A New Way to Make Music: Processing Digital Audio in Virtual Reality

The work of this project attempts to provide new methods of creating music with technology. The product, Fields, is a functional piece of virtual reality software, providing users an immersive and interactive set of tools used to build and design instruments in a modular manner. Each virtual tool is analogous to musical hardware such as guitar pedals, synthesizers, or samplers, and can be thought of as an effect or instrument on its own. Specific configurations of these virtual audio effects can then be played to produce music, and then even saved by the user to load up and play with at a later time. There are still goals to expand this project, and turn it into something more akin to a professional digital audio workstation, but for the time being it remains a modular synthesizer with nearly limitless configurations in a virtual 3D environment. Included is a developer library, giving users the ability to integrate their own musical software solutions into the virtual environment and expand the work of this project

Designing a Model-Based Systems Engineering (MBSE) Template for Satellites

The goal of this project has been to digitally transform SDL systems engineering methods for scoping small satellite missions, developing system architectures, documenting the engineering solution, and verifying design solutions from being document-intensive (gathering non-transformable information in discrete, disjoint documents) to being model-based (employing cohesive, traceable, transformable graphical models). We have produced a set of models that give satellite development programs (and any model-based program) a head start that enables the modeling effort to drive the systems engineering process instead of catching up with a document-driven design. We plan to use these models to develop, train, and encourage consistent modeling techniques across the Lab and lower the barrier of entry for creating focused, useful models

Escherichia coli, an Intestinal Microorganism, as a Biosensor for Quantification of Amino Acid Bioavailability

In animal diets optimal amino acid quantities and balance among amino acids is of great nutritional importance. Essential amino acid deficiencies have negative impacts on animal physiology, most often expressed in sub-optimal body weight gains. Over supplementation of diets with amino acids is costly and can increase the nitrogen emissions from animals. Although in vivo animal assays for quantification of amino acid bioavailability are well established, Escherichia coli-based bioassays are viable potential alternatives in terms of accuracy, cost, and time input. E. coli inhabits the gastrointestinal tract and although more abundant in colon, a relatively high titer of E. coli can also be isolated from the small intestine, where primary absorption of amino acids and peptides occur. After feed proteins are digested, liberated amino acids and small peptides are assimilated by both the small intestine and E. coli. The similar pattern of uptake is a necessary prerequisite to establish E. coli cells as accurate amino acid biosensors. In fact, amino acid transporters in both intestinal and E. coli cells are stereospecific, delivering only the respective biological l-forms. The presence of free amino- and carboxyl groups is critical for amino acid and dipeptide transport in both biological subjects. Di-, tri- and tetrapeptides can enter enterocytes; likewise only di-, tri- and tetrapeptides support E. coli growth. These similarities in addition to the well known bacterial genetics make E. coli an optimal bioassay microorganism for the assessment of nutritionally available amino acids in feeds

Hereditary C1q deficiency is associated with type 1 interferon-pathway activation and a high risk of central nervous system inflammation

Hereditary C1q deficiency (C1QDef) is a rare monogenic disorder leading to defective complement pathway activation and systemic lupus erythematosus (SLE)-like manifestations. The link between impairment of the complement cascade and autoimmunity remains incompletely understood. Here, we assessed type 1 interferon pathway activation in patients with C1QDef. Twelve patients with genetically confirmed C1QDef were recruited through an international collaboration. Clinical, biological and radiological data were collected retrospectively. The expression of a standardized panel of interferon stimulated genes (ISGs) in peripheral blood was measured, and the level of interferon alpha (IFNα) protein in cerebrospinal fluid (CSF) determined using SIMOA technology. Central nervous system (encompassing basal ganglia calcification, encephalitis, vasculitis, chronic pachymeningitis), mucocutaneous and renal involvement were present, respectively, in 10, 11 and 2 of 12 patients, and severe infections recorded in 2/12 patients. Elevated ISG expression was observed in all patients tested (n=10/10), and serum and CSF IFNα elevated in 2/2 patients. Three patients were treated with Janus-kinase inhibitors (JAKi), with variable outcome; one displaying an apparently favourable response in respect of cutaneous and neurological features, and two others experiencing persistent disease despite JAKi therapy. To our knowledge, we report the largest original series of genetically confirmed C1QDef yet described. Additionally, we present a review of all previously described genetically confirmed cases of C1QDef. Overall, individuals with C1QDef demonstrate many characteristics of recognized monogenic interferonopathies: particularly, cutaneous involvement (malar rash, acral vasculitic/papular rash, chilblains), SLE-like disease, basal ganglia calcification, increased expression of ISGs in peripheral blood, and elevated levels of CSF IFNα

