Emerging from the MIST: A Connector Tool for Supporting Programming by Non-programmers

Software development is an iterative process. As user re-quirements emerge software applications must be extended to support the new requirements. Typically, a programmer will add new code to an existing code base of an application to provide a new functionality. Previous research has shown that such extensions are easier when application logic is clearly separated from the user interface logic. Assuming that a programmer is already familiar with the existing code base, the task of writing the new code can be considered to be split into two sub-tasks: writing code for the application logic; that is, the actual functionality of the application; and writing code for the user interface that will expose the functionality to the end user. The goal of this research is to reduce the effort required to create a user interface once the application logic has been created, toward supporting scientists with minimal pro-gramming knowledge to be able to create and modify pro-grams. Using a Model View Controller based architecture, various model components which contain the application logic can be built and extended. The process of creating and extending the views (user interfaces) on these model components is simplified through the use of our Malleable Interactive Software Toolkit (MIST), a tool set an infrastructure intended to simplify the design and extension of dynamically reconfigurable interfaces. This paper focuses on one tool in the MIST suite, a connec-tor tool that enables the programmer to evolve the user interface as the application logic evolves by connecting related pieces of code together; either through simple drag-and-drop interactions or through the authoring of Python code. The connector tool exemplifies the types of tools in the MIST suite, which we expect will encourage collabora-tive development of applications by allowing users to inte-grate various components and minimizing the cost of de-veloping new user interfaces for the combined compo-nents

Scientists in the MIST: Simplifying Interface Design for End Users

We are building a Malleable Interactive Software Toolkit (MIST), a tool set and infrastructure to simplify the design and construction of dynamically-reconfigurable (malleable) interactive software. Malleable software offers the end-user powerful tools to reshape their interactive environment on the fly. We aim to make the construction of such software straightforward, and to make reconfiguration of the resulting systems approachable and manageable to an educated, but non-specialist, user. To do so, we draw on a diverse body of existing research on alternative approaches to user interface (UI) and interactive software construction, including declarative UI languages, constraint-based programming and UI management, reflection and data-driven programming, and visual programming techniques

Computer simulation of web dynamics

Explicit finite difference schemes for modeling one-dimensional, transient web dynamics are designed, developed and tested. A sequence of numerical experiments are performed to ascertain the effects of various parameters on the stability and accuracy of the numerical results. Refinement of the numerical grid led to results which converged to analytical results for stable computations. For a particular web running speed and computational duration, there exists a time-step limit for stability. Longer computational time durations as well as higher web running speeds require reduced time-step size for stable numerical results. Upstream differencing of the Coriolis term to procure stability leads to numerical damping in the computations. A combination of upstream and central differencing yields stable results at larger time-steps than that required using full central differencing as well as less damping than that produced using full upstream differencing.Mechanical and Aerospace Engineerin

Design of a precision calibration unit for Keck NIRC2 AO instrument

High-precision astrometry has the potential to address questions in planet formation, black hole science, Galactic structure, and more. However, in order to achieve a precision of sub-milli arcseconds (mas), we need a calibration method better than the current techniques such as on-sky calibration using calibrated stellar or stellar cluster systems, which have a precision of ~1 mas. Precision calibration unit with a regular grid of photo-lithographically manufactured pinholes combined with self-calibration techniques, on the other hand, is a new and innovative way to potentially achieve a precision of sub-mas over the entire field of view. This technique is beneficial to adaptive optic (AO) instruments for future telescopes like the Thirty Meter Telescope (TMT). In this work, we present our design for a new astrometric calibration unit to feed the NIRC2 AO instrument at the W. M. Keck Observatory. It allows calibration over a large field of view of 47" x 47"

Design of a precision calibration unit for Keck NIRC2 AO instrument

High-precision astrometry has the potential to address questions in planet formation, black hole science, Galactic structure, and more. However, in order to achieve a precision of sub-milli arcseconds (mas), we need a calibration method better than the current techniques such as on-sky calibration using calibrated stellar or stellar cluster systems, which have a precision of ~1 mas. Precision calibration unit with a regular grid of photo-lithographically manufactured pinholes combined with self-calibration techniques, on the other hand, is a new and innovative way to potentially achieve a precision of sub-mas over the entire field of view. This technique is beneficial to adaptive optic (AO) instruments for future telescopes like the Thirty Meter Telescope (TMT). In this work, we present our design for a new astrometric calibration unit to feed the NIRC2 AO instrument at the W. M. Keck Observatory. It allows calibration over a large field of view of 47" x 47"

