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

Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components.

The spliceosome processes RNAs from a pre-RNA state to a mature mRNA thereby influencing RNA availability for translation, localization, and turnover. It consists of complex structures containing RNA-binding proteins (RBPs) essential for post-transcriptional gene expression control. Here we investigate the dynamic modifications of spliceosomal RBPs under stress and in particular drought stress. We do so by mRNA interactome capture in Arabidopsis thaliana using label free quantitation. This approach identified 44 proteins associated with the spliceosome and further 32 proteins associated with stress granules. We noted a high enrichment in the motifs RDRR and RSRSRS that are characteristic of RNA interacting proteins. Identification of splicing factors reflect direct and/or indirect stress induced splicing events that have a direct effect on transcriptome and proteome changes under stress. Furthermore, detection of stress granule components is consistent with transcriptional arrest. Identification of drought induced stress granule components is critical in determining common abiotic stress-induced foci that can have biotechnological applications. This study may therefore open ways to modify plant stress responses at a systems level through the modification of key spliceosome components

Big Foot Art Site, Cania Gorge: Site report

This site report presents a description of archaeological investigations undertaken at Big Foot Art Site, a large rockshelter and art site located at Cania Gorge, eastern Central Queensland. Field and laboratory methods are outlined and results presented. Excavation revealed evidence for occupation spanning from before 7,700 cal BP to at least 300 cal BP, with a significant peak in stone artefact discard between c.4,200-3,200 cal BP. Results are compared to analyses undertaken in the adjacent Central Queensland Highlands

Edge-ground hatchets on the Southern Curtis Coast, Central Queensland: A preliminary Assessment of Technology, Chronology and Provenance

A number of edge-ground hatchets were identified from various locations in central Queensland during recent investigations conducted as part of the Gooreng Gooreng Cultural Heritage Project. Macroscopic examination suggested that some hatchets were manufactured on a distinctive form of rhyolitic tuff which is restricted in occurrence to the Town of Seventeen Seventy - Agnes Water area on the southern Curtis Coast. The hatchets are distributed over an area of some 6000 km2, centred on the town of Lowmead within the ethnohistorically documented linguistic borders of Gooreng Gooreng country. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was employed in an attempt to provenance the hatchets to particular outcrops of rhyolitic tuff on the basis of trace element geochemistry. Preliminary results confirm that all hatchets identified as rhyolitic tuff exhibit a similar geochemical signature. Moreover, this geochemistry can be correlated with the background samples from the Ironbark Site Complex, the only major rhyolite quarry known in the region. The study enhances our understanding of past Aboriginal lifeways in the region by situating strategies of stone procurement and use in the landscape

Roof Fall Cave, Cania Gorge: Site report

This site report presents a description of archaeological investigations undertaken at Roof Fall Cave, an occupied rockshelter and art site located at Cania Gorge, eastern Central Queensland. Excavation yielded quantities of stone artefacts, bone and charcoal, along with some freshwater mussel shell and ochre with an occupational sequence spanning from up to 18,576 cal BP to the historical period. Roof Fall Cave is currently the oldest dated site in Cania Gorge and possibly in the Central Queensland region

Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms.

BACKGROUND: RNA-binding proteins (RBPs) are increasingly recognized as regulatory component of post-transcriptional gene expression. RBPs interact with mRNAs via RNA-binding domains and these interactions affect RNA availability for translation, RNA stability and turn-over thus affecting both RNA and protein expression essential for developmental and stimulus specific responses. Here we investigate the effect of severe drought stress on the RNA-binding proteome to gain insights into the mechanisms that govern drought stress responses at the systems level. RESULTS: Label-free mass spectrometry enabled the identification 567 proteins of which 150 significantly responded to the drought-induced treatment. A gene ontology analysis revealed enrichment in the "RNA binding" and "RNA processing" categories as well as biological processes such as "response to abscisic acid" and "response to water deprivation". Importantly, a large number of the stress responsive proteins have not previously been identified as RBPs and include proteins in carbohydrate metabolism and in the glycolytic and citric acid pathways in particular. This suggests that RBPs have hitherto unknown roles in processes that govern metabolic changes during stress responses. Furthermore, a comparative analysis of RBP domain architectures shows both, plant specific and common domain architectures between plants and animals. The latter could be an indication that RBPs are part of an ancient stress response. CONCLUSION: This study establishes mRNA interactome capture technique as an approach to study stress signal responses implicated in environmental changes. Our findings denote RBP changes in the proteome as critical components in plant adaptation to changing environments and in particular drought stress protein-dependent changes in RNA metabolism