Spatial variation in prostate cancer survival in the Northern and Yorkshire region of England using Bayesian relative survival smoothing

Primary Care Trust (PCT) estimates of survival lack robustness as there are small numbers of deaths per year in each area, even when incidence is high. We assess PCT-level spatial variation in prostate cancer survival using Bayesian spatial models of excess mortality. We extracted data on men diagnosed with prostate cancer between 1990 and 1999 from the Northern and Yorkshire Cancer Registry and Information Service database. Models were adjusted for age at diagnosis, period of diagnosis and deprivation. All covariates had a significant association with excess mortality; men from more deprived areas, older age at diagnosis and diagnosed in 1990–1994 had higher excess mortality. The unadjusted relative excess risks (RER) of death by PCT ranged from 0.75 to 1.66. After adjustment, areas of high and low excess mortality were smoothed towards the mean, and the RERs ranged from 0.74 to 1.49. Using Bayesian smoothing techniques to model cancer survival by geographic area offers many advantages over traditional methods; estimates in areas with small populations or low incidence rates are stabilised and shrunk towards local and global risk estimates improving reliability and precision, complex models are easily handled and adjustment for covariates can be made

Regionally endothermic traits in planktivorous basking sharks Cetorhinus maximus

Few fast-swimming apex fishes are classified as ‘regional endotherms’, having evolved a relatively uncommon suite of traits (e.g. elevated body temperatures, centralised red muscle, and thick-walled hearts) thought to facilitate a fast, predatory lifestyle. Unlike those apex predators, Endangered basking sharks Cetorhinus maximus are massive filter-feeding planktivores assumed to have the anatomy and physiology typical of fully ectothermic fishes. We combined dissections of stranded specimens with biologging of free-swimming individuals and found that basking sharks have red muscle located medially at the trunk, almost 50% compact myo - cardium of the ventricle, and subcutaneous white muscle temperatures consistently 1.0 to 1.5°C above ambient. Collectively, our findings suggest basking sharks are not full ectotherms, instead sharing several traits used to define a regional endotherm, thus deviating from our current understanding of the species and questioning the link between physiology and ecology of regionally endothermic shark species. With successful forecasting of population dynamics and distribution shifts often improved by accurate physiological data, our results may help explain movement patterns of the species, which could ultimately facilitate conservation efforts.http://www.int-res.com/journals/esr/esr-home/Anatomy and PhysiologySDG-14:Life below wate

Trends in non-metastatic prostate cancer management in the Northern and Yorkshire region of England, 2000–2006

Background: Our objective was to analyse variation in non-metastatic prostate cancer management in the Northern and Yorkshire region of England. Methods: We included 21 334 men aged ⩾55, diagnosed between 2000 and 2006. Principal treatment received was categorised into radical prostatectomy (11%), brachytherapy (2%), external beam radiotherapy (16%), hormone therapy (42%) and no treatment (29%). Results: The odds ratio (OR) for receiving a radical prostatectomy was 1.53 in 2006 compared with 2000 (95% CI 1.26–1.86), whereas the OR for receiving hormone therapy was 0.57 (0.51–0.64). Age was strongly associated with treatment received; radical treatments were significantly less likely in men aged ⩾75 compared with men aged 55–64 years, whereas the odds of receiving hormone therapy or no treatment were significantly higher in the older age group. The OR for receiving radical prostatectomy, brachytherapy or external beam radiotherapy were all significantly lower in the most deprived areas when compared with the most affluent (0.64 (0.55–0.75), 0.32 (0.22–0.47) and 0.83 (0.74–0.94), respectively) whereas the OR for receiving hormone therapy was 1.56 (1.42–1.71). Conclusions: This study highlights the variation and inequalities that exist in the management of non-metastatic prostate cancer in the Northern and Yorkshire region of England

