Tables of f/us, ub/ and g/us, ub/ functions for semiconductor surface calculations

Derivation of mathematical functions for calculating changes in semiconductor surfaces due to applied surface charg

Joint and individual analysis of breast cancer histologic images and genomic covariates

A key challenge in modern data analysis is understanding connections between complex and differing modalities of data. For example, two of the main approaches to the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genetics. While histopathology is the gold standard for diagnostics and there have been many recent breakthroughs in genetics, there is little overlap between these two fields. We aim to bridge this gap by developing methods based on Angle-based Joint and Individual Variation Explained (AJIVE) to directly explore similarities and differences between these two modalities. Our approach exploits Convolutional Neural Networks (CNNs) as a powerful, automatic method for image feature extraction to address some of the challenges presented by statistical analysis of histopathology image data. CNNs raise issues of interpretability that we address by developing novel methods to explore visual modes of variation captured by statistical algorithms (e.g. PCA or AJIVE) applied to CNN features. Our results provide many interpretable connections and contrasts between histopathology and genetics

Simulated LSST Survey of RR Lyrae Stars throughout the Local Group

We report on a study to determine the efficiency of the Large Synoptic Survey Telescope (LSST) to recover the periods, brightnesses, and shapes of RR Lyrae stars' light curves in the volume extending to heliocentric distances of 1.5 Mpc. We place the smoothed light curves of 30 type ab and 10 type c RR Lyrae stars in 1007 fields across the sky, each of which represents a different realization of the LSST sampling cadences, and that sample five particular observing modes. A light curve simulation tool was used to sample the idealized RR Lyrae stars' light curves, returning each as it would have been observed by LSST, including realistic photometric scatter, limiting magnitudes, and telescope downtime. We report here the period, brightness, and light curve shape recovery as a function of apparent magnitude and for survey lengths varying from 1 to 10 years. We find that 10 years of LSST data are sufficient to recover the pulsation periods with a fractional precision of ~10^(–5) for ≥90% of ab stars within ≈360 kpc of the Sun in Universal Cadence fields and out to ≈760 kpc for Deep Drilling fields. The 50% completeness level extends to ≈600 kpc and ≈1.0 Mpc for the same fields, respectively. For virtually all stars that had their periods recovered, their light curve shape parameter φ_31 was recovered with sufficient precision to also recover photometric metallicities to within 0.14 dex (the systematic error in the photometric relations). With RR Lyrae stars' periods and metallicities well measured to these distances, LSST will be able to search for halo streams and dwarf satellite galaxies over half of the Local Group, informing galaxy formation models and providing essential data for mapping the Galactic potential. This study also informs the LSST science operations plan for optimizing observing strategies to achieve particular science goals. We additionally present a new [Fe/H]-φ_31 photometric relation in the r band and a new and generally useful metric for defining period recovery for time domain surveys

Safety Performance of Airborne Separation: Preliminary Baseline Testing

The Safety Performance of Airborne Separation (SPAS) study is a suite of Monte Carlo simulation experiments designed to analyze and quantify safety behavior of airborne separation. This paper presents results of preliminary baseline testing. The preliminary baseline scenario is designed to be very challenging, consisting of randomized routes in generic high-density airspace in which all aircraft are constrained to the same flight level. Sustained traffic density is varied from approximately 3 to 15 aircraft per 10,000 square miles, approximating up to about 5 times today s traffic density in a typical sector. Research at high traffic densities and at multiple flight levels are planned within the next two years. Basic safety metrics for aircraft separation are collected and analyzed. During the progression of experiments, various errors, uncertainties, delays, and other variables potentially impacting system safety will be incrementally introduced to analyze the effect on safety of the individual factors as well as their interaction and collective effect. In this paper we report the results of the first experiment that addresses the preliminary baseline condition tested over a range of traffic densities. Early results at five times the typical traffic density in today s NAS indicate that, under the assumptions of this study, airborne separation can be safely performed. In addition, we report on initial observations from an exploration of four additional factors tested at a single traffic density: broadcast surveillance signal interference, extent of intent sharing, pilot delay, and wind prediction error

Intratumor Heterogeneity of the Estrogen Receptor and the Long-term Risk of Fatal Breast Cancer.

