A Semantic Grid Service for Experimentation with an Agent-Based Model of Land-Use Change

Agent-based models, perhaps more than other models, feature large numbers of parameters and potentially generate vast quantities of results data. This paper shows through the FEARLUS-G project (an ESRC e-Social Science Initiative Pilot Demonstrator Project) how deploying an agent-based model on the Semantic Grid facilitates international collaboration on investigations using such a model, and contributes to establishing rigorous working practices with agent-based models as part of good science in social simulation. The experimental workflow is described explicitly using an ontology, and a Semantic Grid service with a web interface implements the workflow. Users are able to compare their parameter settings and results, and relate their work with the model to wider scientific debate.Agent-Based Social Simulation, Experiments, Ontologies, Replication, Semantic Grid

Doing It Again: Repeating Methodology from Published Literature to Learn Field Biology

Repeatability underpins a basic assumption in science which students must learn in order to evaluate others’ research findings as well as to communicate the results of their own research. By attempting to repeat the methods of published studies, students learn the importance of clear written communication, while at the same time developing research skills. I describe three examples of published field studies that can be used as the basis for course exercises on the repeatability of methodology, as well as field sampling techniques, all grounded in the overall topic of environmental change. Two of the exercises returned students to the exact location of the past research that they had previously read from the primary literature, making it possible to clarify the difference between reproducibility and repeatability in field-based research. When student-collected data differed from published results, students explored, through both post-project discussions and written work, factors that could explain this variation, including methodology, ecological succession, and climate change. Assessments and student comments on course evaluations showed that these exercises have a positive impact on students’ communication skills and engagement with the scientific process

IgA-enhancing effects of membrane vesicles derived from Lactobacillus sakei subsp. sakei NBRC15893

Immunoglobulin (Ig) A in the mucus of the intestinal tract plays an important role in preventing the invasion of pathogenic microorganisms and regulating the composition of the gut microbiota. Several strains of probiotic lactic acid bacteria (LAB) are known to promote intestinal IgA production. Bacteria are also known to naturally release spherical membrane vesicles (MVs) that are involved in various biological functions such as quorum sensing, pathogenesis, and host immunomodulation. However, the production of MVs by LAB and their effects on host immunity remain poorly understood. In this study, we investigated the MV production by Lactobacillus sakei subsp. sakei NBRC15893 isolated from kimoto, the traditional seed mash used for brewing sake. MVs were separated from the culture broth of L. sakei NBRC15893 through filtration and density gradient ultracentrifugation and were observed by transmission electron microscopy. The MVs showed a spherical morphology, with a diameter of 30–400 nm, and contained proteins and nucleic acids. In addition, both the LAB cells and purified MVs promoted IgA production by murine Peyer’s patch cells. This MV- and cell-induced IgA production was suppressed by neutralization of Toll-like receptor (TLR) 2, which recognizes cell wall components of gram-positive bacteria, using an anti-TLR2 antibody. Collectively, our results indicate that MVs released from L. sakei NBRC15893 enhance IgA production by activating host TLR2 signaling through its cell wall components. Thus, it is important to consider novel interactions between gut microbiota and hosts via MVs, and MVs derived from probiotic bacteria could have promising applications as safe adjuvants.Japan Society for the Promotion of Science (JSPS) KAKENHI grant (Nos. 16K18302 and 18K04857 [to S.Y.Y]; 15H05790, 16H01373, 17H04134, and 26293111 [to J.K.]

Towards optimisation of load-time conditions for producing viscoelastically prestressed polymeric matrix composites

A viscoelastically prestressed polymeric matrix composite (VPPMC) is produced by applying a tensile creep load to polymeric fibres, the load being released before the fibres are moulded into a polymeric matrix. The viscoelastically recovering fibres induce compressive stresses within the matrix, which can improve mechanical properties by up to 50%. This study investigates the feasibility of reducing the creep loading period for VPPMC production. By using nylon 6,6 fibres, we have demonstrated that the previously adopted viscoelastic creep strain, requiring 330 MPa for 24 h, can be achieved over a shorter duration, tn, using increased creep stress. Thus tn was 92 min at 460 MPa and 37 min at 590 MPa. Subject to avoiding fibre damage however, it may be possible to reduce tn further. From the three creep settings, elapsed recovery strain values were similar, as were the Charpy impact test data from corresponding VPPMC samples; i.e. there were no significant differences in impact energy absorption, these being ∼56% greater than their control (unstressed) counterparts

