Towards incorporating the notion of feature shape in music and text retrieval

Extracted feature data augment information resources with concrete characterizations of their content, but only approximate to the meaningful high-level descriptions typically expected by digital musicology scholars (domain experts with some technological affinity, but with no expertise in signal processing or feature data). Feature shapes provide abstract aggregations of feature types which share common characteristics when applied in extraction workflows. We explore the feasibility of feature shape-based filtering and querying within a large audio dataset of live music performances, employing operation sequences as specified by the Audio Feature Ontology and Vocabulary. We further implement analogous semantic structures for the HathiTrust Extracted Feature Dataset to demonstrate the general applicability of feature shapes in music and text retrieval

An efficient numerical approach to modeling the effects of particle shape on rubble-pile dynamics

We present an approach for the inclusion of non-spherical constituents in high-resolution N-body discrete element method (DEM) simulations. We use aggregates composed of bonded spheres to model non-spherical components. Though the method may be applied more generally, we detail our implementation in the existing N-body code pkdgrav. It has long been acknowledged that non-spherical grains confer additional shear strength and resistance to flow when compared with spheres. As a result, we expect that rubble-pile asteroids will also exhibit these properties and may behave differently than comparable rubble piles composed of idealized spheres. Since spherical particles avoid some significant technical challenges, most DEM gravity codes have used only spherical particles, or have been confined to relatively low resolutions. We also discuss the work that has gone into improving performance with non-spherical grains, building on pkdgrav's existing leading-edge computational efficiency among DEM gravity codes. This allows for the addition of non-spherical shapes while maintaining the efficiencies afforded by pkdgrav's tree implementation and parallelization. As a test, we simulated the gravitational collapse of 25,000 non-spherical bodies in parallel. In this case, the efficiency improvements allowed for an increase in speed by nearly a factor of three when compared with the naive implementation. Without these enhancements, large runs with non-spherical components would remain prohibitively expensive. Finally, we present the results of several small-scale tests: spinup due to the YORP effect, tidal encounters, and the Brazil-nut Effect. In all cases, we find that the inclusion of non-spherical constituents has a measurable impact on simulation outcomes.Comment: 35 pages, 8 figure

Late Holocene wetland transgression and 500 years of vegetation and fire variability in the semi-arid Amboseli landscape, southern Kenya

The semi-arid Amboseli landscape, southern Kenya, is characterised by intermittent groundwater-fed wetlands that form sedimentary geoarchives recording past ecosystem changes. We present a 5000-year environmental history of a radiocarbon dated sediment core from Esambu Swamp adjacent to Amboseli National Park. Although radiocarbon dates suggest an unconformity or sedimentary gap that spans between 3800 and 500 cal year BP, the record provides a unique insight into the long-term ecosystem history and wetland processes, particularly the past 500 years. Climatic shifts, fire activity and recent anthropogenic activity drive changes in ecosystem composition. Prior to 3800 cal year BP the pollen data suggest semi-arid savanna ecosystem persisted near the wetland. The wetland transgressed at some time between 3800 and 500 cal year BP and it is difficult to constrain this timing further, and palustrine peaty sediments have accumulated since 400 cal year BP. Increased abundance of Afromontane forest taxa from adjacent highlands of Kilimanjaro and the Chyulu Hills and local arboreal taxa reflect changes in regional moisture budgets. Particularly transformative changes occurred in the last five centuries, associated with increased local biomass burning coeval with the arrival of Maa-speaking pastoralists and intensification of the ivory trade. Cereal crops occurred consistently from around 300 cal year BP, indicative of further anthropogenic activity. The study provides unique insight in Amboseli ecosystem history and the link between ecosystem drivers of change. Such long-term perspectives are crucial for future climate change and associated livelihood impacts, so that suitable responses to ensure sustainable management practices can be developed in an important conservation landscape

Device assessed activity behaviours in patients with indwelling pleural catheter: A sub-study of the Australasian Malignant PLeural Effusion (AMPLE)-2 randomized trial

Background and Objective: Device-assessed activity behaviours are a novel measure for comparing intervention outcomes in patients with malignant pleural effusion (MPE). Australasian Malignant PLeural Effusion (AMPLE)-2 was a multi-centre clinical trial where participants with MPE treated with an indwelling pleural catheter were randomized to daily (DD) or symptom-guided (SGD) drainage for 60-days. Our aim was to describe activity behaviour patterns in MPE patients, explore the impact of drainage regimen on activity behaviours and examine associations between activity behaviours and quality of life (QoL). Methods: Following randomization to DD or SGD, participants enrolled at the lead site (Perth) completed accelerometry assessment. This was repeated monthly for 5-months. Activity behaviour outcomes were calculated as percent of daily waking-wear time and compared between groups (Mann–Whitney U test; Median [IQR]). Correlations between activity behaviour outcomes and QoL were examined. Results: Forty-one (91%) participants provided ≥ 1 valid accelerometry assessment (DDn = 20, SGD n = 21). Participants spent a large proportion of waking hours sedentary (72%–74% across timepoints), and very little time in moderate-to-vigorous physical activity ( \u3c 1% across timepoints). Compared to SGD group, DD group had a more favourable sedentary-to-light ratio in the week following randomization (2.4 [2.0–3.4] vs. 3.2 [2.4–6.1]; p = 0.047) and at 60-days (2.0 [1.9–2.9] vs. 2.9 [2.8–6.0]; p = 0.016). Sedentary-to-light ratio was correlated with multiple QoL domains at multiple timepoints. Conclusion: Patients with MPE are largely sedentary. Preliminary results suggest that even modest differences in activity behaviours favouring the DD group could be meaningful for this clinical population. Accelerometry reflects QoL and is a useful outcome measure in MPE populations