Closing the loop on e-waste: a multidisciplinary perspective

This paper describes the challenges faced, and oppor tunities identified, by a multidisciplinary team of researchers developing a novel closed loop system to recover valuable metals and reduce e-waste, focusing on mobile phones as a case study. This multidisciplinary approach is contrasted with current top-down approaches to making the transition to the circular economy (CE). The aim of the research presented here is to develop a product service system (PSS) that facilitates the recovery of valuable functional components and metals from mobile phone circuit boards. To create a holistic solution and limit unintended consequences, in addition to technological solutions, this paper considers appropriate component lifetimes; the (often ignored) role of the citizen in the circular economy; customer interaction with the PSS; environmental life cycle assessment; and social impacts of the proposed PSS. Development of enabling technologies and materials to facilitate recovery of components and metals and to provide an emotionally durable external enclosure is described. This research also highlights the impor tance of understanding value in the CE from a multifaceted and interdisciplinary perspective

Distinct microenvironmental cues trigger divergent TLR4-mediated immune signalling in macrophages

Macrophages exhibit a phenotypic plasticity that enables them to orchestrate specific immune responses to distinct threats. However, the factors that control macrophage behaviour in a context dependent manner are not well understood. Lipopolysaccharide (LPS) and the extracellular matrix glycoprotein tenascin-C both activate toll-like receptor 4 (TLR4), and are released during bacterial infection and tissue injury, respectively. Here we report that these two TLR4 ligands induce distinct macrophage signalling pathways and phenotypes. Macrophages activated by LPS or tenascin-C display some common features, including NF-kB and MAP kinase signalling, and cytokine synthesis. However, different subsets of cytokines, and different phosphoproteomic signatures, are produced by each stimulus. Moreover, tenascin-C promotes macrophages more inclined to matrix synthesis and phosphorylation, whilst LPS-activated macrophages exhibit an elevated capacity to degrade matrix. These data reveal how activation of one pattern recognition receptor by different microenvironmental cues, signalling pathogen invasion or tissue damage, can create unique macrophage phenotypes

Inflammatory mediators act at renal pericytes to elicit contraction of vasa recta and reduce pericyte density along the kidney medullary vascular network

Introduction: Regardless of initiating cause, renal injury promotes a potent pro-inflammatory environment in the outer medulla and a concomitant sustained decrease in medullary blood flow (MBF). This decline in MBF is believed to be one of the critical events in the pathogenesis of acute kidney injury (AKI), yet the precise cellular mechanism underlying this are still to be fully elucidated. MBF is regulated by contractile pericyte cells that reside on the descending vasa recta (DVR) capillaries, which are the primary source of blood flow to the medulla. Methods: Using the rat and murine live kidney slice models, we investigated the acute effects of key medullary inflammatory mediators TNF-α, IL-1β, IL-33, IL-18, C3a and C5a on vasa recta pericytes, the effect of AT1-R blocker Losartan on pro-inflammatory mediator activity at vasa recta pericytes, and the effect of 4-hour sustained exposure on immunolabelled NG2+ pericytes. Results and discussion: Exposure of rat and mouse kidney slices to TNF-α, IL-18, IL-33, and C5a demonstrated a real-time pericyte-mediated constriction of DVR. When pro-inflammatory mediators were applied in the presence of Losartan the inflammatory mediator-mediated constriction that had previously been observed was significantly attenuated. When live kidney slices were exposed to inflammatory mediators for 4-h, we noted a significant reduction in the number of NG2+ positive pericytes along vasa recta capillaries in both rat and murine kidney slices. Data collected in this study demonstrate that inflammatory mediators can dysregulate pericytes to constrict DVR diameter and reduce the density of pericytes along vasa recta vessels, further diminishing the regulatory capacity of the capillary network. We postulate that preliminary findings here suggest pericytes play a role in AKI

Predicting coaxial helical stacking in RNA junctions

RNA junctions are important structural elements that form when three or more helices come together in space in the tertiary structures of RNA molecules. Determining their structural configuration is important for predicting RNA 3D structure. We introduce a computational method to predict, at the secondary structure level, the coaxial helical stacking arrangement in junctions, as well as classify the junction topology. Our approach uses a data mining approach known as random forests, which relies on a set of decision trees trained using length, sequence and other variables specified for any given junction. The resulting protocol predicts coaxial stacking within three- and four-way junctions with an accuracy of 81% and 77%, respectively; the accuracy increases to 83% and 87%, respectively, when knowledge from the junction family type is included. Coaxial stacking predictions for the five to ten-way junctions are less accurate (60%) due to sparse data available for training. Additionally, our application predicts the junction family with an accuracy of 85% for three-way junctions and 74% for four-way junctions. Comparisons with other methods, as well applications to unsolved RNAs, are also presented. The web server Junction-Explorer to predict junction topologies is freely available at: http://bioinformatics.njit.edu/junction