Regulatory motif discovery using a population clustering evolutionary algorithm

This paper describes a novel evolutionary algorithm for regulatory motif discovery in DNA promoter sequences. The algorithm uses data clustering to logically distribute the evolving population across the search space. Mating then takes place within local regions of the population, promoting overall solution diversity and encouraging discovery of multiple solutions. Experiments using synthetic data sets have demonstrated the algorithm's capacity to find position frequency matrix models of known regulatory motifs in relatively long promoter sequences. These experiments have also shown the algorithm's ability to maintain diversity during search and discover multiple motifs within a single population. The utility of the algorithm for discovering motifs in real biological data is demonstrated by its ability to find meaningful motifs within muscle-specific regulatory sequences

Experimental effects and causal representations

In experimental settings, scientists often “make” new things, in which case the aim is to intervene in order to produce experimental objects and processes—characterized as ‘effects’. In this discussion, I illuminate an important performative function in measurement and experimentation in general: intervention-based experimental production (IEP). I argue that even though the goal of IEP is the production of new effects, it can be informative for causal details in scientific representations. Specifically, IEP can be informative about causal relations in: regularities under study; ‘intervention systems’, which are measurement/experimental systems; and new technological systems

Integrating Olfaction in a Robotic Telepresence Loop

In this work we propose enhancing a typical robotic telepresence architecture by considering olfactory and wind flow information in addition to the common audio and video channels. The objective is to expand the range of applications where robotics telepresence can be applied, including those related to the detection of volatile chemical substances (e.g. land-mine detection, explosive deactivation, operations in noxious environments, etc.). Concretely, we analyze how the sense of smell can be integrated in the telepresence loop, covering the digitization of the gases and wind flow present in the remote environment, the transmission through the communication network, and their display at the user location. Experiments under different environmental conditions are presented to validate the proposed telepresence system when localizing a gas emission leak at the remote environment.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Reflections on the future of research curation and research reproducibility

In the years since the launch of the World Wide Web in 1993, there have been profoundly transformative changes to the entire concept of publishing—exceeding all the previous combined technical advances of the centuries following the introduction of movable type in medieval Asia around the year 10001 and the subsequent large-scale commercialization of printing several centuries later by J. Gutenberg (circa 1440). Periodicals in print—from daily newspapers to scholarly journals—are now quickly disappearing, never to return, and while no publishing sector has been unaffected, many scholarly journals are almost unrecognizable in comparison with their counterparts of two decades ago. To say that digital delivery of the written word is fundamentally different is a huge understatement. Online publishing permits inclusion of multimedia and interactive content that add new dimensions to what had been available in print-only renderings. As of this writing, the IEEE portfolio of journal titles comprises 59 online only2 (31%) and 132 that are published in both print and online. The migration from print to online is more stark than these numbers indicate because of the 132 periodicals that are both print and online, the print runs are now quite small and continue to decline. In short, most readers prefer to have their subscriptions fulfilled by digital renderings only

Building a Culture of Reproducibility in Academic Research

Reproducibility is an ideal that no researcher would dispute "in the abstract", but when aspirations meet the cold hard reality of the academic grind, reproducibility often "loses out". In this essay, I share some personal experiences grappling with how to operationalize reproducibility while balancing its demands against other priorities. My research group has had some success building a "culture of reproducibility" over the past few years, which I attempt to distill into lessons learned and actionable advice, organized around answering three questions: why, what, and how. I believe that reproducibility efforts should yield easy-to-use, well-packaged, and self-contained software artifacts that allow others to reproduce and generalize research findings. At the core, my approach centers on self interest: I argue that the primary beneficiaries of reproducibility efforts are, in fact, those making the investments. I believe that (unashamedly) appealing to self interest, augmented with expectations of reciprocity, increases the chances of success. Building from repeatability, social processes and standardized tools comprise the two important additional ingredients that help achieve aspirational ideals. The dogfood principle nicely ties these ideas together