Topological Requirements and Signaling Properties of T Cell–activating, Anti-CD28 Antibody Superagonists

Full activation of naive T cells requires both engagement of the T cell antigen receptor (TCR; signal 1) and costimulatory signaling by CD28 (signal 2). We previously identified two types of rat CD28-specific monoclonal antibodies (mAbs): “conventional,” TCR signaling–dependent costimulatory mAbs and “superagonistic” mAbs capable of inducing the full activation of primary resting T cells in the absence of TCR ligation both in vitro and in vivo. Using chimeric rat/mouse CD28 molecules, we show that the superagonists bind exclusively to the laterally exposed C′′D loop of the immunoglobulin-like domain of CD28 whereas conventional, costimulatory mAbs recognize an epitope close to the binding site for the natural CD80/CD86 ligands. Unexpectedly, the C′′D loop reactivity of a panel of new antibodies raised against human CD28 could be predicted solely on the basis of their superagonistic properties. Moreover, mouse CD28 molecules engineered to express the rat or human C′′D loop sequences activated T cell hybridomas without TCR ligation when cross-linked by superagonistic mAbs. Finally, biochemical analysis revealed that superagonistic CD28 signaling activates the nuclear factor κB pathway without inducing phosphorylation of either TCRζ or ZAP70. Our findings indicate that the topologically constrained interactions of anti-CD28 superagonists bypass the requirement for signal 1 in T cell activation. Antibodies with this property may prove useful for the development of T cell stimulatory drugs

Pan-Antarctic analysis aggregating spatial estimates of Adélie penguin abundance reveals robust dynamics despite stochastic noise

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 832, doi:10.1038/s41467-017-00890-0.Colonially-breeding seabirds have long served as indicator species for the health of the oceans on which they depend. Abundance and breeding data are repeatedly collected at fixed study sites in the hopes that changes in abundance and productivity may be useful for adaptive management of marine resources, but their suitability for this purpose is often unknown. To address this, we fit a Bayesian population dynamics model that includes process and observation error to all known Adélie penguin abundance data (1982–2015) in the Antarctic, covering >95% of their population globally. We find that process error exceeds observation error in this system, and that continent-wide “year effects” strongly influence population growth rates. Our findings have important implications for the use of Adélie penguins in Southern Ocean feedback management, and suggest that aggregating abundance across space provides the fastest reliable signal of true population change for species whose dynamics are driven by stochastic processes.H.J.L., C.C.-C., G.H., C.Y., and K.T.S. gratefully acknowledge funding provided by US National Aeronautics and Space Administration Award No. NNX14AC32G and U.S. National Science Foundation Office of Polar Programs Award No. NSF/OPP-1255058. S.J., L.L., M.M.H., Y.L., and R.J. gratefully acknowledge funding provided by US National Aeronautics and Space Administration Award No. NNX14AH74G. H.J.L., C.Y., S.J., Y.L., and R.J. gratefully acknowledge funding provided by U.S. National Science Foundation Office of Polar Programs Award No. NSF/PLR-1341548. S.J. gratefully acknowledges support from the Dalio Explore Fund

CHILES: HI morphology and galaxy environment at z=0.12 and z=0.17

We present a study of 16 HI-detected galaxies found in 178 hours of observations from Epoch 1 of the COSMOS HI Large Extragalactic Survey (CHILES). We focus on two redshift ranges between 0.108 <= z <= 0.127 and 0.162 <= z <= 0.183 which are among the worst affected by radio frequency interference (RFI). While this represents only 10% of the total frequency coverage and 18% of the total expected time on source compared to what will be the full CHILES survey, we demonstrate that our data reduction pipeline recovers high quality data even in regions severely impacted by RFI. We report on our in-depth testing of an automated spectral line source finder to produce HI total intensity maps which we present side-by-side with significance maps to evaluate the reliability of the morphology recovered by the source finder. We recommend that this become a common place manner of presenting data from upcoming HI surveys of resolved objects. We use the COSMOS 20k group catalogue, and we extract filamentary structure using the topological DisPerSE algorithm to evaluate the \hi\ morphology in the context of both local and large-scale environments and we discuss the shortcomings of both methods. Many of the detections show disturbed HI morphologies suggesting they have undergone a recent interaction which is not evident from deep optical imaging alone. Overall, the sample showcases the broad range of ways in which galaxies interact with their environment. This is a first look at the population of galaxies and their local and large-scale environments observed in HI by CHILES at redshifts beyond the z=0.1 Universe.Comment: 23 pages, 12 figures, 1 interactive 3D figure, accepted to MNRA

Decision‐support networks of women newly diagnosed with breast cancer

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138904/1/cncr30848_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138904/2/cncr30848.pd