and exploratory investigations typical of the corpus linguistics methodology. Very large scale text analysis is already carried out in corpus-based language analysis by employing methods such as frequency profiling, keywords, concordancing, collocations and n-grams. However, at present only basic visualisation methods are utilised. In this paper, we describe case studies of multiple types of key word clouds, explorer tools for collocation networks, and compare network and language distance visualisations for online social networks. These are shown to fit better with the iterative data-driven corpus methodology, and permit some level of scalability to cope with ever increasing corpus size and complexity. In addition, they will allow corpus linguistic methods to be used more widely in the digital humanities and social sciences since the learning curve with visualisations is shallower for non-expert

Artificial Intelligence and Machine Learning Approaches to Energy Demand-Side Response: A Systematic Review

Recent years have seen an increasing interest in Demand Response (DR) as a means to provide flexibility, and hence improve the reliability of energy systems in a cost-effective way. Yet, the high complexity of the tasks associated with DR, combined with their use of large-scale data and the frequent need for near real-time de-cisions, means that Artificial Intelligence (AI) and Machine Learning (ML) — a branch of AI — have recently emerged as key technologies for enabling demand-side response. AI methods can be used to tackle various challenges, ranging from selecting the optimal set of consumers to respond, learning their attributes and pref-erences, dynamic pricing, scheduling and control of devices, learning how to incentivise participants in the DR schemes and how to reward them in a fair and economically efficient way. This work provides an overview of AI methods utilised for DR applications, based on a systematic review of over 160 papers, 40 companies and commercial initiatives, and 21 large-scale projects. The papers are classified with regards to both the AI/ML algorithm(s) used and the application area in energy DR. Next, commercial initiatives are presented (including both start-ups and established companies) and large-scale innovation projects, where AI methods have been used for energy DR. The paper concludes with a discussion of advantages and potential limitations of reviewed AI techniques for different DR tasks, and outlines directions for future research in this fast-growing area

Innovative transportable laboratories for Polar science

The Netherlands Organisation for Scientific Research and the British Antarctic Survey have built a transportable laboratory facility, named the Dirck Gerritsz Laboratory, to accommodate new scientific research on and from the westernAntarctic Peninsula. The design provides a flexible,modular, plug-and-play, innovative and sustainable laboratory setup. The docking station houses four 20-foot ISO standard high-cube containers, each of which contains a different laboratory. Special technological features were used to minimise the environmental impact. The four laboratory containers are flexible and can be installed and used as required, and renewed or removedwhen necessary. The container laboratories have provided, since opening in 2013, enhanced facilities for global climate change research through studying the community composition of phytoplankton; the ecological impact of virus-induced mortality in different phytoplankton groups; dimethylsulphide and brominated compound fluxes; and CO2 concentrations and trace elements in sea water. Transportable research laboratory facilities provide an effective and efficient approach for undertaking scientific research in challenging environments and might be the start of a new way of undertaking research, including exchanging laboratory modules between research stations in Antarctica

PATRIC, the bacterial bioinformatics database and analysis resource

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issu

JBrowse: a dynamic web platform for genome visualization and analysis

BACKGROUND: JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. RESULTS: Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. CONCLUSIONS: JBrowse is a mature web application suitable for genome visualization and analysis

Evolutionary timeline and genomic plasticity underlying the lifestyle diversity in rhizobiales

Members of the order include those capable of nitrogen fixation in nodules as well as pathogens of animals and plants. This lifestyle diversity has important implications for agricultural and medical research. Leveraging large-scale genomic data, we infer that originated as a free-living ancestor ∼1,500 million years ago (Mya) and that the later emergence of host-associated lifestyles broadly coincided with the rise of their eukaryotic hosts. In particular, the first nodulating lineage arose from either or 150 to 80 Mya, a time range in general concurrent with the emergence of legumes. The rates of lifestyle transitions are highly variable; nodule association is more likely to be lost than gained, whereas animal association likely represents an evolutionary dead end. We searched for statistical correlations between gene presence and lifestyle and identified genes likely contributing to the transition and adaptation to the same lifestyle in divergent lineages. Among the genes potentially promoting successful transitions to major nodulation lineages, the and clusters for nodulation and nitrogen fixation, respectively, were repeatedly acquired during each transition; the , , and clusters involved in energy conservation under micro-oxic conditions were present in the nonnodulating ancestors; and the secretion systems were acquired in lineage-specific patterns. Our study data suggest that increased eukaryote diversity drives lifestyle diversification of bacteria and highlight both acquired and preexisting traits facilitating the origin of host association. Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the , a clade of strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 genomes. We show that the origins of major host-associated lineages in broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens

Discovery of functionally distinct anti-C7 monoclonal antibodies and stratification of anti-nicotinic AChR positive Myasthenia Gravis patients

Myasthenia Gravis (MG) is mediated by autoantibodies against acetylcholine receptors that cause loss of the receptors in the neuromuscular junction. Eculizumab, a C5-inhibitor, is the only approved treatment for MG that mechanistically addresses complement-mediated loss of nicotinic acetylcholine receptors. It is an expensive drug and was approved despite missing the primary efficacy endpoint in the Phase 3 REGAIN study. There are two observations to highlight. Firstly, further C5 inhibitors are in clinical development, but other terminal pathway proteins, such as C7, have been relatively understudied as therapeutic targets, despite the potential for lower and less frequent dosing. Secondly, given the known heterogenous mechanisms of action of autoantibodies in MG, effective patient stratification in the REGAIN trial may have provided more favorable efficacy readouts. We investigated C7 as a target and assessed the in vitro function, binding epitopes and mechanism of action of three mAbs against C7. We found the mAbs were human, cynomolgus monkey and/or rat cross-reactive and each had a distinct, novel mechanism of C7 inhibition. TPP1820 was effective in preventing experimental MG in rats in both prophylactic and therapeutic dosing regimens. To enable identification of MG patients that are likely to respond to C7 inhibition, we developed a patient stratification assay and showed in a small cohort of MG patients (n=19) that 63% had significant complement activation and C7-dependent loss of AChRs in this in vitro set up. This study provides validation of C7 as a target for treatment of MG and provides a means of identifying patients likely to respond to anti-C7 therapy based on complement-activating properties of patient autoantibodies