Background:Breast cancer patients with estrogen receptor (ER)-positive disease have a continuous long-term risk for fatal breast cancer, but the biological factors influencing this risk are unknown. We aimed to determine whether high intratumor heterogeneity of ER predicts an increased long-term risk (25 years) of fatal breast cancer. Methods:The STO-3 trial enrolled 1780 postmenopausal lymph node-negative breast cancer patients randomly assigned to receive adjuvant tamoxifen vs not. The fraction of cancer cells for each ER intensity level was scored by breast cancer pathologists, and intratumor heterogeneity of ER was calculated using Rao's quadratic entropy and categorized into high and low heterogeneity using a predefined cutoff at the second tertile (67%). Long-term breast cancer-specific survival analyses by intra-tumor heterogeneity of ER were performed using Kaplan-Meier and multivariable Cox proportional hazard modeling adjusting for patient and tumor characteristics. Results:A statistically significant difference in long-term survival by high vs low intratumor heterogeneity of ER was seen for all ER-positive patients (P < .001) and for patients with luminal A subtype tumors (P = .01). In multivariable analyses, patients with high intratumor heterogeneity of ER had a twofold increased long-term risk as compared with patients with low intratumor heterogeneity (ER-positive: hazard ratio [HR] = 1.98, 95% confidence interval [CI] = 1.31 to 3.00; luminal A subtype tumors: HR = 2.43, 95% CI = 1.18 to 4.99). Conclusions:Patients with high intratumor heterogeneity of ER had an increased long-term risk of fatal breast cancer. Interestingly, a similar long-term risk increase was seen in patients with luminal A subtype tumors. Our findings suggest that intratumor heterogeneity of ER is an independent long-term prognosticator with potential to change clinical management, especially for patients with luminal A tumors

Live Coding, Live Notation, Live Performance

This paper/demonstration explores relationships between code, notation including representation, visualisation and performance. Performative aspects of live coding activities are increasingly being investigated as the live coding movement continues to grow and develop. Although live instrumental performance is sometimes included as an accompaniment to live coding, it is often not a fully integrated part of the performance, relying on improvisation and/or basic indicative forms of notation with varying levels of sophistication and universality. Technologies are developing which enable the use of fully explicit music notations as well as more graphic ones, allowing more fully integrated systems of code in and as performance which can also include notations of arbitrary complexity. This itself allows the full skills of instrumental musicians to be utilised and synchronised in the process. This presentation/demonstration presents work and performances already undertaken with these technologies, including technologies for body sensing and data acquisition in the translation of the movements of dancers and musicians into synchronously performable notation, integrated by live and prepared coding. The author together with clarinetist Ian Mitchell present a short live performance utilising these techniques, discuss methods for the dissemination and interpretation of live generated notations and investigate how they take advantage of instrumental musicians’ training-related neuroplasticity skills

Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study

BACKGROUND: Quantitative molecular methods (QMMs) such as quantitative real-time polymerase chain reaction (q-PCR), reverse-transcriptase PCR (qRT-PCR) and quantitative nucleic acid sequence-based amplification (QT-NASBA) are increasingly used to estimate pathogen density in a variety of clinical and epidemiological contexts. These methods are often classified as semi-quantitative, yet estimates of reliability or sensitivity are seldom reported. Here, a statistical framework is developed for assessing the reliability (uncertainty) of pathogen densities estimated using QMMs and the associated diagnostic sensitivity. The method is illustrated with quantification of Plasmodium falciparum gametocytaemia by QT-NASBA. RESULTS: The reliability of pathogen (e.g. gametocyte) densities, and the accompanying diagnostic sensitivity, estimated by two contrasting statistical calibration techniques, are compared; a traditional method and a mixed model Bayesian approach. The latter accounts for statistical dependence of QMM assays run under identical laboratory protocols and permits structural modelling of experimental measurements, allowing precision to vary with pathogen density. Traditional calibration cannot account for inter-assay variability arising from imperfect QMMs and generates estimates of pathogen density that have poor reliability, are variable among assays and inaccurately reflect diagnostic sensitivity. The Bayesian mixed model approach assimilates information from replica QMM assays, improving reliability and inter-assay homogeneity, providing an accurate appraisal of quantitative and diagnostic performance. CONCLUSIONS: Bayesian mixed model statistical calibration supersedes traditional techniques in the context of QMM-derived estimates of pathogen density, offering the potential to improve substantially the depth and quality of clinical and epidemiological inference for a wide variety of pathogens