The impact and significance of tephra deposition on a Holocene forest environment in the North Cascades, Washington, USA.

© 2016 Elsevier Ltd. High-resolution palaeoecological analyses (stratigraphy, tephra geochemistry, radiocarbon dating, pollen and ordination) were used to reconstruct a Holocene vegetation history of a watershed in the Pacific Northwest of America to evaluate the effects and duration of tephra deposition on a forest environment and the significance of these effects compared to long-term trends. Three tephra deposits were detected and evaluated: MLF-T158 and MLC-T324 from the climactic eruption of Mount Mazama, MLC-T480 from a Late Pleistocene eruption of Mount Mazama and MLC-T485 from a Glacier Peak eruption. Records were examined from both the centre and fringe of the basin to elucidate regional and local effects. The significance of tephra impacts independent of underlying long-term trends was confirmed using partial redundancy analysis. Tephra deposition from the climactic eruption of Mount Mazama approximately 7600 cal. years BP caused a significant local impact, reflected in the fringe location by changes to open habitat vegetation (Cyperaceae and Poaceae) and changes in aquatic macrophytes (Myriophyllum spicatum, Potamogeton, Equisetum and the alga Pediastrum). There was no significant impact of the climactic Mazama tephra or other tephras detected on the pollen record of the central core. Changes in this core are potentially climate driven. Overall, significant tephra fall was demonstrated through high resolution analyses indicating a local effect on the terrestrial and aquatic environment, but there was no significant impact on the regional forest dependent of underlying environmental changes

A multilevel study of the determinants of area-level inequalities in colorectal cancer survival

Background: In Australia, associations between geographic remoteness, socioeconomic disadvantage, and colorectal cancer (CRC) survival show that survival rates are lowest among residents of geographically remote regions and those living in disadvantaged areas. At present we know very little about the reasons for these inequalities, hence our capacity to intervene to reduce the inequalities is limited. Methods/Design: This study, the first of its type in Australia, examines the association between CRC survival and key area- and individual-level factors. Specifically, we will use a multilevel framework to investigate the possible determinants of area- and individual-level inequalities in CRC survival and quantify the relative contribution of geographic remoteness, socioeconomic and demographic factors, disease stage, and access to diagnostic and treatment services, to these inequalities. The multilevel analysis will be based on survival data relating to people diagnosed with CRC in Queensland between 1996 and 2005 (n = 22,723) from the Queensland Cancer Registry (QCR), area-level data from other data custodians such as the Australian Bureau of Statistics, and individual-level data from the QCR (including extracting stage from pathology records) and Queensland Hospitals. For a subset of this period (2003 and 2004) we will utilise more detailed, individual-level data (n = 1,966) covering a greater range of risk factors from a concurrent research study. Geo-coding and spatial technology will be used to calculate road travel distances from patients’ residence to treatment centres. The analyses will be conducted using a multilevel Cox proportional hazards model with Level 1 comprising individual-level factors (e.g. occupation) and level 2 area level indicators of remoteness and area socioeconomic disadvantage. Discussion: This study focuses on the health inequalities for rural and disadvantaged populations that have often been documented but poorly understood, hence limiting our capacity to intervene. This study utilises and develops emerging statistical and spatial technologies that can then be applied to other cancers and health outcomes. The findings of this study will have direct implications for the targeting and resourcing of cancer control programs designed to reduce the burden of colorectal cancer, and for the provision of diagnostic and treatment services