The AIROPA software package - Milestones for testing general relativity in the strong gravity regime with AO

General relativity can be tested in the strong gravity regime by monitoring stars orbiting the supermassive black hole at the Galactic Center with adaptive optics. However, the limiting source of uncertainty is the spatial PSF variability due to atmospheric anisoplanatism and instrumental aberrations. The Galactic Center Group at UCLA has completed a project developing algorithms to predict PSF variability for Keck AO images. We have created a new software package (AIROPA), based on modified versions of StarFinder and Arroyo, that takes atmospheric turbulence profiles, instrumental aberration maps, and images as inputs and delivers improved photometry and astrometry on crowded fields. This software package will be made publicly available soon

Robust smoothing of left-censored time series data with a dynamic linear model to infer SARS-CoV-2 RNA concentrations in wastewater

Wastewater sampling for the detection and monitoring of SARS-CoV-2 has been developed and applied at an unprecedented pace, however uncertainty remains when interpreting the measured viral RNA signals and their spatiotemporal variation. The proliferation of measurements that are below a quantifiable threshold, usually during non-endemic periods, poses a further challenge to interpretation and time-series analysis of the data. Inspired by research in the use of a custom Kalman smoother model to estimate the true level of SARS-CoV-2 RNA concentrations in wastewater, we propose an alternative left-censored dynamic linear model. Cross-validation of both models alongside a simple moving average, using data from 286 sewage treatment works across England, allows for a comprehensive validation of the proposed approach. The presented dynamic linear model is more parsimonious, has a faster computational time and is represented by a more flexible modelling framework than the equivalent Kalman smoother. Furthermore we show how the use of wastewater data, transformed by such models, correlates more closely with regional case rate positivity as published by the Office for National Statistics (ONS) Coronavirus (COVID-19) Infection Survey. The modelled output is more robust and is therefore capable of better complementing traditional surveillance than untransformed data or a simple moving average, providing additional confidence and utility for public health decision making. La détection et la surveillance du SARS-CoV-2 dans les eaux usées ont été développées et réalisées à un rythme sans précédent, mais l'interprétation des mesures de concentrations en ARN viral, et de leurs variations spatio-temporelles, pose question. En particulier, l'importante proportion de mesures en deçà du seuil de quantification, généralement pendant les périodes non endémiques, constitue un défi pour l'analyse de ces séries temporelles. Inspirés par un travail de recherche ayant produit un lisseur de Kalman adapté pour estimer les concentrations réelles en ARN de SARS-CoV-2 dans les eaux usées à partir de ce type de données, nous proposons un nouveau modèle linéaire dynamique avec censure à gauche. Une validation croisée de ces lisseurs, ainsi que d'un simple lissage par moyenne glissante, sur des données provenant de 286 stations d'épuration couvrant l'Angleterre, valide de façon complète l'approche proposée. Le modèle présenté est plus parcimonieux, offre un cadre de modélisation plus flexible et nécessite un temps de calcul réduit par rapport au Lisseur de Kalman équivalent. Les données issues des eaux usées ainsi lissées sont en outre plus fortement corrélées avec le taux d'incidence régional produit par le bureau des statistiques nationales (ONS) Coronavirus Infection Survey. Elles se montrent plus robustes que les données brutes, ou lissées par simple moyenne glissante, et donc plus à même de compléter la surveillance traditionnelle, renforçant ainsi la confiance en l'épidémiologie fondée sur les eaux usées et son utilité pour la prise de décisions de santé publique

Keck Planet Imager and Characterizer: A dedicated single-mode fiber injection unit for high resolution exoplanet spectroscopy

The Keck Planet Imager and Characterizer (KPIC) is a purpose-built instrument to demonstrate new tech- nological and instrumental concepts initially developed for the exoplanet direct imaging field. Located downstream of the current Keck II adaptive optic system, KPIC contains a fiber injection unit (FIU) capable of combining the high-contrast imaging capability of the adaptive optic system with the high dispersion spectroscopy capability of the current Keck high resolution infrared spectrograph (NIRSPEC). Deployed at Keck in September 2018, this instrument has already been used to acquire high resolution spectra (R < 35, 000) of multiple targets of interest. In the near term, it will be used to spectrally characterize known directly imaged exoplanets and low-mass brown dwarf companions visible in the northern hemisphere with a spectral resolution high enough to enable spin and planetary radial velocity measurements as well as Doppler imaging of atmospheric weather phenomena. Here we present the design of the FIU, the unique calibration procedures needed to operate a single-mode fiber instrument and the system performance